=>> Building science/plumed build started at Wed Dec 10 06:30:59 EST 2025 port directory: /usr/ports/science/plumed package name: plumed-2.9.3_1 building for: FreeBSD pkg.DaveG.ca 13.5-RELEASE-p7 FreeBSD 13.5-RELEASE-p7 1305000 amd64 maintained by: yuri@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 1487 Jan 31 2025 /usr/ports/science/plumed/Makefile Ports top last git commit: 62d8b1999233 Ports top unclean checkout: no Port dir last git commit: fc4dbd235dee Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500068 Jail OSVERSION: 1305000 Job Id: 13 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1305000 UNAME_v=FreeBSD 13.5-RELEASE-p7 1305000 UNAME_r=13.5-RELEASE-p7 BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin MAKE_OBJDIR_CHECK_WRITABLE=0 LOCALBASE=/usr/local USER=root POUDRIERE_NAME=poudriere-git LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.4.2 MASTERMNT=/usr/local/poudriere/data/.m/freebsd_13_5_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_13_5_x64-HEAD-ALL/13/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=freebsd_13_5_x64-HEAD-ALL SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/freebsd_13_5_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=13.5 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 --End resource limits-- =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> plumed-2.9.3_1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.4.2_1.pkg [pkg.DaveG.ca] Installing pkg-2.4.2_1... [pkg.DaveG.ca] Extracting pkg-2.4.2_1: .......... done ===> plumed-2.9.3_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of plumed-2.9.3_1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by plumed-2.9.3_1 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by plumed-2.9.3_1 for building => SHA256 Checksum OK for plumed-2.9.3.tgz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by plumed-2.9.3_1 for building ===> Extracting for plumed-2.9.3_1 => SHA256 Checksum OK for plumed-2.9.3.tgz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Patching for plumed-2.9.3_1 ===> Applying FreeBSD patches for plumed-2.9.3_1 from /usr/ports/science/plumed/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> plumed-2.9.3_1 depends on executable: bash - not found ===> Installing existing package /packages/All/bash-5.3.8_1.pkg [pkg.DaveG.ca] Installing bash-5.3.8_1... [pkg.DaveG.ca] `-- Installing gettext-runtime-0.23.1... [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-0.23.1: .......... done [pkg.DaveG.ca] Extracting bash-5.3.8_1: .......... done ===> plumed-2.9.3_1 depends on executable: bash - found ===> Returning to build of plumed-2.9.3_1 ===> plumed-2.9.3_1 depends on package: gmake>=4.4.1 - not found ===> Installing existing package /packages/All/gmake-4.4.1.pkg [pkg.DaveG.ca] Installing gmake-4.4.1... [pkg.DaveG.ca] Extracting gmake-4.4.1: .......... done ===> plumed-2.9.3_1 depends on package: gmake>=4.4.1 - found ===> Returning to build of plumed-2.9.3_1 ===> plumed-2.9.3_1 depends on package: pkgconf>=1.3.0_1 - not found ===> Installing existing package /packages/All/pkgconf-2.4.3,1.pkg [pkg.DaveG.ca] Installing pkgconf-2.4.3,1... [pkg.DaveG.ca] Extracting pkgconf-2.4.3,1: .......... done ===> plumed-2.9.3_1 depends on package: pkgconf>=1.3.0_1 - found ===> Returning to build of plumed-2.9.3_1 ===> plumed-2.9.3_1 depends on package: autoconf>=2.72 - not found ===> Installing existing package /packages/All/autoconf-2.72.pkg [pkg.DaveG.ca] Installing autoconf-2.72... [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: .......... done ===> plumed-2.9.3_1 depends on package: autoconf>=2.72 - found ===> Returning to build of plumed-2.9.3_1 ===> plumed-2.9.3_1 depends on package: automake>=1.17 - not found ===> Installing existing package /packages/All/automake-1.17.pkg [pkg.DaveG.ca] Installing automake-1.17... [pkg.DaveG.ca] Extracting automake-1.17: .......... done ===> plumed-2.9.3_1 depends on package: automake>=1.17 - found ===> Returning to build of plumed-2.9.3_1 ===> plumed-2.9.3_1 depends on file: /usr/local/bin/ccache - not found ===> Installing existing package /packages/All/ccache-3.7.12_8.pkg [pkg.DaveG.ca] Installing ccache-3.7.12_8... [pkg.DaveG.ca] Extracting ccache-3.7.12_8: ......... done Create compiler links... create symlink for cc create symlink for cc (world) create symlink for c++ create symlink for c++ (world) create symlink for CC create symlink for CC (world) create symlink for clang create symlink for clang (world) create symlink for clang++ create symlink for clang++ (world) ===== Message from ccache-3.7.12_8: -- NOTE: Please read /usr/local/share/doc/ccache/ccache-howto-freebsd.txt for information on using ccache with FreeBSD ports and src. ===> plumed-2.9.3_1 depends on file: /usr/local/bin/ccache - found ===> Returning to build of plumed-2.9.3_1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> plumed-2.9.3_1 depends on shared library: libblas.so - not found ===> Installing existing package /packages/All/blas-3.12.1.pkg [pkg.DaveG.ca] Installing blas-3.12.1... [pkg.DaveG.ca] `-- Installing gcc13-13.3.0_3... [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 gcc13-13.3.0_3: .......... done create symlink for gcc13 create symlink for gcc13 (world) create symlink for g++13 create symlink for g++13 (world) create symlink for cpp13 create symlink for cpp13 (world) [pkg.DaveG.ca] Extracting blas-3.12.1: ..... done ===== Message from gcc13-13.3.0_3: -- 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/gcc13 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. ===> plumed-2.9.3_1 depends on shared library: libblas.so - found (/usr/local/lib/libblas.so) ===> Returning to build of plumed-2.9.3_1 ===> plumed-2.9.3_1 depends on shared library: libfftw3.so - not found ===> Installing existing package /packages/All/fftw3-3.3.10_5.pkg [pkg.DaveG.ca] Installing fftw3-3.3.10_5... [pkg.DaveG.ca] Extracting fftw3-3.3.10_5: .......... done ===> plumed-2.9.3_1 depends on shared library: libfftw3.so - found (/usr/local/lib/libfftw3.so) ===> Returning to build of plumed-2.9.3_1 ===> plumed-2.9.3_1 depends on shared library: libgsl.so - not found ===> Installing existing package /packages/All/gsl-2.7.1_1.pkg [pkg.DaveG.ca] Installing gsl-2.7.1_1... [pkg.DaveG.ca] Extracting gsl-2.7.1_1: .......... done ===> plumed-2.9.3_1 depends on shared library: libgsl.so - found (/usr/local/lib/libgsl.so) ===> Returning to build of plumed-2.9.3_1 ===> plumed-2.9.3_1 depends on shared library: liblapack.so - not found ===> Installing existing package /packages/All/lapack-3.12.1.pkg [pkg.DaveG.ca] Installing lapack-3.12.1... [pkg.DaveG.ca] Extracting lapack-3.12.1: .......... done ===> plumed-2.9.3_1 depends on shared library: liblapack.so - found (/usr/local/lib/liblapack.so) ===> Returning to build of plumed-2.9.3_1 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for plumed-2.9.3_1 configure: loading site script /usr/ports/Templates/config.site configure: Optional modules are disabled by default checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C++... yes checking whether c++ accepts -g... yes checking for c++ option to enable C++11 features... none needed checking whether the compiler supports GNU C... yes checking whether cc accepts -g... yes checking for cc option to enable C11 features... none needed checking for gfortran... no checking for g95... no checking for xlf95... no checking for f95... no checking for fort... no checking for ifort... no checking for ifc... no checking for efc... no checking for pgfortran... no checking for pgf95... no checking for lf95... no checking for ftn... no checking for nagfor... no checking for xlf90... no checking for f90... no checking for pgf90... no checking for pghpf... no checking for epcf90... no checking for g77... no checking for xlf... no checking for f77... no checking for frt... no checking for pgf77... no checking for cf77... no checking for fort77... no checking for fl32... no checking for af77... no checking whether the compiler supports GNU Fortran... no checking whether accepts -g... no configure: Initial CXX: c++ configure: Initial CXXFLAGS: -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include configure: Initial CPPFLAGS: -isystem /usr/local/include configure: Initial CFLAGS: -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing configure: Initial LDFLAGS: configure: Initial LIBS: -L/usr/local/lib configure: Initial STATIC_LIBS: configure: Initial LD: configure: Initial LDSHARED: c++ configure: Initial SOEXT: checking whether c++ accepts -fPIC... yes checking whether cc accepts -fPIC... yes checking whether c++ accepts -Wall... yes checking whether c++ accepts -pedantic... yes checking whether c++ accepts -std=c++11... yes checking whether c++ declares c++11 support... yes checking whether C++ library supports C++11 exceptions... yes checking whether c++ can generate dependency file with -MM -MF... yes configure: dependency tracking enabled configure: Now we will check compulsory headers and libraries checking for stdio.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for inttypes.h... (cached) yes checking for stdint.h... (cached) yes checking for strings.h... (cached) yes checking for sys/stat.h... (cached) yes checking for sys/types.h... (cached) yes checking for unistd.h... (cached) yes checking for dirent.h... (cached) yes checking for readdir... (cached) yes checking whether dgemv_ can be linked with no library... no checking whether dgemv_ can be linked with no library... no checking for library containing dgemv_... -lblas checking for library containing dsyevr_... -llapack checking whether sdot returns float... yes configure: Now we will check for optional headers and libraries checking for libmolfile_plugin.h... no configure: WARNING: cannot enable __PLUMED_HAS_EXTERNAL_MOLFILE_PLUGINS configure: WARNING: using internal molfile_plugins, which only support dcd/xtc/trr/trj/crd files checking for dlopen in -ldl... yes checking for mpi.h... no configure: WARNING: cannot enable __PLUMED_HAS_MPI checking for c++ option to support OpenMP... -fopenmp checking whether architecture is X86/X64... yes configure: Enabling embedded asmjit checking for regex.h... yes checking for library containing regcomp... none required checking for dlfcn.h... (cached) yes checking for library containing dlopen... none required checking RTLD_DEFAULT without extra libs... yes checking for unistd.h... (cached) yes checking for library containing chdir... none required checking subprocess without extra libs... yes checking for unistd.h... (cached) yes checking for library containing getcwd... none required checking for cstdio... yes checking for library containing popen... none required checking for execinfo.h... yes checking for library containing backtrace... no configure: WARNING: cannot enable __PLUMED_HAS_EXECINFO checking for zlib.h... (cached) yes checking for library containing gzopen... -lz checking for library containing cblas_dgemv... -lgslcblas checking for gsl/gsl_vector.h... yes checking for library containing gsl_vector_alloc... -lgsl checking for fftw3.h... yes checking for library containing fftw_execute... -lfftw3 configure: Release mode, adding -DNDEBUG configure: *** Special settings for dynamic libraries on Linux *** configure: Dynamic library extension is 'so' configure: LDSHARED and LDFLAGS need special flags checking whether LDFLAGS can contain -rdynamic... yes checking whether LDFLAGS can contain -Wl,-Bsymbolic... yes configure: Using LDSHARED='c++ -shared' configure: Using LDFLAGS=' -rdynamic -Wl,-Bsymbolic' checking whether LDSHARED can create dynamic libraries... yes checking for doxygen... no configure: Manuals will not be generated configure: A PDF version of the manual will not be generated checking whether a program can be run on this machine... yes configure: PLUMED seems to be configured properly! configure: ************************** checking whether C++ objects can be grouped with /usr/bin/ld -r -o... yes checking whether static libraries can be created with /usr/bin/ar cr... yes checking whether static-object constructors can be linked from a static archive... yes configure: I will now check if C++ objects can be linked by C/Fortran compilers configure: This is relevant if you want to use plumed patch --static on a non-C++ code checking whether C can link a C++ object... no checking whether C can link a C++ object with library -lstdc++... yes configure: FC compiler not configured checking for pkg-config... /usr/local/bin/pkg-config configure: bash-completion is not installed or it is installed on a different prefix configure: bash completion for plumed will not be installed configure: **** PLUMED will be installed using the following paths: configure: **** prefix: /usr/local configure: **** exec_prefix: ${prefix} configure: **** bindir: ${exec_prefix}/bin configure: **** libdir: ${exec_prefix}/lib configure: **** includedir: ${prefix}/include configure: **** datarootdir: ${prefix}/share configure: **** datadir: ${datarootdir} configure: **** docdir: ${prefix}/share/doc/plumed configure: **** htmldir: ${docdir} configure: **** Executable will be named plumed configure: **** As of PLUMED 2.5, you cannot change paths anymore during "make install" configure: **** Please configure and make clean to change the prefix configure: WARNING: **** Bash completion for plumed will not be installed, please add the following two lines to your bashrc configure: WARNING: **** _plumed() { eval "$(plumed --no-mpi completion 2>/dev/null)";} configure: WARNING: **** complete -F _plumed -o default plumed configure: WARNING: **** PLUMED will NOT be compiled using MPI because MPI have not been found! configure: creating ./config.status config.status: creating Makefile.conf config.status: creating sourceme.sh config.status: creating stamp-h =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for plumed-2.9.3_1 /usr/local/bin/gmake lib gmake[1]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3' /usr/local/bin/gmake -C src gmake[2]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src' /usr/local/bin/gmake -C lib gmake[3]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' /usr/local/bin/gmake dirslinks gmake[4]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' *** Updating links to used modules in all directories *** /usr/local/bin/gmake ../analysis.links ../asmjit.links ../bias.links ../blas.links ../cltools.links ../colvar.links ../config.links ../core.links ../function.links ../generic.links ../gridtools.links ../isdb.links ../lapack.links ../lepton.links ../main.links ../mapping.links ../molfile.links ../multicolvar.links ../reference.links ../secondarystructure.links ../setup.links ../tools.links ../vatom.links ../vesselbase.links ../wrapper.links ../xdrfile.links gmake[5]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' /usr/local/bin/gmake -C ../analysis links gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/analysis' /usr/local/bin/gmake -C ../asmjit links /usr/local/bin/gmake -C ../bias links /usr/local/bin/gmake -C ../blas links Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/analysis /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/bias' gmake[6]: 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/bias Verify modules and create links in /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/asmjit' 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/asmjit /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/config' gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/cltools' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/cltools 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/asmjit' gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/config' /usr/local/bin/gmake -C ../function links /usr/local/bin/gmake -C ../generic links gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/function' /usr/local/bin/gmake -C ../gridtools links Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/function /usr/local/bin/gmake -C ../isdb links /usr/local/bin/gmake -C ../lapack links gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/core' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/core 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/generic' Verify modules and create links in /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/gridtools' /usr/local/bin/gmake -C ../lepton links /usr/local/bin/gmake -C ../main 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/gridtools Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lapack gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/main' /usr/local/bin/gmake -C ../mapping links /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/lepton' /usr/local/bin/gmake -C ../multicolvar links 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/lepton gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/molfile' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/molfile gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/mapping' /usr/local/bin/gmake -C ../reference links gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/molfile' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/mapping gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/main' /usr/local/bin/gmake -C ../secondarystructure links /usr/local/bin/gmake -C ../setup links gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/secondarystructure' /usr/local/bin/gmake -C ../tools links /usr/local/bin/gmake -C ../vatom links 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/secondarystructure 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/setup /usr/local/bin/gmake -C ../vesselbase links gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/vatom' gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/reference' /usr/local/bin/gmake -C ../wrapper links /usr/local/bin/gmake -C ../xdrfile links 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/lepton' 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/wrapper' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/vatom gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lapack' 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' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/vesselbase gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/tools' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/tools gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/bias' gmake[6]: 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[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/xdrfile' 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/core' 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/gridtools' 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/colvar' gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/generic' gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/tools' gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/vesselbase' gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/function' 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/multicolvar' 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/isdb' gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/mapping' gmake[5]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' gmake[4]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' /usr/local/bin/gmake dirs gmake[4]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' *** Compiling all directories *** /usr/local/bin/gmake ../analysis ../asmjit ../bias ../blas ../cltools ../colvar ../config ../core ../function ../generic ../gridtools ../isdb ../lapack ../lepton ../main ../mapping ../molfile ../multicolvar ../reference ../secondarystructure ../setup ../tools ../vatom ../vesselbase ../wrapper ../xdrfile gmake[5]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' /usr/local/bin/gmake -C ../analysis obj /usr/local/bin/gmake -C ../asmjit obj /usr/local/bin/gmake -C ../bias obj /usr/local/bin/gmake -C ../blas obj /usr/local/bin/gmake -C ../cltools obj /usr/local/bin/gmake -C ../colvar obj gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/blas' /usr/local/bin/gmake -C ../config obj /usr/local/bin/gmake -C ../core obj /usr/local/bin/gmake -C ../function obj compiling blas.cpp gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/bias' /usr/local/bin/gmake -C ../generic 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 Bias.cpp compiling ABMD.cpp compiling BiasValue.cpp /usr/local/bin/gmake -C ../gridtools obj gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/config' gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/cltools' Updating ConfigInstall.inc gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/analysis' Updating Config.inc compiling AnalysisBase.cpp compiling Average.cpp compiling AverageVessel.cpp gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/function' compiling ExtendedLagrangian.cpp gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/asmjit' compiling Combine.cpp compiling External.cpp compiling Custom.cpp compiling Ensemble.cpp compiling arch.cpp Updating config.txt file gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/colvar' compiling Angle.cpp compiling Cell.cpp gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/gridtools' gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/generic' gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/core' Updating version.h compiling Action.cpp /usr/local/bin/gmake -C ../isdb obj compiling ActionWithGrid.cpp compiling Debug.cpp compiling DumpAtoms.cpp cmp -s ConfigInstall.inc~ ConfigInstall.inc || cp ConfigInstall.inc~ ConfigInstall.inc compiling ActionWithInputGrid.cpp compiling Colvar.cpp /usr/local/bin/gmake -C ../lapack obj gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lapack' compiling ActionAtomistic.cpp compiling lapack.cpp compiling LWalls.cpp gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/isdb' compiling FuncPathGeneral.cpp /usr/local/bin/gmake -C ../lepton obj /usr/local/bin/gmake -C ../main obj compiling FuncPathMSD.cpp 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' /usr/local/bin/gmake -C ../mapping obj /usr/local/bin/gmake -C ../molfile obj compiling CompiledExpression.cpp compiling ExpressionProgram.cpp rm ConfigInstall.inc~ cmp -s Config.inc~ Config.inc || cp Config.inc~ Config.inc gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/mapping' /usr/local/bin/gmake -C ../multicolvar obj { ../maketools/make-scripts-options.sh ; cat completion.sh ; }| ../maketools/xxd > completion.xxd gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/molfile' compiling AdaptivePath.cpp rm Config.inc~ compiling CLTool.cpp /usr/local/bin/gmake -C ../reference obj /usr/local/bin/gmake -C ../secondarystructure obj gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/secondarystructure' /usr/local/bin/gmake -C ../setup obj compiling main.cpp compiling Operation.cpp compiling ParsedExpression.cpp compiling AlphaRMSD.cpp gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/reference' compiling CS2Backbone.cpp compiling Committor.cpp gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/setup' compiling Driver.cpp compiling ActionAnyorder.cpp compiling assembler.cpp compiling Load.cpp compiling Restart.cpp compiling ActionPilot.cpp /usr/local/bin/gmake -C ../tools obj compiling ActionRegister.cpp compiling ActionWithIntegral.cpp compiling DumpDerivatives.cpp compiling crdplugin.cpp compiling ArgumentOnlyDistance.cpp compiling AverageOnGrid.cpp compiling Mapping.cpp compiling ActionSet.cpp /usr/local/bin/gmake -C ../vatom obj compiling ExpressionTreeNode.cpp compiling gromacsplugin.cpp gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/vatom' gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/tools' compiling ActionWithVirtualAtom.cpp compiling Angle.cpp compiling Units.cpp compiling dcdplugin.cpp compiling PCAVars.cpp compiling ActionSetup.cpp gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/multicolvar' compiling Caliber.cpp compiling MaxEnt.cpp compiling ActionVolume.cpp gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/blas' gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lapack' /usr/local/bin/gmake -C ../vesselbase obj compiling codebuilder.cpp gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/vesselbase' compiling ActionWithAveraging.cpp compiling AntibetaRMSD.cpp compiling DriverDouble.cpp compiling pdbplugin.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. 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 DataCollectionObject.cpp compiling codecompiler.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/main' /usr/local/bin/gmake -C ../wrapper obj compiling DriverFloat.cpp gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/wrapper' compiling PlumedStatic.cpp compiling AtomNumber.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 codeemitter.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. gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/molfile' /usr/local/bin/gmake -C ../xdrfile obj compiling GenExample.cpp gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/xdrfile' compiling xdrfile.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. compiling MetaD.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 ContourFindingBase.cpp compiling codeholder.cpp compiling ActionShortcut.cpp compiling Path.cpp compiling EuclideanDissimilarityMatrix.cpp compiling DumpForces.cpp compiling FarthestPointSampling.cpp compiling FuncSumHills.cpp compiling Plumed.c ParsedExpression.cpp:82:19: warning: reference cannot be bound to dereferenced null pointer in well-defined C++ code; comparison may be assumed to always evaluate to false [-Wtautological-undefined-compare] 82 | if (&rootNode.getOperation() == NULL) | ~~~~~~~~~^~~~~~~~~~~~~~ ~~~~ ./ExpressionTreeNode.h:129:22: note: 'getOperation' returns a reference 129 | const Operation& getOperation() const; | ^ 1 warning generated. compiling Function.cpp compiling Constant.cpp compiling MovingRestraint.cpp compiling Center.cpp compiling ConvertToFES.cpp In file included from Driver.cpp:41: In file included from ./xdrfile/xdrfile_trr.h:1: ./xdrfile/../../xdrfile/xdrfile_trr.h:32:2: warning: '/*' within block comment [-Wcomment] 32 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- | ^ In file included from Driver.cpp:41: In file included from ./xdrfile/xdrfile_trr.h:1: In file included from ./xdrfile/../../xdrfile/xdrfile_trr.h:64: ./xdrfile/../../xdrfile/xdrfile.h:32:2: warning: '/*' within block comment [-Wcomment] 32 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- | ^ In file included from Driver.cpp:42: In file included from ./xdrfile/xdrfile_xtc.h:1: ./xdrfile/../../xdrfile/xdrfile_xtc.h:32:2: warning: '/*' within block comment [-Wcomment] 32 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- | ^ Driver.cpp:184:12: warning: function 'register_cb' is not needed and will not be emitted [-Wunneeded-internal-declaration] 184 | static int register_cb(void *v, vmdplugin_t *p) { | ^~~~~~~~~~~ 4 warnings generated. compiling GenJson.cpp gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/setup' compiling ActionWithArguments.cpp compiling DumpMassCharge.cpp compiling BiasRepresentation.cpp compiling ContactMap.cpp compiling xdrfile_trr.cpp compiling Restraint.cpp compiling PBMetaD.cpp compiling Coordination.cpp compiling LocalEnsemble.cpp compiling DumpCube.cpp compiling DRMSD.cpp compiling ParabetaRMSD.cpp compiling Histogram.cpp compiling SecondaryStructureRMSD.cpp compiling DumpGrid.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 ActionWithValue.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 Piecewise.cpp compiling constpool.cpp compiling ReweightBias.cpp compiling ReweightBase.cpp compiling CoordinationBase.cpp compiling LandmarkSelectionBase.cpp compiling ActionWithVirtualAtom.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 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 Sort.cpp gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/wrapper' compiling cpuinfo.cpp compiling GenTemplate.cpp compiling AlphaBeta.cpp gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/config' /usr/local/bin/gmake Config.o ConfigInstall.o compile_options.sh 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. gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/config' cat ../../Makefile.conf | ../maketools/xxd > Makefile.conf.xxd compiling Atoms.cpp compiling EMMI.cpp compiling func.cpp compiling Brent1DRootSearch.cpp compiling PathReparameterization.cpp compiling PathBase.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 Info.cpp compiling PathTools.cpp compiling FindContour.cpp Building compile_options.sh, a sourceable bash script with some compilation options compiling ReweightMetad.cpp compiling Config.cpp compiling LandmarkStaged.cpp compiling globals.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 Angles.cpp compiling CLTool.cpp compiling ReweightTemperaturePressure.cpp compiling Stats.cpp compiling ActionWithInputVessel.cpp In file included from CompiledExpression.cpp:68: In file included from ./asmjit/asmjit.h:1: In file included from ./asmjit/../../asmjit/asmjit.h:55: In file included from ./asmjit/../../asmjit/./base.h:33: In file included from ./asmjit/../../asmjit/././arch.h:37: ./asmjit/../../asmjit/./././operand.h:341:12: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 341 | return (_packed[0] == other._packed[0]) & | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && 342 | (_packed[1] == other._packed[1]) ; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./asmjit/../../asmjit/./././operand.h:341:12: note: cast one or both operands to int to silence this warning ./asmjit/../../asmjit/./././operand.h:808:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 808 | static ASMJIT_INLINE bool isGp(const Operand_& op, uint32_t rId) noexcept { return isGp(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ./asmjit/../../asmjit/./././operand.h:808:86: note: cast one or both operands to int to silence this warning ./asmjit/../../asmjit/./././operand.h:809:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 809 | static ASMJIT_INLINE bool isVec(const Operand_& op, uint32_t rId) noexcept { return isVec(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ./asmjit/../../asmjit/./././operand.h:809:87: note: cast one or both operands to int to silence this warning In file included from CompiledExpression.cpp:68: In file included from ./asmjit/asmjit.h:1: In file included from ./asmjit/../../asmjit/asmjit.h:59: In file included from ./asmjit/../../asmjit/./x86.h:35: In file included from ./asmjit/../../asmjit/././x86assembler.h:38: In file included from ./asmjit/../../asmjit/./././x86emitter.h:38: ./asmjit/../../asmjit/././././x86operand.h:379:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 379 | static ASMJIT_INLINE bool isGpb(const Operand_& op, uint32_t rId) noexcept { return isGpb(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ./asmjit/../../asmjit/././././x86operand.h:379:87: note: cast one or both operands to int to silence this warning ./asmjit/../../asmjit/././././x86operand.h:381:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 381 | static ASMJIT_INLINE bool isRip(const Operand_& op, uint32_t rId) noexcept { return isRip(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ./asmjit/../../asmjit/././././x86operand.h:381:87: note: cast one or both operands to int to silence this warning ./asmjit/../../asmjit/././././x86operand.h:382:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 382 | static ASMJIT_INLINE bool isSeg(const Operand_& op, uint32_t rId) noexcept { return isSeg(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ./asmjit/../../asmjit/././././x86operand.h:382:87: note: cast one or both operands to int to silence this warning ./asmjit/../../asmjit/././././x86operand.h:383:89: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 383 | static ASMJIT_INLINE bool isGpbLo(const Operand_& op, uint32_t rId) noexcept { return isGpbLo(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ./asmjit/../../asmjit/././././x86operand.h:383:89: note: cast one or both operands to int to silence this warning ./asmjit/../../asmjit/././././x86operand.h:384:89: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 384 | static ASMJIT_INLINE bool isGpbHi(const Operand_& op, uint32_t rId) noexcept { return isGpbHi(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ./asmjit/../../asmjit/././././x86operand.h:384:89: note: cast one or both operands to int to silence this warning ./asmjit/../../asmjit/././././x86operand.h:385:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 385 | static ASMJIT_INLINE bool isGpw(const Operand_& op, uint32_t rId) noexcept { return isGpw(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ./asmjit/../../asmjit/././././x86operand.h:385:87: note: cast one or both operands to int to silence this warning ./asmjit/../../asmjit/././././x86operand.h:386:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 386 | static ASMJIT_INLINE bool isGpd(const Operand_& op, uint32_t rId) noexcept { return isGpd(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ./asmjit/../../asmjit/././././x86operand.h:386:87: note: cast one or both operands to int to silence this warning ./asmjit/../../asmjit/././././x86operand.h:387:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 387 | static ASMJIT_INLINE bool isGpq(const Operand_& op, uint32_t rId) noexcept { return isGpq(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ./asmjit/../../asmjit/././././x86operand.h:387:87: note: cast one or both operands to int to silence this warning ./asmjit/../../asmjit/././././x86operand.h:388:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 388 | static ASMJIT_INLINE bool isFp(const Operand_& op, uint32_t rId) noexcept { return isFp(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ./asmjit/../../asmjit/././././x86operand.h:388:86: note: cast one or both operands to int to silence this warning ./asmjit/../../asmjit/././././x86operand.h:389:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 389 | static ASMJIT_INLINE bool isMm(const Operand_& op, uint32_t rId) noexcept { return isMm(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ./asmjit/../../asmjit/././././x86operand.h:389:86: note: cast one or both operands to int to silence this warning ./asmjit/../../asmjit/././././x86operand.h:390:85: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 390 | static ASMJIT_INLINE bool isK(const Operand_& op, uint32_t rId) noexcept { return isK(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ./asmjit/../../asmjit/././././x86operand.h:390:85: note: cast one or both operands to int to silence this warning ./asmjit/../../asmjit/././././x86operand.h:391:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 391 | static ASMJIT_INLINE bool isXmm(const Operand_& op, uint32_t rId) noexcept { return isXmm(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ./asmjit/../../asmjit/././././x86operand.h:391:87: note: cast one or both operands to int to silence this warning ./asmjit/../../asmjit/././././x86operand.h:392:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 392 | static ASMJIT_INLINE bool isYmm(const Operand_& op, uint32_t rId) noexcept { return isYmm(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ./asmjit/../../asmjit/././././x86operand.h:392:87: note: cast one or both operands to int to silence this warning ./asmjit/../../asmjit/././././x86operand.h:393:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 393 | static ASMJIT_INLINE bool isZmm(const Operand_& op, uint32_t rId) noexcept { return isZmm(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ./asmjit/../../asmjit/././././x86operand.h:393:87: note: cast one or both operands to int to silence this warning ./asmjit/../../asmjit/././././x86operand.h:394:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 394 | static ASMJIT_INLINE bool isBnd(const Operand_& op, uint32_t rId) noexcept { return isBnd(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ./asmjit/../../asmjit/././././x86operand.h:394:87: note: cast one or both operands to int to silence this warning ./asmjit/../../asmjit/././././x86operand.h:395:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 395 | static ASMJIT_INLINE bool isCr(const Operand_& op, uint32_t rId) noexcept { return isCr(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ./asmjit/../../asmjit/././././x86operand.h:395:86: note: cast one or both operands to int to silence this warning ./asmjit/../../asmjit/././././x86operand.h:396:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 396 | static ASMJIT_INLINE bool isDr(const Operand_& op, uint32_t rId) noexcept { return isDr(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ./asmjit/../../asmjit/././././x86operand.h:396:86: note: cast one or both operands to int to silence this warning 20 warnings generated. compiling FindContourSurface.cpp compiling PropertyMap.cpp compiling EffectiveEnergyDrift.cpp compiling DumpProjections.cpp compiling SpathVessel.cpp gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lepton' compiling DHEnergy.cpp compiling Target.cpp ../maketools/makecmd map < CLToolMain.cpp > CLToolMainMap.inc ../maketools/makecmd enum < CLToolMain.cpp > CLToolMainEnum.inc compiling ReweightWham.cpp In file included from cpuinfo.cpp:33: In file included from ././cpuinfo.h:36: In file included from ./././arch.h:37: ././././operand.h:341:12: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 341 | return (_packed[0] == other._packed[0]) & | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && 342 | (_packed[1] == other._packed[1]) ; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ././././operand.h:341:12: note: cast one or both operands to int to silence this warning ././././operand.h:808:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 808 | static ASMJIT_INLINE bool isGp(const Operand_& op, uint32_t rId) noexcept { return isGp(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././operand.h:808:86: note: cast one or both operands to int to silence this warning ././././operand.h:809:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 809 | static ASMJIT_INLINE bool isVec(const Operand_& op, uint32_t rId) noexcept { return isVec(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././operand.h:809:87: note: cast one or both operands to int to silence this warning 3 warnings generated. compiling inst.cpp compiling CLToolRegister.cpp compiling UWalls.cpp compiling DRMSD.cpp compiling Dimer.cpp compiling OutputColvarFile.cpp compiling Colvar.cpp compiling OutputPDBFile.cpp compiling FindSphericalContour.cpp compiling Citations.cpp compiling Direction.cpp compiling logging.cpp compiling EndPlumed.cpp compiling FourierTransform.cpp compiling FixedAtom.cpp compiling Manual.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 operand.cpp compiling Dipole.cpp compiling PdbRenumber.cpp compiling ConfigInstall.cpp compiling FretEfficiency.cpp compiling Communicator.cpp compiling Distance.cpp compiling DataFetchingObject.cpp compiling Jcoupling.cpp compiling osutils.cpp compiling ExchangePatterns.cpp compiling GridPrintingBase.cpp compiling PrintDissimilarityMatrix.cpp compiling GridSearch.cpp compiling FitToTemplate.cpp compiling SimpleMD.cpp GenExample.cpp:248:20: warning: variable 'n' set but not used [-Wunused-but-set-variable] 248 | for(unsigned n=0;; ++n) { | ^ 1 warning generated. compiling SumHills.cpp compiling FlexibleBin.cpp compiling TrigonometricPathVessel.cpp compiling AtomValuePack.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 regalloc.cpp compiling ConjugateGradient.cpp CS2Backbone.cpp:214:14: warning: variable 'nline' set but not used [-Wunused-but-set-variable] 214 | unsigned nline = 0; | ^ 1 warning generated. compiling ZpathVessel.cpp compiling runtime.cpp compiling Metainference.cpp ../maketools/makecmd map < GREX.cpp > GREXMap.inc compiling ReadAnalysisFrames.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 EEFSolv.cpp gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/secondarystructure' 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 kT.cpp compiling ReadDissimilarityMatrix.cpp ../maketools/makecmd enum < GREX.cpp > GREXEnum.inc compiling Flush.cpp compiling GenericMolInfo.cpp compiling Bridge.cpp compiling ActionWithVessel.cpp compiling GridToXYZ.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 string.cpp compiling DLLoader.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 utils.cpp compiling ERMSD.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 vmem.cpp compiling pesmd.cpp compiling MetainferenceBase.cpp compiling MDAtoms.cpp compiling Group.cpp compiling DotProductDistance.cpp compiling BridgedMultiColvarFunction.cpp compiling DynamicList.cpp In file included from regalloc.cpp:37: In file included from ././regalloc_p.h:39: In file included from ./././codecompiler.h:39: In file included from ././././assembler.h:36: In file included from ./././././codeemitter.h:36: In file included from ././././././arch.h:37: ./././././././operand.h:341:12: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 341 | return (_packed[0] == other._packed[0]) & | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && 342 | (_packed[1] == other._packed[1]) ; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./././././././operand.h:341:12: note: cast one or both operands to int to silence this warning ./././././././operand.h:808:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 808 | static ASMJIT_INLINE bool isGp(const Operand_& op, uint32_t rId) noexcept { return isGp(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ./././././././operand.h:808:86: note: cast one or both operands to int to silence this warning ./././././././operand.h:809:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 809 | static ASMJIT_INLINE bool isVec(const Operand_& op, uint32_t rId) noexcept { return isVec(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ./././././././operand.h:809:87: note: cast one or both operands to int to silence this warning 3 warnings generated. compiling Completion.cpp In file included from operand.cpp:33: ././operand.h:341:12: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 341 | return (_packed[0] == other._packed[0]) & | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && 342 | (_packed[1] == other._packed[1]) ; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ././operand.h:341:12: note: cast one or both operands to int to silence this warning ././operand.h:808:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 808 | static ASMJIT_INLINE bool isGp(const Operand_& op, uint32_t rId) noexcept { return isGp(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././operand.h:808:86: note: cast one or both operands to int to silence this warning ././operand.h:809:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 809 | static ASMJIT_INLINE bool isVec(const Operand_& op, uint32_t rId) noexcept { return isVec(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././operand.h:809:87: note: cast one or both operands to int to silence this warning 3 warnings generated. compiling EuclideanDistance.cpp compiling Energy.cpp ../maketools/makeModuleMap ModuleMap.inc compiling x86assembler.cpp compiling x86builder.cpp compiling FakeFrame.cpp compiling Include.cpp gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/function' compiling MolInfo.cpp compiling Plumed.cpp compiling GridVessel.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 x86compiler.cpp compiling HistogramOnGrid.cpp ../maketools/makecmd map < PlumedMain.cpp > PlumedMainMap.inc compiling ExtraCV.cpp ../maketools/makecmd enum < PlumedMain.cpp > PlumedMainEnum.inc compiling Fake.cpp compiling IntegrateGrid.cpp compiling TargetDist.cpp compiling PlumedMainInitializer.cpp compiling ReselectLandmarks.cpp compiling ERMSD.cpp compiling x86inst.cpp compiling x86instimpl.cpp compiling InterpolateGrid.cpp compiling Exception.cpp compiling Ghost.cpp compiling NOE.cpp vmem.cpp:284:13: warning: unused function 'vMemMgrCheckTree' [-Wunused-function] 284 | static bool vMemMgrCheckTree(VMemMgr* self) noexcept { | ^~~~~~~~~~~~~~~~ 1 warning generated. compiling CatomPack.cpp compiling x86internal.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 GHBFIX.cpp compiling Value.cpp compiling WithCmd.cpp compiling SelectRandomFrames.cpp compiling Gyration.cpp compiling PRE.cpp compiling FileBase.cpp compiling AltMin.cpp compiling SelectWithStride.cpp compiling CenterOfMultiColvar.cpp compiling Print.cpp compiling CoordinationNumbers.cpp compiling RandomExchanges.cpp compiling MultiRMSD.cpp compiling RDC.cpp compiling Read.cpp compiling IntermolecularDRMSD.cpp compiling IntramolecularDRMSD.cpp compiling ForwardDecl.cpp compiling CLToolMain.cpp compiling MahalanobisDistance.cpp gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/mapping' compiling Density.cpp compiling ResetCell.cpp compiling Time.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 WhamHistogram.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 Rescale.cpp compiling PCARMSD.cpp compiling WhamWeights.cpp compiling x86operand.cpp compiling Grid.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 UpdateIf.cpp compiling x86operand_regs.cpp compiling GREX.cpp compiling AveragingVessel.cpp compiling PathMSD.cpp compiling DihedralCorrelation.cpp compiling PlumedMain.cpp gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/bias' compiling DistanceFromContour.cpp compiling WholeMolecules.cpp gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/cltools' compiling PathMSDBase.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 x86regalloc.cpp compiling Between.cpp compiling Position.cpp compiling MetricRegister.cpp compiling HistogramBead.cpp compiling ProjectionOnAxis.cpp compiling zone.cpp compiling Distances.cpp compiling MultiDomainRMSD.cpp compiling IFile.cpp compiling PropertyMap.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 Keywords.cpp compiling KernelFunctions.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. gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/vatom' compiling WrapAround.cpp compiling BridgeVessel.cpp compiling FunctionVessel.cpp compiling DumpMultiColvar.cpp In file included from x86logging.cpp:38: In file included from ././x86inst.h:36: In file included from ./././assembler.h:36: In file included from ././././codeemitter.h:36: In file included from ./././././arch.h:37: ././././././operand.h:341:12: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 341 | return (_packed[0] == other._packed[0]) & | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && 342 | (_packed[1] == other._packed[1]) ; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ././././././operand.h:341:12: note: cast one or both operands to int to silence this warning ././././././operand.h:808:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 808 | static ASMJIT_INLINE bool isGp(const Operand_& op, uint32_t rId) noexcept { return isGp(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././././operand.h:808:86: note: cast one or both operands to int to silence this warning ././././././operand.h:809:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 809 | static ASMJIT_INLINE bool isVec(const Operand_& op, uint32_t rId) noexcept { return isVec(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././././././operand.h:809:87: note: cast one or both operands to int to silence this warning In file included from x86logging.cpp:40: ././x86operand.h:379:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 379 | static ASMJIT_INLINE bool isGpb(const Operand_& op, uint32_t rId) noexcept { return isGpb(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:379:87: note: cast one or both operands to int to silence this warning ././x86operand.h:381:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 381 | static ASMJIT_INLINE bool isRip(const Operand_& op, uint32_t rId) noexcept { return isRip(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:381:87: note: cast one or both operands to int to silence this warning ././x86operand.h:382:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 382 | static ASMJIT_INLINE bool isSeg(const Operand_& op, uint32_t rId) noexcept { return isSeg(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:382:87: note: cast one or both operands to int to silence this warning ././x86operand.h:383:89: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 383 | static ASMJIT_INLINE bool isGpbLo(const Operand_& op, uint32_t rId) noexcept { return isGpbLo(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:383:89: note: cast one or both operands to int to silence this warning ././x86operand.h:384:89: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 384 | static ASMJIT_INLINE bool isGpbHi(const Operand_& op, uint32_t rId) noexcept { return isGpbHi(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:384:89: note: cast one or both operands to int to silence this warning ././x86operand.h:385:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 385 | static ASMJIT_INLINE bool isGpw(const Operand_& op, uint32_t rId) noexcept { return isGpw(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:385:87: note: cast one or both operands to int to silence this warning ././x86operand.h:386:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 386 | static ASMJIT_INLINE bool isGpd(const Operand_& op, uint32_t rId) noexcept { return isGpd(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:386:87: note: cast one or both operands to int to silence this warning ././x86operand.h:387:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 387 | static ASMJIT_INLINE bool isGpq(const Operand_& op, uint32_t rId) noexcept { return isGpq(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:387:87: note: cast one or both operands to int to silence this warning ././x86operand.h:388:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 388 | static ASMJIT_INLINE bool isFp(const Operand_& op, uint32_t rId) noexcept { return isFp(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:388:86: note: cast one or both operands to int to silence this warning ././x86operand.h:389:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 389 | static ASMJIT_INLINE bool isMm(const Operand_& op, uint32_t rId) noexcept { return isMm(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:389:86: note: cast one or both operands to int to silence this warning ././x86operand.h:390:85: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 390 | static ASMJIT_INLINE bool isK(const Operand_& op, uint32_t rId) noexcept { return isK(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:390:85: note: cast one or both operands to int to silence this warning ././x86operand.h:391:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 391 | static ASMJIT_INLINE bool isXmm(const Operand_& op, uint32_t rId) noexcept { return isXmm(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:391:87: note: cast one or both operands to int to silence this warning ././x86operand.h:392:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 392 | static ASMJIT_INLINE bool isYmm(const Operand_& op, uint32_t rId) noexcept { return isYmm(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:392:87: note: cast one or both operands to int to silence this warning ././x86operand.h:393:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 393 | static ASMJIT_INLINE bool isZmm(const Operand_& op, uint32_t rId) noexcept { return isZmm(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:393:87: note: cast one or both operands to int to silence this warning ././x86operand.h:394:87: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 394 | static ASMJIT_INLINE bool isBnd(const Operand_& op, uint32_t rId) noexcept { return isBnd(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:394:87: note: cast one or both operands to int to silence this warning ././x86operand.h:395:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 395 | static ASMJIT_INLINE bool isCr(const Operand_& op, uint32_t rId) noexcept { return isCr(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:395:86: note: cast one or both operands to int to silence this warning ././x86operand.h:396:86: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 396 | static ASMJIT_INLINE bool isDr(const Operand_& op, uint32_t rId) noexcept { return isDr(op) & (op.getId() == rId); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && ././x86operand.h:396:86: note: cast one or both operands to int to silence this warning 20 warnings generated. compiling LatticeReduction.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 RMSD.cpp compiling Highest.cpp compiling Puckering.cpp compiling NormalizedEuclideanDistance.cpp compiling FilterBetween.cpp compiling Histogram.cpp compiling SAXS.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 LinkCells.cpp gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/gridtools' compiling Log.cpp compiling OptimalRMSD.cpp compiling RMSDBase.cpp compiling Template.cpp compiling ReferenceArguments.cpp compiling Torsion.cpp compiling LessThan.cpp compiling FilterLessThan.cpp compiling ReferenceAtoms.cpp compiling Volume.cpp compiling ReferenceConfiguration.cpp compiling FilterMoreThan.cpp compiling Select.cpp compiling LoopUnroller.cpp gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/analysis' compiling Selector.cpp compiling Lowest.cpp compiling Max.cpp compiling LocalAverage.cpp compiling InPlaneDistances.cpp compiling Mean.cpp compiling Matrix.cpp compiling ReferenceValuePack.cpp compiling MultiColvarBase.cpp compiling Min.cpp compiling Moments.cpp compiling MatrixSquareBracketsAccess.cpp compiling MultiColvarCombine.cpp compiling MoreThan.cpp compiling OrderingVessel.cpp compiling MinimiseBase.cpp compiling Minimise1DBrent.cpp compiling MolDataClass.cpp compiling MultiColvarDensity.cpp compiling SimpleRMSD.cpp compiling MultiColvarFilter.cpp compiling MultiColvarProduct.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 SingleDomainRMSD.cpp compiling ShortcutVessel.cpp compiling NumberOfLinks.cpp compiling Torsions.cpp compiling VolumeAround.cpp compiling MultiValue.cpp compiling VolumeBetweenContours.cpp compiling NeighborList.cpp compiling OFile.cpp gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/generic' compiling OpenMP.cpp compiling StoreDataVessel.cpp compiling Sum.cpp compiling ValueVessel.cpp compiling Vessel.cpp compiling PDB.cpp compiling Pbc.cpp compiling VolumeCavity.cpp compiling VesselRegister.cpp compiling PlumedHandle.cpp compiling RMSD.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' Grid.cpp:1082:13: warning: variable 'n_examined' set but not used [-Wunused-but-set-variable] 1082 | index_t n_examined = 0; | ^ 1 warning generated. compiling VolumeInCylinder.cpp compiling VolumeInSphere.cpp compiling VolumeTetrapore.cpp compiling XAngle.cpp compiling VolumeGradientBase.cpp compiling Random.cpp compiling XDistances.cpp compiling XYDistances.cpp compiling XYTorsion.cpp compiling RootFindingBase.cpp compiling Stopwatch.cpp compiling Subprocess.cpp compiling SwitchingFunction.cpp compiling Tensor.cpp compiling Tools.cpp compiling Torsion.cpp compiling Tree.cpp compiling TypesafePtr.cpp Keywords.cpp:126:16: warning: variable 'i' set but not used [-Wunused-but-set-variable] 126 | for(unsigned i=0;; ++i) { | ^ 1 warning generated. compiling Vector.cpp compiling h36.cpp compiling Units.cpp PathMSDBase.cpp:143:19: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning] 143 | void PathMSDBase::calculate() { | ^ PathMSDBase.cpp:143:19: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning] PathMSDBase.cpp:143:19: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning] PathMSDBase.cpp:143:19: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning] PathMSDBase.cpp:143:19: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning] PathMSDBase.cpp:143:19: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning] 6 warnings generated. gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/colvar' gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/reference' Vessel.cpp:63:16: warning: variable 'i' set but not used [-Wunused-but-set-variable] 63 | for(unsigned i=0;; ++i) { | ^ 1 warning generated. gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/vesselbase' 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 chmod a+x plumed-config c++ -shared -o libplumedKernel.so ../analysis/AnalysisBase.o ../analysis/Average.o ../analysis/AverageVessel.o ../analysis/Committor.o ../analysis/DataCollectionObject.o ../analysis/EuclideanDissimilarityMatrix.o ../analysis/FarthestPointSampling.o ../analysis/Histogram.o ../analysis/LandmarkSelectionBase.o ../analysis/LandmarkStaged.o ../analysis/OutputColvarFile.o ../analysis/OutputPDBFile.o ../analysis/PrintDissimilarityMatrix.o ../analysis/ReadAnalysisFrames.o ../analysis/ReadDissimilarityMatrix.o ../analysis/ReselectLandmarks.o ../analysis/SelectRandomFrames.o ../analysis/SelectWithStride.o ../analysis/WhamHistogram.o ../analysis/WhamWeights.o ../asmjit/arch.o ../asmjit/assembler.o ../asmjit/codebuilder.o ../asmjit/codecompiler.o ../asmjit/codeemitter.o ../asmjit/codeholder.o ../asmjit/constpool.o ../asmjit/cpuinfo.o ../asmjit/func.o ../asmjit/globals.o ../asmjit/inst.o ../asmjit/logging.o ../asmjit/operand.o ../asmjit/osutils.o ../asmjit/regalloc.o ../asmjit/runtime.o ../asmjit/string.o ../asmjit/utils.o ../asmjit/vmem.o ../asmjit/x86assembler.o ../asmjit/x86builder.o ../asmjit/x86compiler.o ../asmjit/x86inst.o ../asmjit/x86instimpl.o ../asmjit/x86internal.o ../asmjit/x86logging.o ../asmjit/x86operand.o ../asmjit/x86operand_regs.o ../asmjit/x86regalloc.o ../asmjit/zone.o ../bias/ABMD.o ../bias/Bias.o ../bias/BiasValue.o ../bias/ExtendedLagrangian.o ../bias/External.o ../bias/LWalls.o ../bias/MaxEnt.o ../bias/MetaD.o ../bias/MovingRestraint.o ../bias/PBMetaD.o ../bias/Restraint.o ../bias/ReweightBase.o ../bias/ReweightBias.o ../bias/ReweightMetad.o ../bias/ReweightTemperaturePressure.o ../bias/ReweightWham.o ../bias/UWalls.o ../blas/blas.o ../cltools/CLTool.o ../cltools/Completion.o ../cltools/Driver.o ../cltools/DriverDouble.o ../cltools/DriverFloat.o ../cltools/GenExample.o ../cltools/GenJson.o ../cltools/GenTemplate.o ../cltools/Info.o ../cltools/Manual.o ../cltools/PdbRenumber.o ../cltools/SimpleMD.o ../cltools/SumHills.o ../cltools/kT.o ../cltools/pesmd.o ../colvar/Angle.o ../colvar/Cell.o ../colvar/Colvar.o ../colvar/Constant.o ../colvar/ContactMap.o ../colvar/Coordination.o ../colvar/CoordinationBase.o ../colvar/DHEnergy.o ../colvar/DRMSD.o ../colvar/Dimer.o ../colvar/Dipole.o ../colvar/Distance.o ../colvar/EEFSolv.o ../colvar/ERMSD.o ../colvar/Energy.o ../colvar/ExtraCV.o ../colvar/Fake.o ../colvar/GHBFIX.o ../colvar/Gyration.o ../colvar/MultiRMSD.o ../colvar/PCARMSD.o ../colvar/PathMSD.o ../colvar/PathMSDBase.o ../colvar/Position.o ../colvar/ProjectionOnAxis.o ../colvar/PropertyMap.o ../colvar/Puckering.o ../colvar/RMSD.o ../colvar/Template.o ../colvar/Torsion.o ../colvar/Volume.o ../core/Action.o ../core/ActionAnyorder.o ../core/ActionAtomistic.o ../core/ActionPilot.o ../core/ActionRegister.o ../core/ActionSet.o ../core/ActionSetup.o ../core/ActionShortcut.o ../core/ActionWithArguments.o ../core/ActionWithValue.o ../core/ActionWithVirtualAtom.o ../core/Atoms.o ../core/CLTool.o ../core/CLToolMain.o ../core/CLToolRegister.o ../core/Colvar.o ../core/DataFetchingObject.o ../core/ExchangePatterns.o ../core/FlexibleBin.o ../core/GREX.o ../core/GenericMolInfo.o ../core/MDAtoms.o ../core/ModuleMap.o ../core/PlumedMain.o ../core/PlumedMainInitializer.o ../core/TargetDist.o ../core/Value.o ../core/WithCmd.o ../function/Combine.o ../function/Custom.o ../function/Ensemble.o ../function/FuncPathGeneral.o ../function/FuncPathMSD.o ../function/FuncSumHills.o ../function/Function.o ../function/LocalEnsemble.o ../function/Piecewise.o ../function/Sort.o ../function/Stats.o ../function/Target.o ../generic/Debug.o ../generic/DumpAtoms.o ../generic/DumpDerivatives.o ../generic/DumpForces.o ../generic/DumpMassCharge.o ../generic/DumpProjections.o ../generic/EffectiveEnergyDrift.o ../generic/EndPlumed.o ../generic/FitToTemplate.o ../generic/Flush.o ../generic/Group.o ../generic/Include.o ../generic/MolInfo.o ../generic/Plumed.o ../generic/Print.o ../generic/RandomExchanges.o ../generic/Read.o ../generic/ResetCell.o ../generic/Time.o ../generic/UpdateIf.o ../generic/WholeMolecules.o ../generic/WrapAround.o ../gridtools/ActionWithGrid.o ../gridtools/ActionWithInputGrid.o ../gridtools/ActionWithIntegral.o ../gridtools/AverageOnGrid.o ../gridtools/ContourFindingBase.o ../gridtools/ConvertToFES.o ../gridtools/DumpCube.o ../gridtools/DumpGrid.o ../gridtools/FindContour.o ../gridtools/FindContourSurface.o ../gridtools/FindSphericalContour.o ../gridtools/FourierTransform.o ../gridtools/GridPrintingBase.o ../gridtools/GridSearch.o ../gridtools/GridToXYZ.o ../gridtools/GridVessel.o ../gridtools/HistogramOnGrid.o ../gridtools/IntegrateGrid.o ../gridtools/InterpolateGrid.o ../isdb/CS2Backbone.o ../isdb/Caliber.o ../isdb/EMMI.o ../isdb/FretEfficiency.o ../isdb/Jcoupling.o ../isdb/Metainference.o ../isdb/MetainferenceBase.o ../isdb/NOE.o ../isdb/PRE.o ../isdb/RDC.o ../isdb/Rescale.o ../isdb/SAXS.o ../isdb/Select.o ../isdb/Selector.o ../lapack/lapack.o ../lepton/CompiledExpression.o ../lepton/ExpressionProgram.o ../lepton/ExpressionTreeNode.o ../lepton/Operation.o ../lepton/ParsedExpression.o ../lepton/Parser.o ../mapping/AdaptivePath.o ../mapping/Mapping.o ../mapping/PCAVars.o ../mapping/Path.o ../mapping/PathBase.o ../mapping/PathReparameterization.o ../mapping/PathTools.o ../mapping/PropertyMap.o ../mapping/SpathVessel.o ../mapping/TrigonometricPathVessel.o ../mapping/ZpathVessel.o ../molfile/crdplugin.o ../molfile/dcdplugin.o ../molfile/gromacsplugin.o ../molfile/pdbplugin.o ../multicolvar/ActionVolume.o ../multicolvar/AlphaBeta.o ../multicolvar/Angles.o ../multicolvar/AtomValuePack.o ../multicolvar/Bridge.o ../multicolvar/BridgedMultiColvarFunction.o ../multicolvar/CatomPack.o ../multicolvar/CenterOfMultiColvar.o ../multicolvar/CoordinationNumbers.o ../multicolvar/Density.o ../multicolvar/DihedralCorrelation.o ../multicolvar/DistanceFromContour.o ../multicolvar/Distances.o ../multicolvar/DumpMultiColvar.o ../multicolvar/FilterBetween.o ../multicolvar/FilterLessThan.o ../multicolvar/FilterMoreThan.o ../multicolvar/InPlaneDistances.o ../multicolvar/LocalAverage.o ../multicolvar/MultiColvarBase.o ../multicolvar/MultiColvarCombine.o ../multicolvar/MultiColvarDensity.o ../multicolvar/MultiColvarFilter.o ../multicolvar/MultiColvarProduct.o ../multicolvar/NumberOfLinks.o ../multicolvar/Torsions.o ../multicolvar/VolumeAround.o ../multicolvar/VolumeBetweenContours.o ../multicolvar/VolumeCavity.o ../multicolvar/VolumeGradientBase.o ../multicolvar/VolumeInCylinder.o ../multicolvar/VolumeInSphere.o ../multicolvar/VolumeTetrapore.o ../multicolvar/XAngle.o ../multicolvar/XDistances.o ../multicolvar/XYDistances.o ../multicolvar/XYTorsion.o ../reference/ArgumentOnlyDistance.o ../reference/DRMSD.o ../reference/Direction.o ../reference/DotProductDistance.o ../reference/EuclideanDistance.o ../reference/FakeFrame.o ../reference/IntermolecularDRMSD.o ../reference/IntramolecularDRMSD.o ../reference/MahalanobisDistance.o ../reference/MetricRegister.o ../reference/MultiDomainRMSD.o ../reference/NormalizedEuclideanDistance.o ../reference/OptimalRMSD.o ../reference/RMSDBase.o ../reference/ReferenceArguments.o ../reference/ReferenceAtoms.o ../reference/ReferenceConfiguration.o ../reference/ReferenceValuePack.o ../reference/SimpleRMSD.o ../reference/SingleDomainRMSD.o ../secondarystructure/AlphaRMSD.o ../secondarystructure/AntibetaRMSD.o ../secondarystructure/ParabetaRMSD.o ../secondarystructure/SecondaryStructureRMSD.o ../setup/Load.o ../setup/Restart.o ../setup/Units.o ../tools/Angle.o ../tools/AtomNumber.o ../tools/BiasRepresentation.o ../tools/Brent1DRootSearch.o ../tools/Citations.o ../tools/Communicator.o ../tools/ConjugateGradient.o ../tools/DLLoader.o ../tools/DynamicList.o ../tools/ERMSD.o ../tools/Exception.o ../tools/FileBase.o ../tools/ForwardDecl.o ../tools/Grid.o ../tools/HistogramBead.o ../tools/IFile.o ../tools/KernelFunctions.o ../tools/Keywords.o ../tools/LatticeReduction.o ../tools/LinkCells.o ../tools/Log.o ../tools/LoopUnroller.o ../tools/Matrix.o ../tools/MatrixSquareBracketsAccess.o ../tools/Minimise1DBrent.o ../tools/MinimiseBase.o ../tools/MolDataClass.o ../tools/MultiValue.o ../tools/NeighborList.o ../tools/OFile.o ../tools/OpenMP.o ../tools/PDB.o ../tools/Pbc.o ../tools/PlumedHandle.o ../tools/RMSD.o ../tools/Random.o ../tools/RootFindingBase.o ../tools/Stopwatch.o ../tools/Subprocess.o ../tools/SwitchingFunction.o ../tools/Tensor.o ../tools/Tools.o ../tools/Torsion.o ../tools/Tree.o ../tools/TypesafePtr.o ../tools/Units.o ../tools/Vector.o ../tools/h36.o ../vatom/ActionWithVirtualAtom.o ../vatom/Center.o ../vatom/FixedAtom.o ../vatom/Ghost.o ../vesselbase/ActionWithAveraging.o ../vesselbase/ActionWithInputVessel.o ../vesselbase/ActionWithVessel.o ../vesselbase/AltMin.o ../vesselbase/AveragingVessel.o ../vesselbase/Between.o ../vesselbase/BridgeVessel.o ../vesselbase/FunctionVessel.o ../vesselbase/Highest.o ../vesselbase/Histogram.o ../vesselbase/LessThan.o ../vesselbase/Lowest.o ../vesselbase/Max.o ../vesselbase/Mean.o ../vesselbase/Min.o ../vesselbase/Moments.o ../vesselbase/MoreThan.o ../vesselbase/OrderingVessel.o ../vesselbase/ShortcutVessel.o ../vesselbase/StoreDataVessel.o ../vesselbase/Sum.o ../vesselbase/ValueVessel.o ../vesselbase/Vessel.o ../vesselbase/VesselRegister.o ../xdrfile/xdrfile.o ../xdrfile/xdrfile_trr.o ../xdrfile/xdrfile_xtc.o ../config/Config.o -Wl,-soname,"libplumedKernel.so" -lstdc++ -lfftw3 -lgsl -lgslcblas -lz -ldl -llapack -lblas -L/usr/local/lib -rdynamic -Wl,-Bsymbolic -fopenmp c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fPIC -Wall -pedantic -std=c++11 ../main/main.o ../wrapper/Plumed.o -o plumed-runtime -ldl /usr/bin/ar cr libplumedWrapper.a ../wrapper/Plumed.o chmod a+x plumed-mklib Building Plumed.inc, runtime-linking version Building Plumed.inc, shared version Building Plumed.inc, static version Building Plumed.cmake chmod a+x plumed-partial_tempering chmod a+x plumed-newcv chmod a+x plumed-patch chmod a+x plumed-selector Building Plumed.cmake, static version Building Plumed.cmake, runtime-linking version chmod a+x plumed-vim2html Building Plumed.cmake, shared version c++ -shared -o libplumed.so ../wrapper/PlumedStatic.o libplumedKernel.so -Wl,-soname,"libplumed.so" c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fPIC -Wall -pedantic -std=c++11 ../main/main.o ../wrapper/PlumedStatic.o libplumedKernel.so -o plumed -ldl gmake[4]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' /usr/local/bin/gmake install-build gmake[4]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' mkdir -p install/ /usr/local/bin/gmake PLUMED_INSTALL=Install all gmake[5]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' /usr/local/bin/gmake dirslinks gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' *** Updating links to used modules in all directories *** /usr/local/bin/gmake ../analysis.links ../asmjit.links ../bias.links ../blas.links ../cltools.links ../colvar.links ../config.links ../core.links ../function.links ../generic.links ../gridtools.links ../isdb.links ../lapack.links ../lepton.links ../main.links ../mapping.links ../molfile.links ../multicolvar.links ../reference.links ../secondarystructure.links ../setup.links ../tools.links ../vatom.links ../vesselbase.links ../wrapper.links ../xdrfile.links gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' /usr/local/bin/gmake -C ../analysis links /usr/local/bin/gmake -C ../asmjit links /usr/local/bin/gmake -C ../bias links /usr/local/bin/gmake -C ../blas links /usr/local/bin/gmake -C ../cltools links /usr/local/bin/gmake -C ../colvar links /usr/local/bin/gmake -C ../config links /usr/local/bin/gmake -C ../core links /usr/local/bin/gmake -C ../function links /usr/local/bin/gmake -C ../generic links /usr/local/bin/gmake -C ../gridtools links /usr/local/bin/gmake -C ../isdb links /usr/local/bin/gmake -C ../lapack links /usr/local/bin/gmake -C ../lepton links /usr/local/bin/gmake -C ../main links /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/blas' /usr/local/bin/gmake -C ../reference links /usr/local/bin/gmake -C ../secondarystructure links /usr/local/bin/gmake -C ../setup links gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/config' /usr/local/bin/gmake -C ../tools links Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/blas /usr/local/bin/gmake -C ../vatom links /usr/local/bin/gmake -C ../vesselbase links Nothing to do in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/config /usr/local/bin/gmake -C ../wrapper links gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/config' /usr/local/bin/gmake -C ../xdrfile links gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lapack' gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/blas' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lapack gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/main' gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/molfile' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/main Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/molfile gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/wrapper' 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/function' Nothing to do in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/wrapper gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/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/xdrfile' gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/vatom' gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/cltools' gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/molfile' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lepton Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/function gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/secondarystructure' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/xdrfile Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/setup Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/vatom Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/cltools gmake[8]: 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/secondarystructure gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/mapping' gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/xdrfile' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/isdb Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/mapping gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/asmjit' gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/generic' gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/analysis' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/asmjit Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/analysis Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/generic gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/bias' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/bias gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/asmjit' gmake[8]: 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/gridtools' gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/main' gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/colvar' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/reference Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/gridtools 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/core' gmake[8]: Entering 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/lapack' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/core Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/vesselbase gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/tools' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/tools gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lepton' gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/multicolvar' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/multicolvar gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/vatom' gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/setup' gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/bias' 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/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/core' 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/tools' gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/cltools' gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/vesselbase' gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/isdb' gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/mapping' gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/multicolvar' gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/analysis' gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' /usr/local/bin/gmake dirs gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' *** Compiling all directories *** /usr/local/bin/gmake ../analysis ../asmjit ../bias ../blas ../cltools ../colvar ../config ../core ../function ../generic ../gridtools ../isdb ../lapack ../lepton ../main ../mapping ../molfile ../multicolvar ../reference ../secondarystructure ../setup ../tools ../vatom ../vesselbase ../wrapper ../xdrfile gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' /usr/local/bin/gmake -C ../analysis obj /usr/local/bin/gmake -C ../asmjit obj /usr/local/bin/gmake -C ../bias obj /usr/local/bin/gmake -C ../blas obj /usr/local/bin/gmake -C ../cltools obj /usr/local/bin/gmake -C ../colvar obj /usr/local/bin/gmake -C ../config obj /usr/local/bin/gmake -C ../core obj /usr/local/bin/gmake -C ../function obj /usr/local/bin/gmake -C ../generic obj /usr/local/bin/gmake -C ../gridtools obj /usr/local/bin/gmake -C ../isdb obj /usr/local/bin/gmake -C ../lapack obj /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'. gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/blas' /usr/local/bin/gmake -C ../multicolvar obj gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/config' /usr/local/bin/gmake PLUMED_FORCE=yes ConfigInstall.inc Config.inc version.h config.txt /usr/local/bin/gmake -C ../reference obj /usr/local/bin/gmake -C ../secondarystructure obj /usr/local/bin/gmake -C ../setup obj /usr/local/bin/gmake -C ../tools obj /usr/local/bin/gmake -C ../vatom obj /usr/local/bin/gmake -C ../vesselbase obj /usr/local/bin/gmake -C ../wrapper obj gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lapack' gmake[8]: Nothing to be done for 'obj'. gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lapack' /usr/local/bin/gmake -C ../xdrfile obj gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/main' gmake[8]: Nothing to be done for 'obj'. gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/main' gmake[9]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/config' gmake[9]: 'config.txt' is up to date. Updating ConfigInstall.inc Updating Config.inc Updating version.h gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/molfile' gmake[8]: Nothing to be done for 'obj'. gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/molfile' gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lepton' gmake[8]: Nothing to be done for 'obj'. gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lepton' gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/setup' gmake[8]: Nothing to be done for 'obj'. gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/setup' gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/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' 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/vatom' gmake[8]: Nothing to be done for 'obj'. gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/vatom' gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/secondarystructure' gmake[8]: Nothing to be done for 'obj'. gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/secondarystructure' cmp -s ConfigInstall.inc~ ConfigInstall.inc || cp ConfigInstall.inc~ ConfigInstall.inc 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/asmjit' gmake[8]: Nothing to be done for 'obj'. gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/asmjit' gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/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/mapping' gmake[8]: Nothing to be done for 'obj'. gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/mapping' gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/generic' gmake[8]: Nothing to be done for 'obj'. gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/generic' gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/reference' gmake[8]: Nothing to be done for 'obj'. gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/reference' rm ConfigInstall.inc~ gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/isdb' gmake[8]: Nothing to be done for 'obj'. rm Config.inc~ 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/gridtools' gmake[8]: Nothing to be done for 'obj'. 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/gridtools' 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[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[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]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/config' gmake[9]: 'Config.o' is up to date. gmake[9]: 'ConfigInstall.o' is up to date. gmake[9]: 'compile_options.sh' is up to date. gmake[9]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/config' gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/config' gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' /usr/local/bin/gmake lib gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fPIC -Wall -pedantic -std=c++11 ../main/main.o ../analysis/AnalysisBase.o ../analysis/Average.o ../analysis/AverageVessel.o ../analysis/Committor.o ../analysis/DataCollectionObject.o ../analysis/EuclideanDissimilarityMatrix.o ../analysis/FarthestPointSampling.o ../analysis/Histogram.o ../analysis/LandmarkSelectionBase.o ../analysis/LandmarkStaged.o ../analysis/OutputColvarFile.o ../analysis/OutputPDBFile.o ../analysis/PrintDissimilarityMatrix.o ../analysis/ReadAnalysisFrames.o ../analysis/ReadDissimilarityMatrix.o ../analysis/ReselectLandmarks.o ../analysis/SelectRandomFrames.o ../analysis/SelectWithStride.o ../analysis/WhamHistogram.o ../analysis/WhamWeights.o ../asmjit/arch.o ../asmjit/assembler.o ../asmjit/codebuilder.o ../asmjit/codecompiler.o ../asmjit/codeemitter.o ../asmjit/codeholder.o ../asmjit/constpool.o ../asmjit/cpuinfo.o ../asmjit/func.o ../asmjit/globals.o ../asmjit/inst.o ../asmjit/logging.o ../asmjit/operand.o ../asmjit/osutils.o ../asmjit/regalloc.o ../asmjit/runtime.o ../asmjit/string.o ../asmjit/utils.o ../asmjit/vmem.o ../asmjit/x86assembler.o ../asmjit/x86builder.o ../asmjit/x86compiler.o ../asmjit/x86inst.o ../asmjit/x86instimpl.o ../asmjit/x86internal.o ../asmjit/x86logging.o ../asmjit/x86operand.o ../asmjit/x86operand_regs.o ../asmjit/x86regalloc.o ../asmjit/zone.o ../bias/ABMD.o ../bias/Bias.o ../bias/BiasValue.o ../bias/ExtendedLagrangian.o ../bias/External.o ../bias/LWalls.o ../bias/MaxEnt.o ../bias/MetaD.o ../bias/MovingRestraint.o ../bias/PBMetaD.o ../bias/Restraint.o ../bias/ReweightBase.o ../bias/ReweightBias.o ../bias/ReweightMetad.o ../bias/ReweightTemperaturePressure.o ../bias/ReweightWham.o ../bias/UWalls.o ../blas/blas.o ../cltools/CLTool.o ../cltools/Completion.o ../cltools/Driver.o ../cltools/DriverDouble.o ../cltools/DriverFloat.o ../cltools/GenExample.o ../cltools/GenJson.o ../cltools/GenTemplate.o ../cltools/Info.o ../cltools/Manual.o ../cltools/PdbRenumber.o ../cltools/SimpleMD.o ../cltools/SumHills.o ../cltools/kT.o ../cltools/pesmd.o ../colvar/Angle.o ../colvar/Cell.o ../colvar/Colvar.o ../colvar/Constant.o ../colvar/ContactMap.o ../colvar/Coordination.o ../colvar/CoordinationBase.o ../colvar/DHEnergy.o ../colvar/DRMSD.o ../colvar/Dimer.o ../colvar/Dipole.o ../colvar/Distance.o ../colvar/EEFSolv.o ../colvar/ERMSD.o ../colvar/Energy.o ../colvar/ExtraCV.o ../colvar/Fake.o ../colvar/GHBFIX.o ../colvar/Gyration.o ../colvar/MultiRMSD.o ../colvar/PCARMSD.o ../colvar/PathMSD.o ../colvar/PathMSDBase.o ../colvar/Position.o ../colvar/ProjectionOnAxis.o ../colvar/PropertyMap.o ../colvar/Puckering.o ../colvar/RMSD.o ../colvar/Template.o ../colvar/Torsion.o ../colvar/Volume.o ../core/Action.o ../core/ActionAnyorder.o ../core/ActionAtomistic.o ../core/ActionPilot.o ../core/ActionRegister.o ../core/ActionSet.o ../core/ActionSetup.o ../core/ActionShortcut.o ../core/ActionWithArguments.o ../core/ActionWithValue.o ../core/ActionWithVirtualAtom.o ../core/Atoms.o ../core/CLTool.o ../core/CLToolMain.o ../core/CLToolRegister.o ../core/Colvar.o ../core/DataFetchingObject.o ../core/ExchangePatterns.o ../core/FlexibleBin.o ../core/GREX.o ../core/GenericMolInfo.o ../core/MDAtoms.o ../core/ModuleMap.o ../core/PlumedMain.o ../core/PlumedMainInitializer.o ../core/TargetDist.o ../core/Value.o ../core/WithCmd.o ../function/Combine.o ../function/Custom.o ../function/Ensemble.o ../function/FuncPathGeneral.o ../function/FuncPathMSD.o ../function/FuncSumHills.o ../function/Function.o ../function/LocalEnsemble.o ../function/Piecewise.o ../function/Sort.o ../function/Stats.o ../function/Target.o ../generic/Debug.o ../generic/DumpAtoms.o ../generic/DumpDerivatives.o ../generic/DumpForces.o ../generic/DumpMassCharge.o ../generic/DumpProjections.o ../generic/EffectiveEnergyDrift.o ../generic/EndPlumed.o ../generic/FitToTemplate.o ../generic/Flush.o ../generic/Group.o ../generic/Include.o ../generic/MolInfo.o ../generic/Plumed.o ../generic/Print.o ../generic/RandomExchanges.o ../generic/Read.o ../generic/ResetCell.o ../generic/Time.o ../generic/UpdateIf.o ../generic/WholeMolecules.o ../generic/WrapAround.o ../gridtools/ActionWithGrid.o ../gridtools/ActionWithInputGrid.o ../gridtools/ActionWithIntegral.o ../gridtools/AverageOnGrid.o ../gridtools/ContourFindingBase.o ../gridtools/ConvertToFES.o ../gridtools/DumpCube.o ../gridtools/DumpGrid.o ../gridtools/FindContour.o ../gridtools/FindContourSurface.o ../gridtools/FindSphericalContour.o ../gridtools/FourierTransform.o ../gridtools/GridPrintingBase.o ../gridtools/GridSearch.o ../gridtools/GridToXYZ.o ../gridtools/GridVessel.o ../gridtools/HistogramOnGrid.o ../gridtools/IntegrateGrid.o ../gridtools/InterpolateGrid.o ../isdb/CS2Backbone.o ../isdb/Caliber.o ../isdb/EMMI.o ../isdb/FretEfficiency.o ../isdb/Jcoupling.o ../isdb/Metainference.o ../isdb/MetainferenceBase.o ../isdb/NOE.o ../isdb/PRE.o ../isdb/RDC.o ../isdb/Rescale.o ../isdb/SAXS.o ../isdb/Select.o ../isdb/Selector.o ../lapack/lapack.o ../lepton/CompiledExpression.o ../lepton/ExpressionProgram.o ../lepton/ExpressionTreeNode.o ../lepton/Operation.o ../lepton/ParsedExpression.o ../lepton/Parser.o ../mapping/AdaptivePath.o ../mapping/Mapping.o ../mapping/PCAVars.o ../mapping/Path.o ../mapping/PathBase.o ../mapping/PathReparameterization.o ../mapping/PathTools.o ../mapping/PropertyMap.o ../mapping/SpathVessel.o ../mapping/TrigonometricPathVessel.o ../mapping/ZpathVessel.o ../molfile/crdplugin.o ../molfile/dcdplugin.o ../molfile/gromacsplugin.o ../molfile/pdbplugin.o ../multicolvar/ActionVolume.o ../multicolvar/AlphaBeta.o ../multicolvar/Angles.o ../multicolvar/AtomValuePack.o ../multicolvar/Bridge.o ../multicolvar/BridgedMultiColvarFunction.o ../multicolvar/CatomPack.o ../multicolvar/CenterOfMultiColvar.o ../multicolvar/CoordinationNumbers.o ../multicolvar/Density.o ../multicolvar/DihedralCorrelation.o ../multicolvar/DistanceFromContour.o ../multicolvar/Distances.o ../multicolvar/DumpMultiColvar.o ../multicolvar/FilterBetween.o ../multicolvar/FilterLessThan.o ../multicolvar/FilterMoreThan.o ../multicolvar/InPlaneDistances.o ../multicolvar/LocalAverage.o ../multicolvar/MultiColvarBase.o ../multicolvar/MultiColvarCombine.o ../multicolvar/MultiColvarDensity.o ../multicolvar/MultiColvarFilter.o ../multicolvar/MultiColvarProduct.o ../multicolvar/NumberOfLinks.o ../multicolvar/Torsions.o ../multicolvar/VolumeAround.o ../multicolvar/VolumeBetweenContours.o ../multicolvar/VolumeCavity.o ../multicolvar/VolumeGradientBase.o ../multicolvar/VolumeInCylinder.o ../multicolvar/VolumeInSphere.o ../multicolvar/VolumeTetrapore.o ../multicolvar/XAngle.o ../multicolvar/XDistances.o ../multicolvar/XYDistances.o ../multicolvar/XYTorsion.o ../reference/ArgumentOnlyDistance.o ../reference/DRMSD.o ../reference/Direction.o ../reference/DotProductDistance.o ../reference/EuclideanDistance.o ../reference/FakeFrame.o ../reference/IntermolecularDRMSD.o ../reference/IntramolecularDRMSD.o ../reference/MahalanobisDistance.o ../reference/MetricRegister.o ../reference/MultiDomainRMSD.o ../reference/NormalizedEuclideanDistance.o ../reference/OptimalRMSD.o ../reference/RMSDBase.o ../reference/ReferenceArguments.o ../reference/ReferenceAtoms.o ../reference/ReferenceConfiguration.o ../reference/ReferenceValuePack.o ../reference/SimpleRMSD.o ../reference/SingleDomainRMSD.o ../secondarystructure/AlphaRMSD.o ../secondarystructure/AntibetaRMSD.o ../secondarystructure/ParabetaRMSD.o ../secondarystructure/SecondaryStructureRMSD.o ../setup/Load.o ../setup/Restart.o ../setup/Units.o ../tools/Angle.o ../tools/AtomNumber.o ../tools/BiasRepresentation.o ../tools/Brent1DRootSearch.o ../tools/Citations.o ../tools/Communicator.o ../tools/ConjugateGradient.o ../tools/DLLoader.o ../tools/DynamicList.o ../tools/ERMSD.o ../tools/Exception.o ../tools/FileBase.o ../tools/ForwardDecl.o ../tools/Grid.o ../tools/HistogramBead.o ../tools/IFile.o ../tools/KernelFunctions.o ../tools/Keywords.o ../tools/LatticeReduction.o ../tools/LinkCells.o ../tools/Log.o ../tools/LoopUnroller.o ../tools/Matrix.o ../tools/MatrixSquareBracketsAccess.o ../tools/Minimise1DBrent.o ../tools/MinimiseBase.o ../tools/MolDataClass.o ../tools/MultiValue.o ../tools/NeighborList.o ../tools/OFile.o ../tools/OpenMP.o ../tools/PDB.o ../tools/Pbc.o ../tools/PlumedHandle.o ../tools/RMSD.o ../tools/Random.o ../tools/RootFindingBase.o ../tools/Stopwatch.o ../tools/Subprocess.o ../tools/SwitchingFunction.o ../tools/Tensor.o ../tools/Tools.o ../tools/Torsion.o ../tools/Tree.o ../tools/TypesafePtr.o ../tools/Units.o ../tools/Vector.o ../tools/h36.o ../vatom/ActionWithVirtualAtom.o ../vatom/Center.o ../vatom/FixedAtom.o ../vatom/Ghost.o ../vesselbase/ActionWithAveraging.o ../vesselbase/ActionWithInputVessel.o ../vesselbase/ActionWithVessel.o ../vesselbase/AltMin.o ../vesselbase/AveragingVessel.o ../vesselbase/Between.o ../vesselbase/BridgeVessel.o ../vesselbase/FunctionVessel.o ../vesselbase/Highest.o ../vesselbase/Histogram.o ../vesselbase/LessThan.o ../vesselbase/Lowest.o ../vesselbase/Max.o ../vesselbase/Mean.o ../vesselbase/Min.o ../vesselbase/Moments.o ../vesselbase/MoreThan.o ../vesselbase/OrderingVessel.o ../vesselbase/ShortcutVessel.o ../vesselbase/StoreDataVessel.o ../vesselbase/Sum.o ../vesselbase/ValueVessel.o ../vesselbase/Vessel.o ../vesselbase/VesselRegister.o ../xdrfile/xdrfile.o ../xdrfile/xdrfile_trr.o ../xdrfile/xdrfile_xtc.o ../config/ConfigInstall.o ../wrapper/PlumedStatic.o -o install/plumed-static -ldl -lstdc++ -lfftw3 -lgsl -lgslcblas -lz -ldl -llapack -lblas -L/usr/local/lib -rdynamic -Wl,-Bsymbolic -fopenmp Building Plumed.inc mkdir -p install c++ -shared -o install/libplumedKernel.so ../analysis/AnalysisBase.o ../analysis/Average.o ../analysis/AverageVessel.o ../analysis/Committor.o ../analysis/DataCollectionObject.o ../analysis/EuclideanDissimilarityMatrix.o ../analysis/FarthestPointSampling.o ../analysis/Histogram.o ../analysis/LandmarkSelectionBase.o ../analysis/LandmarkStaged.o ../analysis/OutputColvarFile.o ../analysis/OutputPDBFile.o ../analysis/PrintDissimilarityMatrix.o ../analysis/ReadAnalysisFrames.o ../analysis/ReadDissimilarityMatrix.o ../analysis/ReselectLandmarks.o ../analysis/SelectRandomFrames.o ../analysis/SelectWithStride.o ../analysis/WhamHistogram.o ../analysis/WhamWeights.o ../asmjit/arch.o ../asmjit/assembler.o ../asmjit/codebuilder.o ../asmjit/codecompiler.o ../asmjit/codeemitter.o ../asmjit/codeholder.o ../asmjit/constpool.o ../asmjit/cpuinfo.o ../asmjit/func.o ../asmjit/globals.o ../asmjit/inst.o ../asmjit/logging.o ../asmjit/operand.o ../asmjit/osutils.o ../asmjit/regalloc.o ../asmjit/runtime.o ../asmjit/string.o ../asmjit/utils.o ../asmjit/vmem.o ../asmjit/x86assembler.o ../asmjit/x86builder.o ../asmjit/x86compiler.o ../asmjit/x86inst.o ../asmjit/x86instimpl.o ../asmjit/x86internal.o ../asmjit/x86logging.o ../asmjit/x86operand.o ../asmjit/x86operand_regs.o ../asmjit/x86regalloc.o ../asmjit/zone.o ../bias/ABMD.o ../bias/Bias.o ../bias/BiasValue.o ../bias/ExtendedLagrangian.o ../bias/External.o ../bias/LWalls.o ../bias/MaxEnt.o ../bias/MetaD.o ../bias/MovingRestraint.o ../bias/PBMetaD.o ../bias/Restraint.o ../bias/ReweightBase.o ../bias/ReweightBias.o ../bias/ReweightMetad.o ../bias/ReweightTemperaturePressure.o ../bias/ReweightWham.o ../bias/UWalls.o ../blas/blas.o ../cltools/CLTool.o ../cltools/Completion.o ../cltools/Driver.o ../cltools/DriverDouble.o ../cltools/DriverFloat.o ../cltools/GenExample.o ../cltools/GenJson.o ../cltools/GenTemplate.o ../cltools/Info.o ../cltools/Manual.o ../cltools/PdbRenumber.o ../cltools/SimpleMD.o ../cltools/SumHills.o ../cltools/kT.o ../cltools/pesmd.o ../colvar/Angle.o ../colvar/Cell.o ../colvar/Colvar.o ../colvar/Constant.o ../colvar/ContactMap.o ../colvar/Coordination.o ../colvar/CoordinationBase.o ../colvar/DHEnergy.o ../colvar/DRMSD.o ../colvar/Dimer.o ../colvar/Dipole.o ../colvar/Distance.o ../colvar/EEFSolv.o ../colvar/ERMSD.o ../colvar/Energy.o ../colvar/ExtraCV.o ../colvar/Fake.o ../colvar/GHBFIX.o ../colvar/Gyration.o ../colvar/MultiRMSD.o ../colvar/PCARMSD.o ../colvar/PathMSD.o ../colvar/PathMSDBase.o ../colvar/Position.o ../colvar/ProjectionOnAxis.o ../colvar/PropertyMap.o ../colvar/Puckering.o ../colvar/RMSD.o ../colvar/Template.o ../colvar/Torsion.o ../colvar/Volume.o ../core/Action.o ../core/ActionAnyorder.o ../core/ActionAtomistic.o ../core/ActionPilot.o ../core/ActionRegister.o ../core/ActionSet.o ../core/ActionSetup.o ../core/ActionShortcut.o ../core/ActionWithArguments.o ../core/ActionWithValue.o ../core/ActionWithVirtualAtom.o ../core/Atoms.o ../core/CLTool.o ../core/CLToolMain.o ../core/CLToolRegister.o ../core/Colvar.o ../core/DataFetchingObject.o ../core/ExchangePatterns.o ../core/FlexibleBin.o ../core/GREX.o ../core/GenericMolInfo.o ../core/MDAtoms.o ../core/ModuleMap.o ../core/PlumedMain.o ../core/PlumedMainInitializer.o ../core/TargetDist.o ../core/Value.o ../core/WithCmd.o ../function/Combine.o ../function/Custom.o ../function/Ensemble.o ../function/FuncPathGeneral.o ../function/FuncPathMSD.o ../function/FuncSumHills.o ../function/Function.o ../function/LocalEnsemble.o ../function/Piecewise.o ../function/Sort.o ../function/Stats.o ../function/Target.o ../generic/Debug.o ../generic/DumpAtoms.o ../generic/DumpDerivatives.o ../generic/DumpForces.o ../generic/DumpMassCharge.o ../generic/DumpProjections.o ../generic/EffectiveEnergyDrift.o ../generic/EndPlumed.o ../generic/FitToTemplate.o ../generic/Flush.o ../generic/Group.o ../generic/Include.o ../generic/MolInfo.o ../generic/Plumed.o ../generic/Print.o ../generic/RandomExchanges.o ../generic/Read.o ../generic/ResetCell.o ../generic/Time.o ../generic/UpdateIf.o ../generic/WholeMolecules.o ../generic/WrapAround.o ../gridtools/ActionWithGrid.o ../gridtools/ActionWithInputGrid.o ../gridtools/ActionWithIntegral.o ../gridtools/AverageOnGrid.o ../gridtools/ContourFindingBase.o ../gridtools/ConvertToFES.o ../gridtools/DumpCube.o ../gridtools/DumpGrid.o ../gridtools/FindContour.o ../gridtools/FindContourSurface.o ../gridtools/FindSphericalContour.o ../gridtools/FourierTransform.o ../gridtools/GridPrintingBase.o ../gridtools/GridSearch.o ../gridtools/GridToXYZ.o ../gridtools/GridVessel.o ../gridtools/HistogramOnGrid.o ../gridtools/IntegrateGrid.o ../gridtools/InterpolateGrid.o ../isdb/CS2Backbone.o ../isdb/Caliber.o ../isdb/EMMI.o ../isdb/FretEfficiency.o ../isdb/Jcoupling.o ../isdb/Metainference.o ../isdb/MetainferenceBase.o ../isdb/NOE.o ../isdb/PRE.o ../isdb/RDC.o ../isdb/Rescale.o ../isdb/SAXS.o ../isdb/Select.o ../isdb/Selector.o ../lapack/lapack.o ../lepton/CompiledExpression.o ../lepton/ExpressionProgram.o ../lepton/ExpressionTreeNode.o ../lepton/Operation.o ../lepton/ParsedExpression.o ../lepton/Parser.o ../mapping/AdaptivePath.o ../mapping/Mapping.o ../mapping/PCAVars.o ../mapping/Path.o ../mapping/PathBase.o ../mapping/PathReparameterization.o ../mapping/PathTools.o ../mapping/PropertyMap.o ../mapping/SpathVessel.o ../mapping/TrigonometricPathVessel.o ../mapping/ZpathVessel.o ../molfile/crdplugin.o ../molfile/dcdplugin.o ../molfile/gromacsplugin.o ../molfile/pdbplugin.o ../multicolvar/ActionVolume.o ../multicolvar/AlphaBeta.o ../multicolvar/Angles.o ../multicolvar/AtomValuePack.o ../multicolvar/Bridge.o ../multicolvar/BridgedMultiColvarFunction.o ../multicolvar/CatomPack.o ../multicolvar/CenterOfMultiColvar.o ../multicolvar/CoordinationNumbers.o ../multicolvar/Density.o ../multicolvar/DihedralCorrelation.o ../multicolvar/DistanceFromContour.o ../multicolvar/Distances.o ../multicolvar/DumpMultiColvar.o ../multicolvar/FilterBetween.o ../multicolvar/FilterLessThan.o ../multicolvar/FilterMoreThan.o ../multicolvar/InPlaneDistances.o ../multicolvar/LocalAverage.o ../multicolvar/MultiColvarBase.o ../multicolvar/MultiColvarCombine.o ../multicolvar/MultiColvarDensity.o ../multicolvar/MultiColvarFilter.o ../multicolvar/MultiColvarProduct.o ../multicolvar/NumberOfLinks.o ../multicolvar/Torsions.o ../multicolvar/VolumeAround.o ../multicolvar/VolumeBetweenContours.o ../multicolvar/VolumeCavity.o ../multicolvar/VolumeGradientBase.o ../multicolvar/VolumeInCylinder.o ../multicolvar/VolumeInSphere.o ../multicolvar/VolumeTetrapore.o ../multicolvar/XAngle.o ../multicolvar/XDistances.o ../multicolvar/XYDistances.o ../multicolvar/XYTorsion.o ../reference/ArgumentOnlyDistance.o ../reference/DRMSD.o ../reference/Direction.o ../reference/DotProductDistance.o ../reference/EuclideanDistance.o ../reference/FakeFrame.o ../reference/IntermolecularDRMSD.o ../reference/IntramolecularDRMSD.o ../reference/MahalanobisDistance.o ../reference/MetricRegister.o ../reference/MultiDomainRMSD.o ../reference/NormalizedEuclideanDistance.o ../reference/OptimalRMSD.o ../reference/RMSDBase.o ../reference/ReferenceArguments.o ../reference/ReferenceAtoms.o ../reference/ReferenceConfiguration.o ../reference/ReferenceValuePack.o ../reference/SimpleRMSD.o ../reference/SingleDomainRMSD.o ../secondarystructure/AlphaRMSD.o ../secondarystructure/AntibetaRMSD.o ../secondarystructure/ParabetaRMSD.o ../secondarystructure/SecondaryStructureRMSD.o ../setup/Load.o ../setup/Restart.o ../setup/Units.o ../tools/Angle.o ../tools/AtomNumber.o ../tools/BiasRepresentation.o ../tools/Brent1DRootSearch.o ../tools/Citations.o ../tools/Communicator.o ../tools/ConjugateGradient.o ../tools/DLLoader.o ../tools/DynamicList.o ../tools/ERMSD.o ../tools/Exception.o ../tools/FileBase.o ../tools/ForwardDecl.o ../tools/Grid.o ../tools/HistogramBead.o ../tools/IFile.o ../tools/KernelFunctions.o ../tools/Keywords.o ../tools/LatticeReduction.o ../tools/LinkCells.o ../tools/Log.o ../tools/LoopUnroller.o ../tools/Matrix.o ../tools/MatrixSquareBracketsAccess.o ../tools/Minimise1DBrent.o ../tools/MinimiseBase.o ../tools/MolDataClass.o ../tools/MultiValue.o ../tools/NeighborList.o ../tools/OFile.o ../tools/OpenMP.o ../tools/PDB.o ../tools/Pbc.o ../tools/PlumedHandle.o ../tools/RMSD.o ../tools/Random.o ../tools/RootFindingBase.o ../tools/Stopwatch.o ../tools/Subprocess.o ../tools/SwitchingFunction.o ../tools/Tensor.o ../tools/Tools.o ../tools/Torsion.o ../tools/Tree.o ../tools/TypesafePtr.o ../tools/Units.o ../tools/Vector.o ../tools/h36.o ../vatom/ActionWithVirtualAtom.o ../vatom/Center.o ../vatom/FixedAtom.o ../vatom/Ghost.o ../vesselbase/ActionWithAveraging.o ../vesselbase/ActionWithInputVessel.o ../vesselbase/ActionWithVessel.o ../vesselbase/AltMin.o ../vesselbase/AveragingVessel.o ../vesselbase/Between.o ../vesselbase/BridgeVessel.o ../vesselbase/FunctionVessel.o ../vesselbase/Highest.o ../vesselbase/Histogram.o ../vesselbase/LessThan.o ../vesselbase/Lowest.o ../vesselbase/Max.o ../vesselbase/Mean.o ../vesselbase/Min.o ../vesselbase/Moments.o ../vesselbase/MoreThan.o ../vesselbase/OrderingVessel.o ../vesselbase/ShortcutVessel.o ../vesselbase/StoreDataVessel.o ../vesselbase/Sum.o ../vesselbase/ValueVessel.o ../vesselbase/Vessel.o ../vesselbase/VesselRegister.o ../xdrfile/xdrfile.o ../xdrfile/xdrfile_trr.o ../xdrfile/xdrfile_xtc.o ../config/ConfigInstall.o -Wl,-soname,"libplumedKernel.so" -lstdc++ -lfftw3 -lgsl -lgslcblas -lz -ldl -llapack -lblas -L/usr/local/lib -rdynamic -Wl,-Bsymbolic -fopenmp c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fPIC -Wall -pedantic -std=c++11 ../main/main.o ../wrapper/Plumed.o -o install/plumed-runtime -ldl chmod a+x install/plumed-config mkdir -p install Building Plumed.inc, runtime-linking version /usr/bin/ar cr install/libplumedWrapper.a ../wrapper/Plumed.o Building Plumed.inc, shared version chmod a+x install/plumed-mklib Building Plumed.inc, static version chmod a+x install/plumed-partial_tempering chmod a+x install/plumed-patch chmod a+x install/plumed-newcv Building Plumed.cmake chmod a+x install/plumed-selector chmod a+x install/plumed-vim2html Building Plumed.cmake, static version Building Plumed.cmake, runtime-linking version Building Plumed.cmake, shared version mkdir -p install c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fPIC -Wall -pedantic -std=c++11 ../main/main.o ../wrapper/PlumedStatic.o install/libplumedKernel.so -o install/plumed -ldl c++ -shared -o install/libplumed.so ../wrapper/PlumedStatic.o install/libplumedKernel.so -Wl,-soname,"libplumed.so" gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' gmake[5]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' /usr/local/bin/gmake PLUMED_INSTALL=Install install/kernel.o gmake[5]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' /usr/bin/ld -r -o install/kernel.o ../analysis/AnalysisBase.o ../analysis/Average.o ../analysis/AverageVessel.o ../analysis/Committor.o ../analysis/DataCollectionObject.o ../analysis/EuclideanDissimilarityMatrix.o ../analysis/FarthestPointSampling.o ../analysis/Histogram.o ../analysis/LandmarkSelectionBase.o ../analysis/LandmarkStaged.o ../analysis/OutputColvarFile.o ../analysis/OutputPDBFile.o ../analysis/PrintDissimilarityMatrix.o ../analysis/ReadAnalysisFrames.o ../analysis/ReadDissimilarityMatrix.o ../analysis/ReselectLandmarks.o ../analysis/SelectRandomFrames.o ../analysis/SelectWithStride.o ../analysis/WhamHistogram.o ../analysis/WhamWeights.o ../asmjit/arch.o ../asmjit/assembler.o ../asmjit/codebuilder.o ../asmjit/codecompiler.o ../asmjit/codeemitter.o ../asmjit/codeholder.o ../asmjit/constpool.o ../asmjit/cpuinfo.o ../asmjit/func.o ../asmjit/globals.o ../asmjit/inst.o ../asmjit/logging.o ../asmjit/operand.o ../asmjit/osutils.o ../asmjit/regalloc.o ../asmjit/runtime.o ../asmjit/string.o ../asmjit/utils.o ../asmjit/vmem.o ../asmjit/x86assembler.o ../asmjit/x86builder.o ../asmjit/x86compiler.o ../asmjit/x86inst.o ../asmjit/x86instimpl.o ../asmjit/x86internal.o ../asmjit/x86logging.o ../asmjit/x86operand.o ../asmjit/x86operand_regs.o ../asmjit/x86regalloc.o ../asmjit/zone.o ../bias/ABMD.o ../bias/Bias.o ../bias/BiasValue.o ../bias/ExtendedLagrangian.o ../bias/External.o ../bias/LWalls.o ../bias/MaxEnt.o ../bias/MetaD.o ../bias/MovingRestraint.o ../bias/PBMetaD.o ../bias/Restraint.o ../bias/ReweightBase.o ../bias/ReweightBias.o ../bias/ReweightMetad.o ../bias/ReweightTemperaturePressure.o ../bias/ReweightWham.o ../bias/UWalls.o ../blas/blas.o ../cltools/CLTool.o ../cltools/Completion.o ../cltools/Driver.o ../cltools/DriverDouble.o ../cltools/DriverFloat.o ../cltools/GenExample.o ../cltools/GenJson.o ../cltools/GenTemplate.o ../cltools/Info.o ../cltools/Manual.o ../cltools/PdbRenumber.o ../cltools/SimpleMD.o ../cltools/SumHills.o ../cltools/kT.o ../cltools/pesmd.o ../colvar/Angle.o ../colvar/Cell.o ../colvar/Colvar.o ../colvar/Constant.o ../colvar/ContactMap.o ../colvar/Coordination.o ../colvar/CoordinationBase.o ../colvar/DHEnergy.o ../colvar/DRMSD.o ../colvar/Dimer.o ../colvar/Dipole.o ../colvar/Distance.o ../colvar/EEFSolv.o ../colvar/ERMSD.o ../colvar/Energy.o ../colvar/ExtraCV.o ../colvar/Fake.o ../colvar/GHBFIX.o ../colvar/Gyration.o ../colvar/MultiRMSD.o ../colvar/PCARMSD.o ../colvar/PathMSD.o ../colvar/PathMSDBase.o ../colvar/Position.o ../colvar/ProjectionOnAxis.o ../colvar/PropertyMap.o ../colvar/Puckering.o ../colvar/RMSD.o ../colvar/Template.o ../colvar/Torsion.o ../colvar/Volume.o ../core/Action.o ../core/ActionAnyorder.o ../core/ActionAtomistic.o ../core/ActionPilot.o ../core/ActionRegister.o ../core/ActionSet.o ../core/ActionSetup.o ../core/ActionShortcut.o ../core/ActionWithArguments.o ../core/ActionWithValue.o ../core/ActionWithVirtualAtom.o ../core/Atoms.o ../core/CLTool.o ../core/CLToolMain.o ../core/CLToolRegister.o ../core/Colvar.o ../core/DataFetchingObject.o ../core/ExchangePatterns.o ../core/FlexibleBin.o ../core/GREX.o ../core/GenericMolInfo.o ../core/MDAtoms.o ../core/ModuleMap.o ../core/PlumedMain.o ../core/PlumedMainInitializer.o ../core/TargetDist.o ../core/Value.o ../core/WithCmd.o ../function/Combine.o ../function/Custom.o ../function/Ensemble.o ../function/FuncPathGeneral.o ../function/FuncPathMSD.o ../function/FuncSumHills.o ../function/Function.o ../function/LocalEnsemble.o ../function/Piecewise.o ../function/Sort.o ../function/Stats.o ../function/Target.o ../generic/Debug.o ../generic/DumpAtoms.o ../generic/DumpDerivatives.o ../generic/DumpForces.o ../generic/DumpMassCharge.o ../generic/DumpProjections.o ../generic/EffectiveEnergyDrift.o ../generic/EndPlumed.o ../generic/FitToTemplate.o ../generic/Flush.o ../generic/Group.o ../generic/Include.o ../generic/MolInfo.o ../generic/Plumed.o ../generic/Print.o ../generic/RandomExchanges.o ../generic/Read.o ../generic/ResetCell.o ../generic/Time.o ../generic/UpdateIf.o ../generic/WholeMolecules.o ../generic/WrapAround.o ../gridtools/ActionWithGrid.o ../gridtools/ActionWithInputGrid.o ../gridtools/ActionWithIntegral.o ../gridtools/AverageOnGrid.o ../gridtools/ContourFindingBase.o ../gridtools/ConvertToFES.o ../gridtools/DumpCube.o ../gridtools/DumpGrid.o ../gridtools/FindContour.o ../gridtools/FindContourSurface.o ../gridtools/FindSphericalContour.o ../gridtools/FourierTransform.o ../gridtools/GridPrintingBase.o ../gridtools/GridSearch.o ../gridtools/GridToXYZ.o ../gridtools/GridVessel.o ../gridtools/HistogramOnGrid.o ../gridtools/IntegrateGrid.o ../gridtools/InterpolateGrid.o ../isdb/CS2Backbone.o ../isdb/Caliber.o ../isdb/EMMI.o ../isdb/FretEfficiency.o ../isdb/Jcoupling.o ../isdb/Metainference.o ../isdb/MetainferenceBase.o ../isdb/NOE.o ../isdb/PRE.o ../isdb/RDC.o ../isdb/Rescale.o ../isdb/SAXS.o ../isdb/Select.o ../isdb/Selector.o ../lapack/lapack.o ../lepton/CompiledExpression.o ../lepton/ExpressionProgram.o ../lepton/ExpressionTreeNode.o ../lepton/Operation.o ../lepton/ParsedExpression.o ../lepton/Parser.o ../mapping/AdaptivePath.o ../mapping/Mapping.o ../mapping/PCAVars.o ../mapping/Path.o ../mapping/PathBase.o ../mapping/PathReparameterization.o ../mapping/PathTools.o ../mapping/PropertyMap.o ../mapping/SpathVessel.o ../mapping/TrigonometricPathVessel.o ../mapping/ZpathVessel.o ../molfile/crdplugin.o ../molfile/dcdplugin.o ../molfile/gromacsplugin.o ../molfile/pdbplugin.o ../multicolvar/ActionVolume.o ../multicolvar/AlphaBeta.o ../multicolvar/Angles.o ../multicolvar/AtomValuePack.o ../multicolvar/Bridge.o ../multicolvar/BridgedMultiColvarFunction.o ../multicolvar/CatomPack.o ../multicolvar/CenterOfMultiColvar.o ../multicolvar/CoordinationNumbers.o ../multicolvar/Density.o ../multicolvar/DihedralCorrelation.o ../multicolvar/DistanceFromContour.o ../multicolvar/Distances.o ../multicolvar/DumpMultiColvar.o ../multicolvar/FilterBetween.o ../multicolvar/FilterLessThan.o ../multicolvar/FilterMoreThan.o ../multicolvar/InPlaneDistances.o ../multicolvar/LocalAverage.o ../multicolvar/MultiColvarBase.o ../multicolvar/MultiColvarCombine.o ../multicolvar/MultiColvarDensity.o ../multicolvar/MultiColvarFilter.o ../multicolvar/MultiColvarProduct.o ../multicolvar/NumberOfLinks.o ../multicolvar/Torsions.o ../multicolvar/VolumeAround.o ../multicolvar/VolumeBetweenContours.o ../multicolvar/VolumeCavity.o ../multicolvar/VolumeGradientBase.o ../multicolvar/VolumeInCylinder.o ../multicolvar/VolumeInSphere.o ../multicolvar/VolumeTetrapore.o ../multicolvar/XAngle.o ../multicolvar/XDistances.o ../multicolvar/XYDistances.o ../multicolvar/XYTorsion.o ../reference/ArgumentOnlyDistance.o ../reference/DRMSD.o ../reference/Direction.o ../reference/DotProductDistance.o ../reference/EuclideanDistance.o ../reference/FakeFrame.o ../reference/IntermolecularDRMSD.o ../reference/IntramolecularDRMSD.o ../reference/MahalanobisDistance.o ../reference/MetricRegister.o ../reference/MultiDomainRMSD.o ../reference/NormalizedEuclideanDistance.o ../reference/OptimalRMSD.o ../reference/RMSDBase.o ../reference/ReferenceArguments.o ../reference/ReferenceAtoms.o ../reference/ReferenceConfiguration.o ../reference/ReferenceValuePack.o ../reference/SimpleRMSD.o ../reference/SingleDomainRMSD.o ../secondarystructure/AlphaRMSD.o ../secondarystructure/AntibetaRMSD.o ../secondarystructure/ParabetaRMSD.o ../secondarystructure/SecondaryStructureRMSD.o ../setup/Load.o ../setup/Restart.o ../setup/Units.o ../tools/Angle.o ../tools/AtomNumber.o ../tools/BiasRepresentation.o ../tools/Brent1DRootSearch.o ../tools/Citations.o ../tools/Communicator.o ../tools/ConjugateGradient.o ../tools/DLLoader.o ../tools/DynamicList.o ../tools/ERMSD.o ../tools/Exception.o ../tools/FileBase.o ../tools/ForwardDecl.o ../tools/Grid.o ../tools/HistogramBead.o ../tools/IFile.o ../tools/KernelFunctions.o ../tools/Keywords.o ../tools/LatticeReduction.o ../tools/LinkCells.o ../tools/Log.o ../tools/LoopUnroller.o ../tools/Matrix.o ../tools/MatrixSquareBracketsAccess.o ../tools/Minimise1DBrent.o ../tools/MinimiseBase.o ../tools/MolDataClass.o ../tools/MultiValue.o ../tools/NeighborList.o ../tools/OFile.o ../tools/OpenMP.o ../tools/PDB.o ../tools/Pbc.o ../tools/PlumedHandle.o ../tools/RMSD.o ../tools/Random.o ../tools/RootFindingBase.o ../tools/Stopwatch.o ../tools/Subprocess.o ../tools/SwitchingFunction.o ../tools/Tensor.o ../tools/Tools.o ../tools/Torsion.o ../tools/Tree.o ../tools/TypesafePtr.o ../tools/Units.o ../tools/Vector.o ../tools/h36.o ../vatom/ActionWithVirtualAtom.o ../vatom/Center.o ../vatom/FixedAtom.o ../vatom/Ghost.o ../vesselbase/ActionWithAveraging.o ../vesselbase/ActionWithInputVessel.o ../vesselbase/ActionWithVessel.o ../vesselbase/AltMin.o ../vesselbase/AveragingVessel.o ../vesselbase/Between.o ../vesselbase/BridgeVessel.o ../vesselbase/FunctionVessel.o ../vesselbase/Highest.o ../vesselbase/Histogram.o ../vesselbase/LessThan.o ../vesselbase/Lowest.o ../vesselbase/Max.o ../vesselbase/Mean.o ../vesselbase/Min.o ../vesselbase/Moments.o ../vesselbase/MoreThan.o ../vesselbase/OrderingVessel.o ../vesselbase/ShortcutVessel.o ../vesselbase/StoreDataVessel.o ../vesselbase/Sum.o ../vesselbase/ValueVessel.o ../vesselbase/Vessel.o ../vesselbase/VesselRegister.o ../xdrfile/xdrfile.o ../xdrfile/xdrfile_trr.o ../xdrfile/xdrfile_xtc.o ../config/ConfigInstall.o gmake[5]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' /usr/local/bin/gmake PLUMED_INSTALL=Install install/libplumed.a gmake[5]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' rm -f install/libplumed.a /usr/bin/ar cr install/libplumed.a install/kernel.o ../wrapper/PlumedStatic.o gmake[5]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' gmake[4]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' gmake[3]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' gmake[2]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src' gmake[1]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3' /usr/local/bin/gmake -C vim gmake[1]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/vim' ./vimsyntax.sh gmake[1]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/vim' /usr/local/bin/gmake -C python gmake[1]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/python' Python support was not configured gmake[1]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/python' LD_LIBRARY_PATH="/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib": PLUMED_PREPEND_PATH="/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib" /usr/local/bin/gmake -C json gmake[1]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/json' ./get_action_list.sh > action_list ../src/lib/plumed --no-mpi gen_json --actions action_list > syntax.json Could not find jq executable so unable to test if syntax.json is valid json. Consider running sudo apt-get install jq gmake[1]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/json' =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> plumed-2.9.3_1 depends on executable: bash - found =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for plumed-2.9.3_1 ===> Generating temporary packing list /usr/local/bin/gmake -C src install gmake[1]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src' /usr/local/bin/gmake -C lib install gmake[2]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' cd ../config ; /usr/local/bin/gmake gmake[3]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/config' /usr/local/bin/gmake PLUMED_FORCE=yes ConfigInstall.inc Config.inc version.h config.txt gmake[4]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/config' Updating ConfigInstall.inc cmp -s ConfigInstall.inc~ ConfigInstall.inc || cp ConfigInstall.inc~ ConfigInstall.inc rm ConfigInstall.inc~ Updating Config.inc cmp -s Config.inc~ Config.inc || cp Config.inc~ Config.inc rm Config.inc~ Updating version.h gmake[4]: 'config.txt' is up to date. gmake[4]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/config' /usr/local/bin/gmake Config.o ConfigInstall.o compile_options.sh gmake[4]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/config' gmake[4]: 'Config.o' is up to date. gmake[4]: 'ConfigInstall.o' is up to date. gmake[4]: 'compile_options.sh' is up to date. gmake[4]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/config' gmake[3]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/config' # /usr/local/bin/gmake uninstall mkdir -p "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/bin" mkdir -p "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/lib" mkdir -p "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/lib/pkgconfig" mkdir -p "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/include/plumed" mkdir -p "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/lib/plumed/obj" mkdir -p "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/lib/plumed/src/lib" mkdir -p "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/lib/plumed/src/config" mkdir -p "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/lib/plumed/src/colvar" /usr/local/bin/gmake install-build gmake[3]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' mkdir -p install/ /usr/local/bin/gmake PLUMED_INSTALL=Install all gmake[4]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' /usr/local/bin/gmake dirslinks gmake[5]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' *** Updating links to used modules in all directories *** /usr/local/bin/gmake ../analysis.links ../asmjit.links ../bias.links ../blas.links ../cltools.links ../colvar.links ../config.links ../core.links ../function.links ../generic.links ../gridtools.links ../isdb.links ../lapack.links ../lepton.links ../main.links ../mapping.links ../molfile.links ../multicolvar.links ../reference.links ../secondarystructure.links ../setup.links ../tools.links ../vatom.links ../vesselbase.links ../wrapper.links ../xdrfile.links gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' /usr/local/bin/gmake -C ../analysis links gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/analysis' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/analysis gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/analysis' /usr/local/bin/gmake -C ../asmjit links gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/asmjit' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/asmjit gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/asmjit' /usr/local/bin/gmake -C ../bias links gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/bias' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/bias gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/bias' /usr/local/bin/gmake -C ../blas links gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/blas' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/blas gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/blas' /usr/local/bin/gmake -C ../cltools links gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/cltools' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/cltools gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/cltools' /usr/local/bin/gmake -C ../colvar links gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/colvar' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/colvar gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/colvar' /usr/local/bin/gmake -C ../config links gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/config' Nothing to do in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/config gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/config' /usr/local/bin/gmake -C ../core links gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/core' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/core gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/core' /usr/local/bin/gmake -C ../function links gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/function' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/function gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/function' /usr/local/bin/gmake -C ../generic links gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/generic' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/generic gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/generic' /usr/local/bin/gmake -C ../gridtools links gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/gridtools' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/gridtools gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/gridtools' /usr/local/bin/gmake -C ../isdb links gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/isdb' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/isdb gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/isdb' /usr/local/bin/gmake -C ../lapack links gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lapack' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lapack gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lapack' /usr/local/bin/gmake -C ../lepton links gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lepton' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lepton gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lepton' /usr/local/bin/gmake -C ../main links gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/main' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/main gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/main' /usr/local/bin/gmake -C ../mapping links gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/mapping' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/mapping gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/mapping' /usr/local/bin/gmake -C ../molfile links gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/molfile' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/molfile gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/molfile' /usr/local/bin/gmake -C ../multicolvar links gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/multicolvar' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/multicolvar gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/multicolvar' /usr/local/bin/gmake -C ../reference links gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/reference' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/reference gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/reference' /usr/local/bin/gmake -C ../secondarystructure links gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/secondarystructure' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/secondarystructure gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/secondarystructure' /usr/local/bin/gmake -C ../setup links gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/setup' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/setup gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/setup' /usr/local/bin/gmake -C ../tools links gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/tools' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/tools gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/tools' /usr/local/bin/gmake -C ../vatom links gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/vatom' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/vatom gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/vatom' /usr/local/bin/gmake -C ../vesselbase links gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/vesselbase' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/vesselbase gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/vesselbase' /usr/local/bin/gmake -C ../wrapper links gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/wrapper' Nothing to do in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/wrapper gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/wrapper' /usr/local/bin/gmake -C ../xdrfile links gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/xdrfile' Verify modules and create links in /wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/xdrfile gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/xdrfile' gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' gmake[5]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' /usr/local/bin/gmake dirs gmake[5]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' *** Compiling all directories *** /usr/local/bin/gmake ../analysis ../asmjit ../bias ../blas ../cltools ../colvar ../config ../core ../function ../generic ../gridtools ../isdb ../lapack ../lepton ../main ../mapping ../molfile ../multicolvar ../reference ../secondarystructure ../setup ../tools ../vatom ../vesselbase ../wrapper ../xdrfile gmake[6]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' /usr/local/bin/gmake -C ../analysis obj gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/analysis' gmake[7]: Nothing to be done for 'obj'. gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/analysis' /usr/local/bin/gmake -C ../asmjit obj gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/asmjit' gmake[7]: Nothing to be done for 'obj'. gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/asmjit' /usr/local/bin/gmake -C ../bias obj gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/bias' gmake[7]: Nothing to be done for 'obj'. gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/bias' /usr/local/bin/gmake -C ../blas obj gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/blas' gmake[7]: Nothing to be done for 'obj'. gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/blas' /usr/local/bin/gmake -C ../cltools obj gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/cltools' gmake[7]: Nothing to be done for 'obj'. gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/cltools' /usr/local/bin/gmake -C ../colvar obj gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/colvar' gmake[7]: Nothing to be done for 'obj'. gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/colvar' /usr/local/bin/gmake -C ../config obj gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/config' /usr/local/bin/gmake PLUMED_FORCE=yes ConfigInstall.inc Config.inc version.h config.txt gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/config' Updating ConfigInstall.inc cmp -s ConfigInstall.inc~ ConfigInstall.inc || cp ConfigInstall.inc~ ConfigInstall.inc rm ConfigInstall.inc~ Updating Config.inc cmp -s Config.inc~ Config.inc || cp Config.inc~ Config.inc rm Config.inc~ Updating version.h gmake[8]: 'config.txt' is up to date. gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/config' /usr/local/bin/gmake Config.o ConfigInstall.o compile_options.sh gmake[8]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/config' gmake[8]: 'Config.o' is up to date. gmake[8]: 'ConfigInstall.o' is up to date. gmake[8]: 'compile_options.sh' is up to date. gmake[8]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/config' gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/config' /usr/local/bin/gmake -C ../core obj gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/core' gmake[7]: Nothing to be done for 'obj'. gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/core' /usr/local/bin/gmake -C ../function obj gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/function' gmake[7]: Nothing to be done for 'obj'. gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/function' /usr/local/bin/gmake -C ../generic obj gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/generic' gmake[7]: Nothing to be done for 'obj'. gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/generic' /usr/local/bin/gmake -C ../gridtools obj gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/gridtools' gmake[7]: Nothing to be done for 'obj'. gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/gridtools' /usr/local/bin/gmake -C ../isdb obj gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/isdb' gmake[7]: Nothing to be done for 'obj'. gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/isdb' /usr/local/bin/gmake -C ../lapack obj gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lapack' gmake[7]: Nothing to be done for 'obj'. gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lapack' /usr/local/bin/gmake -C ../lepton obj gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lepton' gmake[7]: Nothing to be done for 'obj'. gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lepton' /usr/local/bin/gmake -C ../main obj gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/main' gmake[7]: Nothing to be done for 'obj'. gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/main' /usr/local/bin/gmake -C ../mapping obj gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/mapping' gmake[7]: Nothing to be done for 'obj'. gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/mapping' /usr/local/bin/gmake -C ../molfile obj gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/molfile' gmake[7]: Nothing to be done for 'obj'. gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/molfile' /usr/local/bin/gmake -C ../multicolvar obj gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/multicolvar' gmake[7]: Nothing to be done for 'obj'. gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/multicolvar' /usr/local/bin/gmake -C ../reference obj gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/reference' gmake[7]: Nothing to be done for 'obj'. gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/reference' /usr/local/bin/gmake -C ../secondarystructure obj gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/secondarystructure' gmake[7]: Nothing to be done for 'obj'. gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/secondarystructure' /usr/local/bin/gmake -C ../setup obj gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/setup' gmake[7]: Nothing to be done for 'obj'. gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/setup' /usr/local/bin/gmake -C ../tools obj gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/tools' gmake[7]: Nothing to be done for 'obj'. gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/tools' /usr/local/bin/gmake -C ../vatom obj gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/vatom' gmake[7]: Nothing to be done for 'obj'. gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/vatom' /usr/local/bin/gmake -C ../vesselbase obj gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/vesselbase' gmake[7]: Nothing to be done for 'obj'. gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/vesselbase' /usr/local/bin/gmake -C ../wrapper obj gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/wrapper' gmake[7]: Nothing to be done for 'obj'. gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/wrapper' /usr/local/bin/gmake -C ../xdrfile obj gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/xdrfile' gmake[7]: Nothing to be done for 'obj'. gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/xdrfile' gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' gmake[5]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' /usr/local/bin/gmake lib gmake[5]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' Building Plumed.inc Building Plumed.inc, static version Building Plumed.cmake Building Plumed.cmake, static version chmod a+x install/plumed-config chmod a+x install/plumed-mklib chmod a+x install/plumed-newcv chmod a+x install/plumed-partial_tempering chmod a+x install/plumed-patch chmod a+x install/plumed-selector chmod a+x install/plumed-vim2html Building Plumed.inc, runtime-linking version Building Plumed.inc, shared version Building Plumed.cmake, runtime-linking version Building Plumed.cmake, shared version gmake[5]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' gmake[4]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' /usr/local/bin/gmake PLUMED_INSTALL=Install install/kernel.o gmake[4]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' gmake[4]: 'install/kernel.o' is up to date. gmake[4]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' /usr/local/bin/gmake PLUMED_INSTALL=Install install/libplumed.a gmake[4]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' gmake[4]: 'install/libplumed.a' is up to date. gmake[4]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' gmake[3]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' /usr/local/bin/gmake install-html gmake[3]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' if test -d ../../user-doc/html ; then mkdir -p "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/share/doc/plumed" && cd ../../ && tar cf - user-doc/html | tar xf - -C "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/share/doc/plumed/" ; fi if test -d ../../developer-doc/html ; then mkdir -p "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/share/doc/plumed" && cd ../../ && tar cf - developer-doc/html | tar xf - -C "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/share/doc/plumed/" ; fi if test -d ../../developer-doc/coverage ; then mkdir -p "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/share/doc/plumed" && cd ../../ && tar cf - developer-doc/coverage | tar xf - -C "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/share/doc/plumed/" ; fi if test -f ../../user-doc/manual.pdf ; then mkdir -p "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/share/doc/plumed/user-doc" && cp ../../user-doc/manual.pdf "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/share/doc/plumed/user-doc/" ; fi gmake[3]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' cd ../../ ; tar cf - patches scripts | tar xf - -C "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/lib/plumed/" cp ../colvar/Template.cpp "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/lib/plumed/src/colvar/" grep -v "^link_uninstalled=" ../config/compile_options.sh > "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/lib/plumed/src/config/compile_options.sh" cp ../config/config.txt "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/lib/plumed/src/config/config.txt" cp install/libplumed.a "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/lib/" /usr/local/bin/gmake install-headers gmake[3]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' bash ../maketools/install.headers "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/include/plumed/" analysis asmjit bias blas cltools colvar config core function generic gridtools isdb lapack lepton main mapping molfile multicolvar reference secondarystructure setup tools vatom vesselbase wrapper xdrfile gmake[3]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' cp install/"plumed" "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/bin/" cp install/plumed-patch "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/bin/plumed-patch" cp install/plumed-config "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/bin/plumed-config" cp install/Plumed.cmake* "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/lib/plumed/src/lib/" cp install/Plumed.inc* "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/lib/plumed/src/lib/" for file in config mklib newcv partial_tempering patch selector vim2html ; do cp install/plumed-$file "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/lib/plumed/plumed-$file" ; done cp install/lib"plumed".so "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/lib/" cp install/lib"plumed"Kernel.so "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/lib/" if test -e install/"plumed"-runtime ; then cp install/"plumed"-runtime "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/lib/plumed/plumed-runtime" ; fi cp install/libplumedWrapper.a "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/lib/" cp install/modulefile "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/lib/plumed/modulefile" cp install/pkgconfig "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/lib/pkgconfig/plumed.pc" cp install/pkgconfigWrapper "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/lib/pkgconfig/plumedWrapper.pc" cp install/pkgconfigInternals "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/lib/pkgconfig/plumedInternals.pc" if test -d ../../vim/syntax ; then mkdir -p "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/lib/plumed" && cd ../../ && tar cf - vim/syntax | tar xf - -C "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/lib/plumed/" ; fi if test -d ../../vim/help ; then mkdir -p "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/lib/plumed" && cd ../../ && tar cf - vim/help | tar xf - -C "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/lib/plumed/" ; fi if test -f ../../vim/scripts.vim ; then mkdir -p "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/lib/plumed/vim" && cp ../../vim/scripts.vim "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/lib/plumed/vim/" ; fi if test -f ../../json/syntax.json ; then mkdir -p "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/lib/plumed/json" && cp ../../json/syntax.json "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/lib/plumed/json/" ; fi mkdir -p "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/lib/plumed/fortran" cp ../../fortran/plumed.f90 "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/lib/plumed/fortran/" cp ../../fortran/plumed_f08.f90 "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/lib/plumed/fortran/" chmod -R go+rX,go-w "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/lib/plumed" chmod -R go+rX,go-w "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/include/plumed" chmod -R go+rX,go-w "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/bin/plumed" chmod -R go+rX,go-w "/wrkdirs/usr/ports/science/plumed/work/stage/usr/local/bin/plumed-patch" *** PLUMED has been installed *** WARNING: Staged install with DESTDIR = /wrkdirs/usr/ports/science/plumed/work/stage Install prefix : /usr/local Full name : plumed Setup your environment - Ensure this is in your execution path : /usr/local/bin - Ensure this is in your include path : /usr/local/include - Ensure this is in your library path : /usr/local/lib - Ensure this is in your PKG_CONFIG_PATH path : /usr/local/lib/pkgconfig For runtime binding: - Set this environment variable : PLUMED_KERNEL=/usr/local/lib/libplumedKernel.so To create a tcl module that sets all the variables above, use this one as a starting point: /usr/local/lib/plumed/modulefile To uninstall, remove the following files and directories: /usr/local/lib/plumed /usr/local/share/doc/plumed /usr/local/include/plumed /usr/local/bin/plumed /usr/local/bin/plumed-patch /usr/local/bin/plumed-config /usr/local/lib/pkgconfig/plumed.pc /usr/local/lib/libplumed.so /usr/local/lib/libplumedKernel.so A vim plugin can be found here: /usr/local/lib/plumed/vim/ Copy it to /wrkdirs/usr/ports/science/plumed/work/.vim/ directory Alternatively: - Set this environment variable : PLUMED_VIMPATH=/usr/local/lib/plumed/vim - Add the command 'let &runtimepath.=','.$PLUMED_VIMPATH' to your .vimrc file From vim, you can use :set syntax=plumed to enable it gmake[2]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src/lib' gmake[1]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed-2.9.3/src' ====> Compressing man pages (compress-man) =========================================================================== =================================================== ===== env: 'PKG_NOTES=build_timestamp ports_top_git_hash ports_top_checkout_unclean port_git_hash port_checkout_unclean built_by' 'PKG_NOTE_build_timestamp=2025-12-10T11:30:59+0000' 'PKG_NOTE_ports_top_git_hash=62d8b1999233' 'PKG_NOTE_ports_top_checkout_unclean=no' 'PKG_NOTE_port_git_hash=fc4dbd235dee' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.2' NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building packages for plumed-2.9.3_1 ===> Building plumed-2.9.3_1 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for plumed-2.9.3_1 build of science/plumed | plumed-2.9.3_1 ended at Wed Dec 10 06:34:03 EST 2025 build time: 00:03:05