=>> Building science/plumed build started at Wed Feb 18 13:43:54 EST 2026 port directory: /usr/ports/science/plumed package name: plumed-2.9.3_2 building for: FreeBSD pkg.DaveG.ca 15.0-RELEASE-p3 FreeBSD 15.0-RELEASE-p3 1500068 amd64 maintained by: yuri@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 1487 Feb 17 19:06 /usr/ports/science/plumed/Makefile Ports top last git commit: eac71dbf758c Ports top unclean checkout: no Port dir last git commit: 2e4f3d1acf81 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500068 Jail OSVERSION: 1500068 Job Id: 08 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1500068 UNAME_v=FreeBSD 15.0-RELEASE-p3 1500068 UNAME_r=15.0-RELEASE-p3 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/08/.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_2 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_2 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of plumed-2.9.3_2 =========================================================================== =================================================== ===== 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_2 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by plumed-2.9.3_2 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_2 for building ===> Extracting for plumed-2.9.3_2 => 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_2 ===> Applying FreeBSD patches for plumed-2.9.3_2 from /usr/ports/science/plumed/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> plumed-2.9.3_2 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_2 depends on executable: bash - found ===> Returning to build of plumed-2.9.3_2 ===> plumed-2.9.3_2 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_2 depends on package: gmake>=4.4.1 - found ===> Returning to build of plumed-2.9.3_2 ===> plumed-2.9.3_2 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_2 depends on package: pkgconf>=1.3.0_1 - found ===> Returning to build of plumed-2.9.3_2 ===> plumed-2.9.3_2 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_2 depends on package: autoconf>=2.72_1 - found ===> Returning to build of plumed-2.9.3_2 ===> plumed-2.9.3_2 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_2 depends on package: automake>=1.18.1 - found ===> Returning to build of plumed-2.9.3_2 ===> plumed-2.9.3_2 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_2 depends on file: /usr/local/bin/ccache - found ===> Returning to build of plumed-2.9.3_2 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> plumed-2.9.3_2 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_2 depends on shared library: libblas.so - found (/usr/local/lib/libblas.so) ===> Returning to build of plumed-2.9.3_2 ===> plumed-2.9.3_2 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_2 depends on shared library: libfftw3.so - found (/usr/local/lib/libfftw3.so) ===> Returning to build of plumed-2.9.3_2 ===> plumed-2.9.3_2 depends on shared library: libgsl.so - not found ===> Installing existing package /packages/All/gsl-2.8.pkg [pkg.DaveG.ca] Installing gsl-2.8... [pkg.DaveG.ca] Extracting gsl-2.8: .......... done ===> plumed-2.9.3_2 depends on shared library: libgsl.so - found (/usr/local/lib/libgsl.so) ===> Returning to build of plumed-2.9.3_2 ===> plumed-2.9.3_2 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_2 depends on shared library: liblapack.so - found (/usr/local/lib/liblapack.so) ===> Returning to build of plumed-2.9.3_2 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for plumed-2.9.3_2 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_2 /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 gmake[6]: Entering 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/analysis' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/blas /usr/local/bin/gmake -C ../config links /usr/local/bin/gmake -C ../core links gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/bias' gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/config' gmake[6]: 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/bias Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/analysis Nothing to do in /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' /usr/local/bin/gmake -C ../function links gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/cltools' /usr/local/bin/gmake -C ../generic links /usr/local/bin/gmake -C ../gridtools links gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/blas' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/cltools /usr/local/bin/gmake -C ../isdb links /usr/local/bin/gmake -C ../lapack links /usr/local/bin/gmake -C ../lepton links gmake[6]: 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/asmjit gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/isdb' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lapack 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/generic' gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/colvar' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/isdb gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/asmjit' gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lepton' 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/colvar Verify modules and create links in /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/core' 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/core Verify modules and create links in /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 /usr/local/bin/gmake -C ../main links /usr/local/bin/gmake -C ../mapping links gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/main' /usr/local/bin/gmake -C ../molfile links 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/mapping' Verify modules and create links in /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/bias' /usr/local/bin/gmake -C ../multicolvar links gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/molfile' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/molfile /usr/local/bin/gmake -C ../reference links /usr/local/bin/gmake -C ../secondarystructure links gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/molfile' /usr/local/bin/gmake -C ../setup links /usr/local/bin/gmake -C ../tools links 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/setup 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/multicolvar' 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/multicolvar gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/main' 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/secondarystructure 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 /usr/local/bin/gmake -C ../vatom links gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/generic' /usr/local/bin/gmake -C ../vesselbase links gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/vatom' /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/vatom gmake[6]: 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[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/wrapper' 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/xdrfile gmake[6]: Entering 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/xdrfile' 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/core' 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/setup' 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/tools' 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/vatom' 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/secondarystructure' 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/analysis' 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/vesselbase' 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 gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/blas' /usr/local/bin/gmake -C ../cltools obj /usr/local/bin/gmake -C ../colvar obj gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/bias' /usr/local/bin/gmake -C ../config obj /usr/local/bin/gmake -C ../core obj /usr/local/bin/gmake -C ../function obj compiling ABMD.cpp gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/analysis' gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/asmjit' gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/cltools' /usr/local/bin/gmake -C ../generic obj /usr/local/bin/gmake -C ../gridtools 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 compiling AnalysisBase.cpp compiling Bias.cpp gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/config' compiling CLTool.cpp Updating ConfigInstall.inc /usr/local/bin/gmake -C ../isdb obj Updating Config.inc /usr/local/bin/gmake -C ../lapack obj compiling BiasValue.cpp 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/colvar' compiling Average.cpp compiling blas.cpp compiling Combine.cpp compiling Custom.cpp gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/generic' compiling AverageVessel.cpp gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/isdb' gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/core' compiling Debug.cpp compiling Committor.cpp compiling assembler.cpp compiling codebuilder.cpp compiling codecompiler.cpp compiling CS2Backbone.cpp compiling Caliber.cpp { ../maketools/make-scripts-options.sh ; cat completion.sh ; }| ../maketools/xxd > completion.xxd 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/gridtools' compiling ActionAnyorder.cpp compiling Driver.cpp Updating version.h compiling Angle.cpp compiling DriverDouble.cpp compiling ActionAtomistic.cpp compiling codeemitter.cpp compiling Cell.cpp compiling DriverFloat.cpp compiling Action.cpp gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lapack' compiling Ensemble.cpp compiling DataCollectionObject.cpp compiling ActionWithGrid.cpp /usr/local/bin/gmake -C ../lepton obj compiling arch.cpp rm ConfigInstall.inc~ /usr/local/bin/gmake -C ../main obj compiling ExtendedLagrangian.cpp compiling lapack.cpp /usr/local/bin/gmake -C ../mapping obj /usr/local/bin/gmake -C ../molfile obj compiling codeholder.cpp compiling EMMI.cpp /usr/local/bin/gmake -C ../multicolvar obj 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/molfile' gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/main' gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lepton' compiling GenExample.cpp compiling DumpDerivatives.cpp compiling CompiledExpression.cpp compiling ExpressionProgram.cpp compiling ExpressionTreeNode.cpp Updating config.txt file compiling DumpAtoms.cpp compiling main.cpp compiling AdaptivePath.cpp compiling Colvar.cpp compiling Constant.cpp compiling ActionPilot.cpp compiling EuclideanDissimilarityMatrix.cpp /usr/local/bin/gmake -C ../reference obj compiling Mapping.cpp compiling PCAVars.cpp gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/multicolvar' compiling FretEfficiency.cpp compiling dcdplugin.cpp compiling ActionVolume.cpp compiling ContactMap.cpp cmp -s Config.inc~ Config.inc || cp Config.inc~ Config.inc compiling ActionWithInputGrid.cpp compiling FuncPathGeneral.cpp compiling ParsedExpression.cpp compiling External.cpp compiling FuncPathMSD.cpp compiling Operation.cpp compiling crdplugin.cpp gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/reference' rm Config.inc~ compiling ArgumentOnlyDistance.cpp compiling ActionWithIntegral.cpp compiling GenJson.cpp gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/blas' /usr/local/bin/gmake -C ../secondarystructure obj gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/secondarystructure' compiling Path.cpp compiling AlphaRMSD.cpp gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lapack' /usr/local/bin/gmake -C ../setup obj gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/setup' compiling Load.cpp compiling gromacsplugin.cpp In file included from assembler.cpp:33: In file included from ././assembler.h:36: In file included from ./././codeemitter.h:36: In file included from ././././arch.h:37: ./././././operand.h:341:12: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 341 | return (_packed[0] == other._packed[0]) & | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && 342 | (_packed[1] == other._packed[1]) ; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./././././operand.h:341:12: note: cast one or both operands to int to silence this warning ./././././operand.h:808:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 808 | static ASMJIT_INLINE bool isGp(const Operand_& op, uint32_t rId) noexcept { return isGp(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ./././././operand.h:808:86: note: cast one or both operands to int to silence this warning ./././././operand.h:809:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 809 | static ASMJIT_INLINE bool isVec(const Operand_& op, uint32_t rId) noexcept { return isVec(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ./././././operand.h:809:87: note: cast one or both operands to int to silence this warning 3 warnings generated. compiling constpool.cpp In file included from codebuilder.cpp:37: In file included from ././codebuilder.h:39: In file included from ./././assembler.h:36: In file included from ././././codeemitter.h:36: In file included from ./././././arch.h:37: ././././././operand.h:341:12: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 341 | return (_packed[0] == other._packed[0]) & | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && 342 | (_packed[1] == other._packed[1]) ; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ././././././operand.h:341:12: note: cast one or both operands to int to silence this warning ././././././operand.h:808:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 808 | static ASMJIT_INLINE bool isGp(const Operand_& op, uint32_t rId) noexcept { return isGp(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././././operand.h:808:86: note: cast one or both operands to int to silence this warning ././././././operand.h:809:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 809 | static ASMJIT_INLINE bool isVec(const Operand_& op, uint32_t rId) noexcept { return isVec(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././././operand.h:809:87: note: cast one or both operands to int to silence this warning 3 warnings generated. compiling 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 func.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 pdbplugin.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 globals.cpp In file included from arch.cpp:33: In file included from ././arch.h:37: ./././operand.h:341:12: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 341 | return (_packed[0] == other._packed[0]) & | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && 342 | (_packed[1] == other._packed[1]) ; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./././operand.h:341:12: note: cast one or both operands to int to silence this warning ./././operand.h:808:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 808 | static ASMJIT_INLINE bool isGp(const Operand_& op, uint32_t rId) noexcept { return isGp(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ./././operand.h:808:86: note: cast one or both operands to int to silence this warning ./././operand.h:809:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 809 | static ASMJIT_INLINE bool isVec(const Operand_& op, uint32_t rId) noexcept { return isVec(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ./././operand.h:809:87: note: cast one or both operands to int to silence this warning In file included from arch.cpp:36: ././x86operand.h:379:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 379 | static ASMJIT_INLINE bool isGpb(const Operand_& op, uint32_t rId) noexcept { return isGpb(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:379:87: note: cast one or both operands to int to silence this warning ././x86operand.h:381:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 381 | static ASMJIT_INLINE bool isRip(const Operand_& op, uint32_t rId) noexcept { return isRip(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:381:87: note: cast one or both operands to int to silence this warning ././x86operand.h:382:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 382 | static ASMJIT_INLINE bool isSeg(const Operand_& op, uint32_t rId) noexcept { return isSeg(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:382:87: note: cast one or both operands to int to silence this warning ././x86operand.h:383:89: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 383 | static ASMJIT_INLINE bool isGpbLo(const Operand_& op, uint32_t rId) noexcept { return isGpbLo(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:383:89: note: cast one or both operands to int to silence this warning ././x86operand.h:384:89: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 384 | static ASMJIT_INLINE bool isGpbHi(const Operand_& op, uint32_t rId) noexcept { return isGpbHi(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:384:89: note: cast one or both operands to int to silence this warning ././x86operand.h:385:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 385 | static ASMJIT_INLINE bool isGpw(const Operand_& op, uint32_t rId) noexcept { return isGpw(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:385:87: note: cast one or both operands to int to silence this warning ././x86operand.h:386:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 386 | static ASMJIT_INLINE bool isGpd(const Operand_& op, uint32_t rId) noexcept { return isGpd(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:386:87: note: cast one or both operands to int to silence this warning ././x86operand.h:387:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 387 | static ASMJIT_INLINE bool isGpq(const Operand_& op, uint32_t rId) noexcept { return isGpq(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:387:87: note: cast one or both operands to int to silence this warning ././x86operand.h:388:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 388 | static ASMJIT_INLINE bool isFp(const Operand_& op, uint32_t rId) noexcept { return isFp(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:388:86: note: cast one or both operands to int to silence this warning ././x86operand.h:389:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 389 | static ASMJIT_INLINE bool isMm(const Operand_& op, uint32_t rId) noexcept { return isMm(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:389:86: note: cast one or both operands to int to silence this warning ././x86operand.h:390:85: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 390 | static ASMJIT_INLINE bool isK(const Operand_& op, uint32_t rId) noexcept { return isK(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:390:85: note: cast one or both operands to int to silence this warning ././x86operand.h:391:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 391 | static ASMJIT_INLINE bool isXmm(const Operand_& op, uint32_t rId) noexcept { return isXmm(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:391:87: note: cast one or both operands to int to silence this warning ././x86operand.h:392:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 392 | static ASMJIT_INLINE bool isYmm(const Operand_& op, uint32_t rId) noexcept { return isYmm(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:392:87: note: cast one or both operands to int to silence this warning ././x86operand.h:393:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 393 | static ASMJIT_INLINE bool isZmm(const Operand_& op, uint32_t rId) noexcept { return isZmm(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:393:87: note: cast one or both operands to int to silence this warning ././x86operand.h:394:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 394 | static ASMJIT_INLINE bool isBnd(const Operand_& op, uint32_t rId) noexcept { return isBnd(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:394:87: note: cast one or both operands to int to silence this warning ././x86operand.h:395:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 395 | static ASMJIT_INLINE bool isCr(const Operand_& op, uint32_t rId) noexcept { return isCr(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:395:86: note: cast one or both operands to int to silence this warning ././x86operand.h:396:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 396 | static ASMJIT_INLINE bool isDr(const Operand_& op, uint32_t rId) noexcept { return isDr(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:396:86: note: cast one or both operands to int to silence this warning 20 warnings generated. compiling inst.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 logging.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 Coordination.cpp compiling Parser.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. /usr/local/bin/gmake -C ../tools obj compiling GenTemplate.cpp gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/tools' compiling Angle.cpp compiling LWalls.cpp compiling ActionRegister.cpp compiling MaxEnt.cpp compiling AverageOnGrid.cpp In file included from cpuinfo.cpp:33: In file included from ././cpuinfo.h:36: In file included from ./././arch.h:37: ././././operand.h:341:12: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 341 | return (_packed[0] == other._packed[0]) & | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && 342 | (_packed[1] == other._packed[1]) ; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ././././operand.h:341:12: note: cast one or both operands to int to silence this warning ././././operand.h:808:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 808 | static ASMJIT_INLINE bool isGp(const Operand_& op, uint32_t rId) noexcept { return isGp(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././operand.h:808:86: note: cast one or both operands to int to silence this warning ././././operand.h:809:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 809 | static ASMJIT_INLINE bool isVec(const Operand_& op, uint32_t rId) noexcept { return isVec(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././operand.h:809:87: note: cast one or both operands to int to silence this warning 3 warnings generated. compiling operand.cpp compiling FuncSumHills.cpp compiling DumpForces.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 Info.cpp compiling osutils.cpp /usr/local/bin/gmake -C ../vatom obj compiling DumpMassCharge.cpp gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/main' /usr/local/bin/gmake -C ../vesselbase obj gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/vatom' compiling PathBase.cpp compiling ActionWithVirtualAtom.cpp gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/vesselbase' compiling ActionWithAveraging.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' /usr/local/bin/gmake -C ../wrapper obj 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. gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/wrapper' compiling ActionSet.cpp compiling Histogram.cpp compiling FarthestPointSampling.cpp compiling PlumedStatic.cpp compiling AntibetaRMSD.cpp compiling DRMSD.cpp compiling CoordinationBase.cpp compiling regalloc.cpp compiling LandmarkSelectionBase.cpp compiling PathReparameterization.cpp compiling DHEnergy.cpp compiling AlphaBeta.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 EffectiveEnergyDrift.cpp compiling LandmarkStaged.cpp compiling ContourFindingBase.cpp compiling DRMSD.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 Building compile_options.sh, a sourceable bash script with some compilation options compiling Config.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 ConvertToFES.cpp compiling runtime.cpp compiling Function.cpp compiling MetaD.cpp compiling ActionSetup.cpp compiling MovingRestraint.cpp compiling LocalEnsemble.cpp compiling ParabetaRMSD.cpp compiling Manual.cpp compiling Piecewise.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 Dimer.cpp compiling Restart.cpp compiling string.cpp compiling AtomNumber.cpp compiling DumpCube.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 DumpGrid.cpp compiling PdbRenumber.cpp compiling Jcoupling.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. 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 utils.cpp compiling ActionShortcut.cpp compiling Metainference.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 Angles.cpp compiling Plumed.c compiling Sort.cpp compiling vmem.cpp compiling PathTools.cpp compiling PropertyMap.cpp compiling SimpleMD.cpp compiling ConfigInstall.cpp compiling ActionWithArguments.cpp compiling Dipole.cpp compiling SpathVessel.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 Center.cpp compiling x86assembler.cpp compiling ActionWithValue.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 FindContour.cpp compiling x86builder.cpp compiling ActionWithVirtualAtom.cpp gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/wrapper' /usr/local/bin/gmake -C ../xdrfile obj gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/xdrfile' compiling xdrfile.cpp gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lepton' 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 SumHills.cpp compiling EndPlumed.cpp compiling BiasRepresentation.cpp compiling kT.cpp compiling FindContourSurface.cpp compiling OutputColvarFile.cpp compiling x86compiler.cpp compiling OutputPDBFile.cpp compiling ActionWithInputVessel.cpp vmem.cpp:284:13: warning: unused function 'vMemMgrCheckTree' [-Wunused-function] 284 | static bool vMemMgrCheckTree(VMemMgr* self) noexcept { | ^~~~~~~~~~~~~~~~ 1 warning generated. compiling x86inst.cpp compiling Direction.cpp compiling FitToTemplate.cpp compiling Flush.cpp compiling Distance.cpp compiling pesmd.cpp compiling Atoms.cpp compiling SecondaryStructureRMSD.cpp compiling PrintDissimilarityMatrix.cpp compiling Brent1DRootSearch.cpp compiling FindSphericalContour.cpp compiling x86instimpl.cpp compiling AtomValuePack.cpp compiling PBMetaD.cpp compiling TrigonometricPathVessel.cpp compiling MetainferenceBase.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 Stats.cpp compiling Completion.cpp compiling Group.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 ZpathVessel.cpp compiling NOE.cpp compiling EEFSolv.cpp compiling Target.cpp compiling DotProductDistance.cpp xdrfile.cpp:30:2: warning: '/*' within block comment [-Wcomment] 30 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- | ^ In file included from xdrfile.cpp:85: ./xdrfile.h:32:2: warning: '/*' within block comment [-Wcomment] 32 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- | ^ xdrfile.cpp:819:16: warning: variable 'minidx' set but not used [-Wunused-but-set-variable] 819 | int smallidx, minidx, maxidx; | ^ xdrfile.cpp:822:25: warning: variable 'larger' set but not used [-Wunused-but-set-variable] 822 | int smallnum, smaller, larger, i, is_smaller, run; | ^ xdrfile.cpp:1029:6: warning: variable 'errval' set but not used [-Wunused-but-set-variable] 1029 | int errval=1; | ^ xdrfile.cpp:1086:25: warning: implicit conversion from 'int' to 'float' changes value from 2147483645 to 2147483648 [-Wimplicit-const-int-float-conversion] 1086 | if (fabs(lf) > INT_MAX-2) | ~ ~~~~~~~^~ xdrfile.cpp:1101:25: warning: implicit conversion from 'int' to 'float' changes value from 2147483645 to 2147483648 [-Wimplicit-const-int-float-conversion] 1101 | if (fabs(lf) > INT_MAX-2) | ~ ~~~~~~~^~ xdrfile.cpp:1116:25: warning: implicit conversion from 'int' to 'float' changes value from 2147483645 to 2147483648 [-Wimplicit-const-int-float-conversion] 1116 | if (fabs(lf) > INT_MAX-2) | ~ ~~~~~~~^~ xdrfile.cpp:1137:49: warning: implicit conversion from 'int' to 'float' changes value from 2147483645 to 2147483648 [-Wimplicit-const-int-float-conversion] 1137 | (float)maxint[2] - (float)minint[2] >= INT_MAX-2) { | ~~ ~~~~~~~^~ xdrfile.cpp:1136:49: warning: implicit conversion from 'int' to 'float' changes value from 2147483645 to 2147483648 [-Wimplicit-const-int-float-conversion] 1136 | (float)maxint[1] - (float)minint[1] >= INT_MAX-2 || | ~~ ~~~~~~~^~ xdrfile.cpp:1135:52: warning: implicit conversion from 'int' to 'float' changes value from 2147483645 to 2147483648 [-Wimplicit-const-int-float-conversion] 1135 | if ((float)maxint[0] - (float)minint[0] >= INT_MAX-2 || | ~~ ~~~~~~~^~ xdrfile.cpp:1315:16: warning: variable 'minidx' set but not used [-Wunused-but-set-variable] 1315 | int smallidx, minidx, maxidx; | ^ xdrfile.cpp:1318:25: warning: variable 'larger' set but not used [-Wunused-but-set-variable] 1318 | int smallnum, smaller, larger, i, is_smaller, run; | ^ xdrfile.cpp:1522:6: warning: variable 'errval' set but not used [-Wunused-but-set-variable] 1522 | int errval=1; | ^ xdrfile.cpp:1576:25: warning: implicit conversion from 'int' to 'float' changes value from 2147483645 to 2147483648 [-Wimplicit-const-int-float-conversion] 1576 | if (fabs(lf) > INT_MAX-2) { | ~ ~~~~~~~^~ xdrfile.cpp:1590:25: warning: implicit conversion from 'int' to 'float' changes value from 2147483645 to 2147483648 [-Wimplicit-const-int-float-conversion] 1590 | if (fabs(lf) > INT_MAX-2) { | ~ ~~~~~~~^~ xdrfile.cpp:1604:25: warning: implicit conversion from 'int' to 'float' changes value from 2147483645 to 2147483648 [-Wimplicit-const-int-float-conversion] 1604 | if (fabs(lf) > INT_MAX-2) { | ~ ~~~~~~~^~ xdrfile.cpp:1624:49: warning: implicit conversion from 'int' to 'float' changes value from 2147483645 to 2147483648 [-Wimplicit-const-int-float-conversion] 1624 | (float)maxint[2] - (float)minint[2] >= INT_MAX-2) { | ~~ ~~~~~~~^~ xdrfile.cpp:1623:49: warning: implicit conversion from 'int' to 'float' changes value from 2147483645 to 2147483648 [-Wimplicit-const-int-float-conversion] 1623 | (float)maxint[1] - (float)minint[1] >= INT_MAX-2 || | ~~ ~~~~~~~^~ xdrfile.cpp:1622:52: warning: implicit conversion from 'int' to 'float' changes value from 2147483645 to 2147483648 [-Wimplicit-const-int-float-conversion] 1622 | if ((float)maxint[0] - (float)minint[0] >= INT_MAX-2 || | ~~ ~~~~~~~^~ 20 warnings generated. compiling xdrfile_trr.cpp compiling FixedAtom.cpp compiling ERMSD.cpp compiling Energy.cpp compiling Restraint.cpp In file included from x86builder.cpp:37: In file included from ././x86builder.h:39: In file included from ./././codebuilder.h:39: In file included from ././././assembler.h:36: In file included from ./././././codeemitter.h:36: In file included from ././././././arch.h:37: ./././././././operand.h:341:12: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 341 | return (_packed[0] == other._packed[0]) & | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && 342 | (_packed[1] == other._packed[1]) ; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./././././././operand.h:341:12: note: cast one or both operands to int to silence this warning ./././././././operand.h:808:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 808 | static ASMJIT_INLINE bool isGp(const Operand_& op, uint32_t rId) noexcept { return isGp(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ./././././././operand.h:808:86: note: cast one or both operands to int to silence this warning ./././././././operand.h:809:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 809 | static ASMJIT_INLINE bool isVec(const Operand_& op, uint32_t rId) noexcept { return isVec(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ./././././././operand.h:809:87: note: cast one or both operands to int to silence this warning In file included from x86builder.cpp:37: In file included from ././x86builder.h:41: In file included from ./././x86emitter.h:38: ././././x86operand.h:379:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 379 | static ASMJIT_INLINE bool isGpb(const Operand_& op, uint32_t rId) noexcept { return isGpb(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:379:87: note: cast one or both operands to int to silence this warning ././././x86operand.h:381:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 381 | static ASMJIT_INLINE bool isRip(const Operand_& op, uint32_t rId) noexcept { return isRip(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:381:87: note: cast one or both operands to int to silence this warning ././././x86operand.h:382:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 382 | static ASMJIT_INLINE bool isSeg(const Operand_& op, uint32_t rId) noexcept { return isSeg(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:382:87: note: cast one or both operands to int to silence this warning ././././x86operand.h:383:89: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 383 | static ASMJIT_INLINE bool isGpbLo(const Operand_& op, uint32_t rId) noexcept { return isGpbLo(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:383:89: note: cast one or both operands to int to silence this warning ././././x86operand.h:384:89: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 384 | static ASMJIT_INLINE bool isGpbHi(const Operand_& op, uint32_t rId) noexcept { return isGpbHi(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:384:89: note: cast one or both operands to int to silence this warning ././././x86operand.h:385:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 385 | static ASMJIT_INLINE bool isGpw(const Operand_& op, uint32_t rId) noexcept { return isGpw(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:385:87: note: cast one or both operands to int to silence this warning ././././x86operand.h:386:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 386 | static ASMJIT_INLINE bool isGpd(const Operand_& op, uint32_t rId) noexcept { return isGpd(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:386:87: note: cast one or both operands to int to silence this warning ././././x86operand.h:387:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 387 | static ASMJIT_INLINE bool isGpq(const Operand_& op, uint32_t rId) noexcept { return isGpq(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:387:87: note: cast one or both operands to int to silence this warning ././././x86operand.h:388:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 388 | static ASMJIT_INLINE bool isFp(const Operand_& op, uint32_t rId) noexcept { return isFp(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:388:86: note: cast one or both operands to int to silence this warning ././././x86operand.h:389:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 389 | static ASMJIT_INLINE bool isMm(const Operand_& op, uint32_t rId) noexcept { return isMm(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:389:86: note: cast one or both operands to int to silence this warning ././././x86operand.h:390:85: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 390 | static ASMJIT_INLINE bool isK(const Operand_& op, uint32_t rId) noexcept { return isK(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:390:85: note: cast one or both operands to int to silence this warning ././././x86operand.h:391:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 391 | static ASMJIT_INLINE bool isXmm(const Operand_& op, uint32_t rId) noexcept { return isXmm(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:391:87: note: cast one or both operands to int to silence this warning ././././x86operand.h:392:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 392 | static ASMJIT_INLINE bool isYmm(const Operand_& op, uint32_t rId) noexcept { return isYmm(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:392:87: note: cast one or both operands to int to silence this warning ././././x86operand.h:393:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 393 | static ASMJIT_INLINE bool isZmm(const Operand_& op, uint32_t rId) noexcept { return isZmm(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:393:87: note: cast one or both operands to int to silence this warning ././././x86operand.h:394:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 394 | static ASMJIT_INLINE bool isBnd(const Operand_& op, uint32_t rId) noexcept { return isBnd(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:394:87: note: cast one or both operands to int to silence this warning ././././x86operand.h:395:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 395 | static ASMJIT_INLINE bool isCr(const Operand_& op, uint32_t rId) noexcept { return isCr(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:395:86: note: cast one or both operands to int to silence this warning ././././x86operand.h:396:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 396 | static ASMJIT_INLINE bool isDr(const Operand_& op, uint32_t rId) noexcept { return isDr(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././x86operand.h:396:86: note: cast one or both operands to int to silence this warning 20 warnings generated. compiling x86internal.cpp compiling CLTool.cpp compiling FourierTransform.cpp compiling GridPrintingBase.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 xdrfile_xtc.cpp compiling GridSearch.cpp compiling ReweightBase.cpp compiling ActionWithVessel.cpp compiling Units.cpp compiling ExtraCV.cpp compiling GridToXYZ.cpp compiling ReweightBias.cpp In file included from x86instimpl.cpp:35: In file included from ././x86instimpl_p.h:36: In file included from ./././x86inst.h:36: In file included from ././././assembler.h:36: In file included from ./././././codeemitter.h:36: In file included from ././././././arch.h:37: ./././././././operand.h:341:12: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 341 | return (_packed[0] == other._packed[0]) & | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && 342 | (_packed[1] == other._packed[1]) ; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./././././././operand.h:341:12: note: cast one or both operands to int to silence this warning ./././././././operand.h:808:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 808 | static ASMJIT_INLINE bool isGp(const Operand_& op, uint32_t rId) noexcept { return isGp(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ./././././././operand.h:808:86: note: cast one or both operands to int to silence this warning ./././././././operand.h:809:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 809 | static ASMJIT_INLINE bool isVec(const Operand_& op, uint32_t rId) noexcept { return isVec(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ./././././././operand.h:809:87: note: cast one or both operands to int to silence this warning In file included from x86instimpl.cpp:36: ././x86operand.h:379:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 379 | static ASMJIT_INLINE bool isGpb(const Operand_& op, uint32_t rId) noexcept { return isGpb(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:379:87: note: cast one or both operands to int to silence this warning ././x86operand.h:381:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 381 | static ASMJIT_INLINE bool isRip(const Operand_& op, uint32_t rId) noexcept { return isRip(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:381:87: note: cast one or both operands to int to silence this warning ././x86operand.h:382:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 382 | static ASMJIT_INLINE bool isSeg(const Operand_& op, uint32_t rId) noexcept { return isSeg(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:382:87: note: cast one or both operands to int to silence this warning ././x86operand.h:383:89: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 383 | static ASMJIT_INLINE bool isGpbLo(const Operand_& op, uint32_t rId) noexcept { return isGpbLo(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:383:89: note: cast one or both operands to int to silence this warning ././x86operand.h:384:89: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 384 | static ASMJIT_INLINE bool isGpbHi(const Operand_& op, uint32_t rId) noexcept { return isGpbHi(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:384:89: note: cast one or both operands to int to silence this warning ././x86operand.h:385:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 385 | static ASMJIT_INLINE bool isGpw(const Operand_& op, uint32_t rId) noexcept { return isGpw(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:385:87: note: cast one or both operands to int to silence this warning ././x86operand.h:386:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 386 | static ASMJIT_INLINE bool isGpd(const Operand_& op, uint32_t rId) noexcept { return isGpd(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:386:87: note: cast one or both operands to int to silence this warning ././x86operand.h:387:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 387 | static ASMJIT_INLINE bool isGpq(const Operand_& op, uint32_t rId) noexcept { return isGpq(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:387:87: note: cast one or both operands to int to silence this warning ././x86operand.h:388:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 388 | static ASMJIT_INLINE bool isFp(const Operand_& op, uint32_t rId) noexcept { return isFp(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:388:86: note: cast one or both operands to int to silence this warning ././x86operand.h:389:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 389 | static ASMJIT_INLINE bool isMm(const Operand_& op, uint32_t rId) noexcept { return isMm(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:389:86: note: cast one or both operands to int to silence this warning ././x86operand.h:390:85: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 390 | static ASMJIT_INLINE bool isK(const Operand_& op, uint32_t rId) noexcept { return isK(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:390:85: note: cast one or both operands to int to silence this warning ././x86operand.h:391:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 391 | static ASMJIT_INLINE bool isXmm(const Operand_& op, uint32_t rId) noexcept { return isXmm(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:391:87: note: cast one or both operands to int to silence this warning ././x86operand.h:392:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 392 | static ASMJIT_INLINE bool isYmm(const Operand_& op, uint32_t rId) noexcept { return isYmm(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:392:87: note: cast one or both operands to int to silence this warning ././x86operand.h:393:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 393 | static ASMJIT_INLINE bool isZmm(const Operand_& op, uint32_t rId) noexcept { return isZmm(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:393:87: note: cast one or both operands to int to silence this warning ././x86operand.h:394:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 394 | static ASMJIT_INLINE bool isBnd(const Operand_& op, uint32_t rId) noexcept { return isBnd(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:394:87: note: cast one or both operands to int to silence this warning ././x86operand.h:395:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 395 | static ASMJIT_INLINE bool isCr(const Operand_& op, uint32_t rId) noexcept { return isCr(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:395:86: note: cast one or both operands to int to silence this warning ././x86operand.h:396:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 396 | static ASMJIT_INLINE bool isDr(const Operand_& op, uint32_t rId) noexcept { return isDr(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:396:86: note: cast one or both operands to int to silence this warning 20 warnings generated. compiling x86logging.cpp compiling Include.cpp compiling Fake.cpp ../maketools/makecmd map < CLToolMain.cpp > CLToolMainMap.inc CS2Backbone.cpp:214:14: warning: variable 'nline' set but not used [-Wunused-but-set-variable] 214 | unsigned nline = 0; | ^ 1 warning generated. ../maketools/makecmd enum < CLToolMain.cpp > CLToolMainEnum.inc compiling CLToolRegister.cpp compiling EuclideanDistance.cpp compiling Ghost.cpp compiling PRE.cpp compiling Colvar.cpp compiling RDC.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 DataFetchingObject.cpp compiling x86operand.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. gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/xdrfile' compiling MolInfo.cpp compiling ReadAnalysisFrames.cpp compiling ExchangePatterns.cpp compiling Plumed.cpp compiling FakeFrame.cpp compiling ReadDissimilarityMatrix.cpp compiling Bridge.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 Citations.cpp compiling GHBFIX.cpp compiling ReweightMetad.cpp compiling AltMin.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 x86operand_regs.cpp compiling BridgedMultiColvarFunction.cpp compiling CatomPack.cpp compiling ReweightTemperaturePressure.cpp compiling ReselectLandmarks.cpp compiling GridVessel.cpp compiling SelectRandomFrames.cpp compiling ReweightWham.cpp compiling HistogramOnGrid.cpp compiling Communicator.cpp compiling FlexibleBin.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 IntegrateGrid.cpp compiling x86regalloc.cpp compiling IntermolecularDRMSD.cpp compiling Print.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 RandomExchanges.cpp gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/mapping' compiling CenterOfMultiColvar.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. gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/cltools' compiling Read.cpp compiling AveragingVessel.cpp compiling UWalls.cpp compiling zone.cpp gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/secondarystructure' ../maketools/makecmd map < GREX.cpp > GREXMap.inc compiling InterpolateGrid.cpp ../maketools/makecmd enum < GREX.cpp > GREXEnum.inc compiling GenericMolInfo.cpp compiling Rescale.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 MDAtoms.cpp compiling Gyration.cpp compiling MultiRMSD.cpp gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/function' compiling ConjugateGradient.cpp ../maketools/makeModuleMap ModuleMap.inc compiling IntramolecularDRMSD.cpp compiling DLLoader.cpp compiling DynamicList.cpp compiling MahalanobisDistance.cpp compiling PCARMSD.cpp compiling ResetCell.cpp compiling PathMSD.cpp compiling Time.cpp gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/setup' compiling SelectWithStride.cpp ../maketools/makecmd map < PlumedMain.cpp > PlumedMainMap.inc ../maketools/makecmd enum < PlumedMain.cpp > PlumedMainEnum.inc compiling PlumedMainInitializer.cpp compiling SAXS.cpp gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/vatom' compiling UpdateIf.cpp compiling TargetDist.cpp compiling Select.cpp compiling MetricRegister.cpp compiling CoordinationNumbers.cpp compiling ERMSD.cpp compiling PathMSDBase.cpp compiling Position.cpp compiling ProjectionOnAxis.cpp compiling Value.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 MultiDomainRMSD.cpp compiling Between.cpp compiling Exception.cpp compiling PropertyMap.cpp compiling Selector.cpp compiling BridgeVessel.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 FileBase.cpp 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 WithCmd.cpp compiling WhamHistogram.cpp compiling Density.cpp compiling FunctionVessel.cpp compiling WholeMolecules.cpp compiling WrapAround.cpp compiling WhamWeights.cpp compiling DihedralCorrelation.cpp compiling ForwardDecl.cpp compiling Highest.cpp compiling DistanceFromContour.cpp compiling Puckering.cpp compiling Histogram.cpp compiling Distances.cpp compiling Grid.cpp compiling NormalizedEuclideanDistance.cpp compiling DumpMultiColvar.cpp compiling OptimalRMSD.cpp compiling RMSD.cpp compiling FilterBetween.cpp compiling CLToolMain.cpp compiling LessThan.cpp compiling Template.cpp compiling HistogramBead.cpp compiling GREX.cpp compiling IFile.cpp compiling KernelFunctions.cpp compiling RMSDBase.cpp compiling FilterLessThan.cpp compiling Torsion.cpp compiling Lowest.cpp compiling Keywords.cpp compiling ReferenceArguments.cpp compiling Volume.cpp compiling Max.cpp compiling PlumedMain.cpp compiling LatticeReduction.cpp compiling ReferenceAtoms.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 ReferenceConfiguration.cpp compiling FilterMoreThan.cpp compiling InPlaneDistances.cpp compiling Log.cpp compiling LinkCells.cpp gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/gridtools' compiling LocalAverage.cpp compiling ReferenceValuePack.cpp compiling SimpleRMSD.cpp compiling SingleDomainRMSD.cpp compiling Mean.cpp compiling LoopUnroller.cpp compiling Matrix.cpp compiling Min.cpp compiling Moments.cpp compiling MoreThan.cpp gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/bias' compiling MultiColvarBase.cpp compiling MultiColvarCombine.cpp compiling MatrixSquareBracketsAccess.cpp compiling MultiColvarFilter.cpp compiling MultiColvarDensity.cpp compiling OrderingVessel.cpp compiling ShortcutVessel.cpp compiling MultiColvarProduct.cpp compiling NumberOfLinks.cpp compiling StoreDataVessel.cpp compiling Minimise1DBrent.cpp compiling MinimiseBase.cpp compiling Sum.cpp compiling ValueVessel.cpp gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/analysis' compiling Vessel.cpp compiling VesselRegister.cpp compiling MultiValue.cpp compiling Torsions.cpp compiling MolDataClass.cpp compiling VolumeAround.cpp compiling NeighborList.cpp compiling VolumeBetweenContours.cpp gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/generic' compiling VolumeCavity.cpp compiling VolumeGradientBase.cpp compiling OFile.cpp compiling OpenMP.cpp compiling VolumeInCylinder.cpp compiling VolumeInSphere.cpp compiling VolumeTetrapore.cpp compiling PDB.cpp compiling XAngle.cpp compiling XDistances.cpp compiling PlumedHandle.cpp compiling Pbc.cpp compiling XYTorsion.cpp compiling XYDistances.cpp compiling RMSD.cpp compiling Random.cpp compiling RootFindingBase.cpp PathMSDBase.cpp:143:19: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning] 143 | void PathMSDBase::calculate() { | ^ PathMSDBase.cpp:143:19: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning] PathMSDBase.cpp:143:19: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning] PathMSDBase.cpp:143:19: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning] PathMSDBase.cpp:143:19: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning] PathMSDBase.cpp:143:19: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning] 6 warnings generated. gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/colvar' compiling Stopwatch.cpp compiling Subprocess.cpp compiling SwitchingFunction.cpp compiling Tools.cpp compiling Torsion.cpp compiling Tensor.cpp compiling Tree.cpp compiling TypesafePtr.cpp compiling Units.cpp compiling Vector.cpp gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/reference' compiling h36.cpp Keywords.cpp:126:16: warning: variable 'i' set but not used [-Wunused-but-set-variable] 126 | for(unsigned i=0;; ++i) { | ^ 1 warning generated. Vessel.cpp:63:16: warning: variable 'i' set but not used [-Wunused-but-set-variable] 63 | for(unsigned i=0;; ++i) { | ^ 1 warning generated. 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. 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' RMSD.cpp:93:12: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning] 93 | void RMSD::setReference(const std::vector & reference) { | ^ RMSD.cpp:112:12: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning] 112 | void RMSD::setAlign(const std::vector & align, bool normalize_weights, bool remove_center) { | ^ RMSD.cpp:112:12: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning] RMSD.cpp:152:12: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning] 152 | void RMSD::setDisplace(const std::vector & displace, bool normalize_weights) { | ^ RMSD.cpp:152:12: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning] RMSD.cpp:1118:22: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning] 1118 | double RMSDCoreData::getDistance( bool squared) { | ^ RMSD.cpp:1181:35: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning] 1181 | std::vector RMSDCoreData::getDDistanceDPositions() { | ^ RMSD.cpp:1217:36: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning] 1217 | std::vector RMSDCoreData::getDDistanceDReference() { | ^ 8 warnings generated. gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/tools' gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/core' gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/isdb' gmake[5]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' gmake[4]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' /usr/local/bin/gmake lib gmake[4]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fPIC -Wall -pedantic -std=c++11 ../main/main.o ../analysis/AnalysisBase.o ../analysis/Average.o ../analysis/AverageVessel.o ../analysis/Committor.o ../analysis/DataCollectionObject.o ../analysis/EuclideanDissimilarityMatrix.o ../analysis/FarthestPointSampling.o ../analysis/Histogram.o ../analysis/LandmarkSelectionBase.o ../analysis/LandmarkStaged.o ../analysis/OutputColvarFile.o ../analysis/OutputPDBFile.o ../analysis/PrintDissimilarityMatrix.o ../analysis/ReadAnalysisFrames.o ../analysis/ReadDissimilarityMatrix.o ../analysis/ReselectLandmarks.o ../analysis/SelectRandomFrames.o ../analysis/SelectWithStride.o ../analysis/WhamHistogram.o ../analysis/WhamWeights.o ../asmjit/arch.o ../asmjit/assembler.o ../asmjit/codebuilder.o ../asmjit/codecompiler.o ../asmjit/codeemitter.o ../asmjit/codeholder.o ../asmjit/constpool.o ../asmjit/cpuinfo.o ../asmjit/func.o ../asmjit/globals.o ../asmjit/inst.o ../asmjit/logging.o ../asmjit/operand.o ../asmjit/osutils.o ../asmjit/regalloc.o ../asmjit/runtime.o ../asmjit/string.o ../asmjit/utils.o ../asmjit/vmem.o ../asmjit/x86assembler.o ../asmjit/x86builder.o ../asmjit/x86compiler.o ../asmjit/x86inst.o ../asmjit/x86instimpl.o ../asmjit/x86internal.o ../asmjit/x86logging.o ../asmjit/x86operand.o ../asmjit/x86operand_regs.o ../asmjit/x86regalloc.o ../asmjit/zone.o ../bias/ABMD.o ../bias/Bias.o ../bias/BiasValue.o ../bias/ExtendedLagrangian.o ../bias/External.o ../bias/LWalls.o ../bias/MaxEnt.o ../bias/MetaD.o ../bias/MovingRestraint.o ../bias/PBMetaD.o ../bias/Restraint.o ../bias/ReweightBase.o ../bias/ReweightBias.o ../bias/ReweightMetad.o ../bias/ReweightTemperaturePressure.o ../bias/ReweightWham.o ../bias/UWalls.o ../blas/blas.o ../cltools/CLTool.o ../cltools/Completion.o ../cltools/Driver.o ../cltools/DriverDouble.o ../cltools/DriverFloat.o ../cltools/GenExample.o ../cltools/GenJson.o ../cltools/GenTemplate.o ../cltools/Info.o ../cltools/Manual.o ../cltools/PdbRenumber.o ../cltools/SimpleMD.o ../cltools/SumHills.o ../cltools/kT.o ../cltools/pesmd.o ../colvar/Angle.o ../colvar/Cell.o ../colvar/Colvar.o ../colvar/Constant.o ../colvar/ContactMap.o ../colvar/Coordination.o ../colvar/CoordinationBase.o ../colvar/DHEnergy.o ../colvar/DRMSD.o ../colvar/Dimer.o ../colvar/Dipole.o ../colvar/Distance.o ../colvar/EEFSolv.o ../colvar/ERMSD.o ../colvar/Energy.o ../colvar/ExtraCV.o ../colvar/Fake.o ../colvar/GHBFIX.o ../colvar/Gyration.o ../colvar/MultiRMSD.o ../colvar/PCARMSD.o ../colvar/PathMSD.o ../colvar/PathMSDBase.o ../colvar/Position.o ../colvar/ProjectionOnAxis.o ../colvar/PropertyMap.o ../colvar/Puckering.o ../colvar/RMSD.o ../colvar/Template.o ../colvar/Torsion.o ../colvar/Volume.o ../core/Action.o ../core/ActionAnyorder.o ../core/ActionAtomistic.o ../core/ActionPilot.o ../core/ActionRegister.o ../core/ActionSet.o ../core/ActionSetup.o ../core/ActionShortcut.o ../core/ActionWithArguments.o ../core/ActionWithValue.o ../core/ActionWithVirtualAtom.o ../core/Atoms.o ../core/CLTool.o ../core/CLToolMain.o ../core/CLToolRegister.o ../core/Colvar.o ../core/DataFetchingObject.o ../core/ExchangePatterns.o ../core/FlexibleBin.o ../core/GREX.o ../core/GenericMolInfo.o ../core/MDAtoms.o ../core/ModuleMap.o ../core/PlumedMain.o ../core/PlumedMainInitializer.o ../core/TargetDist.o ../core/Value.o ../core/WithCmd.o ../function/Combine.o ../function/Custom.o ../function/Ensemble.o ../function/FuncPathGeneral.o ../function/FuncPathMSD.o ../function/FuncSumHills.o ../function/Function.o ../function/LocalEnsemble.o ../function/Piecewise.o ../function/Sort.o ../function/Stats.o ../function/Target.o ../generic/Debug.o ../generic/DumpAtoms.o ../generic/DumpDerivatives.o ../generic/DumpForces.o ../generic/DumpMassCharge.o ../generic/DumpProjections.o ../generic/EffectiveEnergyDrift.o ../generic/EndPlumed.o ../generic/FitToTemplate.o ../generic/Flush.o ../generic/Group.o ../generic/Include.o ../generic/MolInfo.o ../generic/Plumed.o ../generic/Print.o ../generic/RandomExchanges.o ../generic/Read.o ../generic/ResetCell.o ../generic/Time.o ../generic/UpdateIf.o ../generic/WholeMolecules.o ../generic/WrapAround.o ../gridtools/ActionWithGrid.o ../gridtools/ActionWithInputGrid.o ../gridtools/ActionWithIntegral.o ../gridtools/AverageOnGrid.o ../gridtools/ContourFindingBase.o ../gridtools/ConvertToFES.o ../gridtools/DumpCube.o ../gridtools/DumpGrid.o ../gridtools/FindContour.o ../gridtools/FindContourSurface.o ../gridtools/FindSphericalContour.o ../gridtools/FourierTransform.o ../gridtools/GridPrintingBase.o ../gridtools/GridSearch.o ../gridtools/GridToXYZ.o ../gridtools/GridVessel.o ../gridtools/HistogramOnGrid.o ../gridtools/IntegrateGrid.o ../gridtools/InterpolateGrid.o ../isdb/CS2Backbone.o ../isdb/Caliber.o ../isdb/EMMI.o ../isdb/FretEfficiency.o ../isdb/Jcoupling.o ../isdb/Metainference.o ../isdb/MetainferenceBase.o ../isdb/NOE.o ../isdb/PRE.o ../isdb/RDC.o ../isdb/Rescale.o ../isdb/SAXS.o ../isdb/Select.o ../isdb/Selector.o ../lapack/lapack.o ../lepton/CompiledExpression.o ../lepton/ExpressionProgram.o ../lepton/ExpressionTreeNode.o ../lepton/Operation.o ../lepton/ParsedExpression.o ../lepton/Parser.o ../mapping/AdaptivePath.o ../mapping/Mapping.o ../mapping/PCAVars.o ../mapping/Path.o ../mapping/PathBase.o ../mapping/PathReparameterization.o ../mapping/PathTools.o ../mapping/PropertyMap.o ../mapping/SpathVessel.o ../mapping/TrigonometricPathVessel.o ../mapping/ZpathVessel.o ../molfile/crdplugin.o ../molfile/dcdplugin.o ../molfile/gromacsplugin.o ../molfile/pdbplugin.o ../multicolvar/ActionVolume.o ../multicolvar/AlphaBeta.o ../multicolvar/Angles.o ../multicolvar/AtomValuePack.o ../multicolvar/Bridge.o ../multicolvar/BridgedMultiColvarFunction.o ../multicolvar/CatomPack.o ../multicolvar/CenterOfMultiColvar.o ../multicolvar/CoordinationNumbers.o ../multicolvar/Density.o ../multicolvar/DihedralCorrelation.o ../multicolvar/DistanceFromContour.o ../multicolvar/Distances.o ../multicolvar/DumpMultiColvar.o ../multicolvar/FilterBetween.o ../multicolvar/FilterLessThan.o ../multicolvar/FilterMoreThan.o ../multicolvar/InPlaneDistances.o ../multicolvar/LocalAverage.o ../multicolvar/MultiColvarBase.o ../multicolvar/MultiColvarCombine.o ../multicolvar/MultiColvarDensity.o ../multicolvar/MultiColvarFilter.o ../multicolvar/MultiColvarProduct.o ../multicolvar/NumberOfLinks.o ../multicolvar/Torsions.o ../multicolvar/VolumeAround.o ../multicolvar/VolumeBetweenContours.o ../multicolvar/VolumeCavity.o ../multicolvar/VolumeGradientBase.o ../multicolvar/VolumeInCylinder.o ../multicolvar/VolumeInSphere.o ../multicolvar/VolumeTetrapore.o ../multicolvar/XAngle.o ../multicolvar/XDistances.o ../multicolvar/XYDistances.o ../multicolvar/XYTorsion.o ../reference/ArgumentOnlyDistance.o ../reference/DRMSD.o ../reference/Direction.o ../reference/DotProductDistance.o ../reference/EuclideanDistance.o ../reference/FakeFrame.o ../reference/IntermolecularDRMSD.o ../reference/IntramolecularDRMSD.o ../reference/MahalanobisDistance.o ../reference/MetricRegister.o ../reference/MultiDomainRMSD.o ../reference/NormalizedEuclideanDistance.o ../reference/OptimalRMSD.o ../reference/RMSDBase.o ../reference/ReferenceArguments.o ../reference/ReferenceAtoms.o ../reference/ReferenceConfiguration.o ../reference/ReferenceValuePack.o ../reference/SimpleRMSD.o ../reference/SingleDomainRMSD.o ../secondarystructure/AlphaRMSD.o ../secondarystructure/AntibetaRMSD.o ../secondarystructure/ParabetaRMSD.o ../secondarystructure/SecondaryStructureRMSD.o ../setup/Load.o ../setup/Restart.o ../setup/Units.o ../tools/Angle.o ../tools/AtomNumber.o ../tools/BiasRepresentation.o ../tools/Brent1DRootSearch.o ../tools/Citations.o ../tools/Communicator.o ../tools/ConjugateGradient.o ../tools/DLLoader.o ../tools/DynamicList.o ../tools/ERMSD.o ../tools/Exception.o ../tools/FileBase.o ../tools/ForwardDecl.o ../tools/Grid.o ../tools/HistogramBead.o ../tools/IFile.o ../tools/KernelFunctions.o ../tools/Keywords.o ../tools/LatticeReduction.o ../tools/LinkCells.o ../tools/Log.o ../tools/LoopUnroller.o ../tools/Matrix.o ../tools/MatrixSquareBracketsAccess.o ../tools/Minimise1DBrent.o ../tools/MinimiseBase.o ../tools/MolDataClass.o ../tools/MultiValue.o ../tools/NeighborList.o ../tools/OFile.o ../tools/OpenMP.o ../tools/PDB.o ../tools/Pbc.o ../tools/PlumedHandle.o ../tools/RMSD.o ../tools/Random.o ../tools/RootFindingBase.o ../tools/Stopwatch.o ../tools/Subprocess.o ../tools/SwitchingFunction.o ../tools/Tensor.o ../tools/Tools.o ../tools/Torsion.o ../tools/Tree.o ../tools/TypesafePtr.o ../tools/Units.o ../tools/Vector.o ../tools/h36.o ../vatom/ActionWithVirtualAtom.o ../vatom/Center.o ../vatom/FixedAtom.o ../vatom/Ghost.o ../vesselbase/ActionWithAveraging.o ../vesselbase/ActionWithInputVessel.o ../vesselbase/ActionWithVessel.o ../vesselbase/AltMin.o ../vesselbase/AveragingVessel.o ../vesselbase/Between.o ../vesselbase/BridgeVessel.o ../vesselbase/FunctionVessel.o ../vesselbase/Highest.o ../vesselbase/Histogram.o ../vesselbase/LessThan.o ../vesselbase/Lowest.o ../vesselbase/Max.o ../vesselbase/Mean.o ../vesselbase/Min.o ../vesselbase/Moments.o ../vesselbase/MoreThan.o ../vesselbase/OrderingVessel.o ../vesselbase/ShortcutVessel.o ../vesselbase/StoreDataVessel.o ../vesselbase/Sum.o ../vesselbase/ValueVessel.o ../vesselbase/Vessel.o ../vesselbase/VesselRegister.o ../xdrfile/xdrfile.o ../xdrfile/xdrfile_trr.o ../xdrfile/xdrfile_xtc.o ../config/Config.o ../wrapper/PlumedStatic.o -o plumed-static -ldl -lstdc++ -lfftw3 -lgsl -lgslcblas -lz -ldl -llapack -lblas -L/usr/local/lib -rdynamic -Wl,-Bsymbolic -fopenmp Building Plumed.inc c++ -shared -o libplumedKernel.so ../analysis/AnalysisBase.o ../analysis/Average.o ../analysis/AverageVessel.o ../analysis/Committor.o ../analysis/DataCollectionObject.o ../analysis/EuclideanDissimilarityMatrix.o ../analysis/FarthestPointSampling.o ../analysis/Histogram.o ../analysis/LandmarkSelectionBase.o ../analysis/LandmarkStaged.o ../analysis/OutputColvarFile.o ../analysis/OutputPDBFile.o ../analysis/PrintDissimilarityMatrix.o ../analysis/ReadAnalysisFrames.o ../analysis/ReadDissimilarityMatrix.o ../analysis/ReselectLandmarks.o ../analysis/SelectRandomFrames.o ../analysis/SelectWithStride.o ../analysis/WhamHistogram.o ../analysis/WhamWeights.o ../asmjit/arch.o ../asmjit/assembler.o ../asmjit/codebuilder.o ../asmjit/codecompiler.o ../asmjit/codeemitter.o ../asmjit/codeholder.o ../asmjit/constpool.o ../asmjit/cpuinfo.o ../asmjit/func.o ../asmjit/globals.o ../asmjit/inst.o ../asmjit/logging.o ../asmjit/operand.o ../asmjit/osutils.o ../asmjit/regalloc.o ../asmjit/runtime.o ../asmjit/string.o ../asmjit/utils.o ../asmjit/vmem.o ../asmjit/x86assembler.o ../asmjit/x86builder.o ../asmjit/x86compiler.o ../asmjit/x86inst.o ../asmjit/x86instimpl.o ../asmjit/x86internal.o ../asmjit/x86logging.o ../asmjit/x86operand.o ../asmjit/x86operand_regs.o ../asmjit/x86regalloc.o ../asmjit/zone.o ../bias/ABMD.o ../bias/Bias.o ../bias/BiasValue.o ../bias/ExtendedLagrangian.o ../bias/External.o ../bias/LWalls.o ../bias/MaxEnt.o ../bias/MetaD.o ../bias/MovingRestraint.o ../bias/PBMetaD.o ../bias/Restraint.o ../bias/ReweightBase.o ../bias/ReweightBias.o ../bias/ReweightMetad.o ../bias/ReweightTemperaturePressure.o ../bias/ReweightWham.o ../bias/UWalls.o ../blas/blas.o ../cltools/CLTool.o ../cltools/Completion.o ../cltools/Driver.o ../cltools/DriverDouble.o ../cltools/DriverFloat.o ../cltools/GenExample.o ../cltools/GenJson.o ../cltools/GenTemplate.o ../cltools/Info.o ../cltools/Manual.o ../cltools/PdbRenumber.o ../cltools/SimpleMD.o ../cltools/SumHills.o ../cltools/kT.o ../cltools/pesmd.o ../colvar/Angle.o ../colvar/Cell.o ../colvar/Colvar.o ../colvar/Constant.o ../colvar/ContactMap.o ../colvar/Coordination.o ../colvar/CoordinationBase.o ../colvar/DHEnergy.o ../colvar/DRMSD.o ../colvar/Dimer.o ../colvar/Dipole.o ../colvar/Distance.o ../colvar/EEFSolv.o ../colvar/ERMSD.o ../colvar/Energy.o ../colvar/ExtraCV.o ../colvar/Fake.o ../colvar/GHBFIX.o ../colvar/Gyration.o ../colvar/MultiRMSD.o ../colvar/PCARMSD.o ../colvar/PathMSD.o ../colvar/PathMSDBase.o ../colvar/Position.o ../colvar/ProjectionOnAxis.o ../colvar/PropertyMap.o ../colvar/Puckering.o ../colvar/RMSD.o ../colvar/Template.o ../colvar/Torsion.o ../colvar/Volume.o ../core/Action.o ../core/ActionAnyorder.o ../core/ActionAtomistic.o ../core/ActionPilot.o ../core/ActionRegister.o ../core/ActionSet.o ../core/ActionSetup.o ../core/ActionShortcut.o ../core/ActionWithArguments.o ../core/ActionWithValue.o ../core/ActionWithVirtualAtom.o ../core/Atoms.o ../core/CLTool.o ../core/CLToolMain.o ../core/CLToolRegister.o ../core/Colvar.o ../core/DataFetchingObject.o ../core/ExchangePatterns.o ../core/FlexibleBin.o ../core/GREX.o ../core/GenericMolInfo.o ../core/MDAtoms.o ../core/ModuleMap.o ../core/PlumedMain.o ../core/PlumedMainInitializer.o ../core/TargetDist.o ../core/Value.o ../core/WithCmd.o ../function/Combine.o ../function/Custom.o ../function/Ensemble.o ../function/FuncPathGeneral.o ../function/FuncPathMSD.o ../function/FuncSumHills.o ../function/Function.o ../function/LocalEnsemble.o ../function/Piecewise.o ../function/Sort.o ../function/Stats.o ../function/Target.o ../generic/Debug.o ../generic/DumpAtoms.o ../generic/DumpDerivatives.o ../generic/DumpForces.o ../generic/DumpMassCharge.o ../generic/DumpProjections.o ../generic/EffectiveEnergyDrift.o ../generic/EndPlumed.o ../generic/FitToTemplate.o ../generic/Flush.o ../generic/Group.o ../generic/Include.o ../generic/MolInfo.o ../generic/Plumed.o ../generic/Print.o ../generic/RandomExchanges.o ../generic/Read.o ../generic/ResetCell.o ../generic/Time.o ../generic/UpdateIf.o ../generic/WholeMolecules.o ../generic/WrapAround.o ../gridtools/ActionWithGrid.o ../gridtools/ActionWithInputGrid.o ../gridtools/ActionWithIntegral.o ../gridtools/AverageOnGrid.o ../gridtools/ContourFindingBase.o ../gridtools/ConvertToFES.o ../gridtools/DumpCube.o ../gridtools/DumpGrid.o ../gridtools/FindContour.o ../gridtools/FindContourSurface.o ../gridtools/FindSphericalContour.o ../gridtools/FourierTransform.o ../gridtools/GridPrintingBase.o ../gridtools/GridSearch.o ../gridtools/GridToXYZ.o ../gridtools/GridVessel.o ../gridtools/HistogramOnGrid.o ../gridtools/IntegrateGrid.o ../gridtools/InterpolateGrid.o ../isdb/CS2Backbone.o ../isdb/Caliber.o ../isdb/EMMI.o ../isdb/FretEfficiency.o ../isdb/Jcoupling.o ../isdb/Metainference.o ../isdb/MetainferenceBase.o ../isdb/NOE.o ../isdb/PRE.o ../isdb/RDC.o ../isdb/Rescale.o ../isdb/SAXS.o ../isdb/Select.o ../isdb/Selector.o ../lapack/lapack.o ../lepton/CompiledExpression.o ../lepton/ExpressionProgram.o ../lepton/ExpressionTreeNode.o ../lepton/Operation.o ../lepton/ParsedExpression.o ../lepton/Parser.o ../mapping/AdaptivePath.o ../mapping/Mapping.o ../mapping/PCAVars.o ../mapping/Path.o ../mapping/PathBase.o ../mapping/PathReparameterization.o ../mapping/PathTools.o ../mapping/PropertyMap.o ../mapping/SpathVessel.o ../mapping/TrigonometricPathVessel.o ../mapping/ZpathVessel.o ../molfile/crdplugin.o ../molfile/dcdplugin.o ../molfile/gromacsplugin.o ../molfile/pdbplugin.o ../multicolvar/ActionVolume.o ../multicolvar/AlphaBeta.o ../multicolvar/Angles.o ../multicolvar/AtomValuePack.o ../multicolvar/Bridge.o ../multicolvar/BridgedMultiColvarFunction.o ../multicolvar/CatomPack.o ../multicolvar/CenterOfMultiColvar.o ../multicolvar/CoordinationNumbers.o ../multicolvar/Density.o ../multicolvar/DihedralCorrelation.o ../multicolvar/DistanceFromContour.o ../multicolvar/Distances.o ../multicolvar/DumpMultiColvar.o ../multicolvar/FilterBetween.o ../multicolvar/FilterLessThan.o ../multicolvar/FilterMoreThan.o ../multicolvar/InPlaneDistances.o ../multicolvar/LocalAverage.o ../multicolvar/MultiColvarBase.o ../multicolvar/MultiColvarCombine.o ../multicolvar/MultiColvarDensity.o ../multicolvar/MultiColvarFilter.o ../multicolvar/MultiColvarProduct.o ../multicolvar/NumberOfLinks.o ../multicolvar/Torsions.o ../multicolvar/VolumeAround.o ../multicolvar/VolumeBetweenContours.o ../multicolvar/VolumeCavity.o ../multicolvar/VolumeGradientBase.o ../multicolvar/VolumeInCylinder.o ../multicolvar/VolumeInSphere.o ../multicolvar/VolumeTetrapore.o ../multicolvar/XAngle.o ../multicolvar/XDistances.o ../multicolvar/XYDistances.o ../multicolvar/XYTorsion.o ../reference/ArgumentOnlyDistance.o ../reference/DRMSD.o ../reference/Direction.o ../reference/DotProductDistance.o ../reference/EuclideanDistance.o ../reference/FakeFrame.o ../reference/IntermolecularDRMSD.o ../reference/IntramolecularDRMSD.o ../reference/MahalanobisDistance.o ../reference/MetricRegister.o ../reference/MultiDomainRMSD.o ../reference/NormalizedEuclideanDistance.o ../reference/OptimalRMSD.o ../reference/RMSDBase.o ../reference/ReferenceArguments.o ../reference/ReferenceAtoms.o ../reference/ReferenceConfiguration.o ../reference/ReferenceValuePack.o ../reference/SimpleRMSD.o ../reference/SingleDomainRMSD.o ../secondarystructure/AlphaRMSD.o ../secondarystructure/AntibetaRMSD.o ../secondarystructure/ParabetaRMSD.o ../secondarystructure/SecondaryStructureRMSD.o ../setup/Load.o ../setup/Restart.o ../setup/Units.o ../tools/Angle.o ../tools/AtomNumber.o ../tools/BiasRepresentation.o ../tools/Brent1DRootSearch.o ../tools/Citations.o ../tools/Communicator.o ../tools/ConjugateGradient.o ../tools/DLLoader.o ../tools/DynamicList.o ../tools/ERMSD.o ../tools/Exception.o ../tools/FileBase.o ../tools/ForwardDecl.o ../tools/Grid.o ../tools/HistogramBead.o ../tools/IFile.o ../tools/KernelFunctions.o ../tools/Keywords.o ../tools/LatticeReduction.o ../tools/LinkCells.o ../tools/Log.o ../tools/LoopUnroller.o ../tools/Matrix.o ../tools/MatrixSquareBracketsAccess.o ../tools/Minimise1DBrent.o ../tools/MinimiseBase.o ../tools/MolDataClass.o ../tools/MultiValue.o ../tools/NeighborList.o ../tools/OFile.o ../tools/OpenMP.o ../tools/PDB.o ../tools/Pbc.o ../tools/PlumedHandle.o ../tools/RMSD.o ../tools/Random.o ../tools/RootFindingBase.o ../tools/Stopwatch.o ../tools/Subprocess.o ../tools/SwitchingFunction.o ../tools/Tensor.o ../tools/Tools.o ../tools/Torsion.o ../tools/Tree.o ../tools/TypesafePtr.o ../tools/Units.o ../tools/Vector.o ../tools/h36.o ../vatom/ActionWithVirtualAtom.o ../vatom/Center.o ../vatom/FixedAtom.o ../vatom/Ghost.o ../vesselbase/ActionWithAveraging.o ../vesselbase/ActionWithInputVessel.o ../vesselbase/ActionWithVessel.o ../vesselbase/AltMin.o ../vesselbase/AveragingVessel.o ../vesselbase/Between.o ../vesselbase/BridgeVessel.o ../vesselbase/FunctionVessel.o ../vesselbase/Highest.o ../vesselbase/Histogram.o ../vesselbase/LessThan.o ../vesselbase/Lowest.o ../vesselbase/Max.o ../vesselbase/Mean.o ../vesselbase/Min.o ../vesselbase/Moments.o ../vesselbase/MoreThan.o ../vesselbase/OrderingVessel.o ../vesselbase/ShortcutVessel.o ../vesselbase/StoreDataVessel.o ../vesselbase/Sum.o ../vesselbase/ValueVessel.o ../vesselbase/Vessel.o ../vesselbase/VesselRegister.o ../xdrfile/xdrfile.o ../xdrfile/xdrfile_trr.o ../xdrfile/xdrfile_xtc.o ../config/Config.o -Wl,-soname,"libplumedKernel.so" -lstdc++ -lfftw3 -lgsl -lgslcblas -lz -ldl -llapack -lblas -L/usr/local/lib -rdynamic -Wl,-Bsymbolic -fopenmp chmod a+x plumed-config c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fPIC -Wall -pedantic -std=c++11 ../main/main.o ../wrapper/Plumed.o -o plumed-runtime -ldl /usr/bin/ar cr libplumedWrapper.a ../wrapper/Plumed.o chmod a+x plumed-mklib Building Plumed.inc, static version Building Plumed.cmake Building Plumed.inc, runtime-linking version Building Plumed.inc, shared version chmod a+x plumed-partial_tempering chmod a+x plumed-newcv chmod a+x plumed-selector chmod a+x plumed-patch Building Plumed.cmake, static version Building Plumed.cmake, runtime-linking version Building Plumed.cmake, shared version chmod a+x plumed-vim2html c++ -shared -o libplumed.so ../wrapper/PlumedStatic.o libplumedKernel.so -Wl,-soname,"libplumed.so" c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fPIC -Wall -pedantic -std=c++11 ../main/main.o ../wrapper/PlumedStatic.o libplumedKernel.so -o plumed -ldl gmake[4]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' /usr/local/bin/gmake install-build gmake[4]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' mkdir -p install/ /usr/local/bin/gmake PLUMED_INSTALL=Install all gmake[5]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' /usr/local/bin/gmake dirslinks gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' *** Updating links to used modules in all directories *** /usr/local/bin/gmake ../analysis.links ../asmjit.links ../bias.links ../blas.links ../cltools.links ../colvar.links ../config.links ../core.links ../function.links ../generic.links ../gridtools.links ../isdb.links ../lapack.links ../lepton.links ../main.links ../mapping.links ../molfile.links ../multicolvar.links ../reference.links ../secondarystructure.links ../setup.links ../tools.links ../vatom.links ../vesselbase.links ../wrapper.links ../xdrfile.links gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' /usr/local/bin/gmake -C ../analysis links /usr/local/bin/gmake -C ../asmjit links /usr/local/bin/gmake -C ../bias links /usr/local/bin/gmake -C ../blas links /usr/local/bin/gmake -C ../cltools links /usr/local/bin/gmake -C ../colvar links /usr/local/bin/gmake -C ../config links /usr/local/bin/gmake -C ../core links /usr/local/bin/gmake -C ../function links /usr/local/bin/gmake -C ../generic links /usr/local/bin/gmake -C ../gridtools links /usr/local/bin/gmake -C ../isdb links /usr/local/bin/gmake -C ../lapack links /usr/local/bin/gmake -C ../lepton links /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 /usr/local/bin/gmake -C ../vesselbase links gmake[8]: Leaving 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/lapack' /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/molfile' 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/asmjit' 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/main gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/wrapper' gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/setup' 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/bias' 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 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/secondarystructure' Nothing to do in /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/bias 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/setup Verify modules and create links in /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/wrapper' 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/secondarystructure gmake[8]: Leaving directory '/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/vatom' 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/xdrfile' Verify modules and create links in /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/generic' 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/isdb' gmake[8]: 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/xdrfile 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/generic 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/mapping 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/xdrfile' gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/reference' gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/core' 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/core Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/reference Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/colvar gmake[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/vesselbase gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/main' gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lapack' gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/tools' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/tools gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/multicolvar' gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lepton' 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/setup' 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/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/core' 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/gridtools' 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/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/isdb' 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 /usr/local/bin/gmake -C ../mapping obj /usr/local/bin/gmake -C ../molfile obj gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/blas' gmake[8]: Nothing to be done for 'obj'. /usr/local/bin/gmake -C ../multicolvar obj gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/blas' /usr/local/bin/gmake -C ../reference 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 ../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[9]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/config' gmake[9]: 'config.txt' is up to date. gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/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[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/bias' gmake[8]: Nothing to be done for 'obj'. gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/bias' Updating Config.inc Updating ConfigInstall.inc 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/lepton' gmake[8]: Nothing to be done for 'obj'. gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lepton' gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/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' Updating version.h 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/cltools' gmake[8]: Nothing to be done for 'obj'. gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/cltools' gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/secondarystructure' gmake[8]: Nothing to be done for 'obj'. gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/vatom' gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/secondarystructure' 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]: Nothing to be done for 'obj'. 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/asmjit' gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/generic' gmake[8]: Nothing to be done for 'obj'. gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/generic' gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/isdb' gmake[8]: Nothing to be done for 'obj'. gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/isdb' 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/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' gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/gridtools' gmake[8]: Nothing to be done for 'obj'. cmp -s ConfigInstall.inc~ ConfigInstall.inc || cp ConfigInstall.inc~ ConfigInstall.inc gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/gridtools' cmp -s Config.inc~ Config.inc || cp Config.inc~ Config.inc gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/mapping' gmake[8]: Nothing to be done for 'obj'. gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/mapping' rm Config.inc~ rm ConfigInstall.inc~ gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/colvar' gmake[8]: Nothing to be done for 'obj'. gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/colvar' 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/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/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/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++ -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 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 chmod a+x install/plumed-config mkdir -p install chmod a+x install/plumed-mklib /usr/bin/ar cr install/libplumedWrapper.a ../wrapper/Plumed.o Building Plumed.inc, runtime-linking version Building Plumed.inc, shared version Building Plumed.inc, static version chmod a+x install/plumed-newcv Building Plumed.cmake chmod a+x install/plumed-partial_tempering chmod a+x install/plumed-patch chmod a+x install/plumed-selector Building Plumed.cmake, static version Building Plumed.cmake, shared version Building Plumed.cmake, runtime-linking version chmod a+x install/plumed-vim2html 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_2 depends on executable: bash - found =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for plumed-2.9.3_2 ===> 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=2026-02-18T18:43:54+0000' 'PKG_NOTE_ports_top_git_hash=eac71dbf758c' 'PKG_NOTE_ports_top_checkout_unclean=no' 'PKG_NOTE_port_git_hash=2e4f3d1acf81' '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_2 ===> Building plumed-2.9.3_2 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for plumed-2.9.3_2 build of science/plumed | plumed-2.9.3_2 ended at Wed Feb 18 13:47:50 EST 2026 build time: 00:03:57