------------------------------------------------------------------------------- -- Phase: Environment ------------------------------------------------------------------------------- NO_DEPENDS=1 UNAME_r=6.5 UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=unknown UNAME_s=DragonFly PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SSL_NO_VERIFY_PEER=1 LANG=C HOME=/root USER=root TERM=dumb SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: showconfig ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: CONFIGURE_ENV ------------------------------------------------------------------------------- MAKE=gmake PKG_CONFIG=pkgconf XDG_DATA_HOME=/construction/science/plumed XDG_CONFIG_HOME=/construction/science/plumed XDG_CACHE_HOME=/construction/science/plumed/.cache HOME=/construction/science/plumed TMPDIR="/tmp" PATH=/construction/science/plumed/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin PKG_CONFIG_LIBDIR=/construction/science/plumed/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc80 DEFAULT_AUTOCONF=2.71 CMAKE_PREFIX_PATH="/usr/local" CONFIG_SITE=/xports/Templates/config.site lt_cv_sys_max_cmd_len=262144 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: CONFIGURE_ARGS ------------------------------------------------------------------------------- --enable-shared --disable-python --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: MAKE_ENV ------------------------------------------------------------------------------- XDG_DATA_HOME=/construction/science/plumed XDG_CONFIG_HOME=/construction/science/plumed XDG_CACHE_HOME=/construction/science/plumed/.cache HOME=/construction/science/plumed TMPDIR="/tmp" PATH=/construction/science/plumed/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin PKG_CONFIG_LIBDIR=/construction/science/plumed/.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 CCVER=gcc80 DEFAULT_AUTOCONF=2.71 PREFIX=/usr/local LOCALBASE=/usr/local NOPROFILE=1 CC="cc" CFLAGS="-pipe -O2 -isystem /usr/local/include -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-isystem /usr/local/include" LDFLAGS=" " LIBS="-L/usr/local/lib" CXX="c++" CXXFLAGS=" -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include " MANPREFIX="/usr/local" 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" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: MAKE_ARGS ------------------------------------------------------------------------------- DESTDIR=/construction/science/plumed/stage SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: PLIST_SUB ------------------------------------------------------------------------------- OSREL=6.5 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/plumed" EXAMPLESDIR="share/examples/plumed" DATADIR="share/plumed" WWWDIR="www/plumed" ETCDIR="etc/plumed" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: 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 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: /etc/make.conf ------------------------------------------------------------------------------- DPORTS_BUILDER=yes DISABLE_LICENSES=yes DEFAULT_VERSIONS=ssl=openssl FORCE_PACKAGE=yes DEVELOPER=yes DFLY_STING_XFAIL=yes USE_PACKAGE_DEPENDS_ONLY=yes PORTSDIR=/xports PORT_DBDIR=/options PKG_DBDIR=/var/db/pkg PKG_CACHEDIR=/var/cache/pkg PKG_COMPRESSION_FORMAT=.tgz DEVELOPER=1 WITH_CCACHE_BUILD=yes CCACHE_DIR=/ccache UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=600503 OSVERSION=9999999 OSREL=6.5 _OSRELEASE=6.5-SYNTH DISTDIR=/distfiles WRKDIRPREFIX=/construction BATCH=yes PACKAGE_BUILDING=yes PKG_CREATE_VERBOSE=yes MAKE_JOBS_NUMBER=13 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/indexinfo-0.3.1.pkg Installing /packages/All/gettext-runtime-0.21.1.pkg Installing /packages/All/ncurses-6.4.pkg ===== Message from ncurses-6.4: -- To get the terminfo database please install the terminfo-db package: pkg install terminfo-db Installing /packages/All/readline-8.2.1.pkg Installing /packages/All/bash-5.2.15.pkg Installing /packages/All/gmake-4.3_2.pkg Installing /packages/All/pkgconf-1.8.1,1.pkg Installing /packages/All/autoconf-switch-20220527.pkg Installing /packages/All/m4-1.4.19,1.pkg Installing /packages/All/perl5-5.32.1_3.pkg Installing /packages/All/autoconf-2.71.pkg Installing /packages/All/automake-1.16.5.pkg Installing /packages/All/ccache-3.7.12_4.pkg 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 gcc create symlink for gcc (world) create symlink for g++ create symlink for g++ (world) ===== Message from ccache-3.7.12_4: -- NOTE: Please read /usr/local/share/doc/ccache/ccache-howto-freebsd.txt for information on using ccache with FreeBSD ports and src. Installing /packages/All/gmp-6.2.1.pkg Installing /packages/All/mpfr-4.2.0_1,1.pkg Installing /packages/All/mpc-1.3.1_1.pkg UNFLAVORED devel/binutils -> use devel/binutils@native Installing /packages/All/liblz4-1.9.4,1.pkg Installing /packages/All/zstd-1.5.5.pkg Installing /packages/All/binutils-2.40_4,1.pkg Installing /packages/All/gcc12-12.2.0_6.pkg create symlink for gcc12 create symlink for gcc12 (world) create symlink for g++12 create symlink for g++12 (world) create symlink for cpp12 create symlink for cpp12 (world) ===== Message from gcc12-12.2.0_6: -- 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/gcc12 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. Installing /packages/All/blas-3.11.0_1.pkg Installing /packages/All/fftw3-3.3.10_3.pkg Installing /packages/All/gsl-2.7.1.pkg Installing /packages/All/lapack-3.11.0_1.pkg UNFLAVORED devel/binutils -> use devel/binutils@native SUCCEEDED 00:00:22 ------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- ===> plumed-2.8.0_1 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> plumed-2.8.0_1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by plumed-2.8.0_1 for building SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> plumed-2.8.0_1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by plumed-2.8.0_1 for building => SHA256 Checksum OK for plumed-2.8.0.tgz. SUCCEEDED 00:00:02 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> plumed-2.8.0_1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by plumed-2.8.0_1 for building ===> Extracting for plumed-2.8.0_1 ===> plumed-2.8.0_1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by plumed-2.8.0_1 for building => SHA256 Checksum OK for plumed-2.8.0.tgz. Extracted Memory Use: 450.76M SUCCEEDED 00:00:06 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for plumed-2.8.0_1 ===> Applying ports patches for plumed-2.8.0_1 from /xports/science/plumed/files /usr/bin/env WRKSRC=/construction/science/plumed/plumed-2.8.0 REWARNFILE=/construction/science/plumed/reinplace_warnings.txt /bin/sh /xports/Mk/Scripts/sed_checked.sh -e 's,FreeBSD,FreeBSD|DragonFly,g' /construction/science/plumed/plumed-2.8.0/configure.ac SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> plumed-2.8.0_1 depends on executable: bash - found ===> plumed-2.8.0_1 depends on package: gmake>=4.3 - found ===> plumed-2.8.0_1 depends on package: pkgconf>=1.3.0_1 - found ===> plumed-2.8.0_1 depends on package: autoconf>=2.71 - found ===> plumed-2.8.0_1 depends on package: automake>=1.16.5 - found ===> plumed-2.8.0_1 depends on file: /usr/local/bin/ccache - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- ===> plumed-2.8.0_1 depends on shared library: libblas.so - found (/usr/local/lib/libblas.so) ===> plumed-2.8.0_1 depends on shared library: libfftw3.so - found (/usr/local/lib/libfftw3.so) ===> plumed-2.8.0_1 depends on shared library: libgsl.so - found (/usr/local/lib/libgsl.so) ===> plumed-2.8.0_1 depends on shared library: liblapack.so - found (/usr/local/lib/liblapack.so) SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> plumed-2.8.0_1 depends on executable: bash - found ===> plumed-2.8.0_1 depends on package: gmake>=4.3 - found ===> plumed-2.8.0_1 depends on package: pkgconf>=1.3.0_1 - found ===> plumed-2.8.0_1 depends on package: autoconf>=2.71 - found ===> plumed-2.8.0_1 depends on package: automake>=1.16.5 - found ===> plumed-2.8.0_1 depends on file: /usr/local/bin/ccache - found ===> plumed-2.8.0_1 depends on shared library: libblas.so - found (/usr/local/lib/libblas.so) ===> plumed-2.8.0_1 depends on shared library: libfftw3.so - found (/usr/local/lib/libfftw3.so) ===> plumed-2.8.0_1 depends on shared library: libgsl.so - found (/usr/local/lib/libgsl.so) ===> plumed-2.8.0_1 depends on shared library: liblapack.so - found (/usr/local/lib/liblapack.so) ===> Configuring for plumed-2.8.0_1 configure: loading site script /xports/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: -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include configure: Initial CPPFLAGS: -isystem /usr/local/include configure: Initial CFLAGS: -pipe -O2 -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... 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 ld -r -o... yes checking whether static libraries can be created with 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 SUCCEEDED 00:00:11 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for plumed-2.8.0_1 gmake[2]: Entering directory '/construction/science/plumed/plumed-2.8.0' gmake lib gmake[3]: Entering directory '/construction/science/plumed/plumed-2.8.0' gmake -C src gmake[4]: Entering directory '/construction/science/plumed/plumed-2.8.0/src' gmake -C lib gmake[5]: Entering directory '/construction/science/plumed/plumed-2.8.0/src/lib' gmake dirslinks gmake[6]: Entering directory '/construction/science/plumed/plumed-2.8.0/src/lib' *** Updating links to used modules in all directories *** 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 '/construction/science/plumed/plumed-2.8.0/src/lib' gmake -C ../analysis links gmake -C ../asmjit links gmake -C ../bias links gmake -C ../blas links gmake -C ../cltools links gmake -C ../colvar links gmake -C ../config links gmake -C ../core links gmake -C ../function links gmake -C ../generic links gmake -C ../gridtools links gmake -C ../isdb links gmake[8]: Entering directory '/construction/science/plumed/plumed-2.8.0/src/blas' Verify modules and create links in /construction/science/plumed/plumed-2.8.0/src/blas gmake[8]: Leaving directory '/construction/science/plumed/plumed-2.8.0/src/blas' gmake[8]: Entering directory '/construction/science/plumed/plumed-2.8.0/src/function' Verify modules and create links in /construction/science/plumed/plumed-2.8.0/src/function gmake[8]: Entering directory '/construction/science/plumed/plumed-2.8.0/src/bias' gmake[8]: Entering directory '/construction/science/plumed/plumed-2.8.0/src/analysis' gmake[8]: Entering directory '/construction/science/plumed/plumed-2.8.0/src/gridtools' gmake[8]: Entering directory '/construction/science/plumed/plumed-2.8.0/src/generic' gmake -C ../lapack links Verify modules and create links in /construction/science/plumed/plumed-2.8.0/src/gridtools Verify modules and create links in /construction/science/plumed/plumed-2.8.0/src/generic gmake -C ../lepton links Verify modules and create links in /construction/science/plumed/plumed-2.8.0/src/analysis gmake[8]: Entering directory '/construction/science/plumed/plumed-2.8.0/src/lapack' Verify modules and create links in /construction/science/plumed/plumed-2.8.0/src/lapack gmake[8]: Entering directory '/construction/science/plumed/plumed-2.8.0/src/asmjit' gmake[8]: Entering directory '/construction/science/plumed/plumed-2.8.0/src/isdb' Verify modules and create links in /construction/science/plumed/plumed-2.8.0/src/bias gmake[8]: Entering directory '/construction/science/plumed/plumed-2.8.0/src/config' Nothing to do in /construction/science/plumed/plumed-2.8.0/src/config gmake[8]: Leaving directory '/construction/science/plumed/plumed-2.8.0/src/config' gmake -C ../main links gmake[8]: Entering directory '/construction/science/plumed/plumed-2.8.0/src/colvar' Verify modules and create links in /construction/science/plumed/plumed-2.8.0/src/isdb gmake[8]: Entering directory '/construction/science/plumed/plumed-2.8.0/src/cltools' gmake[8]: Entering directory '/construction/science/plumed/plumed-2.8.0/src/lepton' Verify modules and create links in /construction/science/plumed/plumed-2.8.0/src/lepton Verify modules and create links in /construction/science/plumed/plumed-2.8.0/src/cltools gmake[8]: Entering directory '/construction/science/plumed/plumed-2.8.0/src/core' Verify modules and create links in /construction/science/plumed/plumed-2.8.0/src/colvar Verify modules and create links in /construction/science/plumed/plumed-2.8.0/src/asmjit gmake[8]: Leaving directory '/construction/science/plumed/plumed-2.8.0/src/lapack' gmake -C ../mapping links gmake[8]: Leaving directory '/construction/science/plumed/plumed-2.8.0/src/asmjit' gmake -C ../molfile links gmake[8]: Entering directory '/construction/science/plumed/plumed-2.8.0/src/main' Verify modules and create links in /construction/science/plumed/plumed-2.8.0/src/main Verify modules and create links in /construction/science/plumed/plumed-2.8.0/src/core gmake[8]: Entering directory '/construction/science/plumed/plumed-2.8.0/src/mapping' Verify modules and create links in /construction/science/plumed/plumed-2.8.0/src/mapping gmake[8]: Entering directory '/construction/science/plumed/plumed-2.8.0/src/molfile' Verify modules and create links in /construction/science/plumed/plumed-2.8.0/src/molfile gmake[8]: Leaving directory '/construction/science/plumed/plumed-2.8.0/src/molfile' gmake -C ../multicolvar links gmake[8]: Entering directory '/construction/science/plumed/plumed-2.8.0/src/multicolvar' Verify modules and create links in /construction/science/plumed/plumed-2.8.0/src/multicolvar gmake[8]: Leaving directory '/construction/science/plumed/plumed-2.8.0/src/main' gmake -C ../reference links gmake[8]: Leaving directory '/construction/science/plumed/plumed-2.8.0/src/gridtools' gmake -C ../secondarystructure links gmake[8]: Entering directory '/construction/science/plumed/plumed-2.8.0/src/secondarystructure' Verify modules and create links in /construction/science/plumed/plumed-2.8.0/src/secondarystructure gmake[8]: Leaving directory '/construction/science/plumed/plumed-2.8.0/src/lepton' gmake[8]: Entering directory '/construction/science/plumed/plumed-2.8.0/src/reference' gmake -C ../setup links Verify modules and create links in /construction/science/plumed/plumed-2.8.0/src/reference gmake[8]: Entering directory '/construction/science/plumed/plumed-2.8.0/src/setup' Verify modules and create links in /construction/science/plumed/plumed-2.8.0/src/setup gmake[8]: Leaving directory '/construction/science/plumed/plumed-2.8.0/src/function' gmake -C ../tools links gmake[8]: Leaving directory '/construction/science/plumed/plumed-2.8.0/src/bias' gmake -C ../vatom links gmake[8]: Leaving directory '/construction/science/plumed/plumed-2.8.0/src/generic' gmake -C ../vesselbase links gmake[8]: Entering directory '/construction/science/plumed/plumed-2.8.0/src/vatom' Verify modules and create links in /construction/science/plumed/plumed-2.8.0/src/vatom gmake[8]: Entering directory '/construction/science/plumed/plumed-2.8.0/src/tools' gmake[8]: Entering directory '/construction/science/plumed/plumed-2.8.0/src/vesselbase' Verify modules and create links in /construction/science/plumed/plumed-2.8.0/src/tools Verify modules and create links in /construction/science/plumed/plumed-2.8.0/src/vesselbase gmake[8]: Leaving directory '/construction/science/plumed/plumed-2.8.0/src/isdb' gmake -C ../wrapper links gmake[8]: Entering directory '/construction/science/plumed/plumed-2.8.0/src/wrapper' Nothing to do in /construction/science/plumed/plumed-2.8.0/src/wrapper gmake[8]: Leaving directory '/construction/science/plumed/plumed-2.8.0/src/wrapper' gmake -C ../xdrfile links gmake[8]: Entering directory '/construction/science/plumed/plumed-2.8.0/src/xdrfile' Verify modules and create links in /construction/science/plumed/plumed-2.8.0/src/xdrfile gmake[8]: Leaving directory '/construction/science/plumed/plumed-2.8.0/src/xdrfile' gmake[8]: Leaving directory '/construction/science/plumed/plumed-2.8.0/src/cltools' gmake[8]: Leaving directory '/construction/science/plumed/plumed-2.8.0/src/vatom' gmake[8]: Leaving directory '/construction/science/plumed/plumed-2.8.0/src/reference' gmake[8]: Leaving directory '/construction/science/plumed/plumed-2.8.0/src/setup' gmake[8]: Leaving directory '/construction/science/plumed/plumed-2.8.0/src/tools' gmake[8]: Leaving directory '/construction/science/plumed/plumed-2.8.0/src/mapping' gmake[8]: Leaving directory '/construction/science/plumed/plumed-2.8.0/src/analysis' gmake[8]: Leaving directory '/construction/science/plumed/plumed-2.8.0/src/secondarystructure' gmake[8]: Leaving directory '/construction/science/plumed/plumed-2.8.0/src/vesselbase' gmake[8]: Leaving directory '/construction/science/plumed/plumed-2.8.0/src/core' gmake[8]: Leaving directory '/construction/science/plumed/plumed-2.8.0/src/multicolvar' gmake[8]: Leaving directory '/construction/science/plumed/plumed-2.8.0/src/colvar' gmake[7]: Leaving directory '/construction/science/plumed/plumed-2.8.0/src/lib' gmake[6]: Leaving directory '/construction/science/plumed/plumed-2.8.0/src/lib' gmake dirs gmake[6]: Entering directory '/construction/science/plumed/plumed-2.8.0/src/lib' *** Compiling all directories *** 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 '/construction/science/plumed/plumed-2.8.0/src/lib' gmake -C ../analysis obj gmake -C ../asmjit obj gmake -C ../bias obj gmake -C ../blas obj gmake -C ../cltools obj gmake -C ../colvar obj gmake -C ../config obj gmake -C ../core obj gmake -C ../function obj gmake -C ../generic obj gmake -C ../gridtools obj gmake -C ../isdb obj gmake[8]: Entering directory '/construction/science/plumed/plumed-2.8.0/src/blas' gmake -C ../lapack obj compiling blas.cpp gmake[8]: Entering directory '/construction/science/plumed/plumed-2.8.0/src/lapack' compiling lapack.cpp gmake[8]: Entering directory '/construction/science/plumed/plumed-2.8.0/src/colvar' compiling Angle.cpp gmake[8]: Entering directory '/construction/science/plumed/plumed-2.8.0/src/asmjit' compiling arch.cpp gmake[8]: Entering directory '/construction/science/plumed/plumed-2.8.0/src/cltools' gmake[8]: Entering directory '/construction/science/plumed/plumed-2.8.0/src/config' gmake PLUMED_FORCE=yes ConfigInstall.inc Config.inc version.h config.txt gmake[8]: Entering directory '/construction/science/plumed/plumed-2.8.0/src/gridtools' gmake[8]: Entering directory '/construction/science/plumed/plumed-2.8.0/src/isdb' gmake[8]: Entering directory '/construction/science/plumed/plumed-2.8.0/src/analysis' compiling CS2Backbone.cpp gmake[8]: Entering directory '/construction/science/plumed/plumed-2.8.0/src/generic' compiling CLTool.cpp compiling ActionWithGrid.cpp gmake[9]: Entering directory '/construction/science/plumed/plumed-2.8.0/src/config' compiling Debug.cpp gmake[8]: Entering directory '/construction/science/plumed/plumed-2.8.0/src/core' gmake[8]: Leaving directory '/construction/science/plumed/plumed-2.8.0/src/blas' Updating ConfigInstall.inc gmake[8]: Entering directory '/construction/science/plumed/plumed-2.8.0/src/function' gmake[8]: Entering directory '/construction/science/plumed/plumed-2.8.0/src/bias' compiling DumpAtoms.cpp compiling Action.cpp compiling Combine.cpp compiling ABMD.cpp cmp -s ConfigInstall.inc~ ConfigInstall.inc || cp ConfigInstall.inc~ ConfigInstall.inc rm ConfigInstall.inc~ compiling AnalysisBase.cpp Updating Config.inc cmp -s Config.inc~ Config.inc || cp Config.inc~ Config.inc rm Config.inc~ Updating version.h gmake[8]: Leaving directory '/construction/science/plumed/plumed-2.8.0/src/lapack' compiling Average.cpp Updating config.txt file compiling Cell.cpp { ../maketools/make-scripts-options.sh ; cat completion.sh ; }| ../maketools/xxd > completion.xxd compiling assembler.cpp compiling ActionWithInputGrid.cpp compiling ActionAnyorder.cpp ../../scripts/selector.sh: line 219: python: command not found compiling Bias.cpp compiling Caliber.cpp compiling Custom.cpp compiling Colvar.cpp In file included from xdrfile/xdrfile_xtc.h:1, from DumpAtoms.cpp:34: xdrfile/../../xdrfile/xdrfile_xtc.h:5:2: warning: "/*" within comment [-Wcomment] /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- In file included from xdrfile/../../xdrfile/xdrfile_xtc.h:37, from xdrfile/xdrfile_xtc.h:1, from DumpAtoms.cpp:34: xdrfile/../../xdrfile/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- In file included from xdrfile/xdrfile_trr.h:1, from DumpAtoms.cpp:35: xdrfile/../../xdrfile/xdrfile_trr.h:5:2: warning: "/*" within comment [-Wcomment] /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- compiling Driver.cpp compiling DriverDouble.cpp compiling codebuilder.cpp compiling DumpDerivatives.cpp compiling ActionAtomistic.cpp compiling AverageVessel.cpp compiling ActionWithIntegral.cpp compiling codecompiler.cpp Caliber.cpp: In member function 'double PLMD::isdb::Caliber::getSpline(unsigned int)': Caliber.cpp:273:14: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] if(tindex+1 Makefile.conf.xxd compiling FretEfficiency.cpp compiling AverageOnGrid.cpp compiling Constant.cpp In file included from xdrfile/xdrfile_trr.h:1, from Driver.cpp:38, from DriverDouble.cpp:23: xdrfile/../../xdrfile/xdrfile_trr.h:5:2: warning: "/*" within comment [-Wcomment] /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- In file included from xdrfile/../../xdrfile/xdrfile_trr.h:37, from xdrfile/xdrfile_trr.h:1, from Driver.cpp:38, from DriverDouble.cpp:23: xdrfile/../../xdrfile/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- In file included from xdrfile/xdrfile_xtc.h:1, from Driver.cpp:39, from DriverDouble.cpp:23: xdrfile/../../xdrfile/xdrfile_xtc.h:5:2: warning: "/*" within comment [-Wcomment] /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- compiling DriverFloat.cpp compiling BiasValue.cpp Building compile_options.sh, a sourceable bash script with some compilation options compiling DumpMassCharge.cpp compiling Jcoupling.cpp compiling Config.cpp compiling FuncPathGeneral.cpp compiling codeholder.cpp compiling Committor.cpp ActionAtomistic.cpp: In member function 'void PLMD::ActionAtomistic::requestAtoms(const std::vector&, bool)': ActionAtomistic.cpp:71:26: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] if(indexes[i].index()>=n) { std::string num; Tools::convert( indexes[i].serial(),num ); error("atom " + num + " out of range"); } ~~~~~~~~~~~~~~~~~~^~~ ActionAtomistic.cpp: In member function 'void PLMD::ActionAtomistic::calculateAtomicNumericalDerivatives(PLMD::ActionWithValue*, const unsigned int&)': ActionAtomistic.cpp:109:17: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long unsigned int'} [-Wsign-compare] for(int i=0; igetOutputQuantity(j); ~^~~~~ ActionAtomistic.cpp:134:17: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long unsigned int'} [-Wsign-compare] for(int j=0; j >&, std::vector&)': ActionAtomistic.cpp:179:28: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'const int' [-Wsign-compare] for(unsigned i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for(int i=0; i PLMD::isdb::EMMI::read_exp_errors(std::__cxx11::string)': EMMI.cpp:954:26: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] for(unsigned i=0; i, int>::value_type' {aka 'int'} and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] if(GMM_d_beta_[i]>=GMM_d_grps_.size()) error("Check Beta values"); compiling Metainference.cpp compiling DumpProjections.cpp compiling ConvertToFES.cpp compiling ActionSet.cpp compiling ExtendedLagrangian.cpp compiling cpuinfo.cpp compiling FuncSumHills.cpp compiling GenTemplate.cpp compiling Coordination.cpp compiling Function.cpp compiling External.cpp compiling FarthestPointSampling.cpp compiling func.cpp compiling EffectiveEnergyDrift.cpp compiling LWalls.cpp compiling LocalEnsemble.cpp compiling ActionSetup.cpp compiling Histogram.cpp compiling CoordinationBase.cpp compiling LandmarkSelectionBase.cpp compiling Info.cpp compiling Piecewise.cpp compiling globals.cpp compiling MetainferenceBase.cpp compiling MaxEnt.cpp compiling DumpCube.cpp compiling EndPlumed.cpp compiling DHEnergy.cpp compiling Manual.cpp compiling inst.cpp compiling MetaD.cpp compiling NOE.cpp compiling MovingRestraint.cpp compiling PdbRenumber.cpp compiling FitToTemplate.cpp compiling DRMSD.cpp compiling LandmarkStaged.cpp compiling DumpGrid.cpp compiling Sort.cpp compiling OutputColvarFile.cpp compiling ActionShortcut.cpp compiling SimpleMD.cpp compiling logging.cpp compiling Flush.cpp MetaD.cpp: In constructor 'PLMD::bias::MetaD::MetaD(const PLMD::ActionOptions&)': MetaD.cpp:1232:25: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] if(result!=0&&result!=mpi_nw_) error("in this WALKERS_MPI run some replica have restarted from GRID while other do not!"); ~~~~~~^~~~~~~~~ MetaD.cpp:1297:25: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] if(result!=0&&result!=mpi_nw_) error("in this WALKERS_MPI run some replica have restarted from FILE while other do not!"); ~~~~~~^~~~~~~~~ compiling Stats.cpp compiling ActionWithArguments.cpp compiling PBMetaD.cpp compiling Target.cpp compiling Dimer.cpp compiling Restraint.cpp compiling SumHills.cpp compiling OutputPDBFile.cpp compiling Group.cpp compiling PrintDissimilarityMatrix.cpp Dimer.cpp: In constructor 'PLMD::colvar::Dimer::Dimer(const PLMD::ActionOptions&)': Dimer.cpp:212:28: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] for(unsigned int i=0; i::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if(dsigmas.size()!=nranks && dsigmas.size()!=1) ~~~~~~~~~~~~~~^~~~~~~~ compiling Dipole.cpp compiling FindContour.cpp compiling Include.cpp compiling kT.cpp gmake[8]: Leaving directory '/construction/science/plumed/plumed-2.8.0/src/function' compiling ReweightBase.cpp compiling PRE.cpp compiling ConfigInstall.cpp compiling ReadAnalysisFrames.cpp compiling operand.cpp compiling ReweightBias.cpp ActionWithArguments.cpp: In member function 'virtual void PLMD::ActionWithArguments::calculateNumericalDerivatives(PLMD::ActionWithValue*)': ActionWithArguments.cpp:281:17: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long unsigned int'} [-Wsign-compare] for(int i=0; ihasDerivatives() ) for(int i=0; iaddDerivative(i,(value[i*nval+j]-a->getOutputQuantity(j))/sqrt(epsilon)); ~^~~~~ compiling ActionWithValue.cpp compiling MolInfo.cpp compiling Distance.cpp compiling ReweightMetad.cpp compiling osutils.cpp compiling ReadDissimilarityMatrix.cpp compiling ReselectLandmarks.cpp compiling ActionWithVirtualAtom.cpp compiling RDC.cpp In file included from tools/../../tools/RootFindingBase.h:26, from tools/RootFindingBase.h:1, from ContourFindingBase.h:26, from FindContour.cpp:24: tools/../../tools/Brent1DRootSearch.h: In member function 'double PLMD::Brent1DRootSearch::search(PLMD::Brent1DRootSearch::eng_pointer) [with FCLASS = PLMD::F1dim]': tools/../../tools/Brent1DRootSearch.h:100:57: warning: 'e' may be used uninitialized in this function [-Wmaybe-uninitialized] p=fabs(p); min1=3.0*xm*q-fabs(tol1*q); min2=fabs(e*q); ~^~ compiling FindContourSurface.cpp compiling SelectRandomFrames.cpp compiling pesmd.cpp compiling ReweightTemperaturePressure.cpp compiling regalloc.cpp compiling Plumed.cpp compiling EEFSolv.cpp compiling Atoms.cpp compiling SelectWithStride.cpp compiling Completion.cpp compiling CLTool.cpp compiling Rescale.cpp ../maketools/makecmd map < CLToolMain.cpp > CLToolMainMap.inc Plumed.cpp: In member function 'virtual void PLMD::generic::Plumed::prepare()': Plumed.cpp:323:26: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] bool redo=(index.size()!=n); ~~~~~~~~~~~~^~~ Plumed.cpp: In member function 'virtual void PLMD::generic::Plumed::calculate()': Plumed.cpp:364:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for(int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for(int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for(int i=0; i::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if( gatindex.size()==natoms ) { ~~~~~~~~~~~~~~~^~~~~~~~ Atoms.cpp:393:22: warning: comparison of integer expressions of different signedness: '__gnu_cxx::__alloc_traits, int>::value_type' {aka 'int'} and 'unsigned int' [-Wsign-compare] if( gatindex[i]!=i ) { shuffledAtoms=1; break; } Atoms.cpp: In member function 'void PLMD::Atoms::setAtomsContiguous(int)': Atoms.cpp:415:21: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if(gatindex.size() CLToolMainEnum.inc compiling CLToolRegister.cpp compiling RandomExchanges.cpp In file included from tools/../../tools/RootFindingBase.h:26, from tools/RootFindingBase.h:1, from ContourFindingBase.h:26, from FindContourSurface.cpp:23: tools/../../tools/Brent1DRootSearch.h: In member function 'double PLMD::Brent1DRootSearch::search(PLMD::Brent1DRootSearch::eng_pointer) [with FCLASS = PLMD::F1dim]': tools/../../tools/Brent1DRootSearch.h:100:57: warning: 'e' may be used uninitialized in this function [-Wmaybe-uninitialized] p=fabs(p); min1=3.0*xm*q-fabs(tol1*q); min2=fabs(e*q); ~^~ compiling FindSphericalContour.cpp compiling SAXS.cpp compiling string.cpp gmake[8]: Leaving directory '/construction/science/plumed/plumed-2.8.0/src/cltools' compiling Select.cpp gmake -C ../lepton obj compiling Energy.cpp gmake[8]: Entering directory '/construction/science/plumed/plumed-2.8.0/src/lepton' compiling CompiledExpression.cpp compiling Selector.cpp compiling Read.cpp compiling utils.cpp compiling ExpressionProgram.cpp compiling Colvar.cpp gmake[8]: Leaving directory '/construction/science/plumed/plumed-2.8.0/src/analysis' compiling ResetCell.cpp compiling vmem.cpp gmake[8]: Leaving directory '/construction/science/plumed/plumed-2.8.0/src/bias' compiling ExpressionTreeNode.cpp compiling ExtraCV.cpp compiling Operation.cpp compiling Time.cpp compiling ParsedExpression.cpp CompiledExpression.cpp: In member function 'void PLMD::lepton::CompiledExpression::compileExpression(const PLMD::lepton::ExpressionTreeNode&, std::vector >&)': CompiledExpression.cpp:157:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i = 0; i < node.getChildren().size(); i++) { ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ CompiledExpression.cpp:179:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i = 1; i < args.size(); i++) ~~^~~~~~~~~~~~~ CompiledExpression.cpp: In member function 'double PLMD::lepton::CompiledExpression::evaluate() const': CompiledExpression.cpp:240:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i = 0; i < variablesToCopy.size(); i++) ~~^~~~~~~~~~~~~~~~~~~~~~~~ CompiledExpression.cpp:245:29: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int step = 0; step < operation.size(); step++) { ~~~~~^~~~~~~~~~~~~~~~~~ CompiledExpression.cpp:250:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i = 0; i < args.size(); i++) ~~^~~~~~~~~~~~~ vmem.cpp:284:13: warning: 'bool PLMD::asmjit::vMemMgrCheckTree(PLMD::asmjit::VMemMgr*)' defined but not used [-Wunused-function] static bool vMemMgrCheckTree(VMemMgr* self) noexcept { ^~~~~~~~~~~~~~~~ compiling x86assembler.cpp compiling DataFetchingObject.cpp compiling x86builder.cpp gmake[8]: Leaving directory '/construction/science/plumed/plumed-2.8.0/src/isdb' compiling Parser.cpp Colvar.cpp: In member function 'virtual void PLMD::Colvar::apply()': Colvar.cpp:62:9: warning: comparison of integer expressions of different signedness: 'const unsigned int' and 'int' [-Wsign-compare] if(ncp>4*comm.Get_size()) { ~~~^~~~~~~~~~~~~~~~~~ Colvar.cpp:102:11: warning: comparison of integer expressions of different signedness: 'const unsigned int' and 'int' [-Wsign-compare] if(ncp>4*comm.Get_size()) { ~~~^~~~~~~~~~~~~~~~~~ compiling x86compiler.cpp compiling ExchangePatterns.cpp compiling FlexibleBin.cpp Parser.cpp: In static member function 'static PLMD::lepton::ParsedExpression PLMD::lepton::Parser::parse(const string&, const std::map, PLMD::lepton::CustomFunction*>&)': Parser.cpp:238:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] if (pos != tokens.size()) ~~~~^~~~~~~~~~~~~~~~ Parser.cpp:247:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] if (pos != tokens.size()) ~~~~^~~~~~~~~~~~~~~~ Parser.cpp: In static member function 'static PLMD::lepton::ExpressionTreeNode PLMD::lepton::Parser::parsePrecedence(const std::vector&, int&, const std::map, PLMD::lepton::CustomFunction*>&, const std::map, PLMD::lepton::ExpressionTreeNode>&, int)': Parser.cpp:258:13: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] if (pos == tokens.size()) ~~~~^~~~~~~~~~~~~~~~ Parser.cpp:284:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] if (pos == tokens.size() || tokens[pos].getType() != ParseToken::RightParen) ~~~~^~~~~~~~~~~~~~~~ Parser.cpp:298:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] if (pos == tokens.size() || tokens[pos].getType() != ParseToken::RightParen) ~~~~^~~~~~~~~~~~~~~~ ../maketools/makecmd map < GREX.cpp > GREXMap.inc ../maketools/makecmd enum < GREX.cpp > GREXEnum.inc ExpressionTreeNode.cpp: In constructor 'PLMD::lepton::ExpressionTreeNode::ExpressionTreeNode(PLMD::lepton::Operation*, const std::vector&)': ExpressionTreeNode.cpp:74:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] if (operation->getNumArguments() != children.size()) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ ExpressionTreeNode.cpp: In constructor 'PLMD::lepton::ExpressionTreeNode::ExpressionTreeNode(PLMD::lepton::Operation*, const PLMD::lepton::ExpressionTreeNode&, const PLMD::lepton::ExpressionTreeNode&)': ExpressionTreeNode.cpp:81:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] if (operation->getNumArguments() != children.size()) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ ExpressionTreeNode.cpp: In constructor 'PLMD::lepton::ExpressionTreeNode::ExpressionTreeNode(PLMD::lepton::Operation*, const PLMD::lepton::ExpressionTreeNode&)': ExpressionTreeNode.cpp:87:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] if (operation->getNumArguments() != children.size()) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ ExpressionTreeNode.cpp: In constructor 'PLMD::lepton::ExpressionTreeNode::ExpressionTreeNode(PLMD::lepton::Operation*)': ExpressionTreeNode.cpp:92:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] if (operation->getNumArguments() != children.size()) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ ExpressionTreeNode.cpp: In member function 'void PLMD::lepton::ExpressionTreeNode::assignTags(std::vector&) const': ExpressionTreeNode.cpp:166:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] if (numTags == examples.size()) { ~~~~~~~~^~~~~~~~~~~~~~~~~~ ExpressionTreeNode.cpp:169:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i = 0; i < examples.size(); i++) { ~~^~~~~~~~~~~~~~~~~ ExpressionTreeNode.cpp:172:42: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j = 0; matches && j < getChildren().size(); j++) ~~^~~~~~~~~~~~~~~~~~~~~~ compiling x86instimpl.cpp DataFetchingObject.cpp: In static member function 'static void PLMD::DataFetchingObject::get_rank(const PLMD::ActionSet&, const string&, const string&, const PLMD::TypesafePtr&)': DataFetchingObject.cpp:78:10: warning: unused variable 'val' [-Wunused-variable] Value* val = myv->copyOutput( key ); ^~~ DataFetchingObject.cpp: In static member function 'static void PLMD::DataFetchingObject::get_shape(const PLMD::ActionSet&, const string&, const string&, const PLMD::TypesafePtr&)': DataFetchingObject.cpp:99:10: warning: unused variable 'val' [-Wunused-variable] Value* val = myv->copyOutput( key ); ^~~ compiling x86internal.cpp compiling x86logging.cpp In file included from tools/../../tools/RootFindingBase.h:26, from tools/RootFindingBase.h:1, from ContourFindingBase.h:26, from FindSphericalContour.cpp:23: tools/../../tools/Brent1DRootSearch.h: In member function 'double PLMD::Brent1DRootSearch::search(PLMD::Brent1DRootSearch::eng_pointer) [with FCLASS = PLMD::F1dim]': tools/../../tools/Brent1DRootSearch.h:100:57: warning: 'e' may be used uninitialized in this function [-Wmaybe-uninitialized] p=fabs(p); min1=3.0*xm*q-fabs(tol1*q); min2=fabs(e*q); ~^~ compiling FourierTransform.cpp compiling x86operand.cpp compiling UpdateIf.cpp ParsedExpression.cpp: In static member function 'static PLMD::lepton::ExpressionTreeNode PLMD::lepton::ParsedExpression::substituteSimplerExpression(const PLMD::lepton::ExpressionTreeNode&, std::map&)': ParsedExpression.cpp:249:84: warning: 'first' may be used uninitialized in this function [-Wmaybe-uninitialized] return ExpressionTreeNode(new Operation::MultiplyConstant(first*dynamic_cast(&children[1].getOperation())->getValue()), children[1].getChildren()[0]); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ParsedExpression.cpp:67: Operation.h:1003:44: warning: 'second' may be used uninitialized in this function [-Wmaybe-uninitialized] AddConstant(double value) : value(value) { ^ ParsedExpression.cpp:191:19: note: 'second' was declared here double first, second; // if yes, value of first and second child ^~~~~~ gmake[8]: Leaving directory '/construction/science/plumed/plumed-2.8.0/src/lepton' compiling WholeMolecules.cpp compiling GenericMolInfo.cpp compiling MDAtoms.cpp ../maketools/makecmd map < PlumedMain.cpp > PlumedMainMap.inc ../maketools/makecmd enum < PlumedMain.cpp > PlumedMainEnum.inc compiling WrapAround.cpp compiling Fake.cpp compiling x86operand_regs.cpp compiling GridPrintingBase.cpp compiling PlumedMainInitializer.cpp compiling TargetDist.cpp compiling GHBFIX.cpp compiling Value.cpp compiling WithCmd.cpp compiling x86regalloc.cpp compiling zone.cpp compiling Gyration.cpp gmake -C ../main obj gmake[8]: Entering directory '/construction/science/plumed/plumed-2.8.0/src/main' compiling main.cpp compiling GridSearch.cpp compiling MultiRMSD.cpp compiling PCARMSD.cpp zone.cpp:223:13: warning: 'bool PLMD::asmjit::ZoneHeap_hasDynamicBlock(PLMD::asmjit::ZoneHeap*, PLMD::asmjit::ZoneHeap::DynamicBlock*)' defined but not used [-Wunused-function] static bool ZoneHeap_hasDynamicBlock(ZoneHeap* self, ZoneHeap::DynamicBlock* block) noexcept { ^~~~~~~~~~~~~~~~~~~~~~~~ compiling PathMSD.cpp gmake[8]: Leaving directory '/construction/science/plumed/plumed-2.8.0/src/main' compiling CLToolMain.cpp gmake[8]: Leaving directory '/construction/science/plumed/plumed-2.8.0/src/generic' compiling GREX.cpp compiling GridToXYZ.cpp gmake -C ../mapping obj gmake[8]: Entering directory '/construction/science/plumed/plumed-2.8.0/src/mapping' compiling AdaptivePath.cpp compiling GridVessel.cpp compiling PathMSDBase.cpp GHBFIX.cpp: In constructor 'PLMD::colvar::GHBFIX::GHBFIX(const PLMD::ActionOptions&)': GHBFIX.cpp:165:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for(auto i=0; i&, const std::vector&, unsigned int&, std::vector&) const': GridVessel.cpp:419:23: warning: comparison of integer expressions of different signedness: 'int' and 'const value_type' {aka 'const unsigned int'} [-Wsign-compare] if(!pbc[i] && i0>=nbin[i]) found=false; GridVessel.cpp:421:23: warning: comparison of integer expressions of different signedness: 'int' and 'const value_type' {aka 'const unsigned int'} [-Wsign-compare] if( pbc[i] && i0>=nbin[i]) i0%=nbin[i]; compiling PropertyMap.cpp compiling Puckering.cpp gmake -C ../reference obj gmake[8]: Entering directory '/construction/science/plumed/plumed-2.8.0/src/reference' compiling ArgumentOnlyDistance.cpp compiling dcdplugin.cpp compiling RMSD.cpp gmake[9]: Leaving directory '/construction/science/plumed/plumed-2.8.0/src/config' gmake[8]: Leaving directory '/construction/science/plumed/plumed-2.8.0/src/config' compiling Template.cpp dcdplugin.cpp: In function 'int PLMD::molfile::read_dcdheader(PLMD::molfile::fio_fd, int*, int*, int*, int*, double*, int*, int**, float**, int*, int*)': dcdplugin.cpp:226:57: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] } else if (input_integer[0] == 84 && input_integer[1] == dcdcordmagic) { ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ dcdplugin.cpp:239:54: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] if (input_integer[0] == 84 && input_integer[1] == dcdcordmagic) { ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ dcdplugin.cpp:257:26: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] if (input_integer[0] != dcdcordmagic) { ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ dcdplugin.cpp:434:45: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] if ((input_integer[0]+input_integer[1]) != ((*N)-(*NAMNF))*4) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ dcdplugin.cpp:451:45: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] if ((input_integer[0]+input_integer[1]) != ((*N)-(*NAMNF))*4) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ dcdplugin.cpp: In function 'int PLMD::molfile::read_dcdstep(PLMD::molfile::fio_fd, int, float*, float*, float*, float*, int, int, int*, float*, int, int)': dcdplugin.cpp:656:23: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] if (tmpbuf[i] != sizeof(float)*N) return DCD_BADFORMAT; ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ dcdplugin.cpp:660:43: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] if ((tmpbuf[2*i]+tmpbuf[2*i+1]) != sizeof(float)*N) return DCD_BADFORMAT; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ dcdplugin.cpp:581:16: warning: variable 'readlen' set but not used [-Wunused-but-set-variable] fio_size_t readlen; /* number of bytes actually read */ ^~~~~~~ In file included from dcdplugin.cpp:92: endianswap.h: At global scope: endianswap.h:136:13: warning: 'void PLMD::molfile::swap2_aligned(void*, long int)' defined but not used [-Wunused-function] static void swap2_aligned(void *v, long ndata) { ^~~~~~~~~~~~~ endianswap.h:72:13: warning: 'void PLMD::molfile::swap2_unaligned(void*, long int)' defined but not used [-Wunused-function] static void swap2_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ In file included from dcdplugin.cpp:83: fastio.h:676:12: warning: 'int PLMD::molfile::fio_write_str(PLMD::molfile::fio_fd, const char*)' defined but not used [-Wunused-function] static int fio_write_str(fio_fd fd, const char *str) { ^~~~~~~~~~~~~ fastio.h:672:12: warning: 'int PLMD::molfile::fio_read_int32(PLMD::molfile::fio_fd, int*)' defined but not used [-Wunused-function] static int fio_read_int32(fio_fd fd, int *i) { ^~~~~~~~~~~~~~ fastio.h:520:19: warning: 'PLMD::molfile::fio_size_t PLMD::molfile::fio_readv(PLMD::molfile::fio_fd, const PLMD::molfile::fio_iovec*, int)' defined but not used [-Wunused-function] static fio_size_t fio_readv(fio_fd fd, const fio_iovec * iov, int iovcnt) { ^~~~~~~~~ compiling gromacsplugin.cpp gmake[8]: Leaving directory '/construction/science/plumed/plumed-2.8.0/src/gridtools' compiling DRMSD.cpp In file included from Gromacs.h:86, from gromacsplugin.cpp:62: endianswap.h:136:13: warning: 'void PLMD::molfile::swap2_aligned(void*, long int)' defined but not used [-Wunused-function] static void swap2_aligned(void *v, long ndata) { ^~~~~~~~~~~~~ endianswap.h:105:13: warning: 'void PLMD::molfile::swap8_unaligned(void*, long int)' defined but not used [-Wunused-function] static void swap8_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ endianswap.h:86:13: warning: 'void PLMD::molfile::swap4_unaligned(void*, long int)' defined but not used [-Wunused-function] static void swap4_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ endianswap.h:72:13: warning: 'void PLMD::molfile::swap2_unaligned(void*, long int)' defined but not used [-Wunused-function] static void swap2_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ In file included from gromacsplugin.cpp:62: Gromacs.h: In function 'int PLMD::molfile::g96_header(PLMD::molfile::md_file*, char*, int, float*)': Gromacs.h:691:32: warning: 'char* strncpy(char*, const char*, size_t)' output may be truncated copying 80 bytes from a string of length 500 [-Wstringop-truncation] if (title && titlelen) strncpy(title, buf, titlelen); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ Gromacs.h: In function 'int PLMD::molfile::gro_header(PLMD::molfile::md_file*, char*, int, float*, int*, int)': Gromacs.h:1059:33: warning: 'char* strncpy(char*, const char*, size_t)' output may be truncated copying between 1 and 80 bytes from a string of length 500 [-Wstringop-truncation] if (title && titlelen) strncpy(title, buf, titlelen); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ gromacsplugin.cpp: In function 'void* PLMD::molfile::open_gro_read(const char*, const char*, int*)': gromacsplugin.cpp:138:12: warning: 'char* strncpy(char*, const char*, size_t)' output may be truncated copying 80 bytes from a string of length 80 [-Wstringop-truncation] strncpy(gmx->meta->title, mdh.title, 80); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gromacsplugin.cpp:62: In function 'int PLMD::molfile::mdio_header(PLMD::molfile::md_file*, PLMD::molfile::md_header*)', inlined from 'void* PLMD::molfile::open_trr_read(const char*, const char*, int*)' at gromacsplugin.cpp:495:20: Gromacs.h:587:10: warning: 'char* strncpy(char*, const char*, size_t)' output may be truncated copying 80 bytes from a string of length 80 [-Wstringop-truncation] strncpy(mdh->title, mf->trx->title, MAX_MDIO_TITLE); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ compiling pdbplugin.cpp compiling Direction.cpp compiling AlphaBeta.cpp In file included from pdbplugin.cpp:64: periodic_table.h:173:12: warning: 'int PLMD::molfile::get_pte_idx(const char*)' defined but not used [-Wunused-function] static int get_pte_idx(const char *label) ^~~~~~~~~~~ In file included from pdbplugin.cpp:63: In function 'void PLMD::molfile::get_pdb_cryst1(const char*, float*, float*, float*, float*, float*, float*)', inlined from 'int PLMD::molfile::read_next_timestep(void*, int, PLMD::molfile::molfile_timestep_t*)' at pdbplugin.cpp:312:23: readpdb.h:160:10: warning: 'char* strncpy(char*, const char*, size_t)' output may be truncated copying 80 bytes from a string of length 82 [-Wstringop-truncation] strncpy(tmp, record, PDB_RECORD_LENGTH); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gmake[8]: Leaving directory '/construction/science/plumed/plumed-2.8.0/src/molfile' compiling Torsion.cpp compiling DotProductDistance.cpp compiling Volume.cpp compiling EuclideanDistance.cpp gmake -C ../secondarystructure obj gmake[8]: Entering directory '/construction/science/plumed/plumed-2.8.0/src/secondarystructure' compiling AlphaRMSD.cpp gmake -C ../setup obj gmake -C ../tools obj gmake[8]: Entering directory '/construction/science/plumed/plumed-2.8.0/src/setup' compiling Load.cpp compiling PCAVars.cpp gmake[8]: Entering directory '/construction/science/plumed/plumed-2.8.0/src/tools' gmake -C ../vatom obj compiling Angle.cpp gmake[8]: Entering directory '/construction/science/plumed/plumed-2.8.0/src/vatom' compiling ActionWithVirtualAtom.cpp compiling AntibetaRMSD.cpp compiling ParabetaRMSD.cpp compiling Center.cpp compiling FixedAtom.cpp compiling Path.cpp compiling FakeFrame.cpp compiling Angles.cpp compiling Ghost.cpp compiling AtomNumber.cpp compiling AtomValuePack.cpp gmake[8]: Leaving directory '/construction/science/plumed/plumed-2.8.0/src/colvar' compiling SecondaryStructureRMSD.cpp compiling Restart.cpp compiling BiasRepresentation.cpp compiling Units.cpp compiling PathBase.cpp compiling IntermolecularDRMSD.cpp compiling IntramolecularDRMSD.cpp compiling MahalanobisDistance.cpp gmake[8]: Leaving directory '/construction/science/plumed/plumed-2.8.0/src/vatom' gmake[8]: Leaving directory '/construction/science/plumed/plumed-2.8.0/src/secondarystructure' compiling MetricRegister.cpp compiling Brent1DRootSearch.cpp compiling PathReparameterization.cpp compiling PathTools.cpp compiling Bridge.cpp compiling Citations.cpp compiling PropertyMap.cpp compiling Communicator.cpp compiling ConjugateGradient.cpp compiling MultiDomainRMSD.cpp compiling NormalizedEuclideanDistance.cpp PathReparameterization.cpp: In member function 'void PLMD::mapping::PathReparameterization::reparameterizePart(const int&, const int&, const double&, const double&)': PathReparameterization.cpp:72:31: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] for(unsigned i=istart; i= iend+1 ) plumed_merror("path reparameterization error"); ~~~~^~~~~~ PathReparameterization.cpp:103:22: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] else if( cfin==(iend+1) && k>=iend ) { k=iend-1; break; } ~~~~^~~~~~~~~~ PathReparameterization.cpp:104:22: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] else if( cfin==(iend-1) && k<=iend ) { k=iend+1; break; } ~~~~^~~~~~~~~~ PathReparameterization.cpp: In member function 'void PLMD::mapping::PathReparameterization::reparameterize(const int&, const int&, const double&)': PathReparameterization.cpp:141:12: warning: comparison of integer expressions of different signedness: 'const int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] if( ifix2<(mypath.size()-1) ) reparameterizePart( ifix2, mypath.size()-1, target, TOL ); ~~~~~^~~~~~~~~~~~~~~~~~ compiling OptimalRMSD.cpp compiling DLLoader.cpp compiling DynamicList.cpp gmake[8]: Leaving directory '/construction/science/plumed/plumed-2.8.0/src/setup' compiling ERMSD.cpp compiling BridgedMultiColvarFunction.cpp compiling RMSDBase.cpp compiling Exception.cpp compiling ReferenceArguments.cpp compiling CatomPack.cpp compiling CenterOfMultiColvar.cpp compiling CoordinationNumbers.cpp PathTools.cpp: In member function 'virtual int PLMD::mapping::PathTools::main(FILE*, FILE*, PLMD::Communicator&)': PathTools.cpp:266:17: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] for(int i=0; i&)': TrigonometricPathVessel.cpp:137:27: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] if( iclose3<0 || iclose3>=mymap->getFullNumberOfTasks() ) { ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ compiling SingleDomainRMSD.cpp compiling IFile.cpp gmake -C ../vesselbase obj compiling DihedralCorrelation.cpp gmake[8]: Entering directory '/construction/science/plumed/plumed-2.8.0/src/vesselbase' compiling ActionWithAveraging.cpp gmake[8]: Leaving directory '/construction/science/plumed/plumed-2.8.0/src/mapping' compiling DistanceFromContour.cpp compiling ActionWithInputVessel.cpp compiling ActionWithVessel.cpp In file included from RootFindingBase.h:26, from Grid.cpp:29: Brent1DRootSearch.h: In member function 'double PLMD::Brent1DRootSearch::search(PLMD::Brent1DRootSearch::eng_pointer) [with FCLASS = PLMD::F1dim]': Brent1DRootSearch.h:100:57: warning: 'e' may be used uninitialized in this function [-Wmaybe-uninitialized] p=fabs(p); min1=3.0*xm*q-fabs(tol1*q); min2=fabs(e*q); ~^~ gmake -C ../wrapper obj gmake[8]: Entering directory '/construction/science/plumed/plumed-2.8.0/src/wrapper' compiling PlumedStatic.cpp compiling Plumed.c compiling KernelFunctions.cpp compiling Keywords.cpp compiling AltMin.cpp In file included from Plumed.c:44: In function 'plumed_attempt_dlopen.part.1', inlined from 'plumed_attempt_dlopen' at Plumed.h:3010:7: Plumed.h:3043:26: warning: 'strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] __PLUMED_WRAPPER_STD strncpy(pathcopy,path,strlenpath+1); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Plumed.h: In function 'plumed_attempt_dlopen': Plumed.h:3037:37: note: length computed here strlenpath=__PLUMED_WRAPPER_STD strlen(path); ^~~~~~~~~~~~ In file included from PlumedStatic.cpp:44: In function 'void* plumed_attempt_dlopen(const char*, int)', inlined from 'plumed plumed_create_dlopen2(const char*, int)' at Plumed.h:3433:42: Plumed.h:3043:33: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] __PLUMED_WRAPPER_STD strncpy(pathcopy,path,strlenpath+1); ^ Plumed.h: In function 'plumed plumed_create_dlopen2(const char*, int)': Plumed.h:3037:43: note: length computed here strlenpath=__PLUMED_WRAPPER_STD strlen(path); ^ compiling LatticeReduction.cpp gmake[8]: Leaving directory '/construction/science/plumed/plumed-2.8.0/src/wrapper' gmake -C ../xdrfile obj gmake[8]: Entering directory '/construction/science/plumed/plumed-2.8.0/src/xdrfile' compiling xdrfile.cpp compiling xdrfile_trr.cpp gmake[8]: Leaving directory '/construction/science/plumed/plumed-2.8.0/src/reference' compiling xdrfile_xtc.cpp xdrfile_trr.cpp:5:2: warning: "/*" within comment [-Wcomment] /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- In file included from xdrfile_trr.cpp:41: xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- In file included from xdrfile_trr.cpp:42: xdrfile_trr.h:5:2: warning: "/*" within comment [-Wcomment] /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- xdrfile_trr.cpp: In function 'int PLMD::xdrfile::do_trnheader(PLMD::xdrfile::XDRFILE*, PLMD::xdrfile::mybool, PLMD::xdrfile::t_trnheader*)': xdrfile_trr.cpp:111:18: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] if (slen != strlen(version)+1) ~~~~~^~~~~~~~~~~~~~~~~~~~ xdrfile_trr.cpp:121:65: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] if (xdrfile_write_string(const_cast(version),xd) != (strlen(version)+1) ) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ compiling AveragingVessel.cpp xdrfile.cpp:5:2: warning: "/*" within comment [-Wcomment] /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- In file included from xdrfile.cpp:60: xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- xdrfile.cpp: In function 'int PLMD::xdrfile::sizeofint(int)': xdrfile.cpp:504:17: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] while (size >= num && num_of_bits < 32) ~~~~~^~~~~~ xdrfile.cpp: In function 'int PLMD::xdrfile::sizeofints(int, unsigned int*)': xdrfile.cpp:550:32: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] while (bytes[num_of_bytes] >= num) ~~~~~~~~~~~~~~~~~~~~^~~~~~ xdrfile.cpp: In function 'void PLMD::xdrfile::encodeints(int*, int, int, unsigned int*, unsigned int*)': xdrfile.cpp:659:21: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] if (num_of_bits >= num_of_bytes * 8) ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ xdrfile.cpp:661:17: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] for (i = 0; i < num_of_bytes; i++) ~~^~~~~~~~~~~~~~ xdrfile.cpp:669:17: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] for (i = 0; i < num_of_bytes-1; i++) ~~^~~~~~~~~~~~~~~~ xdrfile.cpp: In function 'int PLMD::xdrfile::decodebits(int*, int)': xdrfile.cpp:709:16: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] if (lastbits < num_of_bits) ~~~~~~~~~^~~~~~~~~~~~~ xdrfile.cpp: In function 'int PLMD::xdrfile::xdrfile_decompress_coord_float(float*, int*, float*, PLMD::xdrfile::XDRFILE*)': xdrfile.cpp:819:10: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] if(size3>xfp->buf1size) ~~~~~^~~~~~~~~~~~~~ xdrfile.cpp:871:19: warning: comparison of integer expressions of different signedness: 'long unsigned int' and 'int' [-Wsign-compare] maxidx = (LASTIDXxfp->buf1size) ~~~~~^~~~~~~~~~~~~~ xdrfile.cpp:1138:18: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] while (smallidx < LASTIDX && magicints[smallidx] < mindiff) ^ xdrfile.cpp:1144:19: warning: comparison of integer expressions of different signedness: 'long unsigned int' and 'int' [-Wsign-compare] maxidx = (LASTIDXxfp->buf1size) ~~~~~^~~~~~~~~~~~~~ xdrfile.cpp:1371:19: warning: comparison of integer expressions of different signedness: 'long unsigned int' and 'int' [-Wsign-compare] maxidx = (LASTIDXxfp->buf1size) { ~~~~~^~~~~~~~~~~~~~ xdrfile.cpp:1622:18: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] while (smallidx < LASTIDX && magicints[smallidx] < mindiff) { ^ xdrfile.cpp:1627:19: warning: comparison of integer expressions of different signedness: 'long unsigned int' and 'int' [-Wsign-compare] maxidx = (LASTIDX::search(PLMD::Brent1DRootSearch::eng_pointer) [with FCLASS = PLMD::F1dim]': tools/../../tools/Brent1DRootSearch.h:100:57: warning: 'e' may be used uninitialized in this function [-Wmaybe-uninitialized] p=fabs(p); min1=3.0*xm*q-fabs(tol1*q); min2=fabs(e*q); ~^~ compiling LinkCells.cpp In file included from xdrfile_xtc.cpp:31: xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- In file included from xdrfile_xtc.cpp:32: xdrfile_xtc.h:5:2: warning: "/*" within comment [-Wcomment] /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- xdrfile_xtc.cpp: In function 'int PLMD::xdrfile::xtc_coord(PLMD::xdrfile::XDRFILE*, int*, float (*)[3], float (*)[3], float*, PLMD::xdrfile::mybool)': xdrfile_xtc.cpp:69:6: warning: unused variable 'i' [-Wunused-variable] int i,j,result; ^ xdrfile_xtc.cpp:69:8: warning: unused variable 'j' [-Wunused-variable] int i,j,result; ^ compiling DumpMultiColvar.cpp gmake[8]: Leaving directory '/construction/science/plumed/plumed-2.8.0/src/xdrfile' compiling FilterBetween.cpp compiling FilterLessThan.cpp compiling Between.cpp compiling FilterMoreThan.cpp compiling Log.cpp compiling BridgeVessel.cpp compiling LoopUnroller.cpp compiling InPlaneDistances.cpp compiling FunctionVessel.cpp compiling Highest.cpp compiling LocalAverage.cpp compiling Matrix.cpp compiling Histogram.cpp compiling LessThan.cpp compiling MultiColvarBase.cpp compiling MatrixSquareBracketsAccess.cpp compiling Lowest.cpp compiling Max.cpp compiling Minimise1DBrent.cpp compiling Mean.cpp compiling Min.cpp compiling MinimiseBase.cpp compiling Moments.cpp compiling MoreThan.cpp compiling MultiColvarCombine.cpp compiling MolDataClass.cpp compiling MultiValue.cpp compiling MultiColvarDensity.cpp compiling OrderingVessel.cpp compiling MultiColvarFilter.cpp compiling MultiColvarProduct.cpp MultiColvarBase.cpp: In member function 'void PLMD::multicolvar::MultiColvarBase::setupActiveTaskSet(std::vector&, const string&)': MultiColvarBase.cpp:741:34: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] if( atom_lab[itask].first==input_code ) active_tasks[ atom_lab[itask].second ]=1; compiling NeighborList.cpp compiling OFile.cpp compiling OpenMP.cpp compiling ShortcutVessel.cpp compiling PDB.cpp compiling Pbc.cpp compiling StoreDataVessel.cpp compiling NumberOfLinks.cpp NeighborList.cpp: In member function 'void PLMD::NeighborList::update(const std::vector >&)': NeighborList.cpp:158:22: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] for(unsigned i=0; i= digits_size) { ~~~^~~~~~~~~~~~~~ In file included from tools/TypesafePtr.h:1, from WithCmd.h:25, from CLToolMain.h:27, from CLToolMain.cpp:22: tools/../../tools/TypesafePtr.h: In instantiation of 'std::size_t PLMD::typesafePtrSizeof() [with T = __FILE; std::size_t = long unsigned int]': tools/../../tools/TypesafePtr.h:253:44: required from 'T* PLMD::TypesafePtr::get_priv(std::size_t, const size_t*, bool) const [with T = __FILE; std::size_t = long unsigned int]' tools/../../tools/TypesafePtr.h:335:45: required from 'typename std::enable_if::value, T>::type PLMD::TypesafePtr::get() const [with T = __FILE*; typename std::enable_if::value, T>::type = __FILE*]' CLToolMain.cpp:92:25: required from here tools/../../tools/TypesafePtr.h:48:10: error: invalid application of 'sizeof' to incomplete type '__FILE' return sizeof(T); ^~~~~~~~~ gmake[8]: Leaving directory '/construction/science/plumed/plumed-2.8.0/src/tools' gmake[8]: *** [../maketools/make.rules:21: CLToolMain.o] Error 1 gmake[8]: *** Waiting for unfinished jobs.... In file included from tools/TypesafePtr.h:1, from WithCmd.h:25, from PlumedMain.h:25, from PlumedMain.cpp:22: tools/../../tools/TypesafePtr.h: In instantiation of 'std::size_t PLMD::typesafePtrSizeof() [with T = __FILE; std::size_t = long unsigned int]': tools/../../tools/TypesafePtr.h:253:44: required from 'T* PLMD::TypesafePtr::get_priv(std::size_t, const size_t*, bool) const [with T = __FILE; std::size_t = long unsigned int]' tools/../../tools/TypesafePtr.h:335:45: required from 'typename std::enable_if::value, T>::type PLMD::TypesafePtr::get() const [with T = __FILE*; typename std::enable_if::value, T>::type = __FILE*]' PlumedMain.cpp:515:33: required from here tools/../../tools/TypesafePtr.h:48:10: error: invalid application of 'sizeof' to incomplete type '__FILE' return sizeof(T); ^~~~~~~~~ gmake[8]: *** [../maketools/make.rules:21: PlumedMain.o] Error 1 gmake[8]: Leaving directory '/construction/science/plumed/plumed-2.8.0/src/core' gmake[7]: *** [Makefile:426: ../core] Error 2 gmake[7]: Leaving directory '/construction/science/plumed/plumed-2.8.0/src/lib' gmake[6]: *** [Makefile:128: dirs] Error 2 gmake[6]: Leaving directory '/construction/science/plumed/plumed-2.8.0/src/lib' gmake[5]: *** [Makefile:111: all] Error 2 gmake[5]: Leaving directory '/construction/science/plumed/plumed-2.8.0/src/lib' gmake[4]: *** [Makefile:8: lib] Error 2 gmake[4]: Leaving directory '/construction/science/plumed/plumed-2.8.0/src' gmake[3]: *** [Makefile:32: lib] Error 2 gmake[3]: Leaving directory '/construction/science/plumed/plumed-2.8.0' gmake[2]: *** [Makefile:21: all] Error 2 gmake[2]: Leaving directory '/construction/science/plumed/plumed-2.8.0' ===> Compilation failed unexpectedly. Try to set MAKE_JOBS_UNSAFE=yes and rebuild before reporting the failure to the maintainer. *** Error code 1 Stop. make[1]: stopped in /xports/science/plumed *** Error code 1 Stop. make: stopped in /xports/science/plumed FAILED 00:00:14