=>> Building science/plumed build started at Tue Jan 6 15:31:14 EST 2026 port directory: /usr/ports/science/plumed package name: plumed-2.9.3_1 building for: FreeBSD pkg.DaveG.ca 15.0-RELEASE-p1 FreeBSD 15.0-RELEASE-p1 1500068 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: 2d72fe63d004 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: 1500068 Job Id: 10 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1500068 UNAME_v=FreeBSD 15.0-RELEASE-p1 1500068 UNAME_r=15.0-RELEASE-p1 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_15_0_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_15_0_x64-HEAD-ALL/10/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=freebsd_15_0_x64-HEAD-ALL SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/freebsd_15_0_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=15.0 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 /usr/local/bin/gmake -C ../multicolvar links gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/config' /usr/local/bin/gmake -C ../reference links gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/blas' /usr/local/bin/gmake -C ../secondarystructure links /usr/local/bin/gmake -C ../setup links /usr/local/bin/gmake -C ../tools links /usr/local/bin/gmake -C ../vatom links Nothing to do in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/config /usr/local/bin/gmake -C ../vesselbase links Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/blas /usr/local/bin/gmake -C ../wrapper links gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/config' /usr/local/bin/gmake -C ../xdrfile links gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lapack' gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/blas' 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/lapack gmake[6]: Entering 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/main gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/bias' 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/molfile' gmake[6]: Entering 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/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/setup' 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/function 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/secondarystructure 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/vatom' Verify modules and create links in /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/cltools' gmake[6]: 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/lepton 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/isdb' 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/vatom gmake[6]: Entering directory '/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/analysis' Verify modules and create links in /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/isdb 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/mapping gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/generic' gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/colvar' 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/gridtools' 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/colvar 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/asmjit 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/reference' gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/asmjit' gmake[6]: 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/reference 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/lapack' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/core 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/multicolvar 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/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/bias' 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/secondarystructure' 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/generic' 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/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/function' 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/cltools' 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/isdb' 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/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 gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/blas' /usr/local/bin/gmake -C ../gridtools obj /usr/local/bin/gmake -C ../isdb 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 ../lapack obj /usr/local/bin/gmake -C ../lepton obj /usr/local/bin/gmake -C ../main obj compiling blas.cpp /usr/local/bin/gmake -C ../mapping obj /usr/local/bin/gmake -C ../molfile obj /usr/local/bin/gmake -C ../multicolvar obj /usr/local/bin/gmake -C ../reference obj /usr/local/bin/gmake -C ../secondarystructure obj gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lapack' /usr/local/bin/gmake -C ../setup 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/main' /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 compiling lapack.cpp /usr/local/bin/gmake -C ../xdrfile obj Updating ConfigInstall.inc gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lepton' Updating version.h Updating Config.inc compiling main.cpp gmake[6]: Entering directory '/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/bias' { ../maketools/make-scripts-options.sh ; cat completion.sh ; }| ../maketools/xxd > completion.xxd compiling CompiledExpression.cpp gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/molfile' Updating config.txt file compiling ExpressionProgram.cpp gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/analysis' compiling ExpressionTreeNode.cpp compiling ABMD.cpp compiling CLTool.cpp 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/function' gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/wrapper' compiling BiasValue.cpp compiling Bias.cpp compiling Driver.cpp gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/setup' compiling Operation.cpp compiling AnalysisBase.cpp compiling DriverDouble.cpp compiling ExtendedLagrangian.cpp compiling DriverFloat.cpp compiling AlphaRMSD.cpp compiling crdplugin.cpp gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/xdrfile' compiling dcdplugin.cpp compiling LWalls.cpp compiling Combine.cpp compiling External.cpp compiling Plumed.c compiling AntibetaRMSD.cpp gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/mapping' compiling Average.cpp compiling GenExample.cpp compiling Custom.cpp compiling Ensemble.cpp compiling Restart.cpp compiling Load.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/isdb' compiling PlumedStatic.cpp compiling xdrfile.cpp mkdir: deps: File exists gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/gridtools' gmake[6]: [../maketools/make.rules:16: BiasValue.o] Error 1 (ignored) compiling AdaptivePath.cpp compiling gromacsplugin.cpp compiling xdrfile_trr.cpp gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/asmjit' compiling ParabetaRMSD.cpp mkdir: deps: compiling Mapping.cpp File exists compiling CS2Backbone.cpp compiling ActionWithGrid.cpp compiling ActionWithVirtualAtom.cpp mkdir: deps: File exists compiling AverageVessel.cpp gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/reference' gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/generic' mkdir: deps: File exists compiling assembler.cpp compiling arch.cpp compiling SecondaryStructureRMSD.cpp gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/colvar' compiling Center.cpp compiling FuncPathGeneral.cpp compiling ActionWithInputGrid.cpp gmake[6]: [../maketools/make.rules:16: Ensemble.o] Error 1 (ignored) compiling Units.cpp compiling ArgumentOnlyDistance.cpp compiling Caliber.cpp compiling Committor.cpp compiling Debug.cpp compiling Angle.cpp mkdir: deps: File exists compiling PCAVars.cpp gmake[6]: [../maketools/make.rules:15: Combine.o] Error 1 (ignored) gmake[6]: [../maketools/make.rules:16: xdrfile_trr.o] Error 1 (ignored) mkdir: deps: File exists compiling codebuilder.cpp gmake[6]: [../maketools/make.rules:16: AlphaRMSD.o] Error 1 (ignored) cmp -s Config.inc~ Config.inc || cp Config.inc~ Config.inc gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/vesselbase' cmp -s ConfigInstall.inc~ ConfigInstall.inc || cp ConfigInstall.inc~ ConfigInstall.inc gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/core' compiling ActionWithAveraging.cpp rm Config.inc~ compiling Action.cpp gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/multicolvar' compiling ActionVolume.cpp gmake[6]: [../maketools/make.rules:15: gromacsplugin.o] Error 1 (ignored) rm ConfigInstall.inc~ gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/tools' compiling Angle.cpp compiling GenJson.cpp compiling DataCollectionObject.cpp compiling GenTemplate.cpp compiling xdrfile_xtc.cpp gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lapack' compiling Path.cpp gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/blas' compiling FuncPathMSD.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 FixedAtom.cpp compiling pdbplugin.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 AtomNumber.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 Ghost.cpp gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/wrapper' compiling ActionAnyorder.cpp compiling DumpAtoms.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 FuncSumHills.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 Cell.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. 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 codeemitter.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. 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 codeholder.cpp compiling ParsedExpression.cpp compiling Parser.cpp gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/main' compiling PathBase.cpp compiling DRMSD.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 Function.cpp compiling BiasRepresentation.cpp compiling MaxEnt.cpp compiling MetaD.cpp compiling ActionWithInputVessel.cpp compiling DumpDerivatives.cpp compiling Colvar.cpp compiling DumpForces.cpp compiling EuclideanDissimilarityMatrix.cpp compiling AlphaBeta.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 ActionWithIntegral.cpp compiling Info.cpp compiling Brent1DRootSearch.cpp compiling Citations.cpp Building compile_options.sh, a sourceable bash script with some compilation options compiling LocalEnsemble.cpp compiling AverageOnGrid.cpp compiling MovingRestraint.cpp compiling Piecewise.cpp compiling Angles.cpp compiling FarthestPointSampling.cpp compiling PBMetaD.cpp compiling Restraint.cpp compiling constpool.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 Config.cpp compiling Manual.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 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. compiling ActionAtomistic.cpp gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/setup' compiling PathReparameterization.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 DumpMassCharge.cpp compiling func.cpp compiling Histogram.cpp compiling ReweightBase.cpp compiling LandmarkSelectionBase.cpp compiling Sort.cpp compiling inst.cpp compiling EMMI.cpp compiling PathTools.cpp compiling PdbRenumber.cpp compiling LandmarkStaged.cpp compiling SimpleMD.cpp compiling PropertyMap.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 SumHills.cpp compiling Stats.cpp compiling Target.cpp compiling ActionPilot.cpp compiling ActionRegister.cpp compiling AtomValuePack.cpp compiling Bridge.cpp compiling ConfigInstall.cpp 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/vatom' compiling OutputColvarFile.cpp compiling logging.cpp compiling OutputPDBFile.cpp compiling ActionWithVessel.cpp compiling SpathVessel.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 compiling Constant.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. 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 BridgedMultiColvarFunction.cpp compiling Communicator.cpp compiling osutils.cpp compiling TrigonometricPathVessel.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 Direction.cpp 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 DumpProjections.cpp compiling DotProductDistance.cpp compiling ConjugateGradient.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 kT.cpp gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lepton' compiling PrintDissimilarityMatrix.cpp compiling pesmd.cpp compiling EffectiveEnergyDrift.cpp compiling ContourFindingBase.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 regalloc.cpp compiling Completion.cpp compiling runtime.cpp compiling ConvertToFES.cpp compiling ZpathVessel.cpp compiling DLLoader.cpp compiling CatomPack.cpp compiling AltMin.cpp compiling ContactMap.cpp compiling CenterOfMultiColvar.cpp compiling CoordinationNumbers.cpp compiling DumpCube.cpp compiling EndPlumed.cpp compiling ReweightBias.cpp compiling ReadAnalysisFrames.cpp compiling ReadDissimilarityMatrix.cpp compiling string.cpp compiling ReweightMetad.cpp compiling FitToTemplate.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 DumpGrid.cpp compiling utils.cpp compiling AveragingVessel.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 vmem.cpp gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/config' gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/config' compiling Flush.cpp compiling Between.cpp compiling ReselectLandmarks.cpp compiling EuclideanDistance.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 ReweightTemperaturePressure.cpp compiling x86assembler.cpp compiling ActionSet.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 x86builder.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 SelectRandomFrames.cpp compiling FakeFrame.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 x86compiler.cpp compiling Density.cpp compiling BridgeVessel.cpp compiling FretEfficiency.cpp compiling Group.cpp compiling ActionSetup.cpp compiling DynamicList.cpp compiling Coordination.cpp compiling IntermolecularDRMSD.cpp gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/function' compiling ERMSD.cpp compiling FindContour.cpp compiling ActionShortcut.cpp CS2Backbone.cpp:214:14: warning: variable 'nline' set but not used [-Wunused-but-set-variable] 214 | unsigned nline = 0; | ^ 1 warning generated. compiling Jcoupling.cpp compiling Exception.cpp compiling x86instimpl.cpp compiling x86inst.cpp compiling FindContourSurface.cpp compiling DihedralCorrelation.cpp compiling SelectWithStride.cpp compiling IntramolecularDRMSD.cpp compiling Include.cpp compiling DistanceFromContour.cpp compiling CoordinationBase.cpp vmem.cpp:284:13: warning: unused function 'vMemMgrCheckTree' [-Wunused-function] 284 | static bool vMemMgrCheckTree(VMemMgr* self) noexcept { | ^~~~~~~~~~~~~~~~ 1 warning generated. compiling WhamHistogram.cpp compiling x86internal.cpp compiling Distances.cpp compiling Metainference.cpp compiling FindSphericalContour.cpp compiling WhamWeights.cpp compiling FileBase.cpp gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/mapping' compiling FourierTransform.cpp compiling GridPrintingBase.cpp compiling FunctionVessel.cpp compiling Highest.cpp compiling ReweightWham.cpp compiling MolInfo.cpp compiling UWalls.cpp compiling DHEnergy.cpp compiling Plumed.cpp compiling ActionWithArguments.cpp compiling DumpMultiColvar.cpp compiling MahalanobisDistance.cpp compiling Print.cpp compiling GridSearch.cpp compiling DRMSD.cpp compiling GridToXYZ.cpp compiling MetricRegister.cpp compiling Histogram.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. 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. gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/cltools' compiling x86operand.cpp compiling MultiDomainRMSD.cpp compiling GridVessel.cpp compiling LessThan.cpp compiling x86logging.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 ForwardDecl.cpp compiling x86operand_regs.cpp compiling ActionWithValue.cpp compiling MetainferenceBase.cpp compiling NormalizedEuclideanDistance.cpp compiling NOE.cpp compiling Grid.cpp compiling FilterBetween.cpp compiling PRE.cpp compiling RandomExchanges.cpp compiling Dimer.cpp compiling RDC.cpp compiling FilterLessThan.cpp compiling HistogramBead.cpp compiling Lowest.cpp compiling HistogramOnGrid.cpp compiling Dipole.cpp compiling IFile.cpp compiling ActionWithVirtualAtom.cpp compiling OptimalRMSD.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 x86regalloc.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 Read.cpp compiling zone.cpp compiling Max.cpp compiling RMSDBase.cpp compiling ResetCell.cpp compiling KernelFunctions.cpp compiling ReferenceArguments.cpp compiling FilterMoreThan.cpp gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/analysis' compiling Mean.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 Distance.cpp compiling Keywords.cpp compiling ReferenceAtoms.cpp compiling EEFSolv.cpp compiling Time.cpp compiling ReferenceConfiguration.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 UpdateIf.cpp compiling Min.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 InterpolateGrid.cpp compiling WholeMolecules.cpp compiling IntegrateGrid.cpp compiling Moments.cpp compiling InPlaneDistances.cpp compiling ReferenceValuePack.cpp compiling LocalAverage.cpp compiling SimpleRMSD.cpp compiling SingleDomainRMSD.cpp compiling MoreThan.cpp compiling LatticeReduction.cpp gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/bias' compiling MultiColvarBase.cpp compiling Atoms.cpp compiling Rescale.cpp compiling ERMSD.cpp compiling WrapAround.cpp compiling MultiColvarCombine.cpp compiling OrderingVessel.cpp compiling Energy.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 ShortcutVessel.cpp compiling SAXS.cpp compiling Select.cpp compiling StoreDataVessel.cpp compiling MultiColvarDensity.cpp compiling CLTool.cpp compiling LinkCells.cpp compiling MultiColvarFilter.cpp ../maketools/makecmd map < CLToolMain.cpp > CLToolMainMap.inc ../maketools/makecmd enum < CLToolMain.cpp > CLToolMainEnum.inc compiling CLToolRegister.cpp compiling Log.cpp compiling Selector.cpp compiling Colvar.cpp compiling ExtraCV.cpp compiling Sum.cpp compiling LoopUnroller.cpp compiling MultiColvarProduct.cpp compiling NumberOfLinks.cpp compiling Fake.cpp compiling DataFetchingObject.cpp compiling ValueVessel.cpp compiling ExchangePatterns.cpp compiling Matrix.cpp compiling FlexibleBin.cpp compiling Vessel.cpp ../maketools/makecmd map < GREX.cpp > GREXMap.inc ../maketools/makecmd enum < GREX.cpp > GREXEnum.inc compiling VesselRegister.cpp compiling GenericMolInfo.cpp compiling MatrixSquareBracketsAccess.cpp compiling GHBFIX.cpp compiling Minimise1DBrent.cpp compiling MinimiseBase.cpp compiling Gyration.cpp compiling MultiRMSD.cpp compiling PCARMSD.cpp compiling MDAtoms.cpp compiling Torsions.cpp compiling PathMSD.cpp compiling VolumeAround.cpp compiling MolDataClass.cpp ../maketools/makeModuleMap ModuleMap.inc 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. compiling VolumeBetweenContours.cpp compiling VolumeCavity.cpp compiling MultiValue.cpp compiling VolumeGradientBase.cpp 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. gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/asmjit' compiling PathMSDBase.cpp gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/reference' compiling NeighborList.cpp ../maketools/makecmd map < PlumedMain.cpp > PlumedMainMap.inc compiling OFile.cpp ../maketools/makecmd enum < PlumedMain.cpp > PlumedMainEnum.inc compiling PlumedMainInitializer.cpp compiling TargetDist.cpp compiling Position.cpp compiling OpenMP.cpp compiling Value.cpp 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. compiling VolumeInCylinder.cpp compiling ProjectionOnAxis.cpp compiling PropertyMap.cpp compiling PDB.cpp compiling VolumeInSphere.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. compiling Pbc.cpp gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/gridtools' compiling WithCmd.cpp compiling PlumedHandle.cpp compiling VolumeTetrapore.cpp compiling Puckering.cpp compiling XAngle.cpp compiling CLToolMain.cpp compiling GREX.cpp compiling PlumedMain.cpp gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/generic' compiling RMSD.cpp compiling RMSD.cpp compiling Random.cpp compiling Template.cpp compiling XDistances.cpp compiling RootFindingBase.cpp compiling XYDistances.cpp compiling Stopwatch.cpp compiling XYTorsion.cpp compiling Subprocess.cpp compiling SwitchingFunction.cpp compiling Tensor.cpp compiling Torsion.cpp compiling Tools.cpp compiling Torsion.cpp compiling Volume.cpp compiling Tree.cpp compiling TypesafePtr.cpp Vessel.cpp:63:16: warning: variable 'i' set but not used [-Wunused-but-set-variable] 63 | for(unsigned i=0;; ++i) { | ^ 1 warning generated. compiling Units.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 Vector.cpp compiling h36.cpp gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/vesselbase' compiling ModuleMap.cpp gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/multicolvar' 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' 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 chmod a+x plumed-config 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 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 /usr/bin/ar cr libplumedWrapper.a ../wrapper/Plumed.o Building Plumed.inc, runtime-linking version chmod a+x plumed-mklib Building Plumed.inc, shared version chmod a+x plumed-partial_tempering chmod a+x plumed-newcv Building Plumed.inc, static version Building Plumed.cmake chmod a+x plumed-selector chmod a+x plumed-vim2html chmod a+x plumed-patch Building Plumed.cmake, static version Building Plumed.cmake, runtime-linking version Building Plumed.cmake, shared version 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 /usr/local/bin/gmake -C ../main links gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/blas' /usr/local/bin/gmake -C ../mapping links /usr/local/bin/gmake -C ../molfile links /usr/local/bin/gmake -C ../multicolvar links gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/config' /usr/local/bin/gmake -C ../reference links /usr/local/bin/gmake -C ../secondarystructure links Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/blas /usr/local/bin/gmake -C ../setup links /usr/local/bin/gmake -C ../tools links /usr/local/bin/gmake -C ../vatom links Nothing to do in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/config gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lapack' /usr/local/bin/gmake -C ../vesselbase links gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/config' /usr/local/bin/gmake -C ../wrapper links /usr/local/bin/gmake -C ../xdrfile links Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lapack gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/blas' 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/lepton' 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/lepton 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/bias' gmake[8]: Entering 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/cltools Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/molfile 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/vatom' gmake[8]: Entering 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/secondarystructure' 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/function 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/isdb' 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/vatom gmake[8]: 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/setup 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/secondarystructure 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/isdb 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/xdrfile 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/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/asmjit gmake[8]: Entering 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/xdrfile' Verify modules and create links in /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/gridtools' Verify modules and create links in /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/reference 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/asmjit' 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/colvar gmake[8]: Leaving 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/core' gmake[8]: 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/core Verify modules and create links in /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' 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/lapack' 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/multicolvar' Verify modules and create links in /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/bias' 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/setup' 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/gridtools' 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/colvar' 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/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/vesselbase' 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/multicolvar' 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/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 /usr/local/bin/gmake -C ../lepton obj /usr/local/bin/gmake -C ../main 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'. gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/blas' /usr/local/bin/gmake -C ../mapping obj /usr/local/bin/gmake -C ../molfile obj /usr/local/bin/gmake -C ../multicolvar obj gmake[8]: 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 ../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 /usr/local/bin/gmake -C ../xdrfile 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' 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[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]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/molfile' gmake[9]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/config' gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/wrapper' 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[9]: 'config.txt' is up to date. 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' Updating ConfigInstall.inc 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' 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' Updating version.h 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' Updating Config.inc 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/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/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/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/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' 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/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' 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/analysis' gmake[8]: Nothing to be done for 'obj'. gmake[8]: Leaving 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/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/colvar' cmp -s ConfigInstall.inc~ ConfigInstall.inc || cp ConfigInstall.inc~ ConfigInstall.inc gmake[8]: Nothing to be done for 'obj'. gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/colvar' 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/reference' gmake[8]: Nothing to be done for 'obj'. gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/reference' rm ConfigInstall.inc~ rm Config.inc~ 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 Building Plumed.inc, runtime-linking version /usr/bin/ar cr install/libplumedWrapper.a ../wrapper/Plumed.o chmod a+x install/plumed-mklib Building Plumed.inc, static version Building Plumed.inc, shared version chmod a+x install/plumed-newcv chmod a+x install/plumed-config Building Plumed.cmake chmod a+x install/plumed-partial_tempering chmod a+x install/plumed-vim2html chmod a+x install/plumed-patch chmod a+x install/plumed-selector Building Plumed.cmake, static version Building Plumed.cmake, runtime-linking version Building Plumed.cmake, shared 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=2026-01-06T20:31:14+0000' 'PKG_NOTE_ports_top_git_hash=2d72fe63d004' '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 6 15:34:52 EST 2026 build time: 00:03:39