=>> Building science/plumed build started at Tue Jan 20 02:21:22 EST 2026 port directory: /usr/ports/science/plumed package name: plumed-2.9.3_1 building for: FreeBSD pkg.DaveG.ca 14.3-RELEASE-p7 FreeBSD 14.3-RELEASE-p7 1403000 amd64 maintained by: yuri@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 1487 Jan 31 2025 /usr/ports/science/plumed/Makefile Ports top last git commit: 076a295eb33c Ports top unclean checkout: no Port dir last git commit: fc4dbd235dee Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500068 Jail OSVERSION: 1403000 Job Id: 12 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1403000 UNAME_v=FreeBSD 14.3-RELEASE-p7 1403000 UNAME_r=14.3-RELEASE-p7 BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin MAKE_OBJDIR_CHECK_WRITABLE=0 LOCALBASE=/usr/local USER=root POUDRIERE_NAME=poudriere-git LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.4.2 MASTERMNT=/usr/local/poudriere/data/.m/freebsd_14_3_x64-HEAD-ALL/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=tmux-256color OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/freebsd_14_3_x64-HEAD-ALL/12/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=freebsd_14_3_x64-HEAD-ALL SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/freebsd_14_3_x64-HEAD-ALL/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.2 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ---End OPTIONS List--- --MAINTAINER-- yuri@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --enable-shared --disable-python --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=/usr/local/bin/gmake PKG_CONFIG=pkgconf XDG_DATA_HOME=/wrkdirs/usr/ports/science/plumed/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/plumed/work XDG_CACHE_HOME=/wrkdirs/usr/ports/science/plumed/work/.cache HOME=/wrkdirs/usr/ports/science/plumed/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/science/plumed/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/science/plumed/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh DEFAULT_AUTOCONF=2.72 CMAKE_PREFIX_PATH="/usr/local" CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=524288 --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/science/plumed/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/plumed/work XDG_CACHE_HOME=/wrkdirs/usr/ports/science/plumed/work/.cache HOME=/wrkdirs/usr/ports/science/plumed/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/science/plumed/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/science/plumed/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES DEFAULT_AUTOCONF=2.72 PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-isystem /usr/local/include" LDFLAGS=" " LIBS="-L/usr/local/lib" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include " BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- OSREL=14.3 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/plumed" EXAMPLESDIR="share/examples/plumed" DATADIR="share/plumed" WWWDIR="www/plumed" ETCDIR="etc/plumed" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/plumed DOCSDIR=/usr/local/share/doc/plumed EXAMPLESDIR=/usr/local/share/examples/plumed WWWDIR=/usr/local/www/plumed ETCDIR=/usr/local/etc/plumed --End SUB_LIST-- ---Begin make.conf--- DEFAULT_VERSIONS+=pgsql=15 DEFAULT_VERSIONS+=php=82 DISABLE_LICENSES=yes SELECTED_OPTIONS+=OPENBLAS ARCHDEF=AMD64K10h64SSE3 USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles FORCE_PACKAGE=yes PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### DEFAULT_VERSIONS+=pgsql=15 DEFAULT_VERSIONS+=php=82 DISABLE_LICENSES=yes SELECTED_OPTIONS+=OPENBLAS ARCHDEF=AMD64K10h64SSE3 WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 33554432 stack size (kbytes, -s) 524288 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 8192 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited pipebuf (-y) unlimited --End resource limits-- =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> plumed-2.9.3_1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.5.1.pkg [pkg.DaveG.ca] Installing pkg-2.5.1... [pkg.DaveG.ca] Extracting pkg-2.5.1: .......... done ===> plumed-2.9.3_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of plumed-2.9.3_1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by plumed-2.9.3_1 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by plumed-2.9.3_1 for building => SHA256 Checksum OK for plumed-2.9.3.tgz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by plumed-2.9.3_1 for building ===> Extracting for plumed-2.9.3_1 => SHA256 Checksum OK for plumed-2.9.3.tgz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Patching for plumed-2.9.3_1 ===> Applying FreeBSD patches for plumed-2.9.3_1 from /usr/ports/science/plumed/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> plumed-2.9.3_1 depends on executable: bash - not found ===> Installing existing package /packages/All/bash-5.3.9.pkg [pkg.DaveG.ca] Installing bash-5.3.9... [pkg.DaveG.ca] `-- Installing gettext-runtime-0.26... [pkg.DaveG.ca] | `-- Installing indexinfo-0.3.1_1... [pkg.DaveG.ca] | `-- Extracting indexinfo-0.3.1_1: . done [pkg.DaveG.ca] `-- Extracting gettext-runtime-0.26: .......... done [pkg.DaveG.ca] Extracting bash-5.3.9: .......... done ===> plumed-2.9.3_1 depends on executable: bash - found ===> Returning to build of plumed-2.9.3_1 ===> plumed-2.9.3_1 depends on package: gmake>=4.4.1 - not found ===> Installing existing package /packages/All/gmake-4.4.1.pkg [pkg.DaveG.ca] Installing gmake-4.4.1... [pkg.DaveG.ca] Extracting gmake-4.4.1: .......... done ===> plumed-2.9.3_1 depends on package: gmake>=4.4.1 - found ===> Returning to build of plumed-2.9.3_1 ===> plumed-2.9.3_1 depends on package: pkgconf>=1.3.0_1 - not found ===> Installing existing package /packages/All/pkgconf-2.4.3,1.pkg [pkg.DaveG.ca] Installing pkgconf-2.4.3,1... [pkg.DaveG.ca] Extracting pkgconf-2.4.3,1: .......... done ===> plumed-2.9.3_1 depends on package: pkgconf>=1.3.0_1 - found ===> Returning to build of plumed-2.9.3_1 ===> plumed-2.9.3_1 depends on package: autoconf>=2.72_1 - not found ===> Installing existing package /packages/All/autoconf-2.72_1.pkg [pkg.DaveG.ca] Installing autoconf-2.72_1... [pkg.DaveG.ca] `-- Installing autoconf-switch-20220527... [pkg.DaveG.ca] `-- Extracting autoconf-switch-20220527: ....... done [pkg.DaveG.ca] `-- Installing m4-1.4.20,1... [pkg.DaveG.ca] `-- Extracting m4-1.4.20,1: .......... done [pkg.DaveG.ca] `-- Installing perl5-5.42.0_1... [pkg.DaveG.ca] `-- Extracting perl5-5.42.0_1: .......... done [pkg.DaveG.ca] Extracting autoconf-2.72_1: .......... done ===> plumed-2.9.3_1 depends on package: autoconf>=2.72_1 - found ===> Returning to build of plumed-2.9.3_1 ===> plumed-2.9.3_1 depends on package: automake>=1.18.1 - not found ===> Installing existing package /packages/All/automake-1.18.1.pkg [pkg.DaveG.ca] Installing automake-1.18.1... [pkg.DaveG.ca] Extracting automake-1.18.1: .......... done ===> plumed-2.9.3_1 depends on package: automake>=1.18.1 - found ===> Returning to build of plumed-2.9.3_1 ===> plumed-2.9.3_1 depends on file: /usr/local/bin/ccache - not found ===> Installing existing package /packages/All/ccache-3.7.12_8.pkg [pkg.DaveG.ca] Installing ccache-3.7.12_8... [pkg.DaveG.ca] Extracting ccache-3.7.12_8: ......... done Create compiler links... create symlink for cc create symlink for cc (world) create symlink for c++ create symlink for c++ (world) create symlink for CC create symlink for CC (world) create symlink for clang create symlink for clang (world) create symlink for clang++ create symlink for clang++ (world) ===== Message from ccache-3.7.12_8: -- NOTE: Please read /usr/local/share/doc/ccache/ccache-howto-freebsd.txt for information on using ccache with FreeBSD ports and src. ===> plumed-2.9.3_1 depends on file: /usr/local/bin/ccache - found ===> Returning to build of plumed-2.9.3_1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> plumed-2.9.3_1 depends on shared library: libblas.so - not found ===> Installing existing package /packages/All/blas-3.12.1.pkg [pkg.DaveG.ca] Installing blas-3.12.1... [pkg.DaveG.ca] `-- Installing gcc14-14.2.0_4... [pkg.DaveG.ca] | `-- Installing binutils-2.44,1... [pkg.DaveG.ca] | | `-- Installing zstd-1.5.7_1... [pkg.DaveG.ca] | | `-- Extracting zstd-1.5.7_1: .......... done [pkg.DaveG.ca] | `-- Extracting binutils-2.44,1: .......... done [pkg.DaveG.ca] | `-- Installing gmp-6.3.0... [pkg.DaveG.ca] | `-- Extracting gmp-6.3.0: .......... done [pkg.DaveG.ca] | `-- Installing mpc-1.3.1_1... [pkg.DaveG.ca] | | `-- Installing mpfr-4.2.2,1... [pkg.DaveG.ca] | | `-- Extracting mpfr-4.2.2,1: .......... done [pkg.DaveG.ca] | `-- Extracting mpc-1.3.1_1: ...... done [pkg.DaveG.ca] `-- Extracting gcc14-14.2.0_4: .......... done create symlink for gcc14 create symlink for gcc14 (world) create symlink for g++14 create symlink for g++14 (world) create symlink for cpp14 create symlink for cpp14 (world) [pkg.DaveG.ca] Extracting blas-3.12.1: ..... done ===== Message from gcc14-14.2.0_4: -- To ensure binaries built with this toolchain find appropriate versions of the necessary run-time libraries, you may want to link using -Wl,-rpath=/usr/local/lib/gcc14 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. ===> plumed-2.9.3_1 depends on shared library: libblas.so - found (/usr/local/lib/libblas.so) ===> Returning to build of plumed-2.9.3_1 ===> plumed-2.9.3_1 depends on shared library: libfftw3.so - not found ===> Installing existing package /packages/All/fftw3-3.3.10_5.pkg [pkg.DaveG.ca] Installing fftw3-3.3.10_5... [pkg.DaveG.ca] Extracting fftw3-3.3.10_5: .......... done ===> plumed-2.9.3_1 depends on shared library: libfftw3.so - found (/usr/local/lib/libfftw3.so) ===> Returning to build of plumed-2.9.3_1 ===> plumed-2.9.3_1 depends on shared library: libgsl.so - not found ===> Installing existing package /packages/All/gsl-2.7.1_1.pkg [pkg.DaveG.ca] Installing gsl-2.7.1_1... [pkg.DaveG.ca] Extracting gsl-2.7.1_1: .......... done ===> plumed-2.9.3_1 depends on shared library: libgsl.so - found (/usr/local/lib/libgsl.so) ===> Returning to build of plumed-2.9.3_1 ===> plumed-2.9.3_1 depends on shared library: liblapack.so - not found ===> Installing existing package /packages/All/lapack-3.12.1.pkg [pkg.DaveG.ca] Installing lapack-3.12.1... [pkg.DaveG.ca] Extracting lapack-3.12.1: .......... done ===> plumed-2.9.3_1 depends on shared library: liblapack.so - found (/usr/local/lib/liblapack.so) ===> Returning to build of plumed-2.9.3_1 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for plumed-2.9.3_1 configure: loading site script /usr/ports/Templates/config.site configure: Optional modules are disabled by default checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C++... yes checking whether c++ accepts -g... yes checking for c++ option to enable C++11 features... none needed checking whether the compiler supports GNU C... yes checking whether cc accepts -g... yes checking for cc option to enable C11 features... none needed checking for gfortran... no checking for g95... no checking for xlf95... no checking for f95... no checking for fort... no checking for ifort... no checking for ifc... no checking for efc... no checking for pgfortran... no checking for pgf95... no checking for lf95... no checking for ftn... no checking for nagfor... no checking for xlf90... no checking for f90... no checking for pgf90... no checking for pghpf... no checking for epcf90... no checking for g77... no checking for xlf... no checking for f77... no checking for frt... no checking for pgf77... no checking for cf77... no checking for fort77... no checking for fl32... no checking for af77... no checking whether the compiler supports GNU Fortran... no checking whether accepts -g... no configure: Initial CXX: c++ configure: Initial CXXFLAGS: -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include configure: Initial CPPFLAGS: -isystem /usr/local/include configure: Initial CFLAGS: -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing configure: Initial LDFLAGS: configure: Initial LIBS: -L/usr/local/lib configure: Initial STATIC_LIBS: configure: Initial LD: configure: Initial LDSHARED: c++ configure: Initial SOEXT: checking whether c++ accepts -fPIC... yes checking whether cc accepts -fPIC... yes checking whether c++ accepts -Wall... yes checking whether c++ accepts -pedantic... yes checking whether c++ accepts -std=c++11... yes checking whether c++ declares c++11 support... yes checking whether C++ library supports C++11 exceptions... yes checking whether c++ can generate dependency file with -MM -MF... yes configure: dependency tracking enabled configure: Now we will check compulsory headers and libraries checking for stdio.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for inttypes.h... (cached) yes checking for stdint.h... (cached) yes checking for strings.h... (cached) yes checking for sys/stat.h... (cached) yes checking for sys/types.h... (cached) yes checking for unistd.h... (cached) yes checking for dirent.h... (cached) yes checking for readdir... (cached) yes checking whether dgemv_ can be linked with no library... no checking whether dgemv_ can be linked with no library... no checking for library containing dgemv_... -lblas checking for library containing dsyevr_... -llapack checking whether sdot returns float... yes configure: Now we will check for optional headers and libraries checking for libmolfile_plugin.h... no configure: WARNING: cannot enable __PLUMED_HAS_EXTERNAL_MOLFILE_PLUGINS configure: WARNING: using internal molfile_plugins, which only support dcd/xtc/trr/trj/crd files checking for dlopen in -ldl... yes checking for mpi.h... no configure: WARNING: cannot enable __PLUMED_HAS_MPI checking for c++ option to support OpenMP... -fopenmp checking whether architecture is X86/X64... yes configure: Enabling embedded asmjit checking for regex.h... yes checking for library containing regcomp... none required checking for dlfcn.h... (cached) yes checking for library containing dlopen... none required checking RTLD_DEFAULT without extra libs... yes checking for unistd.h... (cached) yes checking for library containing chdir... none required checking subprocess without extra libs... yes checking for unistd.h... (cached) yes checking for library containing getcwd... none required checking for cstdio... yes checking for library containing popen... none required checking for execinfo.h... yes checking for library containing backtrace... no configure: WARNING: cannot enable __PLUMED_HAS_EXECINFO checking for zlib.h... (cached) yes checking for library containing gzopen... -lz checking for library containing cblas_dgemv... -lgslcblas checking for gsl/gsl_vector.h... yes checking for library containing gsl_vector_alloc... -lgsl checking for fftw3.h... yes checking for library containing fftw_execute... -lfftw3 configure: Release mode, adding -DNDEBUG configure: *** Special settings for dynamic libraries on Linux *** configure: Dynamic library extension is 'so' configure: LDSHARED and LDFLAGS need special flags checking whether LDFLAGS can contain -rdynamic... yes checking whether LDFLAGS can contain -Wl,-Bsymbolic... yes configure: Using LDSHARED='c++ -shared' configure: Using LDFLAGS=' -rdynamic -Wl,-Bsymbolic' checking whether LDSHARED can create dynamic libraries... yes checking for doxygen... no configure: Manuals will not be generated configure: A PDF version of the manual will not be generated checking whether a program can be run on this machine... yes configure: PLUMED seems to be configured properly! configure: ************************** checking whether C++ objects can be grouped with /usr/bin/ld -r -o... yes checking whether static libraries can be created with /usr/bin/ar cr... yes checking whether static-object constructors can be linked from a static archive... yes configure: I will now check if C++ objects can be linked by C/Fortran compilers configure: This is relevant if you want to use plumed patch --static on a non-C++ code checking whether C can link a C++ object... no checking whether C can link a C++ object with library -lstdc++... yes configure: FC compiler not configured checking for pkg-config... /usr/local/bin/pkg-config configure: bash-completion is not installed or it is installed on a different prefix configure: bash completion for plumed will not be installed configure: **** PLUMED will be installed using the following paths: configure: **** prefix: /usr/local configure: **** exec_prefix: ${prefix} configure: **** bindir: ${exec_prefix}/bin configure: **** libdir: ${exec_prefix}/lib configure: **** includedir: ${prefix}/include configure: **** datarootdir: ${prefix}/share configure: **** datadir: ${datarootdir} configure: **** docdir: ${prefix}/share/doc/plumed configure: **** htmldir: ${docdir} configure: **** Executable will be named plumed configure: **** As of PLUMED 2.5, you cannot change paths anymore during "make install" configure: **** Please configure and make clean to change the prefix configure: WARNING: **** Bash completion for plumed will not be installed, please add the following two lines to your bashrc configure: WARNING: **** _plumed() { eval "$(plumed --no-mpi completion 2>/dev/null)";} configure: WARNING: **** complete -F _plumed -o default plumed configure: WARNING: **** PLUMED will NOT be compiled using MPI because MPI have not been found! configure: creating ./config.status config.status: creating Makefile.conf config.status: creating sourceme.sh config.status: creating stamp-h =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for plumed-2.9.3_1 /usr/local/bin/gmake lib gmake[1]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3' /usr/local/bin/gmake -C src gmake[2]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src' /usr/local/bin/gmake -C lib gmake[3]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' /usr/local/bin/gmake dirslinks gmake[4]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' *** Updating links to used modules in all directories *** /usr/local/bin/gmake ../analysis.links ../asmjit.links ../bias.links ../blas.links ../cltools.links ../colvar.links ../config.links ../core.links ../function.links ../generic.links ../gridtools.links ../isdb.links ../lapack.links ../lepton.links ../main.links ../mapping.links ../molfile.links ../multicolvar.links ../reference.links ../secondarystructure.links ../setup.links ../tools.links ../vatom.links ../vesselbase.links ../wrapper.links ../xdrfile.links gmake[5]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' /usr/local/bin/gmake -C ../analysis links /usr/local/bin/gmake -C ../asmjit links /usr/local/bin/gmake -C ../bias links /usr/local/bin/gmake -C ../blas links /usr/local/bin/gmake -C ../cltools links /usr/local/bin/gmake -C ../colvar links /usr/local/bin/gmake -C ../config links /usr/local/bin/gmake -C ../core links /usr/local/bin/gmake -C ../function links /usr/local/bin/gmake -C ../generic links /usr/local/bin/gmake -C ../gridtools links /usr/local/bin/gmake -C ../isdb links /usr/local/bin/gmake -C ../lapack links /usr/local/bin/gmake -C ../lepton links /usr/local/bin/gmake -C ../main links /usr/local/bin/gmake -C ../mapping links /usr/local/bin/gmake -C ../molfile links gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/config' /usr/local/bin/gmake -C ../multicolvar links gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/blas' /usr/local/bin/gmake -C ../reference links /usr/local/bin/gmake -C ../secondarystructure links /usr/local/bin/gmake -C ../setup links Nothing to do in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/config /usr/local/bin/gmake -C ../tools links Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/blas gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/config' /usr/local/bin/gmake -C ../vatom links /usr/local/bin/gmake -C ../vesselbase links /usr/local/bin/gmake -C ../wrapper links gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lapack' /usr/local/bin/gmake -C ../xdrfile links gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/blas' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lapack gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/main' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/main gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/wrapper' gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lepton' gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/molfile' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lepton gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/setup' Nothing to do in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/wrapper gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/secondarystructure' gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/xdrfile' gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/function' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/molfile gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/wrapper' gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/cltools' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/setup Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/secondarystructure Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/function Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/xdrfile gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/vatom' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/cltools gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/analysis' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/vatom gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/molfile' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/analysis gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/mapping' gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/xdrfile' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/mapping gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/bias' gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/gridtools' gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/generic' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/bias Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/gridtools gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/asmjit' gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/isdb' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/generic Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/asmjit Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/isdb gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/asmjit' gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/reference' gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/main' gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/colvar' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/reference Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/colvar gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lapack' gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/vesselbase' gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/core' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/vesselbase gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lepton' gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/multicolvar' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/core Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/multicolvar gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/tools' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/tools gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/vatom' gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/setup' gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/bias' gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/reference' gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/secondarystructure' gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/generic' gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/gridtools' gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/core' gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/colvar' gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/function' gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/cltools' gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/tools' gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/vesselbase' gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/multicolvar' gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/mapping' gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/isdb' gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/analysis' gmake[5]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' gmake[4]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' /usr/local/bin/gmake dirs gmake[4]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' *** Compiling all directories *** /usr/local/bin/gmake ../analysis ../asmjit ../bias ../blas ../cltools ../colvar ../config ../core ../function ../generic ../gridtools ../isdb ../lapack ../lepton ../main ../mapping ../molfile ../multicolvar ../reference ../secondarystructure ../setup ../tools ../vatom ../vesselbase ../wrapper ../xdrfile gmake[5]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' /usr/local/bin/gmake -C ../analysis obj /usr/local/bin/gmake -C ../asmjit obj /usr/local/bin/gmake -C ../bias obj /usr/local/bin/gmake -C ../blas obj /usr/local/bin/gmake -C ../cltools obj /usr/local/bin/gmake -C ../colvar obj /usr/local/bin/gmake -C ../config obj /usr/local/bin/gmake -C ../core obj /usr/local/bin/gmake -C ../function obj /usr/local/bin/gmake -C ../generic obj /usr/local/bin/gmake -C ../gridtools obj /usr/local/bin/gmake -C ../isdb obj /usr/local/bin/gmake -C ../lapack obj /usr/local/bin/gmake -C ../lepton obj /usr/local/bin/gmake -C ../main obj /usr/local/bin/gmake -C ../mapping obj /usr/local/bin/gmake -C ../molfile obj gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/config' /usr/local/bin/gmake PLUMED_FORCE=yes ConfigInstall.inc Config.inc version.h config.txt /usr/local/bin/gmake -C ../multicolvar obj /usr/local/bin/gmake -C ../reference obj gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/blas' /usr/local/bin/gmake -C ../secondarystructure obj /usr/local/bin/gmake -C ../setup obj /usr/local/bin/gmake -C ../tools obj /usr/local/bin/gmake -C ../vatom obj /usr/local/bin/gmake -C ../vesselbase obj compiling blas.cpp /usr/local/bin/gmake -C ../wrapper obj /usr/local/bin/gmake -C ../xdrfile obj gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/config' gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lapack' gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/main' Updating ConfigInstall.inc Updating Config.inc compiling lapack.cpp Updating version.h Updating config.txt file compiling main.cpp gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/wrapper' gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/molfile' gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lepton' gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/setup' gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/secondarystructure' compiling PlumedStatic.cpp compiling crdplugin.cpp compiling Plumed.c gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/bias' compiling dcdplugin.cpp gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/vatom' gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/xdrfile' compiling CompiledExpression.cpp gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/isdb' gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/analysis' compiling Load.cpp gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/function' compiling ExpressionProgram.cpp compiling AlphaRMSD.cpp compiling gromacsplugin.cpp compiling pdbplugin.cpp compiling Restart.cpp compiling Units.cpp compiling AntibetaRMSD.cpp compiling ExpressionTreeNode.cpp compiling Operation.cpp gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/mapping' compiling ActionWithVirtualAtom.cpp compiling xdrfile.cpp compiling CS2Backbone.cpp compiling Parser.cpp compiling SecondaryStructureRMSD.cpp compiling ParabetaRMSD.cpp compiling Combine.cpp compiling ParsedExpression.cpp compiling AnalysisBase.cpp compiling Average.cpp compiling FixedAtom.cpp gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/cltools' compiling xdrfile_trr.cpp compiling AdaptivePath.cpp compiling Caliber.cpp compiling xdrfile_xtc.cpp mkdir: compiling Mapping.cpp compiling Center.cpp mkdir: deps: compiling ABMD.cpp File exists { ../maketools/make-scripts-options.sh ; cat completion.sh ; }| ../maketools/xxd > completion.xxd compiling EMMI.cpp deps: File exists compiling AverageVessel.cpp mkdir: compiling Bias.cpp deps: File exists compiling BiasValue.cpp cmp -s ConfigInstall.inc~ ConfigInstall.inc || cp ConfigInstall.inc~ ConfigInstall.inc compiling CLTool.cpp gmake[6]: [../maketools/make.rules:31: Plumed.o] Error 1 (ignored) compiling FretEfficiency.cpp compiling Path.cpp compiling Committor.cpp compiling Custom.cpp mkdir: deps: compiling ExtendedLagrangian.cpp gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/gridtools' File exists compiling Ensemble.cpp compiling PCAVars.cpp mkdir: deps: File exists mkdir: deps: cmp -s Config.inc~ Config.inc || cp Config.inc~ Config.inc File exists compiling FuncPathGeneral.cpp gmake[6]: [../maketools/make.rules:16: dcdplugin.o] Error 1 (ignored) mkdir: deps: compiling Ghost.cpp gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/generic' compiling ActionWithGrid.cpp gmake[6]: [../maketools/make.rules:16: CompiledExpression.o] Error 1 (ignored) File exists mkdir: deps: File exists gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/colvar' gmake[6]: [../maketools/make.rules:16: SecondaryStructureRMSD.o] Error 1 (ignored) mkdir: deps: mkdir: depsFile exists gmake[6]: [../maketools/make.rules:16: AverageVessel.o] Error 1 (ignored) mkdir: deps: : File exists File exists mkdir: deps: File exists gmake[6]: [../maketools/make.rules:15: Operation.o] Error 1 (ignored) mkdir: deps: gmake[6]: [../maketools/make.rules:16: AlphaRMSD.o] Error 1 (ignored) gmake[6]: [../maketools/make.rules:16: Caliber.o] Error 1 (ignored) gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/asmjit' gmake[6]: [../maketools/make.rules:16: ExtendedLagrangian.o] Error 1 (ignored) compiling Debug.cpp mkdir: deps: File exists gmake[6]: [../maketools/make.rules:16: Bias.o] Error 1 (ignored) mkdir: deps: File exists gmake[6]: [../maketools/make.rules:15: FixedAtom.o] Error 1 (ignored) gmake[6]: [../maketools/make.rules:16: Restart.o] Error 1 (ignored) mkdir: deps: File exists File exists compiling Angle.cpp gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/reference' compiling arch.cpp gmake[6]: [../maketools/make.rules:16: AdaptivePath.o] Error 1 (ignored) compiling ArgumentOnlyDistance.cpp gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/vesselbase' gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/core' rm ConfigInstall.inc~ compiling Action.cpp gmake[6]: [../maketools/make.rules:16: AnalysisBase.o] Error 1 (ignored) gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/multicolvar' compiling ActionVolume.cpp rm Config.inc~ gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/tools' gmake[6]: [../maketools/make.rules:16: Ensemble.o] Error 1 (ignored) compiling ActionWithAveraging.cpp compiling Angle.cpp compiling Driver.cpp compiling DRMSD.cpp gmake[6]: [../maketools/make.rules:16: Custom.o] Error 1 (ignored) gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lapack' compiling Jcoupling.cpp compiling Cell.cpp compiling DriverDouble.cpp gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/blas' compiling ActionWithInputGrid.cpp In file included from xdrfile_xtc.cpp:56: ./xdrfile.h:32:2: warning: '/*' within block comment [-Wcomment] 32 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- | ^ In file included from xdrfile_xtc.cpp:57: ./xdrfile_xtc.h:32:2: warning: '/*' within block comment [-Wcomment] 32 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- | ^ xdrfile_xtc.cpp:94:6: warning: unused variable 'i' [-Wunused-variable] 94 | int i,j,result; | ^ xdrfile_xtc.cpp:94:8: warning: unused variable 'j' [-Wunused-variable] 94 | int i,j,result; | ^ 4 warnings generated. compiling ActionAnyorder.cpp compiling DumpAtoms.cpp xdrfile_trr.cpp:30:2: warning: '/*' within block comment [-Wcomment] 30 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- | ^ In file included from xdrfile_trr.cpp:66: ./xdrfile.h:32:2: warning: '/*' within block comment [-Wcomment] 32 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- | ^ In file included from xdrfile_trr.cpp:67: ./xdrfile_trr.h:32:2: warning: '/*' within block comment [-Wcomment] 32 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- | ^ 3 warnings generated. compiling Colvar.cpp In file included from pdbplugin.cpp:64: ./periodic_table.h:107:50: warning: invalid UTF-8 in comment [-Winvalid-utf8] 107 | * either of these publications have RvdW = 2.00 . | ^ ./periodic_table.h:173:12: warning: unused function 'get_pte_idx' [-Wunused-function] 173 | static int get_pte_idx(const char *label) | ^~~~~~~~~~~ 2 warnings generated. compiling ActionWithIntegral.cpp gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/wrapper' compiling Metainference.cpp In file included from dcdplugin.cpp:83: ./fastio.h:474:14: warning: variable 'len' set but not used [-Wunused-but-set-variable] 474 | fio_size_t len = 0; | ^ ./fastio.h:593:14: warning: variable 'len' set but not used [-Wunused-but-set-variable] 593 | fio_size_t len = 0; | ^ ./fastio.h:520:19: warning: unused function 'fio_readv' [-Wunused-function] 520 | static fio_size_t fio_readv(fio_fd fd, const fio_iovec * iov, int iovcnt) { | ^~~~~~~~~ ./fastio.h:672:12: warning: unused function 'fio_read_int32' [-Wunused-function] 672 | static int fio_read_int32(fio_fd fd, int *i) { | ^~~~~~~~~~~~~~ ./fastio.h:676:12: warning: unused function 'fio_write_str' [-Wunused-function] 676 | static int fio_write_str(fio_fd fd, const char *str) { | ^~~~~~~~~~~~~ In file included from dcdplugin.cpp:93: ./endianswap.h:74:13: warning: unused function 'swap2_unaligned' [-Wunused-function] 74 | static void swap2_unaligned(void *v, ptrdiff_t ndata) { | ^~~~~~~~~~~~~~~ ./endianswap.h:138:13: warning: unused function 'swap2_aligned' [-Wunused-function] 138 | static void swap2_aligned(void *v, ptrdiff_t ndata) { | ^~~~~~~~~~~~~ 7 warnings generated. compiling AverageOnGrid.cpp compiling DataCollectionObject.cpp In file included from gromacsplugin.cpp:62: In file included from ./Gromacs.h:86: ./endianswap.h:74:13: warning: unused function 'swap2_unaligned' [-Wunused-function] 74 | static void swap2_unaligned(void *v, ptrdiff_t ndata) { | ^~~~~~~~~~~~~~~ ./endianswap.h:88:13: warning: unused function 'swap4_unaligned' [-Wunused-function] 88 | static void swap4_unaligned(void *v, ptrdiff_t ndata) { | ^~~~~~~~~~~~~~~ ./endianswap.h:107:13: warning: unused function 'swap8_unaligned' [-Wunused-function] 107 | static void swap8_unaligned(void *v, ptrdiff_t ndata) { | ^~~~~~~~~~~~~~~ ./endianswap.h:138:13: warning: unused function 'swap2_aligned' [-Wunused-function] 138 | static void swap2_aligned(void *v, ptrdiff_t ndata) { | ^~~~~~~~~~~~~ 4 warnings generated. gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/molfile' compiling DriverFloat.cpp In file included from arch.cpp:33: In file included from ././arch.h:37: ./././operand.h:341:12: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 341 | return (_packed[0] == other._packed[0]) & | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && 342 | (_packed[1] == other._packed[1]) ; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./././operand.h:341:12: note: cast one or both operands to int to silence this warning ./././operand.h:808:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 808 | static ASMJIT_INLINE bool isGp(const Operand_& op, uint32_t rId) noexcept { return isGp(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ./././operand.h:808:86: note: cast one or both operands to int to silence this warning ./././operand.h:809:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 809 | static ASMJIT_INLINE bool isVec(const Operand_& op, uint32_t rId) noexcept { return isVec(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ./././operand.h:809:87: note: cast one or both operands to int to silence this warning In file included from arch.cpp:36: ././x86operand.h:379:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 379 | static ASMJIT_INLINE bool isGpb(const Operand_& op, uint32_t rId) noexcept { return isGpb(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:379:87: note: cast one or both operands to int to silence this warning ././x86operand.h:381:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 381 | static ASMJIT_INLINE bool isRip(const Operand_& op, uint32_t rId) noexcept { return isRip(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:381:87: note: cast one or both operands to int to silence this warning ././x86operand.h:382:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 382 | static ASMJIT_INLINE bool isSeg(const Operand_& op, uint32_t rId) noexcept { return isSeg(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:382:87: note: cast one or both operands to int to silence this warning ././x86operand.h:383:89: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 383 | static ASMJIT_INLINE bool isGpbLo(const Operand_& op, uint32_t rId) noexcept { return isGpbLo(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:383:89: note: cast one or both operands to int to silence this warning ././x86operand.h:384:89: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 384 | static ASMJIT_INLINE bool isGpbHi(const Operand_& op, uint32_t rId) noexcept { return isGpbHi(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:384:89: note: cast one or both operands to int to silence this warning ././x86operand.h:385:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 385 | static ASMJIT_INLINE bool isGpw(const Operand_& op, uint32_t rId) noexcept { return isGpw(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:385:87: note: cast one or both operands to int to silence this warning ././x86operand.h:386:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 386 | static ASMJIT_INLINE bool isGpd(const Operand_& op, uint32_t rId) noexcept { return isGpd(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:386:87: note: cast one or both operands to int to silence this warning ././x86operand.h:387:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 387 | static ASMJIT_INLINE bool isGpq(const Operand_& op, uint32_t rId) noexcept { return isGpq(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:387:87: note: cast one or both operands to int to silence this warning ././x86operand.h:388:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 388 | static ASMJIT_INLINE bool isFp(const Operand_& op, uint32_t rId) noexcept { return isFp(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:388:86: note: cast one or both operands to int to silence this warning ././x86operand.h:389:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 389 | static ASMJIT_INLINE bool isMm(const Operand_& op, uint32_t rId) noexcept { return isMm(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:389:86: note: cast one or both operands to int to silence this warning ././x86operand.h:390:85: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 390 | static ASMJIT_INLINE bool isK(const Operand_& op, uint32_t rId) noexcept { return isK(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:390:85: note: cast one or both operands to int to silence this warning ././x86operand.h:391:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 391 | static ASMJIT_INLINE bool isXmm(const Operand_& op, uint32_t rId) noexcept { return isXmm(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:391:87: note: cast one or both operands to int to silence this warning ././x86operand.h:392:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 392 | static ASMJIT_INLINE bool isYmm(const Operand_& op, uint32_t rId) noexcept { return isYmm(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:392:87: note: cast one or both operands to int to silence this warning ././x86operand.h:393:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 393 | static ASMJIT_INLINE bool isZmm(const Operand_& op, uint32_t rId) noexcept { return isZmm(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:393:87: note: cast one or both operands to int to silence this warning ././x86operand.h:394:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 394 | static ASMJIT_INLINE bool isBnd(const Operand_& op, uint32_t rId) noexcept { return isBnd(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:394:87: note: cast one or both operands to int to silence this warning ././x86operand.h:395:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 395 | static ASMJIT_INLINE bool isCr(const Operand_& op, uint32_t rId) noexcept { return isCr(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:395:86: note: cast one or both operands to int to silence this warning ././x86operand.h:396:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 396 | static ASMJIT_INLINE bool isDr(const Operand_& op, uint32_t rId) noexcept { return isDr(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:396:86: note: cast one or both operands to int to silence this warning 20 warnings generated. compiling assembler.cpp xdrfile.cpp:30:2: warning: '/*' within block comment [-Wcomment] 30 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- | ^ In file included from xdrfile.cpp:85: ./xdrfile.h:32:2: warning: '/*' within block comment [-Wcomment] 32 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- | ^ xdrfile.cpp:819:16: warning: variable 'minidx' set but not used [-Wunused-but-set-variable] 819 | int smallidx, minidx, maxidx; | ^ xdrfile.cpp:822:25: warning: variable 'larger' set but not used [-Wunused-but-set-variable] 822 | int smallnum, smaller, larger, i, is_smaller, run; | ^ xdrfile.cpp:1029:6: warning: variable 'errval' set but not used [-Wunused-but-set-variable] 1029 | int errval=1; | ^ xdrfile.cpp:1086:25: warning: implicit conversion from 'int' to 'float' changes value from 2147483645 to 2147483648 [-Wimplicit-const-int-float-conversion] 1086 | if (fabs(lf) > INT_MAX-2) | ~ ~~~~~~~^~ xdrfile.cpp:1101:25: warning: implicit conversion from 'int' to 'float' changes value from 2147483645 to 2147483648 [-Wimplicit-const-int-float-conversion] 1101 | if (fabs(lf) > INT_MAX-2) | ~ ~~~~~~~^~ xdrfile.cpp:1116:25: warning: implicit conversion from 'int' to 'float' changes value from 2147483645 to 2147483648 [-Wimplicit-const-int-float-conversion] 1116 | if (fabs(lf) > INT_MAX-2) | ~ ~~~~~~~^~ xdrfile.cpp:1137:49: warning: implicit conversion from 'int' to 'float' changes value from 2147483645 to 2147483648 [-Wimplicit-const-int-float-conversion] 1137 | (float)maxint[2] - (float)minint[2] >= INT_MAX-2) { | ~~ ~~~~~~~^~ xdrfile.cpp:1136:49: warning: implicit conversion from 'int' to 'float' changes value from 2147483645 to 2147483648 [-Wimplicit-const-int-float-conversion] 1136 | (float)maxint[1] - (float)minint[1] >= INT_MAX-2 || | ~~ ~~~~~~~^~ xdrfile.cpp:1135:52: warning: implicit conversion from 'int' to 'float' changes value from 2147483645 to 2147483648 [-Wimplicit-const-int-float-conversion] 1135 | if ((float)maxint[0] - (float)minint[0] >= INT_MAX-2 || | ~~ ~~~~~~~^~ xdrfile.cpp:1315:16: warning: variable 'minidx' set but not used [-Wunused-but-set-variable] 1315 | int smallidx, minidx, maxidx; | ^ xdrfile.cpp:1318:25: warning: variable 'larger' set but not used [-Wunused-but-set-variable] 1318 | int smallnum, smaller, larger, i, is_smaller, run; | ^ xdrfile.cpp:1522:6: warning: variable 'errval' set but not used [-Wunused-but-set-variable] 1522 | int errval=1; | ^ xdrfile.cpp:1576:25: warning: implicit conversion from 'int' to 'float' changes value from 2147483645 to 2147483648 [-Wimplicit-const-int-float-conversion] 1576 | if (fabs(lf) > INT_MAX-2) { | ~ ~~~~~~~^~ xdrfile.cpp:1590:25: warning: implicit conversion from 'int' to 'float' changes value from 2147483645 to 2147483648 [-Wimplicit-const-int-float-conversion] 1590 | if (fabs(lf) > INT_MAX-2) { | ~ ~~~~~~~^~ xdrfile.cpp:1604:25: warning: implicit conversion from 'int' to 'float' changes value from 2147483645 to 2147483648 [-Wimplicit-const-int-float-conversion] 1604 | if (fabs(lf) > INT_MAX-2) { | ~ ~~~~~~~^~ xdrfile.cpp:1624:49: warning: implicit conversion from 'int' to 'float' changes value from 2147483645 to 2147483648 [-Wimplicit-const-int-float-conversion] 1624 | (float)maxint[2] - (float)minint[2] >= INT_MAX-2) { | ~~ ~~~~~~~^~ xdrfile.cpp:1623:49: warning: implicit conversion from 'int' to 'float' changes value from 2147483645 to 2147483648 [-Wimplicit-const-int-float-conversion] 1623 | (float)maxint[1] - (float)minint[1] >= INT_MAX-2 || | ~~ ~~~~~~~^~ xdrfile.cpp:1622:52: warning: implicit conversion from 'int' to 'float' changes value from 2147483645 to 2147483648 [-Wimplicit-const-int-float-conversion] 1622 | if ((float)maxint[0] - (float)minint[0] >= INT_MAX-2 || | ~~ ~~~~~~~^~ 20 warnings generated. gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/xdrfile' compiling ActionAtomistic.cpp compiling AtomNumber.cpp gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/main' compiling GenExample.cpp compiling PathBase.cpp ExpressionTreeNode.cpp:99:105: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 99 | ExpressionTreeNode::ExpressionTreeNode(ExpressionTreeNode&& node) : operation(node.operation), children(move(node.children)) { | ^ | std:: ExpressionTreeNode.cpp:144:16: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 144 | children = move(node.children); | ^ | std:: 2 warnings generated. compiling DumpDerivatives.cpp compiling LWalls.cpp compiling External.cpp compiling Constant.cpp gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/config' /usr/local/bin/gmake Config.o ConfigInstall.o compile_options.sh gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/config' cat ../../Makefile.conf | ../maketools/xxd > Makefile.conf.xxd compiling ActionPilot.cpp compiling EuclideanDissimilarityMatrix.cpp compiling DumpForces.cpp compiling ActionWithInputVessel.cpp compiling ActionWithVessel.cpp compiling ContactMap.cpp compiling Direction.cpp Building compile_options.sh, a sourceable bash script with some compilation options compiling ContourFindingBase.cpp compiling DotProductDistance.cpp compiling ActionRegister.cpp In file included from Driver.cpp:41: In file included from ./xdrfile/xdrfile_trr.h:1: ./xdrfile/../../xdrfile/xdrfile_trr.h:32:2: warning: '/*' within block comment [-Wcomment] 32 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- | ^ In file included from Driver.cpp:41: In file included from ./xdrfile/xdrfile_trr.h:1: In file included from ./xdrfile/../../xdrfile/xdrfile_trr.h:64: ./xdrfile/../../xdrfile/xdrfile.h:32:2: warning: '/*' within block comment [-Wcomment] 32 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- | ^ In file included from Driver.cpp:42: In file included from ./xdrfile/xdrfile_xtc.h:1: ./xdrfile/../../xdrfile/xdrfile_xtc.h:32:2: warning: '/*' within block comment [-Wcomment] 32 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- | ^ Driver.cpp:184:12: warning: function 'register_cb' is not needed and will not be emitted [-Wunneeded-internal-declaration] 184 | static int register_cb(void *v, vmdplugin_t *p) { | ^~~~~~~~~~~ 4 warnings generated. compiling GenJson.cpp gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/setup' compiling ConvertToFES.cpp compiling AlphaBeta.cpp compiling Coordination.cpp compiling DumpMassCharge.cpp compiling MetainferenceBase.cpp compiling Config.cpp compiling codebuilder.cpp compiling DumpProjections.cpp compiling NOE.cpp compiling MaxEnt.cpp In file included from assembler.cpp:33: In file included from ././assembler.h:36: In file included from ./././codeemitter.h:36: In file included from ././././arch.h:37: ./././././operand.h:341:12: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 341 | return (_packed[0] == other._packed[0]) & | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && 342 | (_packed[1] == other._packed[1]) ; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./././././operand.h:341:12: note: cast one or both operands to int to silence this warning ./././././operand.h:808:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 808 | static ASMJIT_INLINE bool isGp(const Operand_& op, uint32_t rId) noexcept { return isGp(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ./././././operand.h:808:86: note: cast one or both operands to int to silence this warning ./././././operand.h:809:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 809 | static ASMJIT_INLINE bool isVec(const Operand_& op, uint32_t rId) noexcept { return isVec(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ./././././operand.h:809:87: note: cast one or both operands to int to silence this warning 3 warnings generated. compiling codecompiler.cpp compiling FarthestPointSampling.cpp compiling MetaD.cpp compiling EffectiveEnergyDrift.cpp compiling codeemitter.cpp compiling DumpCube.cpp compiling GenTemplate.cpp compiling FuncPathMSD.cpp compiling Histogram.cpp compiling FuncSumHills.cpp compiling Angles.cpp compiling LandmarkSelectionBase.cpp compiling ActionSet.cpp compiling Function.cpp compiling LocalEnsemble.cpp ParsedExpression.cpp:82:19: warning: reference cannot be bound to dereferenced null pointer in well-defined C++ code; comparison may be assumed to always evaluate to false [-Wtautological-undefined-compare] 82 | if (&rootNode.getOperation() == NULL) | ~~~~~~~~~^~~~~~~~~~~~~~ ~~~~ ./ExpressionTreeNode.h:129:22: note: 'getOperation' returns a reference 129 | const Operation& getOperation() const; | ^ 1 warning generated. compiling BiasRepresentation.cpp compiling DumpGrid.cpp gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/vatom' compiling ConfigInstall.cpp compiling AltMin.cpp compiling AtomValuePack.cpp compiling EndPlumed.cpp compiling PathReparameterization.cpp compiling LandmarkStaged.cpp compiling PRE.cpp compiling FindContour.cpp compiling AveragingVessel.cpp gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/secondarystructure' compiling FindContourSurface.cpp compiling EuclideanDistance.cpp compiling PathTools.cpp In file included from codebuilder.cpp:37: In file included from ././codebuilder.h:39: In file included from ./././assembler.h:36: In file included from ././././codeemitter.h:36: In file included from ./././././arch.h:37: ././././././operand.h:341:12: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 341 | return (_packed[0] == other._packed[0]) & | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && 342 | (_packed[1] == other._packed[1]) ; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ././././././operand.h:341:12: note: cast one or both operands to int to silence this warning ././././././operand.h:808:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 808 | static ASMJIT_INLINE bool isGp(const Operand_& op, uint32_t rId) noexcept { return isGp(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././././operand.h:808:86: note: cast one or both operands to int to silence this warning ././././././operand.h:809:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 809 | static ASMJIT_INLINE bool isVec(const Operand_& op, uint32_t rId) noexcept { return isVec(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././././operand.h:809:87: note: cast one or both operands to int to silence this warning 3 warnings generated. compiling codeholder.cpp In file included from codecompiler.cpp:37: In file included from ././assembler.h:36: In file included from ./././codeemitter.h:36: In file included from ././././arch.h:37: ./././././operand.h:341:12: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 341 | return (_packed[0] == other._packed[0]) & | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && 342 | (_packed[1] == other._packed[1]) ; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./././././operand.h:341:12: note: cast one or both operands to int to silence this warning ./././././operand.h:808:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 808 | static ASMJIT_INLINE bool isGp(const Operand_& op, uint32_t rId) noexcept { return isGp(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ./././././operand.h:808:86: note: cast one or both operands to int to silence this warning ./././././operand.h:809:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 809 | static ASMJIT_INLINE bool isVec(const Operand_& op, uint32_t rId) noexcept { return isVec(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ./././././operand.h:809:87: note: cast one or both operands to int to silence this warning 3 warnings generated. In file included from DumpAtoms.cpp:34: In file included from ./xdrfile/xdrfile_xtc.h:1: ./xdrfile/../../xdrfile/xdrfile_xtc.h:32:2: warning: '/*' within block comment [-Wcomment] 32 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- | ^ In file included from DumpAtoms.cpp:34: In file included from ./xdrfile/xdrfile_xtc.h:1: In file included from ./xdrfile/../../xdrfile/xdrfile_xtc.h:64: ./xdrfile/../../xdrfile/xdrfile.h:32:2: warning: '/*' within block comment [-Wcomment] 32 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- | ^ In file included from DumpAtoms.cpp:35: In file included from ./xdrfile/xdrfile_trr.h:1: ./xdrfile/../../xdrfile/xdrfile_trr.h:32:2: warning: '/*' within block comment [-Wcomment] 32 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- | ^ 3 warnings generated. compiling FitToTemplate.cpp compiling constpool.cpp In file included from codeemitter.cpp:33: In file included from ././assembler.h:36: In file included from ./././codeemitter.h:36: In file included from ././././arch.h:37: ./././././operand.h:341:12: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 341 | return (_packed[0] == other._packed[0]) & | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && 342 | (_packed[1] == other._packed[1]) ; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./././././operand.h:341:12: note: cast one or both operands to int to silence this warning ./././././operand.h:808:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 808 | static ASMJIT_INLINE bool isGp(const Operand_& op, uint32_t rId) noexcept { return isGp(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ./././././operand.h:808:86: note: cast one or both operands to int to silence this warning ./././././operand.h:809:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 809 | static ASMJIT_INLINE bool isVec(const Operand_& op, uint32_t rId) noexcept { return isVec(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ./././././operand.h:809:87: note: cast one or both operands to int to silence this warning 3 warnings generated. compiling cpuinfo.cpp compiling PropertyMap.cpp compiling ActionSetup.cpp compiling Flush.cpp compiling Group.cpp compiling FakeFrame.cpp In file included from CompiledExpression.cpp:68: In file included from ./asmjit/asmjit.h:1: In file included from ./asmjit/../../asmjit/asmjit.h:55: In file included from ./asmjit/../../asmjit/./base.h:33: In file included from ./asmjit/../../asmjit/././arch.h:37: ./asmjit/../../asmjit/./././operand.h:341:12: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 341 | return (_packed[0] == other._packed[0]) & | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && 342 | (_packed[1] == other._packed[1]) ; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./asmjit/../../asmjit/./././operand.h:341:12: note: cast one or both operands to int to silence this warning ./asmjit/../../asmjit/./././operand.h:808:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 808 | static ASMJIT_INLINE bool isGp(const Operand_& op, uint32_t rId) noexcept { return isGp(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ./asmjit/../../asmjit/./././operand.h:808:86: note: cast one or both operands to int to silence this warning ./asmjit/../../asmjit/./././operand.h:809:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 809 | static ASMJIT_INLINE bool isVec(const Operand_& op, uint32_t rId) noexcept { return isVec(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ./asmjit/../../asmjit/./././operand.h:809:87: note: cast one or both operands to int to silence this warning In file included from CompiledExpression.cpp:68: In file included from ./asmjit/asmjit.h:1: In file included from ./asmjit/../../asmjit/asmjit.h:59: In file included from ./asmjit/../../asmjit/./x86.h:35: In file included from ./asmjit/../../asmjit/././x86assembler.h:38: In file included from ./asmjit/../../asmjit/./././x86emitter.h:38: ./asmjit/../../asmjit/././././x86operand.h:379:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 379 | static ASMJIT_INLINE bool isGpb(const Operand_& op, uint32_t rId) noexcept { return isGpb(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ./asmjit/../../asmjit/././././x86operand.h:379:87: note: cast one or both operands to int to silence this warning ./asmjit/../../asmjit/././././x86operand.h:381:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 381 | static ASMJIT_INLINE bool isRip(const Operand_& op, uint32_t rId) noexcept { return isRip(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ./asmjit/../../asmjit/././././x86operand.h:381:87: note: cast one or both operands to int to silence this warning ./asmjit/../../asmjit/././././x86operand.h:382:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 382 | static ASMJIT_INLINE bool isSeg(const Operand_& op, uint32_t rId) noexcept { return isSeg(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ./asmjit/../../asmjit/././././x86operand.h:382:87: note: cast one or both operands to int to silence this warning ./asmjit/../../asmjit/././././x86operand.h:383:89: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 383 | static ASMJIT_INLINE bool isGpbLo(const Operand_& op, uint32_t rId) noexcept { return isGpbLo(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ./asmjit/../../asmjit/././././x86operand.h:383:89: note: cast one or both operands to int to silence this warning ./asmjit/../../asmjit/././././x86operand.h:384:89: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 384 | static ASMJIT_INLINE bool isGpbHi(const Operand_& op, uint32_t rId) noexcept { return isGpbHi(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ./asmjit/../../asmjit/././././x86operand.h:384:89: note: cast one or both operands to int to silence this warning ./asmjit/../../asmjit/././././x86operand.h:385:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 385 | static ASMJIT_INLINE bool isGpw(const Operand_& op, uint32_t rId) noexcept { return isGpw(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ./asmjit/../../asmjit/././././x86operand.h:385:87: note: cast one or both operands to int to silence this warning ./asmjit/../../asmjit/././././x86operand.h:386:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 386 | static ASMJIT_INLINE bool isGpd(const Operand_& op, uint32_t rId) noexcept { return isGpd(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ./asmjit/../../asmjit/././././x86operand.h:386:87: note: cast one or both operands to int to silence this warning ./asmjit/../../asmjit/././././x86operand.h:387:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 387 | static ASMJIT_INLINE bool isGpq(const Operand_& op, uint32_t rId) noexcept { return isGpq(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ./asmjit/../../asmjit/././././x86operand.h:387:87: note: cast one or both operands to int to silence this warning ./asmjit/../../asmjit/././././x86operand.h:388:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 388 | static ASMJIT_INLINE bool isFp(const Operand_& op, uint32_t rId) noexcept { return isFp(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ./asmjit/../../asmjit/././././x86operand.h:388:86: note: cast one or both operands to int to silence this warning ./asmjit/../../asmjit/././././x86operand.h:389:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 389 | static ASMJIT_INLINE bool isMm(const Operand_& op, uint32_t rId) noexcept { return isMm(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ./asmjit/../../asmjit/././././x86operand.h:389:86: note: cast one or both operands to int to silence this warning ./asmjit/../../asmjit/././././x86operand.h:390:85: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 390 | static ASMJIT_INLINE bool isK(const Operand_& op, uint32_t rId) noexcept { return isK(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ./asmjit/../../asmjit/././././x86operand.h:390:85: note: cast one or both operands to int to silence this warning ./asmjit/../../asmjit/././././x86operand.h:391:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 391 | static ASMJIT_INLINE bool isXmm(const Operand_& op, uint32_t rId) noexcept { return isXmm(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ./asmjit/../../asmjit/././././x86operand.h:391:87: note: cast one or both operands to int to silence this warning ./asmjit/../../asmjit/././././x86operand.h:392:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 392 | static ASMJIT_INLINE bool isYmm(const Operand_& op, uint32_t rId) noexcept { return isYmm(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ./asmjit/../../asmjit/././././x86operand.h:392:87: note: cast one or both operands to int to silence this warning ./asmjit/../../asmjit/././././x86operand.h:393:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 393 | static ASMJIT_INLINE bool isZmm(const Operand_& op, uint32_t rId) noexcept { return isZmm(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ./asmjit/../../asmjit/././././x86operand.h:393:87: note: cast one or both operands to int to silence this warning ./asmjit/../../asmjit/././././x86operand.h:394:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 394 | static ASMJIT_INLINE bool isBnd(const Operand_& op, uint32_t rId) noexcept { return isBnd(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ./asmjit/../../asmjit/././././x86operand.h:394:87: note: cast one or both operands to int to silence this warning ./asmjit/../../asmjit/././././x86operand.h:395:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 395 | static ASMJIT_INLINE bool isCr(const Operand_& op, uint32_t rId) noexcept { return isCr(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ./asmjit/../../asmjit/././././x86operand.h:395:86: note: cast one or both operands to int to silence this warning ./asmjit/../../asmjit/././././x86operand.h:396:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 396 | static ASMJIT_INLINE bool isDr(const Operand_& op, uint32_t rId) noexcept { return isDr(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ./asmjit/../../asmjit/././././x86operand.h:396:86: note: cast one or both operands to int to silence this warning 20 warnings generated. compiling MovingRestraint.cpp gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lepton' compiling Bridge.cpp compiling CoordinationBase.cpp gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/config' compiling Info.cpp gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/config' compiling IntermolecularDRMSD.cpp compiling FindSphericalContour.cpp compiling OutputColvarFile.cpp compiling ActionWithArguments.cpp compiling RDC.cpp compiling ActionShortcut.cpp compiling SpathVessel.cpp compiling Include.cpp compiling Between.cpp compiling Manual.cpp compiling MolInfo.cpp compiling DHEnergy.cpp compiling FourierTransform.cpp compiling BridgedMultiColvarFunction.cpp compiling ActionWithValue.cpp compiling Plumed.cpp compiling OutputPDBFile.cpp compiling Rescale.cpp In file included from DriverDouble.cpp:23: In file included from ./Driver.cpp:41: In file included from ./xdrfile/xdrfile_trr.h:1: ./xdrfile/../../xdrfile/xdrfile_trr.h:32:2: warning: '/*' within block comment [-Wcomment] 32 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- | ^ In file included from DriverDouble.cpp:23: In file included from ./Driver.cpp:41: In file included from ./xdrfile/xdrfile_trr.h:1: In file included from ./xdrfile/../../xdrfile/xdrfile_trr.h:64: ./xdrfile/../../xdrfile/xdrfile.h:32:2: warning: '/*' within block comment [-Wcomment] 32 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- | ^ In file included from DriverDouble.cpp:23: In file included from ./Driver.cpp:42: In file included from ./xdrfile/xdrfile_xtc.h:1: ./xdrfile/../../xdrfile/xdrfile_xtc.h:32:2: warning: '/*' within block comment [-Wcomment] 32 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- | ^ 3 warnings generated. compiling PdbRenumber.cpp compiling PrintDissimilarityMatrix.cpp compiling ReadAnalysisFrames.cpp compiling func.cpp In file included from codeholder.cpp:33: In file included from ././assembler.h:36: In file included from ./././codeemitter.h:36: In file included from ././././arch.h:37: ./././././operand.h:341:12: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 341 | return (_packed[0] == other._packed[0]) & | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && 342 | (_packed[1] == other._packed[1]) ; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./././././operand.h:341:12: note: cast one or both operands to int to silence this warning ./././././operand.h:808:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 808 | static ASMJIT_INLINE bool isGp(const Operand_& op, uint32_t rId) noexcept { return isGp(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ./././././operand.h:808:86: note: cast one or both operands to int to silence this warning ./././././operand.h:809:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 809 | static ASMJIT_INLINE bool isVec(const Operand_& op, uint32_t rId) noexcept { return isVec(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ./././././operand.h:809:87: note: cast one or both operands to int to silence this warning 3 warnings generated. compiling globals.cpp compiling Piecewise.cpp compiling CatomPack.cpp compiling GridPrintingBase.cpp In file included from cpuinfo.cpp:33: In file included from ././cpuinfo.h:36: In file included from ./././arch.h:37: ././././operand.h:341:12: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 341 | return (_packed[0] == other._packed[0]) & | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && 342 | (_packed[1] == other._packed[1]) ; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ././././operand.h:341:12: note: cast one or both operands to int to silence this warning ././././operand.h:808:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 808 | static ASMJIT_INLINE bool isGp(const Operand_& op, uint32_t rId) noexcept { return isGp(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././operand.h:808:86: note: cast one or both operands to int to silence this warning ././././operand.h:809:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 809 | static ASMJIT_INLINE bool isVec(const Operand_& op, uint32_t rId) noexcept { return isVec(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././operand.h:809:87: note: cast one or both operands to int to silence this warning 3 warnings generated. compiling inst.cpp compiling BridgeVessel.cpp compiling Stats.cpp GenExample.cpp:248:20: warning: variable 'n' set but not used [-Wunused-but-set-variable] 248 | for(unsigned n=0;; ++n) { | ^ 1 warning generated. compiling Sort.cpp compiling GridSearch.cpp compiling SimpleMD.cpp compiling FunctionVessel.cpp compiling CenterOfMultiColvar.cpp compiling TrigonometricPathVessel.cpp compiling Highest.cpp compiling DRMSD.cpp compiling Brent1DRootSearch.cpp compiling ZpathVessel.cpp compiling IntramolecularDRMSD.cpp compiling SAXS.cpp compiling ReadDissimilarityMatrix.cpp compiling CoordinationNumbers.cpp compiling Density.cpp compiling PBMetaD.cpp compiling Print.cpp compiling MahalanobisDistance.cpp compiling logging.cpp In file included from DriverFloat.cpp:23: In file included from ./Driver.cpp:41: In file included from ./xdrfile/xdrfile_trr.h:1: ./xdrfile/../../xdrfile/xdrfile_trr.h:32:2: warning: '/*' within block comment [-Wcomment] 32 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- | ^ In file included from DriverFloat.cpp:23: In file included from ./Driver.cpp:41: In file included from ./xdrfile/xdrfile_trr.h:1: In file included from ./xdrfile/../../xdrfile/xdrfile_trr.h:64: ./xdrfile/../../xdrfile/xdrfile.h:32:2: warning: '/*' within block comment [-Wcomment] 32 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- | ^ In file included from DriverFloat.cpp:23: In file included from ./Driver.cpp:42: In file included from ./xdrfile/xdrfile_xtc.h:1: ./xdrfile/../../xdrfile/xdrfile_xtc.h:32:2: warning: '/*' within block comment [-Wcomment] 32 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- | ^ 3 warnings generated. compiling Histogram.cpp compiling SumHills.cpp compiling Select.cpp In file included from inst.cpp:37: In file included from ././arch.h:37: ./././operand.h:341:12: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 341 | return (_packed[0] == other._packed[0]) & | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && 342 | (_packed[1] == other._packed[1]) ; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./././operand.h:341:12: note: cast one or both operands to int to silence this warning ./././operand.h:808:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 808 | static ASMJIT_INLINE bool isGp(const Operand_& op, uint32_t rId) noexcept { return isGp(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ./././operand.h:808:86: note: cast one or both operands to int to silence this warning ./././operand.h:809:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 809 | static ASMJIT_INLINE bool isVec(const Operand_& op, uint32_t rId) noexcept { return isVec(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ./././operand.h:809:87: note: cast one or both operands to int to silence this warning 3 warnings generated. compiling operand.cpp CS2Backbone.cpp:214:14: warning: variable 'nline' set but not used [-Wunused-but-set-variable] 214 | unsigned nline = 0; | ^ 1 warning generated. compiling Selector.cpp compiling ActionWithVirtualAtom.cpp compiling GridToXYZ.cpp compiling GridVessel.cpp PathTools.cpp:280:48: warning: variable 'nframes' set but not used [-Wunused-but-set-variable] 280 | OFile ofile; ofile.open(ofilename); unsigned nframes=0; | ^ 1 warning generated. compiling osutils.cpp compiling Citations.cpp compiling DihedralCorrelation.cpp compiling MetricRegister.cpp compiling RandomExchanges.cpp In file included from func.cpp:33: In file included from ././arch.h:37: ./././operand.h:341:12: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 341 | return (_packed[0] == other._packed[0]) & | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && 342 | (_packed[1] == other._packed[1]) ; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./././operand.h:341:12: note: cast one or both operands to int to silence this warning ./././operand.h:808:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 808 | static ASMJIT_INLINE bool isGp(const Operand_& op, uint32_t rId) noexcept { return isGp(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ./././operand.h:808:86: note: cast one or both operands to int to silence this warning ./././operand.h:809:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 809 | static ASMJIT_INLINE bool isVec(const Operand_& op, uint32_t rId) noexcept { return isVec(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ./././operand.h:809:87: note: cast one or both operands to int to silence this warning In file included from func.cpp:37: In file included from ././x86internal_p.h:39: In file included from ./././x86emitter.h:38: ././././x86operand.h:379:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 379 | static ASMJIT_INLINE bool isGpb(const Operand_& op, uint32_t rId) noexcept { return isGpb(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:379:87: note: cast one or both operands to int to silence this warning ././././x86operand.h:381:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 381 | static ASMJIT_INLINE bool isRip(const Operand_& op, uint32_t rId) noexcept { return isRip(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:381:87: note: cast one or both operands to int to silence this warning ././././x86operand.h:382:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 382 | static ASMJIT_INLINE bool isSeg(const Operand_& op, uint32_t rId) noexcept { return isSeg(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:382:87: note: cast one or both operands to int to silence this warning ././././x86operand.h:383:89: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 383 | static ASMJIT_INLINE bool isGpbLo(const Operand_& op, uint32_t rId) noexcept { return isGpbLo(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:383:89: note: cast one or both operands to int to silence this warning ././././x86operand.h:384:89: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 384 | static ASMJIT_INLINE bool isGpbHi(const Operand_& op, uint32_t rId) noexcept { return isGpbHi(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:384:89: note: cast one or both operands to int to silence this warning ././././x86operand.h:385:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 385 | static ASMJIT_INLINE bool isGpw(const Operand_& op, uint32_t rId) noexcept { return isGpw(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:385:87: note: cast one or both operands to int to silence this warning ././././x86operand.h:386:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 386 | static ASMJIT_INLINE bool isGpd(const Operand_& op, uint32_t rId) noexcept { return isGpd(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:386:87: note: cast one or both operands to int to silence this warning ././././x86operand.h:387:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 387 | static ASMJIT_INLINE bool isGpq(const Operand_& op, uint32_t rId) noexcept { return isGpq(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:387:87: note: cast one or both operands to int to silence this warning ././././x86operand.h:388:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 388 | static ASMJIT_INLINE bool isFp(const Operand_& op, uint32_t rId) noexcept { return isFp(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:388:86: note: cast one or both operands to int to silence this warning ././././x86operand.h:389:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 389 | static ASMJIT_INLINE bool isMm(const Operand_& op, uint32_t rId) noexcept { return isMm(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:389:86: note: cast one or both operands to int to silence this warning ././././x86operand.h:390:85: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 390 | static ASMJIT_INLINE bool isK(const Operand_& op, uint32_t rId) noexcept { return isK(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:390:85: note: cast one or both operands to int to silence this warning ././././x86operand.h:391:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 391 | static ASMJIT_INLINE bool isXmm(const Operand_& op, uint32_t rId) noexcept { return isXmm(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:391:87: note: cast one or both operands to int to silence this warning ././././x86operand.h:392:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 392 | static ASMJIT_INLINE bool isYmm(const Operand_& op, uint32_t rId) noexcept { return isYmm(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:392:87: note: cast one or both operands to int to silence this warning ././././x86operand.h:393:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 393 | static ASMJIT_INLINE bool isZmm(const Operand_& op, uint32_t rId) noexcept { return isZmm(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:393:87: note: cast one or both operands to int to silence this warning ././././x86operand.h:394:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 394 | static ASMJIT_INLINE bool isBnd(const Operand_& op, uint32_t rId) noexcept { return isBnd(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:394:87: note: cast one or both operands to int to silence this warning ././././x86operand.h:395:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 395 | static ASMJIT_INLINE bool isCr(const Operand_& op, uint32_t rId) noexcept { return isCr(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:395:86: note: cast one or both operands to int to silence this warning ././././x86operand.h:396:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 396 | static ASMJIT_INLINE bool isDr(const Operand_& op, uint32_t rId) noexcept { return isDr(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:396:86: note: cast one or both operands to int to silence this warning 20 warnings generated. compiling Read.cpp compiling regalloc.cpp compiling ResetCell.cpp compiling kT.cpp compiling Time.cpp compiling LessThan.cpp compiling ReselectLandmarks.cpp compiling Dimer.cpp compiling HistogramOnGrid.cpp compiling Atoms.cpp compiling Restraint.cpp compiling Communicator.cpp compiling pesmd.cpp compiling Dipole.cpp compiling DistanceFromContour.cpp compiling SelectRandomFrames.cpp compiling CLTool.cpp ../maketools/makecmd map < CLToolMain.cpp > CLToolMainMap.inc ../maketools/makecmd enum < CLToolMain.cpp > CLToolMainEnum.inc compiling CLToolRegister.cpp compiling ConjugateGradient.cpp compiling Distances.cpp compiling IntegrateGrid.cpp compiling Max.cpp In file included from logging.cpp:37: In file included from ././codeholder.h:36: In file included from ./././arch.h:37: ././././operand.h:341:12: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 341 | return (_packed[0] == other._packed[0]) & | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && 342 | (_packed[1] == other._packed[1]) ; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ././././operand.h:341:12: note: cast one or both operands to int to silence this warning ././././operand.h:808:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 808 | static ASMJIT_INLINE bool isGp(const Operand_& op, uint32_t rId) noexcept { return isGp(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././operand.h:808:86: note: cast one or both operands to int to silence this warning ././././operand.h:809:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 809 | static ASMJIT_INLINE bool isVec(const Operand_& op, uint32_t rId) noexcept { return isVec(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././operand.h:809:87: note: cast one or both operands to int to silence this warning 3 warnings generated. compiling DLLoader.cpp compiling Lowest.cpp compiling Target.cpp compiling Distance.cpp compiling string.cpp compiling Mean.cpp compiling runtime.cpp compiling SelectWithStride.cpp compiling DumpMultiColvar.cpp compiling UpdateIf.cpp compiling InterpolateGrid.cpp compiling WholeMolecules.cpp compiling MultiDomainRMSD.cpp compiling DynamicList.cpp In file included from regalloc.cpp:37: In file included from ././regalloc_p.h:39: In file included from ./././codecompiler.h:39: In file included from ././././assembler.h:36: In file included from ./././././codeemitter.h:36: In file included from ././././././arch.h:37: ./././././././operand.h:341:12: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 341 | return (_packed[0] == other._packed[0]) & | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && 342 | (_packed[1] == other._packed[1]) ; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./././././././operand.h:341:12: note: cast one or both operands to int to silence this warning ./././././././operand.h:808:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 808 | static ASMJIT_INLINE bool isGp(const Operand_& op, uint32_t rId) noexcept { return isGp(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ./././././././operand.h:808:86: note: cast one or both operands to int to silence this warning ./././././././operand.h:809:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 809 | static ASMJIT_INLINE bool isVec(const Operand_& op, uint32_t rId) noexcept { return isVec(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ./././././././operand.h:809:87: note: cast one or both operands to int to silence this warning 3 warnings generated. compiling utils.cpp compiling FilterBetween.cpp compiling NormalizedEuclideanDistance.cpp In file included from operand.cpp:33: ././operand.h:341:12: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 341 | return (_packed[0] == other._packed[0]) & | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && 342 | (_packed[1] == other._packed[1]) ; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ././operand.h:341:12: note: cast one or both operands to int to silence this warning ././operand.h:808:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 808 | static ASMJIT_INLINE bool isGp(const Operand_& op, uint32_t rId) noexcept { return isGp(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././operand.h:808:86: note: cast one or both operands to int to silence this warning ././operand.h:809:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 809 | static ASMJIT_INLINE bool isVec(const Operand_& op, uint32_t rId) noexcept { return isVec(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././operand.h:809:87: note: cast one or both operands to int to silence this warning 3 warnings generated. compiling FilterLessThan.cpp compiling vmem.cpp compiling Completion.cpp compiling WhamHistogram.cpp compiling OptimalRMSD.cpp compiling FilterMoreThan.cpp compiling ERMSD.cpp In file included from runtime.cpp:33: In file included from ././assembler.h:36: In file included from ./././codeemitter.h:36: In file included from ././././arch.h:37: ./././././operand.h:341:12: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 341 | return (_packed[0] == other._packed[0]) & | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && 342 | (_packed[1] == other._packed[1]) ; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./././././operand.h:341:12: note: cast one or both operands to int to silence this warning ./././././operand.h:808:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 808 | static ASMJIT_INLINE bool isGp(const Operand_& op, uint32_t rId) noexcept { return isGp(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ./././././operand.h:808:86: note: cast one or both operands to int to silence this warning ./././././operand.h:809:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 809 | static ASMJIT_INLINE bool isVec(const Operand_& op, uint32_t rId) noexcept { return isVec(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ./././././operand.h:809:87: note: cast one or both operands to int to silence this warning 3 warnings generated. compiling x86builder.cpp compiling x86assembler.cpp compiling EEFSolv.cpp compiling RMSDBase.cpp gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/mapping' compiling WrapAround.cpp compiling ReferenceArguments.cpp compiling Min.cpp compiling ReweightBase.cpp compiling FileBase.cpp compiling Exception.cpp compiling ReweightBias.cpp compiling InPlaneDistances.cpp compiling LocalAverage.cpp compiling Moments.cpp compiling ForwardDecl.cpp compiling Colvar.cpp compiling MoreThan.cpp compiling ERMSD.cpp compiling Energy.cpp compiling Grid.cpp compiling WhamWeights.cpp compiling x86compiler.cpp compiling MultiColvarBase.cpp compiling HistogramBead.cpp vmem.cpp:284:13: warning: unused function 'vMemMgrCheckTree' [-Wunused-function] 284 | static bool vMemMgrCheckTree(VMemMgr* self) noexcept { | ^~~~~~~~~~~~~~~~ 1 warning generated. compiling ReweightMetad.cpp compiling ReweightTemperaturePressure.cpp compiling x86inst.cpp compiling ExtraCV.cpp compiling Fake.cpp compiling OrderingVessel.cpp compiling IFile.cpp compiling KernelFunctions.cpp compiling Keywords.cpp compiling ShortcutVessel.cpp compiling DataFetchingObject.cpp compiling LatticeReduction.cpp compiling ExchangePatterns.cpp compiling ReferenceAtoms.cpp compiling StoreDataVessel.cpp compiling x86instimpl.cpp compiling LinkCells.cpp compiling x86internal.cpp compiling GHBFIX.cpp compiling ReweightWham.cpp gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/function' compiling Sum.cpp compiling MultiColvarCombine.cpp gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/cltools' compiling FlexibleBin.cpp compiling Gyration.cpp In file included from x86builder.cpp:37: In file included from ././x86builder.h:39: In file included from ./././codebuilder.h:39: In file included from ././././assembler.h:36: In file included from ./././././codeemitter.h:36: In file included from ././././././arch.h:37: ./././././././operand.h:341:12: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 341 | return (_packed[0] == other._packed[0]) & | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && 342 | (_packed[1] == other._packed[1]) ; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./././././././operand.h:341:12: note: cast one or both operands to int to silence this warning ./././././././operand.h:808:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 808 | static ASMJIT_INLINE bool isGp(const Operand_& op, uint32_t rId) noexcept { return isGp(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ./././././././operand.h:808:86: note: cast one or both operands to int to silence this warning ./././././././operand.h:809:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 809 | static ASMJIT_INLINE bool isVec(const Operand_& op, uint32_t rId) noexcept { return isVec(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ./././././././operand.h:809:87: note: cast one or both operands to int to silence this warning In file included from x86builder.cpp:37: In file included from ././x86builder.h:41: In file included from ./././x86emitter.h:38: ././././x86operand.h:379:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 379 | static ASMJIT_INLINE bool isGpb(const Operand_& op, uint32_t rId) noexcept { return isGpb(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:379:87: note: cast one or both operands to int to silence this warning ././././x86operand.h:381:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 381 | static ASMJIT_INLINE bool isRip(const Operand_& op, uint32_t rId) noexcept { return isRip(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:381:87: note: cast one or both operands to int to silence this warning ././././x86operand.h:382:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 382 | static ASMJIT_INLINE bool isSeg(const Operand_& op, uint32_t rId) noexcept { return isSeg(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:382:87: note: cast one or both operands to int to silence this warning ././././x86operand.h:383:89: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 383 | static ASMJIT_INLINE bool isGpbLo(const Operand_& op, uint32_t rId) noexcept { return isGpbLo(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:383:89: note: cast one or both operands to int to silence this warning ././././x86operand.h:384:89: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 384 | static ASMJIT_INLINE bool isGpbHi(const Operand_& op, uint32_t rId) noexcept { return isGpbHi(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:384:89: note: cast one or both operands to int to silence this warning ././././x86operand.h:385:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 385 | static ASMJIT_INLINE bool isGpw(const Operand_& op, uint32_t rId) noexcept { return isGpw(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:385:87: note: cast one or both operands to int to silence this warning ././././x86operand.h:386:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 386 | static ASMJIT_INLINE bool isGpd(const Operand_& op, uint32_t rId) noexcept { return isGpd(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:386:87: note: cast one or both operands to int to silence this warning ././././x86operand.h:387:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 387 | static ASMJIT_INLINE bool isGpq(const Operand_& op, uint32_t rId) noexcept { return isGpq(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:387:87: note: cast one or both operands to int to silence this warning ././././x86operand.h:388:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 388 | static ASMJIT_INLINE bool isFp(const Operand_& op, uint32_t rId) noexcept { return isFp(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:388:86: note: cast one or both operands to int to silence this warning ././././x86operand.h:389:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 389 | static ASMJIT_INLINE bool isMm(const Operand_& op, uint32_t rId) noexcept { return isMm(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:389:86: note: cast one or both operands to int to silence this warning ././././x86operand.h:390:85: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 390 | static ASMJIT_INLINE bool isK(const Operand_& op, uint32_t rId) noexcept { return isK(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:390:85: note: cast one or both operands to int to silence this warning ././././x86operand.h:391:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 391 | static ASMJIT_INLINE bool isXmm(const Operand_& op, uint32_t rId) noexcept { return isXmm(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:391:87: note: cast one or both operands to int to silence this warning ././././x86operand.h:392:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 392 | static ASMJIT_INLINE bool isYmm(const Operand_& op, uint32_t rId) noexcept { return isYmm(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:392:87: note: cast one or both operands to int to silence this warning ././././x86operand.h:393:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 393 | static ASMJIT_INLINE bool isZmm(const Operand_& op, uint32_t rId) noexcept { return isZmm(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:393:87: note: cast one or both operands to int to silence this warning ././././x86operand.h:394:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 394 | static ASMJIT_INLINE bool isBnd(const Operand_& op, uint32_t rId) noexcept { return isBnd(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:394:87: note: cast one or both operands to int to silence this warning ././././x86operand.h:395:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 395 | static ASMJIT_INLINE bool isCr(const Operand_& op, uint32_t rId) noexcept { return isCr(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:395:86: note: cast one or both operands to int to silence this warning ././././x86operand.h:396:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 396 | static ASMJIT_INLINE bool isDr(const Operand_& op, uint32_t rId) noexcept { return isDr(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:396:86: note: cast one or both operands to int to silence this warning 20 warnings generated. compiling x86logging.cpp compiling ReferenceConfiguration.cpp compiling ReferenceValuePack.cpp compiling MultiColvarDensity.cpp compiling MultiColvarFilter.cpp compiling MultiColvarProduct.cpp compiling Log.cpp compiling UWalls.cpp gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/gridtools' compiling MultiRMSD.cpp ../maketools/makecmd map < GREX.cpp > GREXMap.inc ../maketools/makecmd enum < GREX.cpp > GREXEnum.inc compiling NumberOfLinks.cpp compiling SimpleRMSD.cpp compiling Torsions.cpp compiling MDAtoms.cpp compiling GenericMolInfo.cpp compiling SingleDomainRMSD.cpp compiling LoopUnroller.cpp compiling x86operand.cpp compiling ValueVessel.cpp compiling Vessel.cpp ../maketools/makeModuleMap ModuleMap.inc compiling VolumeAround.cpp ../maketools/makecmd map < PlumedMain.cpp > PlumedMainMap.inc ../maketools/makecmd enum < PlumedMain.cpp > PlumedMainEnum.inc compiling PlumedMainInitializer.cpp compiling MatrixSquareBracketsAccess.cpp compiling Matrix.cpp In file included from x86instimpl.cpp:35: In file included from ././x86instimpl_p.h:36: In file included from ./././x86inst.h:36: In file included from ././././assembler.h:36: In file included from ./././././codeemitter.h:36: In file included from ././././././arch.h:37: ./././././././operand.h:341:12: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 341 | return (_packed[0] == other._packed[0]) & | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && 342 | (_packed[1] == other._packed[1]) ; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./././././././operand.h:341:12: note: cast one or both operands to int to silence this warning ./././././././operand.h:808:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 808 | static ASMJIT_INLINE bool isGp(const Operand_& op, uint32_t rId) noexcept { return isGp(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ./././././././operand.h:808:86: note: cast one or both operands to int to silence this warning ./././././././operand.h:809:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 809 | static ASMJIT_INLINE bool isVec(const Operand_& op, uint32_t rId) noexcept { return isVec(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ./././././././operand.h:809:87: note: cast one or both operands to int to silence this warning In file included from x86instimpl.cpp:36: ././x86operand.h:379:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 379 | static ASMJIT_INLINE bool isGpb(const Operand_& op, uint32_t rId) noexcept { return isGpb(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:379:87: note: cast one or both operands to int to silence this warning ././x86operand.h:381:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 381 | static ASMJIT_INLINE bool isRip(const Operand_& op, uint32_t rId) noexcept { return isRip(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:381:87: note: cast one or both operands to int to silence this warning ././x86operand.h:382:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 382 | static ASMJIT_INLINE bool isSeg(const Operand_& op, uint32_t rId) noexcept { return isSeg(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:382:87: note: cast one or both operands to int to silence this warning ././x86operand.h:383:89: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 383 | static ASMJIT_INLINE bool isGpbLo(const Operand_& op, uint32_t rId) noexcept { return isGpbLo(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:383:89: note: cast one or both operands to int to silence this warning ././x86operand.h:384:89: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 384 | static ASMJIT_INLINE bool isGpbHi(const Operand_& op, uint32_t rId) noexcept { return isGpbHi(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:384:89: note: cast one or both operands to int to silence this warning ././x86operand.h:385:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 385 | static ASMJIT_INLINE bool isGpw(const Operand_& op, uint32_t rId) noexcept { return isGpw(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:385:87: note: cast one or both operands to int to silence this warning ././x86operand.h:386:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 386 | static ASMJIT_INLINE bool isGpd(const Operand_& op, uint32_t rId) noexcept { return isGpd(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:386:87: note: cast one or both operands to int to silence this warning ././x86operand.h:387:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 387 | static ASMJIT_INLINE bool isGpq(const Operand_& op, uint32_t rId) noexcept { return isGpq(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:387:87: note: cast one or both operands to int to silence this warning ././x86operand.h:388:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 388 | static ASMJIT_INLINE bool isFp(const Operand_& op, uint32_t rId) noexcept { return isFp(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:388:86: note: cast one or both operands to int to silence this warning ././x86operand.h:389:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 389 | static ASMJIT_INLINE bool isMm(const Operand_& op, uint32_t rId) noexcept { return isMm(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:389:86: note: cast one or both operands to int to silence this warning ././x86operand.h:390:85: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 390 | static ASMJIT_INLINE bool isK(const Operand_& op, uint32_t rId) noexcept { return isK(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:390:85: note: cast one or both operands to int to silence this warning ././x86operand.h:391:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 391 | static ASMJIT_INLINE bool isXmm(const Operand_& op, uint32_t rId) noexcept { return isXmm(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:391:87: note: cast one or both operands to int to silence this warning ././x86operand.h:392:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 392 | static ASMJIT_INLINE bool isYmm(const Operand_& op, uint32_t rId) noexcept { return isYmm(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:392:87: note: cast one or both operands to int to silence this warning ././x86operand.h:393:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 393 | static ASMJIT_INLINE bool isZmm(const Operand_& op, uint32_t rId) noexcept { return isZmm(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:393:87: note: cast one or both operands to int to silence this warning ././x86operand.h:394:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 394 | static ASMJIT_INLINE bool isBnd(const Operand_& op, uint32_t rId) noexcept { return isBnd(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:394:87: note: cast one or both operands to int to silence this warning ././x86operand.h:395:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 395 | static ASMJIT_INLINE bool isCr(const Operand_& op, uint32_t rId) noexcept { return isCr(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:395:86: note: cast one or both operands to int to silence this warning ././x86operand.h:396:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 396 | static ASMJIT_INLINE bool isDr(const Operand_& op, uint32_t rId) noexcept { return isDr(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:396:86: note: cast one or both operands to int to silence this warning 20 warnings generated. compiling Minimise1DBrent.cpp compiling PCARMSD.cpp In file included from x86compiler.cpp:38: In file included from ././x86compiler.h:39: In file included from ./././codecompiler.h:39: In file included from ././././assembler.h:36: In file included from ./././././codeemitter.h:36: In file included from ././././././arch.h:37: ./././././././operand.h:341:12: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 341 | return (_packed[0] == other._packed[0]) & | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && 342 | (_packed[1] == other._packed[1]) ; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./././././././operand.h:341:12: note: cast one or both operands to int to silence this warning ./././././././operand.h:808:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 808 | static ASMJIT_INLINE bool isGp(const Operand_& op, uint32_t rId) noexcept { return isGp(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ./././././././operand.h:808:86: note: cast one or both operands to int to silence this warning ./././././././operand.h:809:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 809 | static ASMJIT_INLINE bool isVec(const Operand_& op, uint32_t rId) noexcept { return isVec(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ./././././././operand.h:809:87: note: cast one or both operands to int to silence this warning In file included from x86compiler.cpp:38: In file included from ././x86compiler.h:41: In file included from ./././x86emitter.h:38: ././././x86operand.h:379:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 379 | static ASMJIT_INLINE bool isGpb(const Operand_& op, uint32_t rId) noexcept { return isGpb(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:379:87: note: cast one or both operands to int to silence this warning ././././x86operand.h:381:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 381 | static ASMJIT_INLINE bool isRip(const Operand_& op, uint32_t rId) noexcept { return isRip(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:381:87: note: cast one or both operands to int to silence this warning ././././x86operand.h:382:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 382 | static ASMJIT_INLINE bool isSeg(const Operand_& op, uint32_t rId) noexcept { return isSeg(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:382:87: note: cast one or both operands to int to silence this warning ././././x86operand.h:383:89: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 383 | static ASMJIT_INLINE bool isGpbLo(const Operand_& op, uint32_t rId) noexcept { return isGpbLo(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:383:89: note: cast one or both operands to int to silence this warning ././././x86operand.h:384:89: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 384 | static ASMJIT_INLINE bool isGpbHi(const Operand_& op, uint32_t rId) noexcept { return isGpbHi(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:384:89: note: cast one or both operands to int to silence this warning ././././x86operand.h:385:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 385 | static ASMJIT_INLINE bool isGpw(const Operand_& op, uint32_t rId) noexcept { return isGpw(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:385:87: note: cast one or both operands to int to silence this warning ././././x86operand.h:386:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 386 | static ASMJIT_INLINE bool isGpd(const Operand_& op, uint32_t rId) noexcept { return isGpd(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:386:87: note: cast one or both operands to int to silence this warning ././././x86operand.h:387:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 387 | static ASMJIT_INLINE bool isGpq(const Operand_& op, uint32_t rId) noexcept { return isGpq(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:387:87: note: cast one or both operands to int to silence this warning ././././x86operand.h:388:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 388 | static ASMJIT_INLINE bool isFp(const Operand_& op, uint32_t rId) noexcept { return isFp(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:388:86: note: cast one or both operands to int to silence this warning ././././x86operand.h:389:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 389 | static ASMJIT_INLINE bool isMm(const Operand_& op, uint32_t rId) noexcept { return isMm(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:389:86: note: cast one or both operands to int to silence this warning ././././x86operand.h:390:85: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 390 | static ASMJIT_INLINE bool isK(const Operand_& op, uint32_t rId) noexcept { return isK(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:390:85: note: cast one or both operands to int to silence this warning ././././x86operand.h:391:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 391 | static ASMJIT_INLINE bool isXmm(const Operand_& op, uint32_t rId) noexcept { return isXmm(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:391:87: note: cast one or both operands to int to silence this warning ././././x86operand.h:392:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 392 | static ASMJIT_INLINE bool isYmm(const Operand_& op, uint32_t rId) noexcept { return isYmm(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:392:87: note: cast one or both operands to int to silence this warning ././././x86operand.h:393:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 393 | static ASMJIT_INLINE bool isZmm(const Operand_& op, uint32_t rId) noexcept { return isZmm(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:393:87: note: cast one or both operands to int to silence this warning ././././x86operand.h:394:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 394 | static ASMJIT_INLINE bool isBnd(const Operand_& op, uint32_t rId) noexcept { return isBnd(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:394:87: note: cast one or both operands to int to silence this warning ././././x86operand.h:395:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 395 | static ASMJIT_INLINE bool isCr(const Operand_& op, uint32_t rId) noexcept { return isCr(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:395:86: note: cast one or both operands to int to silence this warning ././././x86operand.h:396:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 396 | static ASMJIT_INLINE bool isDr(const Operand_& op, uint32_t rId) noexcept { return isDr(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:396:86: note: cast one or both operands to int to silence this warning 20 warnings generated. compiling x86operand_regs.cpp gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/generic' compiling VesselRegister.cpp compiling PathMSD.cpp compiling TargetDist.cpp compiling x86regalloc.cpp compiling Value.cpp compiling PathMSDBase.cpp compiling MinimiseBase.cpp In file included from x86logging.cpp:38: In file included from ././x86inst.h:36: In file included from ./././assembler.h:36: In file included from ././././codeemitter.h:36: In file included from ./././././arch.h:37: ././././././operand.h:341:12: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 341 | return (_packed[0] == other._packed[0]) & | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && 342 | (_packed[1] == other._packed[1]) ; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ././././././operand.h:341:12: note: cast one or both operands to int to silence this warning ././././././operand.h:808:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 808 | static ASMJIT_INLINE bool isGp(const Operand_& op, uint32_t rId) noexcept { return isGp(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././././operand.h:808:86: note: cast one or both operands to int to silence this warning ././././././operand.h:809:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 809 | static ASMJIT_INLINE bool isVec(const Operand_& op, uint32_t rId) noexcept { return isVec(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././././operand.h:809:87: note: cast one or both operands to int to silence this warning In file included from x86logging.cpp:40: ././x86operand.h:379:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 379 | static ASMJIT_INLINE bool isGpb(const Operand_& op, uint32_t rId) noexcept { return isGpb(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:379:87: note: cast one or both operands to int to silence this warning ././x86operand.h:381:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 381 | static ASMJIT_INLINE bool isRip(const Operand_& op, uint32_t rId) noexcept { return isRip(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:381:87: note: cast one or both operands to int to silence this warning ././x86operand.h:382:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 382 | static ASMJIT_INLINE bool isSeg(const Operand_& op, uint32_t rId) noexcept { return isSeg(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:382:87: note: cast one or both operands to int to silence this warning ././x86operand.h:383:89: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 383 | static ASMJIT_INLINE bool isGpbLo(const Operand_& op, uint32_t rId) noexcept { return isGpbLo(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:383:89: note: cast one or both operands to int to silence this warning ././x86operand.h:384:89: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 384 | static ASMJIT_INLINE bool isGpbHi(const Operand_& op, uint32_t rId) noexcept { return isGpbHi(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:384:89: note: cast one or both operands to int to silence this warning ././x86operand.h:385:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 385 | static ASMJIT_INLINE bool isGpw(const Operand_& op, uint32_t rId) noexcept { return isGpw(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:385:87: note: cast one or both operands to int to silence this warning ././x86operand.h:386:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 386 | static ASMJIT_INLINE bool isGpd(const Operand_& op, uint32_t rId) noexcept { return isGpd(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:386:87: note: cast one or both operands to int to silence this warning ././x86operand.h:387:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 387 | static ASMJIT_INLINE bool isGpq(const Operand_& op, uint32_t rId) noexcept { return isGpq(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:387:87: note: cast one or both operands to int to silence this warning ././x86operand.h:388:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 388 | static ASMJIT_INLINE bool isFp(const Operand_& op, uint32_t rId) noexcept { return isFp(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:388:86: note: cast one or both operands to int to silence this warning ././x86operand.h:389:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 389 | static ASMJIT_INLINE bool isMm(const Operand_& op, uint32_t rId) noexcept { return isMm(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:389:86: note: cast one or both operands to int to silence this warning ././x86operand.h:390:85: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 390 | static ASMJIT_INLINE bool isK(const Operand_& op, uint32_t rId) noexcept { return isK(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:390:85: note: cast one or both operands to int to silence this warning ././x86operand.h:391:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 391 | static ASMJIT_INLINE bool isXmm(const Operand_& op, uint32_t rId) noexcept { return isXmm(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:391:87: note: cast one or both operands to int to silence this warning ././x86operand.h:392:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 392 | static ASMJIT_INLINE bool isYmm(const Operand_& op, uint32_t rId) noexcept { return isYmm(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:392:87: note: cast one or both operands to int to silence this warning ././x86operand.h:393:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 393 | static ASMJIT_INLINE bool isZmm(const Operand_& op, uint32_t rId) noexcept { return isZmm(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:393:87: note: cast one or both operands to int to silence this warning ././x86operand.h:394:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 394 | static ASMJIT_INLINE bool isBnd(const Operand_& op, uint32_t rId) noexcept { return isBnd(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:394:87: note: cast one or both operands to int to silence this warning ././x86operand.h:395:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 395 | static ASMJIT_INLINE bool isCr(const Operand_& op, uint32_t rId) noexcept { return isCr(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:395:86: note: cast one or both operands to int to silence this warning ././x86operand.h:396:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 396 | static ASMJIT_INLINE bool isDr(const Operand_& op, uint32_t rId) noexcept { return isDr(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:396:86: note: cast one or both operands to int to silence this warning 20 warnings generated. compiling MolDataClass.cpp compiling Position.cpp compiling zone.cpp compiling VolumeBetweenContours.cpp In file included from x86inst.cpp:56: In file included from ././cpuinfo.h:36: In file included from ./././arch.h:37: ././././operand.h:341:12: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 341 | return (_packed[0] == other._packed[0]) & | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && 342 | (_packed[1] == other._packed[1]) ; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ././././operand.h:341:12: note: cast one or both operands to int to silence this warning ././././operand.h:808:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 808 | static ASMJIT_INLINE bool isGp(const Operand_& op, uint32_t rId) noexcept { return isGp(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././operand.h:808:86: note: cast one or both operands to int to silence this warning ././././operand.h:809:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 809 | static ASMJIT_INLINE bool isVec(const Operand_& op, uint32_t rId) noexcept { return isVec(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././operand.h:809:87: note: cast one or both operands to int to silence this warning In file included from x86inst.cpp:59: ././x86operand.h:379:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 379 | static ASMJIT_INLINE bool isGpb(const Operand_& op, uint32_t rId) noexcept { return isGpb(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:379:87: note: cast one or both operands to int to silence this warning ././x86operand.h:381:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 381 | static ASMJIT_INLINE bool isRip(const Operand_& op, uint32_t rId) noexcept { return isRip(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:381:87: note: cast one or both operands to int to silence this warning ././x86operand.h:382:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 382 | static ASMJIT_INLINE bool isSeg(const Operand_& op, uint32_t rId) noexcept { return isSeg(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:382:87: note: cast one or both operands to int to silence this warning ././x86operand.h:383:89: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 383 | static ASMJIT_INLINE bool isGpbLo(const Operand_& op, uint32_t rId) noexcept { return isGpbLo(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:383:89: note: cast one or both operands to int to silence this warning ././x86operand.h:384:89: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 384 | static ASMJIT_INLINE bool isGpbHi(const Operand_& op, uint32_t rId) noexcept { return isGpbHi(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:384:89: note: cast one or both operands to int to silence this warning ././x86operand.h:385:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 385 | static ASMJIT_INLINE bool isGpw(const Operand_& op, uint32_t rId) noexcept { return isGpw(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:385:87: note: cast one or both operands to int to silence this warning ././x86operand.h:386:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 386 | static ASMJIT_INLINE bool isGpd(const Operand_& op, uint32_t rId) noexcept { return isGpd(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:386:87: note: cast one or both operands to int to silence this warning ././x86operand.h:387:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 387 | static ASMJIT_INLINE bool isGpq(const Operand_& op, uint32_t rId) noexcept { return isGpq(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:387:87: note: cast one or both operands to int to silence this warning ././x86operand.h:388:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 388 | static ASMJIT_INLINE bool isFp(const Operand_& op, uint32_t rId) noexcept { return isFp(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:388:86: note: cast one or both operands to int to silence this warning ././x86operand.h:389:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 389 | static ASMJIT_INLINE bool isMm(const Operand_& op, uint32_t rId) noexcept { return isMm(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:389:86: note: cast one or both operands to int to silence this warning ././x86operand.h:390:85: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 390 | static ASMJIT_INLINE bool isK(const Operand_& op, uint32_t rId) noexcept { return isK(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:390:85: note: cast one or both operands to int to silence this warning ././x86operand.h:391:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 391 | static ASMJIT_INLINE bool isXmm(const Operand_& op, uint32_t rId) noexcept { return isXmm(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:391:87: note: cast one or both operands to int to silence this warning ././x86operand.h:392:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 392 | static ASMJIT_INLINE bool isYmm(const Operand_& op, uint32_t rId) noexcept { return isYmm(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:392:87: note: cast one or both operands to int to silence this warning ././x86operand.h:393:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 393 | static ASMJIT_INLINE bool isZmm(const Operand_& op, uint32_t rId) noexcept { return isZmm(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:393:87: note: cast one or both operands to int to silence this warning ././x86operand.h:394:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 394 | static ASMJIT_INLINE bool isBnd(const Operand_& op, uint32_t rId) noexcept { return isBnd(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:394:87: note: cast one or both operands to int to silence this warning ././x86operand.h:395:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 395 | static ASMJIT_INLINE bool isCr(const Operand_& op, uint32_t rId) noexcept { return isCr(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:395:86: note: cast one or both operands to int to silence this warning ././x86operand.h:396:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 396 | static ASMJIT_INLINE bool isDr(const Operand_& op, uint32_t rId) noexcept { return isDr(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:396:86: note: cast one or both operands to int to silence this warning 20 warnings generated. compiling VolumeCavity.cpp compiling WithCmd.cpp compiling MultiValue.cpp compiling VolumeGradientBase.cpp gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/analysis' compiling ProjectionOnAxis.cpp compiling PropertyMap.cpp compiling CLToolMain.cpp In file included from x86internal.cpp:37: In file included from ././x86internal_p.h:38: In file included from ./././func.h:38: In file included from ././././arch.h:37: ./././././operand.h:341:12: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 341 | return (_packed[0] == other._packed[0]) & | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && 342 | (_packed[1] == other._packed[1]) ; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./././././operand.h:341:12: note: cast one or both operands to int to silence this warning ./././././operand.h:808:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 808 | static ASMJIT_INLINE bool isGp(const Operand_& op, uint32_t rId) noexcept { return isGp(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ./././././operand.h:808:86: note: cast one or both operands to int to silence this warning ./././././operand.h:809:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 809 | static ASMJIT_INLINE bool isVec(const Operand_& op, uint32_t rId) noexcept { return isVec(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ./././././operand.h:809:87: note: cast one or both operands to int to silence this warning In file included from x86internal.cpp:37: In file included from ././x86internal_p.h:39: In file included from ./././x86emitter.h:38: ././././x86operand.h:379:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 379 | static ASMJIT_INLINE bool isGpb(const Operand_& op, uint32_t rId) noexcept { return isGpb(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:379:87: note: cast one or both operands to int to silence this warning ././././x86operand.h:381:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 381 | static ASMJIT_INLINE bool isRip(const Operand_& op, uint32_t rId) noexcept { return isRip(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:381:87: note: cast one or both operands to int to silence this warning ././././x86operand.h:382:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 382 | static ASMJIT_INLINE bool isSeg(const Operand_& op, uint32_t rId) noexcept { return isSeg(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:382:87: note: cast one or both operands to int to silence this warning ././././x86operand.h:383:89: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 383 | static ASMJIT_INLINE bool isGpbLo(const Operand_& op, uint32_t rId) noexcept { return isGpbLo(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:383:89: note: cast one or both operands to int to silence this warning ././././x86operand.h:384:89: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 384 | static ASMJIT_INLINE bool isGpbHi(const Operand_& op, uint32_t rId) noexcept { return isGpbHi(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:384:89: note: cast one or both operands to int to silence this warning ././././x86operand.h:385:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 385 | static ASMJIT_INLINE bool isGpw(const Operand_& op, uint32_t rId) noexcept { return isGpw(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:385:87: note: cast one or both operands to int to silence this warning ././././x86operand.h:386:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 386 | static ASMJIT_INLINE bool isGpd(const Operand_& op, uint32_t rId) noexcept { return isGpd(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:386:87: note: cast one or both operands to int to silence this warning ././././x86operand.h:387:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 387 | static ASMJIT_INLINE bool isGpq(const Operand_& op, uint32_t rId) noexcept { return isGpq(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:387:87: note: cast one or both operands to int to silence this warning ././././x86operand.h:388:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 388 | static ASMJIT_INLINE bool isFp(const Operand_& op, uint32_t rId) noexcept { return isFp(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:388:86: note: cast one or both operands to int to silence this warning ././././x86operand.h:389:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 389 | static ASMJIT_INLINE bool isMm(const Operand_& op, uint32_t rId) noexcept { return isMm(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:389:86: note: cast one or both operands to int to silence this warning ././././x86operand.h:390:85: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 390 | static ASMJIT_INLINE bool isK(const Operand_& op, uint32_t rId) noexcept { return isK(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:390:85: note: cast one or both operands to int to silence this warning ././././x86operand.h:391:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 391 | static ASMJIT_INLINE bool isXmm(const Operand_& op, uint32_t rId) noexcept { return isXmm(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:391:87: note: cast one or both operands to int to silence this warning ././././x86operand.h:392:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 392 | static ASMJIT_INLINE bool isYmm(const Operand_& op, uint32_t rId) noexcept { return isYmm(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:392:87: note: cast one or both operands to int to silence this warning ././././x86operand.h:393:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 393 | static ASMJIT_INLINE bool isZmm(const Operand_& op, uint32_t rId) noexcept { return isZmm(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:393:87: note: cast one or both operands to int to silence this warning ././././x86operand.h:394:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 394 | static ASMJIT_INLINE bool isBnd(const Operand_& op, uint32_t rId) noexcept { return isBnd(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:394:87: note: cast one or both operands to int to silence this warning ././././x86operand.h:395:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 395 | static ASMJIT_INLINE bool isCr(const Operand_& op, uint32_t rId) noexcept { return isCr(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:395:86: note: cast one or both operands to int to silence this warning ././././x86operand.h:396:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 396 | static ASMJIT_INLINE bool isDr(const Operand_& op, uint32_t rId) noexcept { return isDr(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:396:86: note: cast one or both operands to int to silence this warning 20 warnings generated. compiling NeighborList.cpp compiling Puckering.cpp compiling GREX.cpp compiling OFile.cpp In file included from x86operand.cpp:37: In file included from ././x86operand.h:36: In file included from ./././arch.h:37: ././././operand.h:341:12: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 341 | return (_packed[0] == other._packed[0]) & | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && 342 | (_packed[1] == other._packed[1]) ; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ././././operand.h:341:12: note: cast one or both operands to int to silence this warning ././././operand.h:808:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 808 | static ASMJIT_INLINE bool isGp(const Operand_& op, uint32_t rId) noexcept { return isGp(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././operand.h:808:86: note: cast one or both operands to int to silence this warning ././././operand.h:809:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 809 | static ASMJIT_INLINE bool isVec(const Operand_& op, uint32_t rId) noexcept { return isVec(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././operand.h:809:87: note: cast one or both operands to int to silence this warning In file included from x86operand.cpp:37: ././x86operand.h:379:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 379 | static ASMJIT_INLINE bool isGpb(const Operand_& op, uint32_t rId) noexcept { return isGpb(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:379:87: note: cast one or both operands to int to silence this warning ././x86operand.h:381:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 381 | static ASMJIT_INLINE bool isRip(const Operand_& op, uint32_t rId) noexcept { return isRip(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:381:87: note: cast one or both operands to int to silence this warning ././x86operand.h:382:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 382 | static ASMJIT_INLINE bool isSeg(const Operand_& op, uint32_t rId) noexcept { return isSeg(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:382:87: note: cast one or both operands to int to silence this warning ././x86operand.h:383:89: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 383 | static ASMJIT_INLINE bool isGpbLo(const Operand_& op, uint32_t rId) noexcept { return isGpbLo(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:383:89: note: cast one or both operands to int to silence this warning ././x86operand.h:384:89: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 384 | static ASMJIT_INLINE bool isGpbHi(const Operand_& op, uint32_t rId) noexcept { return isGpbHi(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:384:89: note: cast one or both operands to int to silence this warning ././x86operand.h:385:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 385 | static ASMJIT_INLINE bool isGpw(const Operand_& op, uint32_t rId) noexcept { return isGpw(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:385:87: note: cast one or both operands to int to silence this warning ././x86operand.h:386:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 386 | static ASMJIT_INLINE bool isGpd(const Operand_& op, uint32_t rId) noexcept { return isGpd(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:386:87: note: cast one or both operands to int to silence this warning ././x86operand.h:387:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 387 | static ASMJIT_INLINE bool isGpq(const Operand_& op, uint32_t rId) noexcept { return isGpq(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:387:87: note: cast one or both operands to int to silence this warning ././x86operand.h:388:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 388 | static ASMJIT_INLINE bool isFp(const Operand_& op, uint32_t rId) noexcept { return isFp(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:388:86: note: cast one or both operands to int to silence this warning ././x86operand.h:389:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 389 | static ASMJIT_INLINE bool isMm(const Operand_& op, uint32_t rId) noexcept { return isMm(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:389:86: note: cast one or both operands to int to silence this warning ././x86operand.h:390:85: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 390 | static ASMJIT_INLINE bool isK(const Operand_& op, uint32_t rId) noexcept { return isK(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:390:85: note: cast one or both operands to int to silence this warning ././x86operand.h:391:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 391 | static ASMJIT_INLINE bool isXmm(const Operand_& op, uint32_t rId) noexcept { return isXmm(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:391:87: note: cast one or both operands to int to silence this warning ././x86operand.h:392:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 392 | static ASMJIT_INLINE bool isYmm(const Operand_& op, uint32_t rId) noexcept { return isYmm(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:392:87: note: cast one or both operands to int to silence this warning ././x86operand.h:393:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 393 | static ASMJIT_INLINE bool isZmm(const Operand_& op, uint32_t rId) noexcept { return isZmm(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:393:87: note: cast one or both operands to int to silence this warning ././x86operand.h:394:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 394 | static ASMJIT_INLINE bool isBnd(const Operand_& op, uint32_t rId) noexcept { return isBnd(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:394:87: note: cast one or both operands to int to silence this warning ././x86operand.h:395:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 395 | static ASMJIT_INLINE bool isCr(const Operand_& op, uint32_t rId) noexcept { return isCr(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:395:86: note: cast one or both operands to int to silence this warning ././x86operand.h:396:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 396 | static ASMJIT_INLINE bool isDr(const Operand_& op, uint32_t rId) noexcept { return isDr(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:396:86: note: cast one or both operands to int to silence this warning 20 warnings generated. compiling OpenMP.cpp compiling PDB.cpp compiling PlumedMain.cpp compiling Pbc.cpp compiling RMSD.cpp compiling PlumedHandle.cpp compiling RMSD.cpp compiling VolumeInCylinder.cpp In file included from x86operand_regs.cpp:39: In file included from ././x86operand.h:36: In file included from ./././arch.h:37: ././././operand.h:341:12: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 341 | return (_packed[0] == other._packed[0]) & | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && 342 | (_packed[1] == other._packed[1]) ; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ././././operand.h:341:12: note: cast one or both operands to int to silence this warning ././././operand.h:808:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 808 | static ASMJIT_INLINE bool isGp(const Operand_& op, uint32_t rId) noexcept { return isGp(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././operand.h:808:86: note: cast one or both operands to int to silence this warning ././././operand.h:809:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 809 | static ASMJIT_INLINE bool isVec(const Operand_& op, uint32_t rId) noexcept { return isVec(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././operand.h:809:87: note: cast one or both operands to int to silence this warning In file included from x86operand_regs.cpp:39: ././x86operand.h:379:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 379 | static ASMJIT_INLINE bool isGpb(const Operand_& op, uint32_t rId) noexcept { return isGpb(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:379:87: note: cast one or both operands to int to silence this warning ././x86operand.h:381:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 381 | static ASMJIT_INLINE bool isRip(const Operand_& op, uint32_t rId) noexcept { return isRip(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:381:87: note: cast one or both operands to int to silence this warning ././x86operand.h:382:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 382 | static ASMJIT_INLINE bool isSeg(const Operand_& op, uint32_t rId) noexcept { return isSeg(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:382:87: note: cast one or both operands to int to silence this warning ././x86operand.h:383:89: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 383 | static ASMJIT_INLINE bool isGpbLo(const Operand_& op, uint32_t rId) noexcept { return isGpbLo(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:383:89: note: cast one or both operands to int to silence this warning ././x86operand.h:384:89: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 384 | static ASMJIT_INLINE bool isGpbHi(const Operand_& op, uint32_t rId) noexcept { return isGpbHi(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:384:89: note: cast one or both operands to int to silence this warning ././x86operand.h:385:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 385 | static ASMJIT_INLINE bool isGpw(const Operand_& op, uint32_t rId) noexcept { return isGpw(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:385:87: note: cast one or both operands to int to silence this warning ././x86operand.h:386:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 386 | static ASMJIT_INLINE bool isGpd(const Operand_& op, uint32_t rId) noexcept { return isGpd(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:386:87: note: cast one or both operands to int to silence this warning ././x86operand.h:387:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 387 | static ASMJIT_INLINE bool isGpq(const Operand_& op, uint32_t rId) noexcept { return isGpq(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:387:87: note: cast one or both operands to int to silence this warning ././x86operand.h:388:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 388 | static ASMJIT_INLINE bool isFp(const Operand_& op, uint32_t rId) noexcept { return isFp(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:388:86: note: cast one or both operands to int to silence this warning ././x86operand.h:389:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 389 | static ASMJIT_INLINE bool isMm(const Operand_& op, uint32_t rId) noexcept { return isMm(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:389:86: note: cast one or both operands to int to silence this warning ././x86operand.h:390:85: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 390 | static ASMJIT_INLINE bool isK(const Operand_& op, uint32_t rId) noexcept { return isK(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:390:85: note: cast one or both operands to int to silence this warning ././x86operand.h:391:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 391 | static ASMJIT_INLINE bool isXmm(const Operand_& op, uint32_t rId) noexcept { return isXmm(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:391:87: note: cast one or both operands to int to silence this warning ././x86operand.h:392:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 392 | static ASMJIT_INLINE bool isYmm(const Operand_& op, uint32_t rId) noexcept { return isYmm(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:392:87: note: cast one or both operands to int to silence this warning ././x86operand.h:393:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 393 | static ASMJIT_INLINE bool isZmm(const Operand_& op, uint32_t rId) noexcept { return isZmm(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:393:87: note: cast one or both operands to int to silence this warning ././x86operand.h:394:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 394 | static ASMJIT_INLINE bool isBnd(const Operand_& op, uint32_t rId) noexcept { return isBnd(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:394:87: note: cast one or both operands to int to silence this warning ././x86operand.h:395:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 395 | static ASMJIT_INLINE bool isCr(const Operand_& op, uint32_t rId) noexcept { return isCr(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:395:86: note: cast one or both operands to int to silence this warning ././x86operand.h:396:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 396 | static ASMJIT_INLINE bool isDr(const Operand_& op, uint32_t rId) noexcept { return isDr(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:396:86: note: cast one or both operands to int to silence this warning 20 warnings generated. compiling VolumeInSphere.cpp compiling Template.cpp zone.cpp:223:13: warning: unused function 'ZoneHeap_hasDynamicBlock' [-Wunused-function] 223 | static bool ZoneHeap_hasDynamicBlock(ZoneHeap* self, ZoneHeap::DynamicBlock* block) noexcept { | ^~~~~~~~~~~~~~~~~~~~~~~~ 1 warning generated. compiling VolumeTetrapore.cpp compiling Random.cpp DataFetchingObject.cpp:78:10: warning: unused variable 'val' [-Wunused-variable] 78 | Value* val = myv->copyOutput( key ); | ^~~ DataFetchingObject.cpp:99:10: warning: unused variable 'val' [-Wunused-variable] 99 | Value* val = myv->copyOutput( key ); | ^~~ 2 warnings generated. compiling Torsion.cpp compiling Volume.cpp compiling RootFindingBase.cpp compiling XAngle.cpp compiling XDistances.cpp gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/bias' compiling Stopwatch.cpp compiling XYDistances.cpp compiling Subprocess.cpp gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/reference' compiling XYTorsion.cpp compiling SwitchingFunction.cpp compiling Tensor.cpp compiling Tools.cpp compiling Torsion.cpp compiling Tree.cpp compiling TypesafePtr.cpp compiling Units.cpp compiling Vector.cpp compiling h36.cpp Keywords.cpp:126:16: warning: variable 'i' set but not used [-Wunused-but-set-variable] 126 | for(unsigned i=0;; ++i) { | ^ 1 warning generated. Vessel.cpp:63:16: warning: variable 'i' set but not used [-Wunused-but-set-variable] 63 | for(unsigned i=0;; ++i) { | ^ 1 warning generated. gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/vesselbase' Grid.cpp:1082:13: warning: variable 'n_examined' set but not used [-Wunused-but-set-variable] 1082 | index_t n_examined = 0; | ^ 1 warning generated. In file included from x86regalloc.cpp:37: In file included from ././cpuinfo.h:36: In file included from ./././arch.h:37: ././././operand.h:341:12: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 341 | return (_packed[0] == other._packed[0]) & | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && 342 | (_packed[1] == other._packed[1]) ; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ././././operand.h:341:12: note: cast one or both operands to int to silence this warning ././././operand.h:808:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 808 | static ASMJIT_INLINE bool isGp(const Operand_& op, uint32_t rId) noexcept { return isGp(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././operand.h:808:86: note: cast one or both operands to int to silence this warning ././././operand.h:809:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 809 | static ASMJIT_INLINE bool isVec(const Operand_& op, uint32_t rId) noexcept { return isVec(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././operand.h:809:87: note: cast one or both operands to int to silence this warning In file included from x86regalloc.cpp:39: In file included from ././x86assembler.h:38: In file included from ./././x86emitter.h:38: ././././x86operand.h:379:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 379 | static ASMJIT_INLINE bool isGpb(const Operand_& op, uint32_t rId) noexcept { return isGpb(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:379:87: note: cast one or both operands to int to silence this warning ././././x86operand.h:381:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 381 | static ASMJIT_INLINE bool isRip(const Operand_& op, uint32_t rId) noexcept { return isRip(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:381:87: note: cast one or both operands to int to silence this warning ././././x86operand.h:382:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 382 | static ASMJIT_INLINE bool isSeg(const Operand_& op, uint32_t rId) noexcept { return isSeg(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:382:87: note: cast one or both operands to int to silence this warning ././././x86operand.h:383:89: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 383 | static ASMJIT_INLINE bool isGpbLo(const Operand_& op, uint32_t rId) noexcept { return isGpbLo(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:383:89: note: cast one or both operands to int to silence this warning ././././x86operand.h:384:89: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 384 | static ASMJIT_INLINE bool isGpbHi(const Operand_& op, uint32_t rId) noexcept { return isGpbHi(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:384:89: note: cast one or both operands to int to silence this warning ././././x86operand.h:385:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 385 | static ASMJIT_INLINE bool isGpw(const Operand_& op, uint32_t rId) noexcept { return isGpw(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:385:87: note: cast one or both operands to int to silence this warning ././././x86operand.h:386:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 386 | static ASMJIT_INLINE bool isGpd(const Operand_& op, uint32_t rId) noexcept { return isGpd(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:386:87: note: cast one or both operands to int to silence this warning ././././x86operand.h:387:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 387 | static ASMJIT_INLINE bool isGpq(const Operand_& op, uint32_t rId) noexcept { return isGpq(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:387:87: note: cast one or both operands to int to silence this warning ././././x86operand.h:388:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 388 | static ASMJIT_INLINE bool isFp(const Operand_& op, uint32_t rId) noexcept { return isFp(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:388:86: note: cast one or both operands to int to silence this warning ././././x86operand.h:389:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 389 | static ASMJIT_INLINE bool isMm(const Operand_& op, uint32_t rId) noexcept { return isMm(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:389:86: note: cast one or both operands to int to silence this warning ././././x86operand.h:390:85: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 390 | static ASMJIT_INLINE bool isK(const Operand_& op, uint32_t rId) noexcept { return isK(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:390:85: note: cast one or both operands to int to silence this warning ././././x86operand.h:391:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 391 | static ASMJIT_INLINE bool isXmm(const Operand_& op, uint32_t rId) noexcept { return isXmm(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:391:87: note: cast one or both operands to int to silence this warning ././././x86operand.h:392:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 392 | static ASMJIT_INLINE bool isYmm(const Operand_& op, uint32_t rId) noexcept { return isYmm(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:392:87: note: cast one or both operands to int to silence this warning ././././x86operand.h:393:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 393 | static ASMJIT_INLINE bool isZmm(const Operand_& op, uint32_t rId) noexcept { return isZmm(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:393:87: note: cast one or both operands to int to silence this warning ././././x86operand.h:394:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 394 | static ASMJIT_INLINE bool isBnd(const Operand_& op, uint32_t rId) noexcept { return isBnd(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:394:87: note: cast one or both operands to int to silence this warning ././././x86operand.h:395:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 395 | static ASMJIT_INLINE bool isCr(const Operand_& op, uint32_t rId) noexcept { return isCr(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:395:86: note: cast one or both operands to int to silence this warning ././././x86operand.h:396:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 396 | static ASMJIT_INLINE bool isDr(const Operand_& op, uint32_t rId) noexcept { return isDr(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:396:86: note: cast one or both operands to int to silence this warning 20 warnings generated. In file included from x86assembler.cpp:37: In file included from ././cpuinfo.h:36: In file included from ./././arch.h:37: ././././operand.h:341:12: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 341 | return (_packed[0] == other._packed[0]) & | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && 342 | (_packed[1] == other._packed[1]) ; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ././././operand.h:341:12: note: cast one or both operands to int to silence this warning ././././operand.h:808:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 808 | static ASMJIT_INLINE bool isGp(const Operand_& op, uint32_t rId) noexcept { return isGp(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././operand.h:808:86: note: cast one or both operands to int to silence this warning ././././operand.h:809:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 809 | static ASMJIT_INLINE bool isVec(const Operand_& op, uint32_t rId) noexcept { return isVec(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././operand.h:809:87: note: cast one or both operands to int to silence this warning In file included from x86assembler.cpp:41: In file included from ././x86assembler.h:38: In file included from ./././x86emitter.h:38: ././././x86operand.h:379:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 379 | static ASMJIT_INLINE bool isGpb(const Operand_& op, uint32_t rId) noexcept { return isGpb(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:379:87: note: cast one or both operands to int to silence this warning ././././x86operand.h:381:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 381 | static ASMJIT_INLINE bool isRip(const Operand_& op, uint32_t rId) noexcept { return isRip(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:381:87: note: cast one or both operands to int to silence this warning ././././x86operand.h:382:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 382 | static ASMJIT_INLINE bool isSeg(const Operand_& op, uint32_t rId) noexcept { return isSeg(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:382:87: note: cast one or both operands to int to silence this warning ././././x86operand.h:383:89: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 383 | static ASMJIT_INLINE bool isGpbLo(const Operand_& op, uint32_t rId) noexcept { return isGpbLo(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:383:89: note: cast one or both operands to int to silence this warning ././././x86operand.h:384:89: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 384 | static ASMJIT_INLINE bool isGpbHi(const Operand_& op, uint32_t rId) noexcept { return isGpbHi(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:384:89: note: cast one or both operands to int to silence this warning ././././x86operand.h:385:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 385 | static ASMJIT_INLINE bool isGpw(const Operand_& op, uint32_t rId) noexcept { return isGpw(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:385:87: note: cast one or both operands to int to silence this warning ././././x86operand.h:386:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 386 | static ASMJIT_INLINE bool isGpd(const Operand_& op, uint32_t rId) noexcept { return isGpd(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:386:87: note: cast one or both operands to int to silence this warning ././././x86operand.h:387:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 387 | static ASMJIT_INLINE bool isGpq(const Operand_& op, uint32_t rId) noexcept { return isGpq(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:387:87: note: cast one or both operands to int to silence this warning ././././x86operand.h:388:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 388 | static ASMJIT_INLINE bool isFp(const Operand_& op, uint32_t rId) noexcept { return isFp(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:388:86: note: cast one or both operands to int to silence this warning ././././x86operand.h:389:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 389 | static ASMJIT_INLINE bool isMm(const Operand_& op, uint32_t rId) noexcept { return isMm(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:389:86: note: cast one or both operands to int to silence this warning ././././x86operand.h:390:85: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 390 | static ASMJIT_INLINE bool isK(const Operand_& op, uint32_t rId) noexcept { return isK(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:390:85: note: cast one or both operands to int to silence this warning ././././x86operand.h:391:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 391 | static ASMJIT_INLINE bool isXmm(const Operand_& op, uint32_t rId) noexcept { return isXmm(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:391:87: note: cast one or both operands to int to silence this warning ././././x86operand.h:392:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 392 | static ASMJIT_INLINE bool isYmm(const Operand_& op, uint32_t rId) noexcept { return isYmm(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:392:87: note: cast one or both operands to int to silence this warning ././././x86operand.h:393:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 393 | static ASMJIT_INLINE bool isZmm(const Operand_& op, uint32_t rId) noexcept { return isZmm(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:393:87: note: cast one or both operands to int to silence this warning ././././x86operand.h:394:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 394 | static ASMJIT_INLINE bool isBnd(const Operand_& op, uint32_t rId) noexcept { return isBnd(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:394:87: note: cast one or both operands to int to silence this warning ././././x86operand.h:395:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 395 | static ASMJIT_INLINE bool isCr(const Operand_& op, uint32_t rId) noexcept { return isCr(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:395:86: note: cast one or both operands to int to silence this warning ././././x86operand.h:396:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 396 | static ASMJIT_INLINE bool isDr(const Operand_& op, uint32_t rId) noexcept { return isDr(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:396:86: note: cast one or both operands to int to silence this warning 20 warnings generated. gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/asmjit' compiling ModuleMap.cpp PathMSDBase.cpp:143:19: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning] 143 | void PathMSDBase::calculate() { | ^ PathMSDBase.cpp:143:19: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning] PathMSDBase.cpp:143:19: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning] PathMSDBase.cpp:143:19: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning] PathMSDBase.cpp:143:19: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning] PathMSDBase.cpp:143:19: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning] 6 warnings generated. gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/colvar' gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/multicolvar' RMSD.cpp:93:12: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning] 93 | void RMSD::setReference(const std::vector & reference) { | ^ RMSD.cpp:112:12: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning] 112 | void RMSD::setAlign(const std::vector & align, bool normalize_weights, bool remove_center) { | ^ RMSD.cpp:112:12: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning] RMSD.cpp:152:12: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning] 152 | void RMSD::setDisplace(const std::vector & displace, bool normalize_weights) { | ^ RMSD.cpp:152:12: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning] RMSD.cpp:1118:22: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning] 1118 | double RMSDCoreData::getDistance( bool squared) { | ^ RMSD.cpp:1181:35: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning] 1181 | std::vector RMSDCoreData::getDDistanceDPositions() { | ^ RMSD.cpp:1217:36: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning] 1217 | std::vector RMSDCoreData::getDDistanceDReference() { | ^ 8 warnings generated. gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/tools' gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/core' gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/isdb' gmake[5]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' gmake[4]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' /usr/local/bin/gmake lib gmake[4]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fPIC -Wall -pedantic -std=c++11 ../main/main.o ../analysis/AnalysisBase.o ../analysis/Average.o ../analysis/AverageVessel.o ../analysis/Committor.o ../analysis/DataCollectionObject.o ../analysis/EuclideanDissimilarityMatrix.o ../analysis/FarthestPointSampling.o ../analysis/Histogram.o ../analysis/LandmarkSelectionBase.o ../analysis/LandmarkStaged.o ../analysis/OutputColvarFile.o ../analysis/OutputPDBFile.o ../analysis/PrintDissimilarityMatrix.o ../analysis/ReadAnalysisFrames.o ../analysis/ReadDissimilarityMatrix.o ../analysis/ReselectLandmarks.o ../analysis/SelectRandomFrames.o ../analysis/SelectWithStride.o ../analysis/WhamHistogram.o ../analysis/WhamWeights.o ../asmjit/arch.o ../asmjit/assembler.o ../asmjit/codebuilder.o ../asmjit/codecompiler.o ../asmjit/codeemitter.o ../asmjit/codeholder.o ../asmjit/constpool.o ../asmjit/cpuinfo.o ../asmjit/func.o ../asmjit/globals.o ../asmjit/inst.o ../asmjit/logging.o ../asmjit/operand.o ../asmjit/osutils.o ../asmjit/regalloc.o ../asmjit/runtime.o ../asmjit/string.o ../asmjit/utils.o ../asmjit/vmem.o ../asmjit/x86assembler.o ../asmjit/x86builder.o ../asmjit/x86compiler.o ../asmjit/x86inst.o ../asmjit/x86instimpl.o ../asmjit/x86internal.o ../asmjit/x86logging.o ../asmjit/x86operand.o ../asmjit/x86operand_regs.o ../asmjit/x86regalloc.o ../asmjit/zone.o ../bias/ABMD.o ../bias/Bias.o ../bias/BiasValue.o ../bias/ExtendedLagrangian.o ../bias/External.o ../bias/LWalls.o ../bias/MaxEnt.o ../bias/MetaD.o ../bias/MovingRestraint.o ../bias/PBMetaD.o ../bias/Restraint.o ../bias/ReweightBase.o ../bias/ReweightBias.o ../bias/ReweightMetad.o ../bias/ReweightTemperaturePressure.o ../bias/ReweightWham.o ../bias/UWalls.o ../blas/blas.o ../cltools/CLTool.o ../cltools/Completion.o ../cltools/Driver.o ../cltools/DriverDouble.o ../cltools/DriverFloat.o ../cltools/GenExample.o ../cltools/GenJson.o ../cltools/GenTemplate.o ../cltools/Info.o ../cltools/Manual.o ../cltools/PdbRenumber.o ../cltools/SimpleMD.o ../cltools/SumHills.o ../cltools/kT.o ../cltools/pesmd.o ../colvar/Angle.o ../colvar/Cell.o ../colvar/Colvar.o ../colvar/Constant.o ../colvar/ContactMap.o ../colvar/Coordination.o ../colvar/CoordinationBase.o ../colvar/DHEnergy.o ../colvar/DRMSD.o ../colvar/Dimer.o ../colvar/Dipole.o ../colvar/Distance.o ../colvar/EEFSolv.o ../colvar/ERMSD.o ../colvar/Energy.o ../colvar/ExtraCV.o ../colvar/Fake.o ../colvar/GHBFIX.o ../colvar/Gyration.o ../colvar/MultiRMSD.o ../colvar/PCARMSD.o ../colvar/PathMSD.o ../colvar/PathMSDBase.o ../colvar/Position.o ../colvar/ProjectionOnAxis.o ../colvar/PropertyMap.o ../colvar/Puckering.o ../colvar/RMSD.o ../colvar/Template.o ../colvar/Torsion.o ../colvar/Volume.o ../core/Action.o ../core/ActionAnyorder.o ../core/ActionAtomistic.o ../core/ActionPilot.o ../core/ActionRegister.o ../core/ActionSet.o ../core/ActionSetup.o ../core/ActionShortcut.o ../core/ActionWithArguments.o ../core/ActionWithValue.o ../core/ActionWithVirtualAtom.o ../core/Atoms.o ../core/CLTool.o ../core/CLToolMain.o ../core/CLToolRegister.o ../core/Colvar.o ../core/DataFetchingObject.o ../core/ExchangePatterns.o ../core/FlexibleBin.o ../core/GREX.o ../core/GenericMolInfo.o ../core/MDAtoms.o ../core/ModuleMap.o ../core/PlumedMain.o ../core/PlumedMainInitializer.o ../core/TargetDist.o ../core/Value.o ../core/WithCmd.o ../function/Combine.o ../function/Custom.o ../function/Ensemble.o ../function/FuncPathGeneral.o ../function/FuncPathMSD.o ../function/FuncSumHills.o ../function/Function.o ../function/LocalEnsemble.o ../function/Piecewise.o ../function/Sort.o ../function/Stats.o ../function/Target.o ../generic/Debug.o ../generic/DumpAtoms.o ../generic/DumpDerivatives.o ../generic/DumpForces.o ../generic/DumpMassCharge.o ../generic/DumpProjections.o ../generic/EffectiveEnergyDrift.o ../generic/EndPlumed.o ../generic/FitToTemplate.o ../generic/Flush.o ../generic/Group.o ../generic/Include.o ../generic/MolInfo.o ../generic/Plumed.o ../generic/Print.o ../generic/RandomExchanges.o ../generic/Read.o ../generic/ResetCell.o ../generic/Time.o ../generic/UpdateIf.o ../generic/WholeMolecules.o ../generic/WrapAround.o ../gridtools/ActionWithGrid.o ../gridtools/ActionWithInputGrid.o ../gridtools/ActionWithIntegral.o ../gridtools/AverageOnGrid.o ../gridtools/ContourFindingBase.o ../gridtools/ConvertToFES.o ../gridtools/DumpCube.o ../gridtools/DumpGrid.o ../gridtools/FindContour.o ../gridtools/FindContourSurface.o ../gridtools/FindSphericalContour.o ../gridtools/FourierTransform.o ../gridtools/GridPrintingBase.o ../gridtools/GridSearch.o ../gridtools/GridToXYZ.o ../gridtools/GridVessel.o ../gridtools/HistogramOnGrid.o ../gridtools/IntegrateGrid.o ../gridtools/InterpolateGrid.o ../isdb/CS2Backbone.o ../isdb/Caliber.o ../isdb/EMMI.o ../isdb/FretEfficiency.o ../isdb/Jcoupling.o ../isdb/Metainference.o ../isdb/MetainferenceBase.o ../isdb/NOE.o ../isdb/PRE.o ../isdb/RDC.o ../isdb/Rescale.o ../isdb/SAXS.o ../isdb/Select.o ../isdb/Selector.o ../lapack/lapack.o ../lepton/CompiledExpression.o ../lepton/ExpressionProgram.o ../lepton/ExpressionTreeNode.o ../lepton/Operation.o ../lepton/ParsedExpression.o ../lepton/Parser.o ../mapping/AdaptivePath.o ../mapping/Mapping.o ../mapping/PCAVars.o ../mapping/Path.o ../mapping/PathBase.o ../mapping/PathReparameterization.o ../mapping/PathTools.o ../mapping/PropertyMap.o ../mapping/SpathVessel.o ../mapping/TrigonometricPathVessel.o ../mapping/ZpathVessel.o ../molfile/crdplugin.o ../molfile/dcdplugin.o ../molfile/gromacsplugin.o ../molfile/pdbplugin.o ../multicolvar/ActionVolume.o ../multicolvar/AlphaBeta.o ../multicolvar/Angles.o ../multicolvar/AtomValuePack.o ../multicolvar/Bridge.o ../multicolvar/BridgedMultiColvarFunction.o ../multicolvar/CatomPack.o ../multicolvar/CenterOfMultiColvar.o ../multicolvar/CoordinationNumbers.o ../multicolvar/Density.o ../multicolvar/DihedralCorrelation.o ../multicolvar/DistanceFromContour.o ../multicolvar/Distances.o ../multicolvar/DumpMultiColvar.o ../multicolvar/FilterBetween.o ../multicolvar/FilterLessThan.o ../multicolvar/FilterMoreThan.o ../multicolvar/InPlaneDistances.o ../multicolvar/LocalAverage.o ../multicolvar/MultiColvarBase.o ../multicolvar/MultiColvarCombine.o ../multicolvar/MultiColvarDensity.o ../multicolvar/MultiColvarFilter.o ../multicolvar/MultiColvarProduct.o ../multicolvar/NumberOfLinks.o ../multicolvar/Torsions.o ../multicolvar/VolumeAround.o ../multicolvar/VolumeBetweenContours.o ../multicolvar/VolumeCavity.o ../multicolvar/VolumeGradientBase.o ../multicolvar/VolumeInCylinder.o ../multicolvar/VolumeInSphere.o ../multicolvar/VolumeTetrapore.o ../multicolvar/XAngle.o ../multicolvar/XDistances.o ../multicolvar/XYDistances.o ../multicolvar/XYTorsion.o ../reference/ArgumentOnlyDistance.o ../reference/DRMSD.o ../reference/Direction.o ../reference/DotProductDistance.o ../reference/EuclideanDistance.o ../reference/FakeFrame.o ../reference/IntermolecularDRMSD.o ../reference/IntramolecularDRMSD.o ../reference/MahalanobisDistance.o ../reference/MetricRegister.o ../reference/MultiDomainRMSD.o ../reference/NormalizedEuclideanDistance.o ../reference/OptimalRMSD.o ../reference/RMSDBase.o ../reference/ReferenceArguments.o ../reference/ReferenceAtoms.o ../reference/ReferenceConfiguration.o ../reference/ReferenceValuePack.o ../reference/SimpleRMSD.o ../reference/SingleDomainRMSD.o ../secondarystructure/AlphaRMSD.o ../secondarystructure/AntibetaRMSD.o ../secondarystructure/ParabetaRMSD.o ../secondarystructure/SecondaryStructureRMSD.o ../setup/Load.o ../setup/Restart.o ../setup/Units.o ../tools/Angle.o ../tools/AtomNumber.o ../tools/BiasRepresentation.o ../tools/Brent1DRootSearch.o ../tools/Citations.o ../tools/Communicator.o ../tools/ConjugateGradient.o ../tools/DLLoader.o ../tools/DynamicList.o ../tools/ERMSD.o ../tools/Exception.o ../tools/FileBase.o ../tools/ForwardDecl.o ../tools/Grid.o ../tools/HistogramBead.o ../tools/IFile.o ../tools/KernelFunctions.o ../tools/Keywords.o ../tools/LatticeReduction.o ../tools/LinkCells.o ../tools/Log.o ../tools/LoopUnroller.o ../tools/Matrix.o ../tools/MatrixSquareBracketsAccess.o ../tools/Minimise1DBrent.o ../tools/MinimiseBase.o ../tools/MolDataClass.o ../tools/MultiValue.o ../tools/NeighborList.o ../tools/OFile.o ../tools/OpenMP.o ../tools/PDB.o ../tools/Pbc.o ../tools/PlumedHandle.o ../tools/RMSD.o ../tools/Random.o ../tools/RootFindingBase.o ../tools/Stopwatch.o ../tools/Subprocess.o ../tools/SwitchingFunction.o ../tools/Tensor.o ../tools/Tools.o ../tools/Torsion.o ../tools/Tree.o ../tools/TypesafePtr.o ../tools/Units.o ../tools/Vector.o ../tools/h36.o ../vatom/ActionWithVirtualAtom.o ../vatom/Center.o ../vatom/FixedAtom.o ../vatom/Ghost.o ../vesselbase/ActionWithAveraging.o ../vesselbase/ActionWithInputVessel.o ../vesselbase/ActionWithVessel.o ../vesselbase/AltMin.o ../vesselbase/AveragingVessel.o ../vesselbase/Between.o ../vesselbase/BridgeVessel.o ../vesselbase/FunctionVessel.o ../vesselbase/Highest.o ../vesselbase/Histogram.o ../vesselbase/LessThan.o ../vesselbase/Lowest.o ../vesselbase/Max.o ../vesselbase/Mean.o ../vesselbase/Min.o ../vesselbase/Moments.o ../vesselbase/MoreThan.o ../vesselbase/OrderingVessel.o ../vesselbase/ShortcutVessel.o ../vesselbase/StoreDataVessel.o ../vesselbase/Sum.o ../vesselbase/ValueVessel.o ../vesselbase/Vessel.o ../vesselbase/VesselRegister.o ../xdrfile/xdrfile.o ../xdrfile/xdrfile_trr.o ../xdrfile/xdrfile_xtc.o ../config/Config.o ../wrapper/PlumedStatic.o -o plumed-static -ldl -lstdc++ -lfftw3 -lgsl -lgslcblas -lz -ldl -llapack -lblas -L/usr/local/lib -rdynamic -Wl,-Bsymbolic -fopenmp Building Plumed.inc c++ -shared -o libplumedKernel.so ../analysis/AnalysisBase.o ../analysis/Average.o ../analysis/AverageVessel.o ../analysis/Committor.o ../analysis/DataCollectionObject.o ../analysis/EuclideanDissimilarityMatrix.o ../analysis/FarthestPointSampling.o ../analysis/Histogram.o ../analysis/LandmarkSelectionBase.o ../analysis/LandmarkStaged.o ../analysis/OutputColvarFile.o ../analysis/OutputPDBFile.o ../analysis/PrintDissimilarityMatrix.o ../analysis/ReadAnalysisFrames.o ../analysis/ReadDissimilarityMatrix.o ../analysis/ReselectLandmarks.o ../analysis/SelectRandomFrames.o ../analysis/SelectWithStride.o ../analysis/WhamHistogram.o ../analysis/WhamWeights.o ../asmjit/arch.o ../asmjit/assembler.o ../asmjit/codebuilder.o ../asmjit/codecompiler.o ../asmjit/codeemitter.o ../asmjit/codeholder.o ../asmjit/constpool.o ../asmjit/cpuinfo.o ../asmjit/func.o ../asmjit/globals.o ../asmjit/inst.o ../asmjit/logging.o ../asmjit/operand.o ../asmjit/osutils.o ../asmjit/regalloc.o ../asmjit/runtime.o ../asmjit/string.o ../asmjit/utils.o ../asmjit/vmem.o ../asmjit/x86assembler.o ../asmjit/x86builder.o ../asmjit/x86compiler.o ../asmjit/x86inst.o ../asmjit/x86instimpl.o ../asmjit/x86internal.o ../asmjit/x86logging.o ../asmjit/x86operand.o ../asmjit/x86operand_regs.o ../asmjit/x86regalloc.o ../asmjit/zone.o ../bias/ABMD.o ../bias/Bias.o ../bias/BiasValue.o ../bias/ExtendedLagrangian.o ../bias/External.o ../bias/LWalls.o ../bias/MaxEnt.o ../bias/MetaD.o ../bias/MovingRestraint.o ../bias/PBMetaD.o ../bias/Restraint.o ../bias/ReweightBase.o ../bias/ReweightBias.o ../bias/ReweightMetad.o ../bias/ReweightTemperaturePressure.o ../bias/ReweightWham.o ../bias/UWalls.o ../blas/blas.o ../cltools/CLTool.o ../cltools/Completion.o ../cltools/Driver.o ../cltools/DriverDouble.o ../cltools/DriverFloat.o ../cltools/GenExample.o ../cltools/GenJson.o ../cltools/GenTemplate.o ../cltools/Info.o ../cltools/Manual.o ../cltools/PdbRenumber.o ../cltools/SimpleMD.o ../cltools/SumHills.o ../cltools/kT.o ../cltools/pesmd.o ../colvar/Angle.o ../colvar/Cell.o ../colvar/Colvar.o ../colvar/Constant.o ../colvar/ContactMap.o ../colvar/Coordination.o ../colvar/CoordinationBase.o ../colvar/DHEnergy.o ../colvar/DRMSD.o ../colvar/Dimer.o ../colvar/Dipole.o ../colvar/Distance.o ../colvar/EEFSolv.o ../colvar/ERMSD.o ../colvar/Energy.o ../colvar/ExtraCV.o ../colvar/Fake.o ../colvar/GHBFIX.o ../colvar/Gyration.o ../colvar/MultiRMSD.o ../colvar/PCARMSD.o ../colvar/PathMSD.o ../colvar/PathMSDBase.o ../colvar/Position.o ../colvar/ProjectionOnAxis.o ../colvar/PropertyMap.o ../colvar/Puckering.o ../colvar/RMSD.o ../colvar/Template.o ../colvar/Torsion.o ../colvar/Volume.o ../core/Action.o ../core/ActionAnyorder.o ../core/ActionAtomistic.o ../core/ActionPilot.o ../core/ActionRegister.o ../core/ActionSet.o ../core/ActionSetup.o ../core/ActionShortcut.o ../core/ActionWithArguments.o ../core/ActionWithValue.o ../core/ActionWithVirtualAtom.o ../core/Atoms.o ../core/CLTool.o ../core/CLToolMain.o ../core/CLToolRegister.o ../core/Colvar.o ../core/DataFetchingObject.o ../core/ExchangePatterns.o ../core/FlexibleBin.o ../core/GREX.o ../core/GenericMolInfo.o ../core/MDAtoms.o ../core/ModuleMap.o ../core/PlumedMain.o ../core/PlumedMainInitializer.o ../core/TargetDist.o ../core/Value.o ../core/WithCmd.o ../function/Combine.o ../function/Custom.o ../function/Ensemble.o ../function/FuncPathGeneral.o ../function/FuncPathMSD.o ../function/FuncSumHills.o ../function/Function.o ../function/LocalEnsemble.o ../function/Piecewise.o ../function/Sort.o ../function/Stats.o ../function/Target.o ../generic/Debug.o ../generic/DumpAtoms.o ../generic/DumpDerivatives.o ../generic/DumpForces.o ../generic/DumpMassCharge.o ../generic/DumpProjections.o ../generic/EffectiveEnergyDrift.o ../generic/EndPlumed.o ../generic/FitToTemplate.o ../generic/Flush.o ../generic/Group.o ../generic/Include.o ../generic/MolInfo.o ../generic/Plumed.o ../generic/Print.o ../generic/RandomExchanges.o ../generic/Read.o ../generic/ResetCell.o ../generic/Time.o ../generic/UpdateIf.o ../generic/WholeMolecules.o ../generic/WrapAround.o ../gridtools/ActionWithGrid.o ../gridtools/ActionWithInputGrid.o ../gridtools/ActionWithIntegral.o ../gridtools/AverageOnGrid.o ../gridtools/ContourFindingBase.o ../gridtools/ConvertToFES.o ../gridtools/DumpCube.o ../gridtools/DumpGrid.o ../gridtools/FindContour.o ../gridtools/FindContourSurface.o ../gridtools/FindSphericalContour.o ../gridtools/FourierTransform.o ../gridtools/GridPrintingBase.o ../gridtools/GridSearch.o ../gridtools/GridToXYZ.o ../gridtools/GridVessel.o ../gridtools/HistogramOnGrid.o ../gridtools/IntegrateGrid.o ../gridtools/InterpolateGrid.o ../isdb/CS2Backbone.o ../isdb/Caliber.o ../isdb/EMMI.o ../isdb/FretEfficiency.o ../isdb/Jcoupling.o ../isdb/Metainference.o ../isdb/MetainferenceBase.o ../isdb/NOE.o ../isdb/PRE.o ../isdb/RDC.o ../isdb/Rescale.o ../isdb/SAXS.o ../isdb/Select.o ../isdb/Selector.o ../lapack/lapack.o ../lepton/CompiledExpression.o ../lepton/ExpressionProgram.o ../lepton/ExpressionTreeNode.o ../lepton/Operation.o ../lepton/ParsedExpression.o ../lepton/Parser.o ../mapping/AdaptivePath.o ../mapping/Mapping.o ../mapping/PCAVars.o ../mapping/Path.o ../mapping/PathBase.o ../mapping/PathReparameterization.o ../mapping/PathTools.o ../mapping/PropertyMap.o ../mapping/SpathVessel.o ../mapping/TrigonometricPathVessel.o ../mapping/ZpathVessel.o ../molfile/crdplugin.o ../molfile/dcdplugin.o ../molfile/gromacsplugin.o ../molfile/pdbplugin.o ../multicolvar/ActionVolume.o ../multicolvar/AlphaBeta.o ../multicolvar/Angles.o ../multicolvar/AtomValuePack.o ../multicolvar/Bridge.o ../multicolvar/BridgedMultiColvarFunction.o ../multicolvar/CatomPack.o ../multicolvar/CenterOfMultiColvar.o ../multicolvar/CoordinationNumbers.o ../multicolvar/Density.o ../multicolvar/DihedralCorrelation.o ../multicolvar/DistanceFromContour.o ../multicolvar/Distances.o ../multicolvar/DumpMultiColvar.o ../multicolvar/FilterBetween.o ../multicolvar/FilterLessThan.o ../multicolvar/FilterMoreThan.o ../multicolvar/InPlaneDistances.o ../multicolvar/LocalAverage.o ../multicolvar/MultiColvarBase.o ../multicolvar/MultiColvarCombine.o ../multicolvar/MultiColvarDensity.o ../multicolvar/MultiColvarFilter.o ../multicolvar/MultiColvarProduct.o ../multicolvar/NumberOfLinks.o ../multicolvar/Torsions.o ../multicolvar/VolumeAround.o ../multicolvar/VolumeBetweenContours.o ../multicolvar/VolumeCavity.o ../multicolvar/VolumeGradientBase.o ../multicolvar/VolumeInCylinder.o ../multicolvar/VolumeInSphere.o ../multicolvar/VolumeTetrapore.o ../multicolvar/XAngle.o ../multicolvar/XDistances.o ../multicolvar/XYDistances.o ../multicolvar/XYTorsion.o ../reference/ArgumentOnlyDistance.o ../reference/DRMSD.o ../reference/Direction.o ../reference/DotProductDistance.o ../reference/EuclideanDistance.o ../reference/FakeFrame.o ../reference/IntermolecularDRMSD.o ../reference/IntramolecularDRMSD.o ../reference/MahalanobisDistance.o ../reference/MetricRegister.o ../reference/MultiDomainRMSD.o ../reference/NormalizedEuclideanDistance.o ../reference/OptimalRMSD.o ../reference/RMSDBase.o ../reference/ReferenceArguments.o ../reference/ReferenceAtoms.o ../reference/ReferenceConfiguration.o ../reference/ReferenceValuePack.o ../reference/SimpleRMSD.o ../reference/SingleDomainRMSD.o ../secondarystructure/AlphaRMSD.o ../secondarystructure/AntibetaRMSD.o ../secondarystructure/ParabetaRMSD.o ../secondarystructure/SecondaryStructureRMSD.o ../setup/Load.o ../setup/Restart.o ../setup/Units.o ../tools/Angle.o ../tools/AtomNumber.o ../tools/BiasRepresentation.o ../tools/Brent1DRootSearch.o ../tools/Citations.o ../tools/Communicator.o ../tools/ConjugateGradient.o ../tools/DLLoader.o ../tools/DynamicList.o ../tools/ERMSD.o ../tools/Exception.o ../tools/FileBase.o ../tools/ForwardDecl.o ../tools/Grid.o ../tools/HistogramBead.o ../tools/IFile.o ../tools/KernelFunctions.o ../tools/Keywords.o ../tools/LatticeReduction.o ../tools/LinkCells.o ../tools/Log.o ../tools/LoopUnroller.o ../tools/Matrix.o ../tools/MatrixSquareBracketsAccess.o ../tools/Minimise1DBrent.o ../tools/MinimiseBase.o ../tools/MolDataClass.o ../tools/MultiValue.o ../tools/NeighborList.o ../tools/OFile.o ../tools/OpenMP.o ../tools/PDB.o ../tools/Pbc.o ../tools/PlumedHandle.o ../tools/RMSD.o ../tools/Random.o ../tools/RootFindingBase.o ../tools/Stopwatch.o ../tools/Subprocess.o ../tools/SwitchingFunction.o ../tools/Tensor.o ../tools/Tools.o ../tools/Torsion.o ../tools/Tree.o ../tools/TypesafePtr.o ../tools/Units.o ../tools/Vector.o ../tools/h36.o ../vatom/ActionWithVirtualAtom.o ../vatom/Center.o ../vatom/FixedAtom.o ../vatom/Ghost.o ../vesselbase/ActionWithAveraging.o ../vesselbase/ActionWithInputVessel.o ../vesselbase/ActionWithVessel.o ../vesselbase/AltMin.o ../vesselbase/AveragingVessel.o ../vesselbase/Between.o ../vesselbase/BridgeVessel.o ../vesselbase/FunctionVessel.o ../vesselbase/Highest.o ../vesselbase/Histogram.o ../vesselbase/LessThan.o ../vesselbase/Lowest.o ../vesselbase/Max.o ../vesselbase/Mean.o ../vesselbase/Min.o ../vesselbase/Moments.o ../vesselbase/MoreThan.o ../vesselbase/OrderingVessel.o ../vesselbase/ShortcutVessel.o ../vesselbase/StoreDataVessel.o ../vesselbase/Sum.o ../vesselbase/ValueVessel.o ../vesselbase/Vessel.o ../vesselbase/VesselRegister.o ../xdrfile/xdrfile.o ../xdrfile/xdrfile_trr.o ../xdrfile/xdrfile_xtc.o ../config/Config.o -Wl,-soname,"libplumedKernel.so" -lstdc++ -lfftw3 -lgsl -lgslcblas -lz -ldl -llapack -lblas -L/usr/local/lib -rdynamic -Wl,-Bsymbolic -fopenmp chmod a+x plumed-config c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fPIC -Wall -pedantic -std=c++11 ../main/main.o ../wrapper/Plumed.o -o plumed-runtime -ldl chmod a+x plumed-mklib /usr/bin/ar cr libplumedWrapper.a ../wrapper/Plumed.o Building Plumed.inc, runtime-linking version Building Plumed.inc, shared version Building Plumed.inc, static version chmod a+x plumed-partial_tempering chmod a+x plumed-patch chmod a+x plumed-newcv Building Plumed.cmake chmod a+x plumed-selector Building Plumed.cmake, static version Building Plumed.cmake, runtime-linking version Building Plumed.cmake, shared version chmod a+x plumed-vim2html c++ -shared -o libplumed.so ../wrapper/PlumedStatic.o libplumedKernel.so -Wl,-soname,"libplumed.so" c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fPIC -Wall -pedantic -std=c++11 ../main/main.o ../wrapper/PlumedStatic.o libplumedKernel.so -o plumed -ldl gmake[4]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' /usr/local/bin/gmake install-build gmake[4]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' mkdir -p install/ /usr/local/bin/gmake PLUMED_INSTALL=Install all gmake[5]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' /usr/local/bin/gmake dirslinks gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' *** Updating links to used modules in all directories *** /usr/local/bin/gmake ../analysis.links ../asmjit.links ../bias.links ../blas.links ../cltools.links ../colvar.links ../config.links ../core.links ../function.links ../generic.links ../gridtools.links ../isdb.links ../lapack.links ../lepton.links ../main.links ../mapping.links ../molfile.links ../multicolvar.links ../reference.links ../secondarystructure.links ../setup.links ../tools.links ../vatom.links ../vesselbase.links ../wrapper.links ../xdrfile.links gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' /usr/local/bin/gmake -C ../analysis links /usr/local/bin/gmake -C ../asmjit links /usr/local/bin/gmake -C ../bias links /usr/local/bin/gmake -C ../blas links /usr/local/bin/gmake -C ../cltools links /usr/local/bin/gmake -C ../colvar links /usr/local/bin/gmake -C ../config links /usr/local/bin/gmake -C ../core links /usr/local/bin/gmake -C ../function links /usr/local/bin/gmake -C ../generic links /usr/local/bin/gmake -C ../gridtools links /usr/local/bin/gmake -C ../isdb links /usr/local/bin/gmake -C ../lapack links /usr/local/bin/gmake -C ../lepton links gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/blas' /usr/local/bin/gmake -C ../main links /usr/local/bin/gmake -C ../mapping links /usr/local/bin/gmake -C ../molfile links gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/config' /usr/local/bin/gmake -C ../multicolvar links Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/blas /usr/local/bin/gmake -C ../reference links /usr/local/bin/gmake -C ../secondarystructure links /usr/local/bin/gmake -C ../setup links Nothing to do in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/config /usr/local/bin/gmake -C ../tools links /usr/local/bin/gmake -C ../vatom links gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/config' /usr/local/bin/gmake -C ../vesselbase links gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/blas' /usr/local/bin/gmake -C ../wrapper links /usr/local/bin/gmake -C ../xdrfile links gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lapack' gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/main' gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/molfile' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/main gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/cltools' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lapack gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lepton' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/molfile Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/cltools gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/wrapper' gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/setup' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lepton gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/function' gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/asmjit' gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/secondarystructure' Nothing to do in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/wrapper gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/xdrfile' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/setup gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/vatom' gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/wrapper' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/function gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/isdb' gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/molfile' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/asmjit Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/secondarystructure Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/vatom Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/isdb Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/xdrfile gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/mapping' gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/analysis' gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/bias' gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/asmjit' gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/xdrfile' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/analysis Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/bias Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/mapping gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/generic' gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/reference' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/generic Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/reference gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/gridtools' gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/colvar' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/gridtools gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/main' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/colvar gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/vesselbase' gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/core' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/vesselbase Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/core gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/multicolvar' gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lapack' gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/tools' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/multicolvar Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/tools gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lepton' gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/setup' gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/vatom' gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/reference' gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/secondarystructure' gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/bias' gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/generic' gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/core' gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/tools' gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/colvar' gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/gridtools' gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/function' gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/cltools' gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/isdb' gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/vesselbase' gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/mapping' gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/multicolvar' gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/analysis' gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' /usr/local/bin/gmake dirs gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' *** Compiling all directories *** /usr/local/bin/gmake ../analysis ../asmjit ../bias ../blas ../cltools ../colvar ../config ../core ../function ../generic ../gridtools ../isdb ../lapack ../lepton ../main ../mapping ../molfile ../multicolvar ../reference ../secondarystructure ../setup ../tools ../vatom ../vesselbase ../wrapper ../xdrfile gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' /usr/local/bin/gmake -C ../analysis obj /usr/local/bin/gmake -C ../asmjit obj /usr/local/bin/gmake -C ../bias obj /usr/local/bin/gmake -C ../blas obj /usr/local/bin/gmake -C ../cltools obj /usr/local/bin/gmake -C ../colvar obj /usr/local/bin/gmake -C ../config obj /usr/local/bin/gmake -C ../core obj /usr/local/bin/gmake -C ../function obj /usr/local/bin/gmake -C ../generic obj /usr/local/bin/gmake -C ../gridtools obj /usr/local/bin/gmake -C ../isdb obj /usr/local/bin/gmake -C ../lapack obj gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/blas' gmake[8]: Nothing to be done for 'obj'. /usr/local/bin/gmake -C ../lepton obj gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/blas' /usr/local/bin/gmake -C ../main obj /usr/local/bin/gmake -C ../mapping obj gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/config' /usr/local/bin/gmake -C ../molfile obj /usr/local/bin/gmake PLUMED_FORCE=yes ConfigInstall.inc Config.inc version.h config.txt /usr/local/bin/gmake -C ../multicolvar obj /usr/local/bin/gmake -C ../reference obj /usr/local/bin/gmake -C ../secondarystructure obj /usr/local/bin/gmake -C ../setup obj /usr/local/bin/gmake -C ../tools obj /usr/local/bin/gmake -C ../vatom obj /usr/local/bin/gmake -C ../vesselbase obj /usr/local/bin/gmake -C ../wrapper obj gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lapack' gmake[8]: Nothing to be done for 'obj'. gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lapack' /usr/local/bin/gmake -C ../xdrfile obj gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/main' gmake[8]: Nothing to be done for 'obj'. gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/main' gmake[9]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/config' gmake[9]: 'config.txt' is up to date. gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/molfile' gmake[8]: Nothing to be done for 'obj'. gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/wrapper' gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/molfile' gmake[8]: Nothing to be done for 'obj'. gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/wrapper' gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/bias' gmake[8]: Nothing to be done for 'obj'. gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/bias' Updating ConfigInstall.inc Updating Config.inc Updating version.h gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lepton' gmake[8]: Nothing to be done for 'obj'. gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lepton' gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/setup' gmake[8]: Nothing to be done for 'obj'. gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/setup' gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/xdrfile' gmake[8]: Nothing to be done for 'obj'. gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/xdrfile' gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/asmjit' gmake[8]: Nothing to be done for 'obj'. gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/asmjit' gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/vatom' gmake[8]: Nothing to be done for 'obj'. gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/vatom' gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/secondarystructure' gmake[8]: Nothing to be done for 'obj'. gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/secondarystructure' gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/cltools' gmake[8]: Nothing to be done for 'obj'. gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/cltools' gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/function' gmake[8]: Nothing to be done for 'obj'. gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/function' gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/generic' gmake[8]: Nothing to be done for 'obj'. gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/generic' gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/isdb' gmake[8]: Nothing to be done for 'obj'. gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/isdb' cmp -s Config.inc~ Config.inc || cp Config.inc~ Config.inc gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/mapping' gmake[8]: Nothing to be done for 'obj'. gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/mapping' cmp -s ConfigInstall.inc~ ConfigInstall.inc || cp ConfigInstall.inc~ ConfigInstall.inc gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/analysis' gmake[8]: Nothing to be done for 'obj'. gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/reference' gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/analysis' gmake[8]: Nothing to be done for 'obj'. gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/reference' gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/colvar' gmake[8]: Nothing to be done for 'obj'. gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/colvar' rm Config.inc~ rm ConfigInstall.inc~ gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/gridtools' gmake[8]: Nothing to be done for 'obj'. gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/gridtools' gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/vesselbase' gmake[8]: Nothing to be done for 'obj'. gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/vesselbase' gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/tools' gmake[8]: Nothing to be done for 'obj'. gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/tools' gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/core' gmake[8]: Nothing to be done for 'obj'. gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/core' gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/multicolvar' gmake[8]: Nothing to be done for 'obj'. gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/multicolvar' gmake[9]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/config' /usr/local/bin/gmake Config.o ConfigInstall.o compile_options.sh gmake[9]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/config' gmake[9]: 'Config.o' is up to date. gmake[9]: 'ConfigInstall.o' is up to date. gmake[9]: 'compile_options.sh' is up to date. gmake[9]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/config' gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/config' gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' /usr/local/bin/gmake lib gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fPIC -Wall -pedantic -std=c++11 ../main/main.o ../analysis/AnalysisBase.o ../analysis/Average.o ../analysis/AverageVessel.o ../analysis/Committor.o ../analysis/DataCollectionObject.o ../analysis/EuclideanDissimilarityMatrix.o ../analysis/FarthestPointSampling.o ../analysis/Histogram.o ../analysis/LandmarkSelectionBase.o ../analysis/LandmarkStaged.o ../analysis/OutputColvarFile.o ../analysis/OutputPDBFile.o ../analysis/PrintDissimilarityMatrix.o ../analysis/ReadAnalysisFrames.o ../analysis/ReadDissimilarityMatrix.o ../analysis/ReselectLandmarks.o ../analysis/SelectRandomFrames.o ../analysis/SelectWithStride.o ../analysis/WhamHistogram.o ../analysis/WhamWeights.o ../asmjit/arch.o ../asmjit/assembler.o ../asmjit/codebuilder.o ../asmjit/codecompiler.o ../asmjit/codeemitter.o ../asmjit/codeholder.o ../asmjit/constpool.o ../asmjit/cpuinfo.o ../asmjit/func.o ../asmjit/globals.o ../asmjit/inst.o ../asmjit/logging.o ../asmjit/operand.o ../asmjit/osutils.o ../asmjit/regalloc.o ../asmjit/runtime.o ../asmjit/string.o ../asmjit/utils.o ../asmjit/vmem.o ../asmjit/x86assembler.o ../asmjit/x86builder.o ../asmjit/x86compiler.o ../asmjit/x86inst.o ../asmjit/x86instimpl.o ../asmjit/x86internal.o ../asmjit/x86logging.o ../asmjit/x86operand.o ../asmjit/x86operand_regs.o ../asmjit/x86regalloc.o ../asmjit/zone.o ../bias/ABMD.o ../bias/Bias.o ../bias/BiasValue.o ../bias/ExtendedLagrangian.o ../bias/External.o ../bias/LWalls.o ../bias/MaxEnt.o ../bias/MetaD.o ../bias/MovingRestraint.o ../bias/PBMetaD.o ../bias/Restraint.o ../bias/ReweightBase.o ../bias/ReweightBias.o ../bias/ReweightMetad.o ../bias/ReweightTemperaturePressure.o ../bias/ReweightWham.o ../bias/UWalls.o ../blas/blas.o ../cltools/CLTool.o ../cltools/Completion.o ../cltools/Driver.o ../cltools/DriverDouble.o ../cltools/DriverFloat.o ../cltools/GenExample.o ../cltools/GenJson.o ../cltools/GenTemplate.o ../cltools/Info.o ../cltools/Manual.o ../cltools/PdbRenumber.o ../cltools/SimpleMD.o ../cltools/SumHills.o ../cltools/kT.o ../cltools/pesmd.o ../colvar/Angle.o ../colvar/Cell.o ../colvar/Colvar.o ../colvar/Constant.o ../colvar/ContactMap.o ../colvar/Coordination.o ../colvar/CoordinationBase.o ../colvar/DHEnergy.o ../colvar/DRMSD.o ../colvar/Dimer.o ../colvar/Dipole.o ../colvar/Distance.o ../colvar/EEFSolv.o ../colvar/ERMSD.o ../colvar/Energy.o ../colvar/ExtraCV.o ../colvar/Fake.o ../colvar/GHBFIX.o ../colvar/Gyration.o ../colvar/MultiRMSD.o ../colvar/PCARMSD.o ../colvar/PathMSD.o ../colvar/PathMSDBase.o ../colvar/Position.o ../colvar/ProjectionOnAxis.o ../colvar/PropertyMap.o ../colvar/Puckering.o ../colvar/RMSD.o ../colvar/Template.o ../colvar/Torsion.o ../colvar/Volume.o ../core/Action.o ../core/ActionAnyorder.o ../core/ActionAtomistic.o ../core/ActionPilot.o ../core/ActionRegister.o ../core/ActionSet.o ../core/ActionSetup.o ../core/ActionShortcut.o ../core/ActionWithArguments.o ../core/ActionWithValue.o ../core/ActionWithVirtualAtom.o ../core/Atoms.o ../core/CLTool.o ../core/CLToolMain.o ../core/CLToolRegister.o ../core/Colvar.o ../core/DataFetchingObject.o ../core/ExchangePatterns.o ../core/FlexibleBin.o ../core/GREX.o ../core/GenericMolInfo.o ../core/MDAtoms.o ../core/ModuleMap.o ../core/PlumedMain.o ../core/PlumedMainInitializer.o ../core/TargetDist.o ../core/Value.o ../core/WithCmd.o ../function/Combine.o ../function/Custom.o ../function/Ensemble.o ../function/FuncPathGeneral.o ../function/FuncPathMSD.o ../function/FuncSumHills.o ../function/Function.o ../function/LocalEnsemble.o ../function/Piecewise.o ../function/Sort.o ../function/Stats.o ../function/Target.o ../generic/Debug.o ../generic/DumpAtoms.o ../generic/DumpDerivatives.o ../generic/DumpForces.o ../generic/DumpMassCharge.o ../generic/DumpProjections.o ../generic/EffectiveEnergyDrift.o ../generic/EndPlumed.o ../generic/FitToTemplate.o ../generic/Flush.o ../generic/Group.o ../generic/Include.o ../generic/MolInfo.o ../generic/Plumed.o ../generic/Print.o ../generic/RandomExchanges.o ../generic/Read.o ../generic/ResetCell.o ../generic/Time.o ../generic/UpdateIf.o ../generic/WholeMolecules.o ../generic/WrapAround.o ../gridtools/ActionWithGrid.o ../gridtools/ActionWithInputGrid.o ../gridtools/ActionWithIntegral.o ../gridtools/AverageOnGrid.o ../gridtools/ContourFindingBase.o ../gridtools/ConvertToFES.o ../gridtools/DumpCube.o ../gridtools/DumpGrid.o ../gridtools/FindContour.o ../gridtools/FindContourSurface.o ../gridtools/FindSphericalContour.o ../gridtools/FourierTransform.o ../gridtools/GridPrintingBase.o ../gridtools/GridSearch.o ../gridtools/GridToXYZ.o ../gridtools/GridVessel.o ../gridtools/HistogramOnGrid.o ../gridtools/IntegrateGrid.o ../gridtools/InterpolateGrid.o ../isdb/CS2Backbone.o ../isdb/Caliber.o ../isdb/EMMI.o ../isdb/FretEfficiency.o ../isdb/Jcoupling.o ../isdb/Metainference.o ../isdb/MetainferenceBase.o ../isdb/NOE.o ../isdb/PRE.o ../isdb/RDC.o ../isdb/Rescale.o ../isdb/SAXS.o ../isdb/Select.o ../isdb/Selector.o ../lapack/lapack.o ../lepton/CompiledExpression.o ../lepton/ExpressionProgram.o ../lepton/ExpressionTreeNode.o ../lepton/Operation.o ../lepton/ParsedExpression.o ../lepton/Parser.o ../mapping/AdaptivePath.o ../mapping/Mapping.o ../mapping/PCAVars.o ../mapping/Path.o ../mapping/PathBase.o ../mapping/PathReparameterization.o ../mapping/PathTools.o ../mapping/PropertyMap.o ../mapping/SpathVessel.o ../mapping/TrigonometricPathVessel.o ../mapping/ZpathVessel.o ../molfile/crdplugin.o ../molfile/dcdplugin.o ../molfile/gromacsplugin.o ../molfile/pdbplugin.o ../multicolvar/ActionVolume.o ../multicolvar/AlphaBeta.o ../multicolvar/Angles.o ../multicolvar/AtomValuePack.o ../multicolvar/Bridge.o ../multicolvar/BridgedMultiColvarFunction.o ../multicolvar/CatomPack.o ../multicolvar/CenterOfMultiColvar.o ../multicolvar/CoordinationNumbers.o ../multicolvar/Density.o ../multicolvar/DihedralCorrelation.o ../multicolvar/DistanceFromContour.o ../multicolvar/Distances.o ../multicolvar/DumpMultiColvar.o ../multicolvar/FilterBetween.o ../multicolvar/FilterLessThan.o ../multicolvar/FilterMoreThan.o ../multicolvar/InPlaneDistances.o ../multicolvar/LocalAverage.o ../multicolvar/MultiColvarBase.o ../multicolvar/MultiColvarCombine.o ../multicolvar/MultiColvarDensity.o ../multicolvar/MultiColvarFilter.o ../multicolvar/MultiColvarProduct.o ../multicolvar/NumberOfLinks.o ../multicolvar/Torsions.o ../multicolvar/VolumeAround.o ../multicolvar/VolumeBetweenContours.o ../multicolvar/VolumeCavity.o ../multicolvar/VolumeGradientBase.o ../multicolvar/VolumeInCylinder.o ../multicolvar/VolumeInSphere.o ../multicolvar/VolumeTetrapore.o ../multicolvar/XAngle.o ../multicolvar/XDistances.o ../multicolvar/XYDistances.o ../multicolvar/XYTorsion.o ../reference/ArgumentOnlyDistance.o ../reference/DRMSD.o ../reference/Direction.o ../reference/DotProductDistance.o ../reference/EuclideanDistance.o ../reference/FakeFrame.o ../reference/IntermolecularDRMSD.o ../reference/IntramolecularDRMSD.o ../reference/MahalanobisDistance.o ../reference/MetricRegister.o ../reference/MultiDomainRMSD.o ../reference/NormalizedEuclideanDistance.o ../reference/OptimalRMSD.o ../reference/RMSDBase.o ../reference/ReferenceArguments.o ../reference/ReferenceAtoms.o ../reference/ReferenceConfiguration.o ../reference/ReferenceValuePack.o ../reference/SimpleRMSD.o ../reference/SingleDomainRMSD.o ../secondarystructure/AlphaRMSD.o ../secondarystructure/AntibetaRMSD.o ../secondarystructure/ParabetaRMSD.o ../secondarystructure/SecondaryStructureRMSD.o ../setup/Load.o ../setup/Restart.o ../setup/Units.o ../tools/Angle.o ../tools/AtomNumber.o ../tools/BiasRepresentation.o ../tools/Brent1DRootSearch.o ../tools/Citations.o ../tools/Communicator.o ../tools/ConjugateGradient.o ../tools/DLLoader.o ../tools/DynamicList.o ../tools/ERMSD.o ../tools/Exception.o ../tools/FileBase.o ../tools/ForwardDecl.o ../tools/Grid.o ../tools/HistogramBead.o ../tools/IFile.o ../tools/KernelFunctions.o ../tools/Keywords.o ../tools/LatticeReduction.o ../tools/LinkCells.o ../tools/Log.o ../tools/LoopUnroller.o ../tools/Matrix.o ../tools/MatrixSquareBracketsAccess.o ../tools/Minimise1DBrent.o ../tools/MinimiseBase.o ../tools/MolDataClass.o ../tools/MultiValue.o ../tools/NeighborList.o ../tools/OFile.o ../tools/OpenMP.o ../tools/PDB.o ../tools/Pbc.o ../tools/PlumedHandle.o ../tools/RMSD.o ../tools/Random.o ../tools/RootFindingBase.o ../tools/Stopwatch.o ../tools/Subprocess.o ../tools/SwitchingFunction.o ../tools/Tensor.o ../tools/Tools.o ../tools/Torsion.o ../tools/Tree.o ../tools/TypesafePtr.o ../tools/Units.o ../tools/Vector.o ../tools/h36.o ../vatom/ActionWithVirtualAtom.o ../vatom/Center.o ../vatom/FixedAtom.o ../vatom/Ghost.o ../vesselbase/ActionWithAveraging.o ../vesselbase/ActionWithInputVessel.o ../vesselbase/ActionWithVessel.o ../vesselbase/AltMin.o ../vesselbase/AveragingVessel.o ../vesselbase/Between.o ../vesselbase/BridgeVessel.o ../vesselbase/FunctionVessel.o ../vesselbase/Highest.o ../vesselbase/Histogram.o ../vesselbase/LessThan.o ../vesselbase/Lowest.o ../vesselbase/Max.o ../vesselbase/Mean.o ../vesselbase/Min.o ../vesselbase/Moments.o ../vesselbase/MoreThan.o ../vesselbase/OrderingVessel.o ../vesselbase/ShortcutVessel.o ../vesselbase/StoreDataVessel.o ../vesselbase/Sum.o ../vesselbase/ValueVessel.o ../vesselbase/Vessel.o ../vesselbase/VesselRegister.o ../xdrfile/xdrfile.o ../xdrfile/xdrfile_trr.o ../xdrfile/xdrfile_xtc.o ../config/ConfigInstall.o ../wrapper/PlumedStatic.o -o install/plumed-static -ldl -lstdc++ -lfftw3 -lgsl -lgslcblas -lz -ldl -llapack -lblas -L/usr/local/lib -rdynamic -Wl,-Bsymbolic -fopenmp Building Plumed.inc mkdir -p install c++ -shared -o install/libplumedKernel.so ../analysis/AnalysisBase.o ../analysis/Average.o ../analysis/AverageVessel.o ../analysis/Committor.o ../analysis/DataCollectionObject.o ../analysis/EuclideanDissimilarityMatrix.o ../analysis/FarthestPointSampling.o ../analysis/Histogram.o ../analysis/LandmarkSelectionBase.o ../analysis/LandmarkStaged.o ../analysis/OutputColvarFile.o ../analysis/OutputPDBFile.o ../analysis/PrintDissimilarityMatrix.o ../analysis/ReadAnalysisFrames.o ../analysis/ReadDissimilarityMatrix.o ../analysis/ReselectLandmarks.o ../analysis/SelectRandomFrames.o ../analysis/SelectWithStride.o ../analysis/WhamHistogram.o ../analysis/WhamWeights.o ../asmjit/arch.o ../asmjit/assembler.o ../asmjit/codebuilder.o ../asmjit/codecompiler.o ../asmjit/codeemitter.o ../asmjit/codeholder.o ../asmjit/constpool.o ../asmjit/cpuinfo.o ../asmjit/func.o ../asmjit/globals.o ../asmjit/inst.o ../asmjit/logging.o ../asmjit/operand.o ../asmjit/osutils.o ../asmjit/regalloc.o ../asmjit/runtime.o ../asmjit/string.o ../asmjit/utils.o ../asmjit/vmem.o ../asmjit/x86assembler.o ../asmjit/x86builder.o ../asmjit/x86compiler.o ../asmjit/x86inst.o ../asmjit/x86instimpl.o ../asmjit/x86internal.o ../asmjit/x86logging.o ../asmjit/x86operand.o ../asmjit/x86operand_regs.o ../asmjit/x86regalloc.o ../asmjit/zone.o ../bias/ABMD.o ../bias/Bias.o ../bias/BiasValue.o ../bias/ExtendedLagrangian.o ../bias/External.o ../bias/LWalls.o ../bias/MaxEnt.o ../bias/MetaD.o ../bias/MovingRestraint.o ../bias/PBMetaD.o ../bias/Restraint.o ../bias/ReweightBase.o ../bias/ReweightBias.o ../bias/ReweightMetad.o ../bias/ReweightTemperaturePressure.o ../bias/ReweightWham.o ../bias/UWalls.o ../blas/blas.o ../cltools/CLTool.o ../cltools/Completion.o ../cltools/Driver.o ../cltools/DriverDouble.o ../cltools/DriverFloat.o ../cltools/GenExample.o ../cltools/GenJson.o ../cltools/GenTemplate.o ../cltools/Info.o ../cltools/Manual.o ../cltools/PdbRenumber.o ../cltools/SimpleMD.o ../cltools/SumHills.o ../cltools/kT.o ../cltools/pesmd.o ../colvar/Angle.o ../colvar/Cell.o ../colvar/Colvar.o ../colvar/Constant.o ../colvar/ContactMap.o ../colvar/Coordination.o ../colvar/CoordinationBase.o ../colvar/DHEnergy.o ../colvar/DRMSD.o ../colvar/Dimer.o ../colvar/Dipole.o ../colvar/Distance.o ../colvar/EEFSolv.o ../colvar/ERMSD.o ../colvar/Energy.o ../colvar/ExtraCV.o ../colvar/Fake.o ../colvar/GHBFIX.o ../colvar/Gyration.o ../colvar/MultiRMSD.o ../colvar/PCARMSD.o ../colvar/PathMSD.o ../colvar/PathMSDBase.o ../colvar/Position.o ../colvar/ProjectionOnAxis.o ../colvar/PropertyMap.o ../colvar/Puckering.o ../colvar/RMSD.o ../colvar/Template.o ../colvar/Torsion.o ../colvar/Volume.o ../core/Action.o ../core/ActionAnyorder.o ../core/ActionAtomistic.o ../core/ActionPilot.o ../core/ActionRegister.o ../core/ActionSet.o ../core/ActionSetup.o ../core/ActionShortcut.o ../core/ActionWithArguments.o ../core/ActionWithValue.o ../core/ActionWithVirtualAtom.o ../core/Atoms.o ../core/CLTool.o ../core/CLToolMain.o ../core/CLToolRegister.o ../core/Colvar.o ../core/DataFetchingObject.o ../core/ExchangePatterns.o ../core/FlexibleBin.o ../core/GREX.o ../core/GenericMolInfo.o ../core/MDAtoms.o ../core/ModuleMap.o ../core/PlumedMain.o ../core/PlumedMainInitializer.o ../core/TargetDist.o ../core/Value.o ../core/WithCmd.o ../function/Combine.o ../function/Custom.o ../function/Ensemble.o ../function/FuncPathGeneral.o ../function/FuncPathMSD.o ../function/FuncSumHills.o ../function/Function.o ../function/LocalEnsemble.o ../function/Piecewise.o ../function/Sort.o ../function/Stats.o ../function/Target.o ../generic/Debug.o ../generic/DumpAtoms.o ../generic/DumpDerivatives.o ../generic/DumpForces.o ../generic/DumpMassCharge.o ../generic/DumpProjections.o ../generic/EffectiveEnergyDrift.o ../generic/EndPlumed.o ../generic/FitToTemplate.o ../generic/Flush.o ../generic/Group.o ../generic/Include.o ../generic/MolInfo.o ../generic/Plumed.o ../generic/Print.o ../generic/RandomExchanges.o ../generic/Read.o ../generic/ResetCell.o ../generic/Time.o ../generic/UpdateIf.o ../generic/WholeMolecules.o ../generic/WrapAround.o ../gridtools/ActionWithGrid.o ../gridtools/ActionWithInputGrid.o ../gridtools/ActionWithIntegral.o ../gridtools/AverageOnGrid.o ../gridtools/ContourFindingBase.o ../gridtools/ConvertToFES.o ../gridtools/DumpCube.o ../gridtools/DumpGrid.o ../gridtools/FindContour.o ../gridtools/FindContourSurface.o ../gridtools/FindSphericalContour.o ../gridtools/FourierTransform.o ../gridtools/GridPrintingBase.o ../gridtools/GridSearch.o ../gridtools/GridToXYZ.o ../gridtools/GridVessel.o ../gridtools/HistogramOnGrid.o ../gridtools/IntegrateGrid.o ../gridtools/InterpolateGrid.o ../isdb/CS2Backbone.o ../isdb/Caliber.o ../isdb/EMMI.o ../isdb/FretEfficiency.o ../isdb/Jcoupling.o ../isdb/Metainference.o ../isdb/MetainferenceBase.o ../isdb/NOE.o ../isdb/PRE.o ../isdb/RDC.o ../isdb/Rescale.o ../isdb/SAXS.o ../isdb/Select.o ../isdb/Selector.o ../lapack/lapack.o ../lepton/CompiledExpression.o ../lepton/ExpressionProgram.o ../lepton/ExpressionTreeNode.o ../lepton/Operation.o ../lepton/ParsedExpression.o ../lepton/Parser.o ../mapping/AdaptivePath.o ../mapping/Mapping.o ../mapping/PCAVars.o ../mapping/Path.o ../mapping/PathBase.o ../mapping/PathReparameterization.o ../mapping/PathTools.o ../mapping/PropertyMap.o ../mapping/SpathVessel.o ../mapping/TrigonometricPathVessel.o ../mapping/ZpathVessel.o ../molfile/crdplugin.o ../molfile/dcdplugin.o ../molfile/gromacsplugin.o ../molfile/pdbplugin.o ../multicolvar/ActionVolume.o ../multicolvar/AlphaBeta.o ../multicolvar/Angles.o ../multicolvar/AtomValuePack.o ../multicolvar/Bridge.o ../multicolvar/BridgedMultiColvarFunction.o ../multicolvar/CatomPack.o ../multicolvar/CenterOfMultiColvar.o ../multicolvar/CoordinationNumbers.o ../multicolvar/Density.o ../multicolvar/DihedralCorrelation.o ../multicolvar/DistanceFromContour.o ../multicolvar/Distances.o ../multicolvar/DumpMultiColvar.o ../multicolvar/FilterBetween.o ../multicolvar/FilterLessThan.o ../multicolvar/FilterMoreThan.o ../multicolvar/InPlaneDistances.o ../multicolvar/LocalAverage.o ../multicolvar/MultiColvarBase.o ../multicolvar/MultiColvarCombine.o ../multicolvar/MultiColvarDensity.o ../multicolvar/MultiColvarFilter.o ../multicolvar/MultiColvarProduct.o ../multicolvar/NumberOfLinks.o ../multicolvar/Torsions.o ../multicolvar/VolumeAround.o ../multicolvar/VolumeBetweenContours.o ../multicolvar/VolumeCavity.o ../multicolvar/VolumeGradientBase.o ../multicolvar/VolumeInCylinder.o ../multicolvar/VolumeInSphere.o ../multicolvar/VolumeTetrapore.o ../multicolvar/XAngle.o ../multicolvar/XDistances.o ../multicolvar/XYDistances.o ../multicolvar/XYTorsion.o ../reference/ArgumentOnlyDistance.o ../reference/DRMSD.o ../reference/Direction.o ../reference/DotProductDistance.o ../reference/EuclideanDistance.o ../reference/FakeFrame.o ../reference/IntermolecularDRMSD.o ../reference/IntramolecularDRMSD.o ../reference/MahalanobisDistance.o ../reference/MetricRegister.o ../reference/MultiDomainRMSD.o ../reference/NormalizedEuclideanDistance.o ../reference/OptimalRMSD.o ../reference/RMSDBase.o ../reference/ReferenceArguments.o ../reference/ReferenceAtoms.o ../reference/ReferenceConfiguration.o ../reference/ReferenceValuePack.o ../reference/SimpleRMSD.o ../reference/SingleDomainRMSD.o ../secondarystructure/AlphaRMSD.o ../secondarystructure/AntibetaRMSD.o ../secondarystructure/ParabetaRMSD.o ../secondarystructure/SecondaryStructureRMSD.o ../setup/Load.o ../setup/Restart.o ../setup/Units.o ../tools/Angle.o ../tools/AtomNumber.o ../tools/BiasRepresentation.o ../tools/Brent1DRootSearch.o ../tools/Citations.o ../tools/Communicator.o ../tools/ConjugateGradient.o ../tools/DLLoader.o ../tools/DynamicList.o ../tools/ERMSD.o ../tools/Exception.o ../tools/FileBase.o ../tools/ForwardDecl.o ../tools/Grid.o ../tools/HistogramBead.o ../tools/IFile.o ../tools/KernelFunctions.o ../tools/Keywords.o ../tools/LatticeReduction.o ../tools/LinkCells.o ../tools/Log.o ../tools/LoopUnroller.o ../tools/Matrix.o ../tools/MatrixSquareBracketsAccess.o ../tools/Minimise1DBrent.o ../tools/MinimiseBase.o ../tools/MolDataClass.o ../tools/MultiValue.o ../tools/NeighborList.o ../tools/OFile.o ../tools/OpenMP.o ../tools/PDB.o ../tools/Pbc.o ../tools/PlumedHandle.o ../tools/RMSD.o ../tools/Random.o ../tools/RootFindingBase.o ../tools/Stopwatch.o ../tools/Subprocess.o ../tools/SwitchingFunction.o ../tools/Tensor.o ../tools/Tools.o ../tools/Torsion.o ../tools/Tree.o ../tools/TypesafePtr.o ../tools/Units.o ../tools/Vector.o ../tools/h36.o ../vatom/ActionWithVirtualAtom.o ../vatom/Center.o ../vatom/FixedAtom.o ../vatom/Ghost.o ../vesselbase/ActionWithAveraging.o ../vesselbase/ActionWithInputVessel.o ../vesselbase/ActionWithVessel.o ../vesselbase/AltMin.o ../vesselbase/AveragingVessel.o ../vesselbase/Between.o ../vesselbase/BridgeVessel.o ../vesselbase/FunctionVessel.o ../vesselbase/Highest.o ../vesselbase/Histogram.o ../vesselbase/LessThan.o ../vesselbase/Lowest.o ../vesselbase/Max.o ../vesselbase/Mean.o ../vesselbase/Min.o ../vesselbase/Moments.o ../vesselbase/MoreThan.o ../vesselbase/OrderingVessel.o ../vesselbase/ShortcutVessel.o ../vesselbase/StoreDataVessel.o ../vesselbase/Sum.o ../vesselbase/ValueVessel.o ../vesselbase/Vessel.o ../vesselbase/VesselRegister.o ../xdrfile/xdrfile.o ../xdrfile/xdrfile_trr.o ../xdrfile/xdrfile_xtc.o ../config/ConfigInstall.o -Wl,-soname,"libplumedKernel.so" -lstdc++ -lfftw3 -lgsl -lgslcblas -lz -ldl -llapack -lblas -L/usr/local/lib -rdynamic -Wl,-Bsymbolic -fopenmp c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fPIC -Wall -pedantic -std=c++11 ../main/main.o ../wrapper/Plumed.o -o install/plumed-runtime -ldl mkdir -p install chmod a+x install/plumed-config /usr/bin/ar cr install/libplumedWrapper.a ../wrapper/Plumed.o Building Plumed.inc, runtime-linking version chmod a+x install/plumed-newcv chmod a+x install/plumed-mklib Building Plumed.inc, shared version Building Plumed.inc, static version Building Plumed.cmake chmod a+x install/plumed-partial_tempering chmod a+x install/plumed-vim2html chmod a+x install/plumed-selector chmod a+x install/plumed-patch Building Plumed.cmake, runtime-linking version Building Plumed.cmake, shared version Building Plumed.cmake, static version mkdir -p install c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fPIC -Wall -pedantic -std=c++11 ../main/main.o ../wrapper/PlumedStatic.o install/libplumedKernel.so -o install/plumed -ldl c++ -shared -o install/libplumed.so ../wrapper/PlumedStatic.o install/libplumedKernel.so -Wl,-soname,"libplumed.so" gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' gmake[5]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' /usr/local/bin/gmake PLUMED_INSTALL=Install install/kernel.o gmake[5]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' /usr/bin/ld -r -o install/kernel.o ../analysis/AnalysisBase.o ../analysis/Average.o ../analysis/AverageVessel.o ../analysis/Committor.o ../analysis/DataCollectionObject.o ../analysis/EuclideanDissimilarityMatrix.o ../analysis/FarthestPointSampling.o ../analysis/Histogram.o ../analysis/LandmarkSelectionBase.o ../analysis/LandmarkStaged.o ../analysis/OutputColvarFile.o ../analysis/OutputPDBFile.o ../analysis/PrintDissimilarityMatrix.o ../analysis/ReadAnalysisFrames.o ../analysis/ReadDissimilarityMatrix.o ../analysis/ReselectLandmarks.o ../analysis/SelectRandomFrames.o ../analysis/SelectWithStride.o ../analysis/WhamHistogram.o ../analysis/WhamWeights.o ../asmjit/arch.o ../asmjit/assembler.o ../asmjit/codebuilder.o ../asmjit/codecompiler.o ../asmjit/codeemitter.o ../asmjit/codeholder.o ../asmjit/constpool.o ../asmjit/cpuinfo.o ../asmjit/func.o ../asmjit/globals.o ../asmjit/inst.o ../asmjit/logging.o ../asmjit/operand.o ../asmjit/osutils.o ../asmjit/regalloc.o ../asmjit/runtime.o ../asmjit/string.o ../asmjit/utils.o ../asmjit/vmem.o ../asmjit/x86assembler.o ../asmjit/x86builder.o ../asmjit/x86compiler.o ../asmjit/x86inst.o ../asmjit/x86instimpl.o ../asmjit/x86internal.o ../asmjit/x86logging.o ../asmjit/x86operand.o ../asmjit/x86operand_regs.o ../asmjit/x86regalloc.o ../asmjit/zone.o ../bias/ABMD.o ../bias/Bias.o ../bias/BiasValue.o ../bias/ExtendedLagrangian.o ../bias/External.o ../bias/LWalls.o ../bias/MaxEnt.o ../bias/MetaD.o ../bias/MovingRestraint.o ../bias/PBMetaD.o ../bias/Restraint.o ../bias/ReweightBase.o ../bias/ReweightBias.o ../bias/ReweightMetad.o ../bias/ReweightTemperaturePressure.o ../bias/ReweightWham.o ../bias/UWalls.o ../blas/blas.o ../cltools/CLTool.o ../cltools/Completion.o ../cltools/Driver.o ../cltools/DriverDouble.o ../cltools/DriverFloat.o ../cltools/GenExample.o ../cltools/GenJson.o ../cltools/GenTemplate.o ../cltools/Info.o ../cltools/Manual.o ../cltools/PdbRenumber.o ../cltools/SimpleMD.o ../cltools/SumHills.o ../cltools/kT.o ../cltools/pesmd.o ../colvar/Angle.o ../colvar/Cell.o ../colvar/Colvar.o ../colvar/Constant.o ../colvar/ContactMap.o ../colvar/Coordination.o ../colvar/CoordinationBase.o ../colvar/DHEnergy.o ../colvar/DRMSD.o ../colvar/Dimer.o ../colvar/Dipole.o ../colvar/Distance.o ../colvar/EEFSolv.o ../colvar/ERMSD.o ../colvar/Energy.o ../colvar/ExtraCV.o ../colvar/Fake.o ../colvar/GHBFIX.o ../colvar/Gyration.o ../colvar/MultiRMSD.o ../colvar/PCARMSD.o ../colvar/PathMSD.o ../colvar/PathMSDBase.o ../colvar/Position.o ../colvar/ProjectionOnAxis.o ../colvar/PropertyMap.o ../colvar/Puckering.o ../colvar/RMSD.o ../colvar/Template.o ../colvar/Torsion.o ../colvar/Volume.o ../core/Action.o ../core/ActionAnyorder.o ../core/ActionAtomistic.o ../core/ActionPilot.o ../core/ActionRegister.o ../core/ActionSet.o ../core/ActionSetup.o ../core/ActionShortcut.o ../core/ActionWithArguments.o ../core/ActionWithValue.o ../core/ActionWithVirtualAtom.o ../core/Atoms.o ../core/CLTool.o ../core/CLToolMain.o ../core/CLToolRegister.o ../core/Colvar.o ../core/DataFetchingObject.o ../core/ExchangePatterns.o ../core/FlexibleBin.o ../core/GREX.o ../core/GenericMolInfo.o ../core/MDAtoms.o ../core/ModuleMap.o ../core/PlumedMain.o ../core/PlumedMainInitializer.o ../core/TargetDist.o ../core/Value.o ../core/WithCmd.o ../function/Combine.o ../function/Custom.o ../function/Ensemble.o ../function/FuncPathGeneral.o ../function/FuncPathMSD.o ../function/FuncSumHills.o ../function/Function.o ../function/LocalEnsemble.o ../function/Piecewise.o ../function/Sort.o ../function/Stats.o ../function/Target.o ../generic/Debug.o ../generic/DumpAtoms.o ../generic/DumpDerivatives.o ../generic/DumpForces.o ../generic/DumpMassCharge.o ../generic/DumpProjections.o ../generic/EffectiveEnergyDrift.o ../generic/EndPlumed.o ../generic/FitToTemplate.o ../generic/Flush.o ../generic/Group.o ../generic/Include.o ../generic/MolInfo.o ../generic/Plumed.o ../generic/Print.o ../generic/RandomExchanges.o ../generic/Read.o ../generic/ResetCell.o ../generic/Time.o ../generic/UpdateIf.o ../generic/WholeMolecules.o ../generic/WrapAround.o ../gridtools/ActionWithGrid.o ../gridtools/ActionWithInputGrid.o ../gridtools/ActionWithIntegral.o ../gridtools/AverageOnGrid.o ../gridtools/ContourFindingBase.o ../gridtools/ConvertToFES.o ../gridtools/DumpCube.o ../gridtools/DumpGrid.o ../gridtools/FindContour.o ../gridtools/FindContourSurface.o ../gridtools/FindSphericalContour.o ../gridtools/FourierTransform.o ../gridtools/GridPrintingBase.o ../gridtools/GridSearch.o ../gridtools/GridToXYZ.o ../gridtools/GridVessel.o ../gridtools/HistogramOnGrid.o ../gridtools/IntegrateGrid.o ../gridtools/InterpolateGrid.o ../isdb/CS2Backbone.o ../isdb/Caliber.o ../isdb/EMMI.o ../isdb/FretEfficiency.o ../isdb/Jcoupling.o ../isdb/Metainference.o ../isdb/MetainferenceBase.o ../isdb/NOE.o ../isdb/PRE.o ../isdb/RDC.o ../isdb/Rescale.o ../isdb/SAXS.o ../isdb/Select.o ../isdb/Selector.o ../lapack/lapack.o ../lepton/CompiledExpression.o ../lepton/ExpressionProgram.o ../lepton/ExpressionTreeNode.o ../lepton/Operation.o ../lepton/ParsedExpression.o ../lepton/Parser.o ../mapping/AdaptivePath.o ../mapping/Mapping.o ../mapping/PCAVars.o ../mapping/Path.o ../mapping/PathBase.o ../mapping/PathReparameterization.o ../mapping/PathTools.o ../mapping/PropertyMap.o ../mapping/SpathVessel.o ../mapping/TrigonometricPathVessel.o ../mapping/ZpathVessel.o ../molfile/crdplugin.o ../molfile/dcdplugin.o ../molfile/gromacsplugin.o ../molfile/pdbplugin.o ../multicolvar/ActionVolume.o ../multicolvar/AlphaBeta.o ../multicolvar/Angles.o ../multicolvar/AtomValuePack.o ../multicolvar/Bridge.o ../multicolvar/BridgedMultiColvarFunction.o ../multicolvar/CatomPack.o ../multicolvar/CenterOfMultiColvar.o ../multicolvar/CoordinationNumbers.o ../multicolvar/Density.o ../multicolvar/DihedralCorrelation.o ../multicolvar/DistanceFromContour.o ../multicolvar/Distances.o ../multicolvar/DumpMultiColvar.o ../multicolvar/FilterBetween.o ../multicolvar/FilterLessThan.o ../multicolvar/FilterMoreThan.o ../multicolvar/InPlaneDistances.o ../multicolvar/LocalAverage.o ../multicolvar/MultiColvarBase.o ../multicolvar/MultiColvarCombine.o ../multicolvar/MultiColvarDensity.o ../multicolvar/MultiColvarFilter.o ../multicolvar/MultiColvarProduct.o ../multicolvar/NumberOfLinks.o ../multicolvar/Torsions.o ../multicolvar/VolumeAround.o ../multicolvar/VolumeBetweenContours.o ../multicolvar/VolumeCavity.o ../multicolvar/VolumeGradientBase.o ../multicolvar/VolumeInCylinder.o ../multicolvar/VolumeInSphere.o ../multicolvar/VolumeTetrapore.o ../multicolvar/XAngle.o ../multicolvar/XDistances.o ../multicolvar/XYDistances.o ../multicolvar/XYTorsion.o ../reference/ArgumentOnlyDistance.o ../reference/DRMSD.o ../reference/Direction.o ../reference/DotProductDistance.o ../reference/EuclideanDistance.o ../reference/FakeFrame.o ../reference/IntermolecularDRMSD.o ../reference/IntramolecularDRMSD.o ../reference/MahalanobisDistance.o ../reference/MetricRegister.o ../reference/MultiDomainRMSD.o ../reference/NormalizedEuclideanDistance.o ../reference/OptimalRMSD.o ../reference/RMSDBase.o ../reference/ReferenceArguments.o ../reference/ReferenceAtoms.o ../reference/ReferenceConfiguration.o ../reference/ReferenceValuePack.o ../reference/SimpleRMSD.o ../reference/SingleDomainRMSD.o ../secondarystructure/AlphaRMSD.o ../secondarystructure/AntibetaRMSD.o ../secondarystructure/ParabetaRMSD.o ../secondarystructure/SecondaryStructureRMSD.o ../setup/Load.o ../setup/Restart.o ../setup/Units.o ../tools/Angle.o ../tools/AtomNumber.o ../tools/BiasRepresentation.o ../tools/Brent1DRootSearch.o ../tools/Citations.o ../tools/Communicator.o ../tools/ConjugateGradient.o ../tools/DLLoader.o ../tools/DynamicList.o ../tools/ERMSD.o ../tools/Exception.o ../tools/FileBase.o ../tools/ForwardDecl.o ../tools/Grid.o ../tools/HistogramBead.o ../tools/IFile.o ../tools/KernelFunctions.o ../tools/Keywords.o ../tools/LatticeReduction.o ../tools/LinkCells.o ../tools/Log.o ../tools/LoopUnroller.o ../tools/Matrix.o ../tools/MatrixSquareBracketsAccess.o ../tools/Minimise1DBrent.o ../tools/MinimiseBase.o ../tools/MolDataClass.o ../tools/MultiValue.o ../tools/NeighborList.o ../tools/OFile.o ../tools/OpenMP.o ../tools/PDB.o ../tools/Pbc.o ../tools/PlumedHandle.o ../tools/RMSD.o ../tools/Random.o ../tools/RootFindingBase.o ../tools/Stopwatch.o ../tools/Subprocess.o ../tools/SwitchingFunction.o ../tools/Tensor.o ../tools/Tools.o ../tools/Torsion.o ../tools/Tree.o ../tools/TypesafePtr.o ../tools/Units.o ../tools/Vector.o ../tools/h36.o ../vatom/ActionWithVirtualAtom.o ../vatom/Center.o ../vatom/FixedAtom.o ../vatom/Ghost.o ../vesselbase/ActionWithAveraging.o ../vesselbase/ActionWithInputVessel.o ../vesselbase/ActionWithVessel.o ../vesselbase/AltMin.o ../vesselbase/AveragingVessel.o ../vesselbase/Between.o ../vesselbase/BridgeVessel.o ../vesselbase/FunctionVessel.o ../vesselbase/Highest.o ../vesselbase/Histogram.o ../vesselbase/LessThan.o ../vesselbase/Lowest.o ../vesselbase/Max.o ../vesselbase/Mean.o ../vesselbase/Min.o ../vesselbase/Moments.o ../vesselbase/MoreThan.o ../vesselbase/OrderingVessel.o ../vesselbase/ShortcutVessel.o ../vesselbase/StoreDataVessel.o ../vesselbase/Sum.o ../vesselbase/ValueVessel.o ../vesselbase/Vessel.o ../vesselbase/VesselRegister.o ../xdrfile/xdrfile.o ../xdrfile/xdrfile_trr.o ../xdrfile/xdrfile_xtc.o ../config/ConfigInstall.o gmake[5]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' /usr/local/bin/gmake PLUMED_INSTALL=Install install/libplumed.a gmake[5]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' rm -f install/libplumed.a /usr/bin/ar cr install/libplumed.a install/kernel.o ../wrapper/PlumedStatic.o gmake[5]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' gmake[4]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' gmake[3]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' gmake[2]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src' gmake[1]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3' /usr/local/bin/gmake -C vim gmake[1]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/vim' ./vimsyntax.sh gmake[1]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/vim' /usr/local/bin/gmake -C python gmake[1]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/python' Python support was not configured gmake[1]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/python' LD_LIBRARY_PATH="/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib": PLUMED_PREPEND_PATH="/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib" /usr/local/bin/gmake -C json gmake[1]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/json' ./get_action_list.sh > action_list ../src/lib/plumed --no-mpi gen_json --actions action_list > syntax.json Could not find jq executable so unable to test if syntax.json is valid json. Consider running sudo apt-get install jq gmake[1]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/json' =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> plumed-2.9.3_1 depends on executable: bash - found =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for plumed-2.9.3_1 ===> Generating temporary packing list /usr/local/bin/gmake -C src install gmake[1]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src' /usr/local/bin/gmake -C lib install gmake[2]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' cd ../config ; /usr/local/bin/gmake gmake[3]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/config' /usr/local/bin/gmake PLUMED_FORCE=yes ConfigInstall.inc Config.inc version.h config.txt gmake[4]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/config' Updating ConfigInstall.inc cmp -s ConfigInstall.inc~ ConfigInstall.inc || cp ConfigInstall.inc~ ConfigInstall.inc rm ConfigInstall.inc~ Updating Config.inc cmp -s Config.inc~ Config.inc || cp Config.inc~ Config.inc rm Config.inc~ Updating version.h gmake[4]: 'config.txt' is up to date. gmake[4]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/config' /usr/local/bin/gmake Config.o ConfigInstall.o compile_options.sh gmake[4]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/config' gmake[4]: 'Config.o' is up to date. gmake[4]: 'ConfigInstall.o' is up to date. gmake[4]: 'compile_options.sh' is up to date. gmake[4]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/config' gmake[3]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/config' # /usr/local/bin/gmake uninstall mkdir -p "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/bin" mkdir -p "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/lib" mkdir -p "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/lib/pkgconfig" mkdir -p "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/include/plumed" mkdir -p "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/lib/plumed/obj" mkdir -p "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/lib/plumed/src/lib" mkdir -p "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/lib/plumed/src/config" mkdir -p "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/lib/plumed/src/colvar" /usr/local/bin/gmake install-build gmake[3]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' mkdir -p install/ /usr/local/bin/gmake PLUMED_INSTALL=Install all gmake[4]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' /usr/local/bin/gmake dirslinks gmake[5]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' *** Updating links to used modules in all directories *** /usr/local/bin/gmake ../analysis.links ../asmjit.links ../bias.links ../blas.links ../cltools.links ../colvar.links ../config.links ../core.links ../function.links ../generic.links ../gridtools.links ../isdb.links ../lapack.links ../lepton.links ../main.links ../mapping.links ../molfile.links ../multicolvar.links ../reference.links ../secondarystructure.links ../setup.links ../tools.links ../vatom.links ../vesselbase.links ../wrapper.links ../xdrfile.links gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' /usr/local/bin/gmake -C ../analysis links gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/analysis' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/analysis gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/analysis' /usr/local/bin/gmake -C ../asmjit links gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/asmjit' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/asmjit gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/asmjit' /usr/local/bin/gmake -C ../bias links gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/bias' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/bias gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/bias' /usr/local/bin/gmake -C ../blas links gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/blas' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/blas gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/blas' /usr/local/bin/gmake -C ../cltools links gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/cltools' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/cltools gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/cltools' /usr/local/bin/gmake -C ../colvar links gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/colvar' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/colvar gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/colvar' /usr/local/bin/gmake -C ../config links gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/config' Nothing to do in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/config gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/config' /usr/local/bin/gmake -C ../core links gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/core' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/core gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/core' /usr/local/bin/gmake -C ../function links gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/function' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/function gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/function' /usr/local/bin/gmake -C ../generic links gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/generic' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/generic gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/generic' /usr/local/bin/gmake -C ../gridtools links gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/gridtools' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/gridtools gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/gridtools' /usr/local/bin/gmake -C ../isdb links gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/isdb' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/isdb gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/isdb' /usr/local/bin/gmake -C ../lapack links gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lapack' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lapack gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lapack' /usr/local/bin/gmake -C ../lepton links gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lepton' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lepton gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lepton' /usr/local/bin/gmake -C ../main links gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/main' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/main gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/main' /usr/local/bin/gmake -C ../mapping links gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/mapping' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/mapping gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/mapping' /usr/local/bin/gmake -C ../molfile links gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/molfile' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/molfile gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/molfile' /usr/local/bin/gmake -C ../multicolvar links gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/multicolvar' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/multicolvar gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/multicolvar' /usr/local/bin/gmake -C ../reference links gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/reference' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/reference gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/reference' /usr/local/bin/gmake -C ../secondarystructure links gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/secondarystructure' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/secondarystructure gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/secondarystructure' /usr/local/bin/gmake -C ../setup links gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/setup' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/setup gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/setup' /usr/local/bin/gmake -C ../tools links gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/tools' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/tools gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/tools' /usr/local/bin/gmake -C ../vatom links gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/vatom' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/vatom gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/vatom' /usr/local/bin/gmake -C ../vesselbase links gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/vesselbase' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/vesselbase gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/vesselbase' /usr/local/bin/gmake -C ../wrapper links gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/wrapper' Nothing to do in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/wrapper gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/wrapper' /usr/local/bin/gmake -C ../xdrfile links gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/xdrfile' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/xdrfile gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/xdrfile' gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' gmake[5]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' /usr/local/bin/gmake dirs gmake[5]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' *** Compiling all directories *** /usr/local/bin/gmake ../analysis ../asmjit ../bias ../blas ../cltools ../colvar ../config ../core ../function ../generic ../gridtools ../isdb ../lapack ../lepton ../main ../mapping ../molfile ../multicolvar ../reference ../secondarystructure ../setup ../tools ../vatom ../vesselbase ../wrapper ../xdrfile gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' /usr/local/bin/gmake -C ../analysis obj gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/analysis' gmake[7]: Nothing to be done for 'obj'. gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/analysis' /usr/local/bin/gmake -C ../asmjit obj gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/asmjit' gmake[7]: Nothing to be done for 'obj'. gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/asmjit' /usr/local/bin/gmake -C ../bias obj gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/bias' gmake[7]: Nothing to be done for 'obj'. gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/bias' /usr/local/bin/gmake -C ../blas obj gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/blas' gmake[7]: Nothing to be done for 'obj'. gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/blas' /usr/local/bin/gmake -C ../cltools obj gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/cltools' gmake[7]: Nothing to be done for 'obj'. gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/cltools' /usr/local/bin/gmake -C ../colvar obj gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/colvar' gmake[7]: Nothing to be done for 'obj'. gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/colvar' /usr/local/bin/gmake -C ../config obj gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/config' /usr/local/bin/gmake PLUMED_FORCE=yes ConfigInstall.inc Config.inc version.h config.txt gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/config' Updating ConfigInstall.inc cmp -s ConfigInstall.inc~ ConfigInstall.inc || cp ConfigInstall.inc~ ConfigInstall.inc rm ConfigInstall.inc~ Updating Config.inc cmp -s Config.inc~ Config.inc || cp Config.inc~ Config.inc rm Config.inc~ Updating version.h gmake[8]: 'config.txt' is up to date. gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/config' /usr/local/bin/gmake Config.o ConfigInstall.o compile_options.sh gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/config' gmake[8]: 'Config.o' is up to date. gmake[8]: 'ConfigInstall.o' is up to date. gmake[8]: 'compile_options.sh' is up to date. gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/config' gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/config' /usr/local/bin/gmake -C ../core obj gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/core' gmake[7]: Nothing to be done for 'obj'. gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/core' /usr/local/bin/gmake -C ../function obj gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/function' gmake[7]: Nothing to be done for 'obj'. gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/function' /usr/local/bin/gmake -C ../generic obj gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/generic' gmake[7]: Nothing to be done for 'obj'. gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/generic' /usr/local/bin/gmake -C ../gridtools obj gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/gridtools' gmake[7]: Nothing to be done for 'obj'. gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/gridtools' /usr/local/bin/gmake -C ../isdb obj gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/isdb' gmake[7]: Nothing to be done for 'obj'. gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/isdb' /usr/local/bin/gmake -C ../lapack obj gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lapack' gmake[7]: Nothing to be done for 'obj'. gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lapack' /usr/local/bin/gmake -C ../lepton obj gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lepton' gmake[7]: Nothing to be done for 'obj'. gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lepton' /usr/local/bin/gmake -C ../main obj gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/main' gmake[7]: Nothing to be done for 'obj'. gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/main' /usr/local/bin/gmake -C ../mapping obj gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/mapping' gmake[7]: Nothing to be done for 'obj'. gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/mapping' /usr/local/bin/gmake -C ../molfile obj gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/molfile' gmake[7]: Nothing to be done for 'obj'. gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/molfile' /usr/local/bin/gmake -C ../multicolvar obj gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/multicolvar' gmake[7]: Nothing to be done for 'obj'. gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/multicolvar' /usr/local/bin/gmake -C ../reference obj gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/reference' gmake[7]: Nothing to be done for 'obj'. gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/reference' /usr/local/bin/gmake -C ../secondarystructure obj gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/secondarystructure' gmake[7]: Nothing to be done for 'obj'. gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/secondarystructure' /usr/local/bin/gmake -C ../setup obj gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/setup' gmake[7]: Nothing to be done for 'obj'. gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/setup' /usr/local/bin/gmake -C ../tools obj gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/tools' gmake[7]: Nothing to be done for 'obj'. gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/tools' /usr/local/bin/gmake -C ../vatom obj gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/vatom' gmake[7]: Nothing to be done for 'obj'. gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/vatom' /usr/local/bin/gmake -C ../vesselbase obj gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/vesselbase' gmake[7]: Nothing to be done for 'obj'. gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/vesselbase' /usr/local/bin/gmake -C ../wrapper obj gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/wrapper' gmake[7]: Nothing to be done for 'obj'. gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/wrapper' /usr/local/bin/gmake -C ../xdrfile obj gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/xdrfile' gmake[7]: Nothing to be done for 'obj'. gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/xdrfile' gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' gmake[5]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' /usr/local/bin/gmake lib gmake[5]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' Building Plumed.inc Building Plumed.inc, static version Building Plumed.cmake Building Plumed.cmake, static version chmod a+x install/plumed-config chmod a+x install/plumed-mklib chmod a+x install/plumed-newcv chmod a+x install/plumed-partial_tempering chmod a+x install/plumed-patch chmod a+x install/plumed-selector chmod a+x install/plumed-vim2html Building Plumed.inc, runtime-linking version Building Plumed.inc, shared version Building Plumed.cmake, runtime-linking version Building Plumed.cmake, shared version gmake[5]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' gmake[4]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' /usr/local/bin/gmake PLUMED_INSTALL=Install install/kernel.o gmake[4]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' gmake[4]: 'install/kernel.o' is up to date. gmake[4]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' /usr/local/bin/gmake PLUMED_INSTALL=Install install/libplumed.a gmake[4]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' gmake[4]: 'install/libplumed.a' is up to date. gmake[4]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' gmake[3]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' /usr/local/bin/gmake install-html gmake[3]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' if test -d ../../user-doc/html ; then mkdir -p "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/share/doc/plumed" && cd ../../ && tar cf - user-doc/html | tar xf - -C "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/share/doc/plumed/" ; fi if test -d ../../developer-doc/html ; then mkdir -p "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/share/doc/plumed" && cd ../../ && tar cf - developer-doc/html | tar xf - -C "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/share/doc/plumed/" ; fi if test -d ../../developer-doc/coverage ; then mkdir -p "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/share/doc/plumed" && cd ../../ && tar cf - developer-doc/coverage | tar xf - -C "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/share/doc/plumed/" ; fi if test -f ../../user-doc/manual.pdf ; then mkdir -p "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/share/doc/plumed/user-doc" && cp ../../user-doc/manual.pdf "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/share/doc/plumed/user-doc/" ; fi gmake[3]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' cd ../../ ; tar cf - patches scripts | tar xf - -C "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/lib/plumed/" cp ../colvar/Template.cpp "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/lib/plumed/src/colvar/" grep -v "^link_uninstalled=" ../config/compile_options.sh > "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/lib/plumed/src/config/compile_options.sh" cp ../config/config.txt "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/lib/plumed/src/config/config.txt" cp install/libplumed.a "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/lib/" /usr/local/bin/gmake install-headers gmake[3]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' bash ../maketools/install.headers "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/include/plumed/" analysis asmjit bias blas cltools colvar config core function generic gridtools isdb lapack lepton main mapping molfile multicolvar reference secondarystructure setup tools vatom vesselbase wrapper xdrfile gmake[3]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' cp install/"plumed" "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/bin/" cp install/plumed-patch "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/bin/plumed-patch" cp install/plumed-config "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/bin/plumed-config" cp install/Plumed.cmake* "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/lib/plumed/src/lib/" cp install/Plumed.inc* "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/lib/plumed/src/lib/" for file in config mklib newcv partial_tempering patch selector vim2html ; do cp install/plumed-$file "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/lib/plumed/plumed-$file" ; done cp install/lib"plumed".so "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/lib/" cp install/lib"plumed"Kernel.so "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/lib/" if test -e install/"plumed"-runtime ; then cp install/"plumed"-runtime "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/lib/plumed/plumed-runtime" ; fi cp install/libplumedWrapper.a "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/lib/" cp install/modulefile "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/lib/plumed/modulefile" cp install/pkgconfig "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/lib/pkgconfig/plumed.pc" cp install/pkgconfigWrapper "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/lib/pkgconfig/plumedWrapper.pc" cp install/pkgconfigInternals "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/lib/pkgconfig/plumedInternals.pc" if test -d ../../vim/syntax ; then mkdir -p "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/lib/plumed" && cd ../../ && tar cf - vim/syntax | tar xf - -C "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/lib/plumed/" ; fi if test -d ../../vim/help ; then mkdir -p "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/lib/plumed" && cd ../../ && tar cf - vim/help | tar xf - -C "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/lib/plumed/" ; fi if test -f ../../vim/scripts.vim ; then mkdir -p "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/lib/plumed/vim" && cp ../../vim/scripts.vim "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/lib/plumed/vim/" ; fi if test -f ../../json/syntax.json ; then mkdir -p "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/lib/plumed/json" && cp ../../json/syntax.json "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/lib/plumed/json/" ; fi mkdir -p "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/lib/plumed/fortran" cp ../../fortran/plumed.f90 "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/lib/plumed/fortran/" cp ../../fortran/plumed_f08.f90 "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/lib/plumed/fortran/" chmod -R go+rX,go-w "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/lib/plumed" chmod -R go+rX,go-w "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/include/plumed" chmod -R go+rX,go-w "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/bin/plumed" chmod -R go+rX,go-w "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/bin/plumed-patch" *** PLUMED has been installed *** WARNING: Staged install with DESTDIR = /wrkdirs/usr/ports/science/plumed/work/stage Install prefix : /usr/local Full name : plumed Setup your environment - Ensure this is in your execution path : /usr/local/bin - Ensure this is in your include path : /usr/local/include - Ensure this is in your library path : /usr/local/lib - Ensure this is in your PKG_CONFIG_PATH path : /usr/local/lib/pkgconfig For runtime binding: - Set this environment variable : PLUMED_KERNEL=/usr/local/lib/libplumedKernel.so To create a tcl module that sets all the variables above, use this one as a starting point: /usr/local/lib/plumed/modulefile To uninstall, remove the following files and directories: /usr/local/lib/plumed /usr/local/share/doc/plumed /usr/local/include/plumed /usr/local/bin/plumed /usr/local/bin/plumed-patch /usr/local/bin/plumed-config /usr/local/lib/pkgconfig/plumed.pc /usr/local/lib/libplumed.so /usr/local/lib/libplumedKernel.so A vim plugin can be found here: /usr/local/lib/plumed/vim/ Copy it to /wrkdirs/usr/ports/science/plumed/work/.vim/ directory Alternatively: - Set this environment variable : PLUMED_VIMPATH=/usr/local/lib/plumed/vim - Add the command 'let &runtimepath.=','.$PLUMED_VIMPATH' to your .vimrc file From vim, you can use :set syntax=plumed to enable it gmake[2]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' gmake[1]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src' ====> Compressing man pages (compress-man) =========================================================================== =================================================== ===== env: 'PKG_NOTES=build_timestamp ports_top_git_hash ports_top_checkout_unclean port_git_hash port_checkout_unclean built_by' 'PKG_NOTE_build_timestamp=2026-01-20T07:21:22+0000' 'PKG_NOTE_ports_top_git_hash=076a295eb33c' 'PKG_NOTE_ports_top_checkout_unclean=no' 'PKG_NOTE_port_git_hash=fc4dbd235dee' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.2' NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building packages for plumed-2.9.3_1 ===> Building plumed-2.9.3_1 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for plumed-2.9.3_1 build of science/plumed | plumed-2.9.3_1 ended at Tue Jan 20 02:23:36 EST 2026 build time: 00:02:15