------------------------------------------------------------------------------- -- 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 00:00:16 ------------------------------------------------------------------------------- -- 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 00:00:00 ------------------------------------------------------------------------------- -- 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 00:00:07 ------------------------------------------------------------------------------- -- 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 00:00:00 ------------------------------------------------------------------------------- -- 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 00:00:01 ------------------------------------------------------------------------------- -- 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 00:00:14 ------------------------------------------------------------------------------- -- 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 -C ../lapack 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 -C ../lepton links 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/isdb' 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/isdb 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/generic' 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' Verify modules and create links in /construction/science/plumed/plumed-2.8.0/src/generic Verify modules and create links in /construction/science/plumed/plumed-2.8.0/src/gridtools gmake[8]: Entering directory '/construction/science/plumed/plumed-2.8.0/src/config' 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 gmake[8]: Entering directory '/construction/science/plumed/plumed-2.8.0/src/asmjit' Verify modules and create links in /construction/science/plumed/plumed-2.8.0/src/asmjit 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]: Leaving directory '/construction/science/plumed/plumed-2.8.0/src/asmjit' Verify modules and create links in /construction/science/plumed/plumed-2.8.0/src/analysis gmake -C ../mapping links gmake[8]: Leaving directory '/construction/science/plumed/plumed-2.8.0/src/lapack' gmake -C ../molfile 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/colvar 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/lepton' gmake -C ../multicolvar links gmake[8]: Entering directory '/construction/science/plumed/plumed-2.8.0/src/bias' Verify modules and create links in /construction/science/plumed/plumed-2.8.0/src/bias 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/cltools' 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/molfile' 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]: 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/molfile gmake[8]: Leaving directory '/construction/science/plumed/plumed-2.8.0/src/molfile' gmake -C ../reference 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/mapping Verify modules and create links in /construction/science/plumed/plumed-2.8.0/src/main gmake[8]: Entering directory '/construction/science/plumed/plumed-2.8.0/src/reference' Verify modules and create links in /construction/science/plumed/plumed-2.8.0/src/reference 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/generic' gmake -C ../setup links gmake[8]: Leaving directory '/construction/science/plumed/plumed-2.8.0/src/main' gmake -C ../tools links gmake[8]: Entering directory '/construction/science/plumed/plumed-2.8.0/src/setup' gmake[8]: Leaving directory '/construction/science/plumed/plumed-2.8.0/src/function' gmake -C ../vatom links gmake[8]: Leaving directory '/construction/science/plumed/plumed-2.8.0/src/core' gmake -C ../vesselbase links 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/colvar' gmake[8]: Leaving directory '/construction/science/plumed/plumed-2.8.0/src/reference' gmake -C ../wrapper links gmake[8]: Entering directory '/construction/science/plumed/plumed-2.8.0/src/vatom' gmake -C ../xdrfile links 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/wrapper' gmake[8]: Entering directory '/construction/science/plumed/plumed-2.8.0/src/xdrfile' 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' 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/multicolvar' 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/vesselbase Verify modules and create links in /construction/science/plumed/plumed-2.8.0/src/tools gmake[8]: Leaving directory '/construction/science/plumed/plumed-2.8.0/src/bias' gmake[8]: Leaving directory '/construction/science/plumed/plumed-2.8.0/src/isdb' 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/analysis' 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/cltools' 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/tools' 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[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[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[9]: Entering directory '/construction/science/plumed/plumed-2.8.0/src/config' gmake[8]: Entering directory '/construction/science/plumed/plumed-2.8.0/src/cltools' { ../maketools/make-scripts-options.sh ; cat completion.sh ; }| ../maketools/xxd > completion.xxd Updating Config.inc Updating config.txt file Updating ConfigInstall.inc compiling CLTool.cpp gmake[8]: Entering directory '/construction/science/plumed/plumed-2.8.0/src/analysis' Updating version.h compiling AnalysisBase.cpp compiling Driver.cpp gmake[8]: Entering directory '/construction/science/plumed/plumed-2.8.0/src/asmjit' cmp -s Config.inc~ Config.inc || cp Config.inc~ Config.inc rm Config.inc~ gmake[8]: Entering directory '/construction/science/plumed/plumed-2.8.0/src/bias' cmp -s ConfigInstall.inc~ ConfigInstall.inc || cp ConfigInstall.inc~ ConfigInstall.inc gmake -C ../function obj 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/blas' compiling ABMD.cpp compiling Combine.cpp compiling arch.cpp gmake[8]: Entering directory '/construction/science/plumed/plumed-2.8.0/src/colvar' rm ConfigInstall.inc~ gmake[8]: Entering directory '/construction/science/plumed/plumed-2.8.0/src/core' compiling Action.cpp compiling assembler.cpp compiling Angle.cpp compiling blas.cpp ../../scripts/selector.sh: line 219: python: command not found compiling codebuilder.cpp compiling Custom.cpp gmake[8]: Leaving directory '/construction/science/plumed/plumed-2.8.0/src/blas' In file included from xdrfile/xdrfile_trr.h:1, from Driver.cpp:38: 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: 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: 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 Ensemble.cpp compiling DriverDouble.cpp compiling Cell.cpp compiling Bias.cpp compiling BiasValue.cpp compiling Average.cpp compiling ExtendedLagrangian.cpp compiling FuncPathGeneral.cpp compiling FuncPathMSD.cpp compiling codecompiler.cpp compiling External.cpp compiling ActionAnyorder.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 Colvar.cpp compiling AverageVessel.cpp compiling Constant.cpp compiling ContactMap.cpp compiling codeemitter.cpp compiling LWalls.cpp compiling ActionAtomistic.cpp compiling MaxEnt.cpp compiling Coordination.cpp In file included from xdrfile/xdrfile_trr.h:1, from Driver.cpp:38, from DriverFloat.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 DriverFloat.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 DriverFloat.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 FuncSumHills.cpp compiling GenExample.cpp compiling Function.cpp compiling LocalEnsemble.cpp compiling Committor.cpp compiling MetaD.cpp compiling codeholder.cpp gmake[9]: Leaving directory '/construction/science/plumed/plumed-2.8.0/src/config' gmake Config.o ConfigInstall.o compile_options.sh gmake[9]: Entering directory '/construction/science/plumed/plumed-2.8.0/src/config' cat ../../Makefile.conf | ../maketools/xxd > Makefile.conf.xxd Building compile_options.sh, a sourceable bash script with some compilation options compiling Piecewise.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 CLToolMainMap.inc compiling FarthestPointSampling.cpp compiling string.cpp compiling utils.cpp gmake[8]: Leaving directory '/construction/science/plumed/plumed-2.8.0/src/bias' compiling vmem.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 x86assembler.cpp compiling x86builder.cpp Atoms.cpp: In member function 'void PLMD::Atoms::wait()': Atoms.cpp:296:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::size_t' {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 Dipole.cpp 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 Distance.cpp compiling pesmd.cpp gmake -C ../generic obj gmake[8]: Entering directory '/construction/science/plumed/plumed-2.8.0/src/generic' compiling Debug.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 x86inst.cpp compiling Colvar.cpp compiling DumpAtoms.cpp compiling DumpDerivatives.cpp compiling DumpForces.cpp compiling Completion.cpp compiling DumpMassCharge.cpp compiling EEFSolv.cpp compiling DumpProjections.cpp gmake[8]: Leaving directory '/construction/science/plumed/plumed-2.8.0/src/cltools' 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 ERMSD.cpp compiling DataFetchingObject.cpp compiling x86instimpl.cpp compiling EffectiveEnergyDrift.cpp compiling x86internal.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 LandmarkSelectionBase.cpp compiling EndPlumed.cpp compiling LandmarkStaged.cpp compiling FitToTemplate.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 ExchangePatterns.cpp compiling Flush.cpp compiling x86logging.cpp compiling Group.cpp compiling Include.cpp compiling Energy.cpp compiling ExtraCV.cpp compiling FlexibleBin.cpp compiling MolInfo.cpp compiling Plumed.cpp compiling Fake.cpp compiling GHBFIX.cpp compiling x86operand.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 Print.cpp compiling Read.cpp compiling RandomExchanges.cpp compiling OutputColvarFile.cpp compiling OutputPDBFile.cpp ../maketools/makecmd map < GREX.cpp > GREXMap.inc ../maketools/makecmd enum < GREX.cpp > GREXEnum.inc gmake -C ../gridtools obj compiling GenericMolInfo.cpp gmake[8]: Entering directory '/construction/science/plumed/plumed-2.8.0/src/gridtools' compiling ActionWithGrid.cpp compiling Gyration.cpp compiling x86operand_regs.cpp compiling MDAtoms.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 PlumedMainMap.inc compiling ActionWithIntegral.cpp compiling AverageOnGrid.cpp compiling ContourFindingBase.cpp ../maketools/makecmd enum < PlumedMain.cpp > PlumedMainEnum.inc compiling ConvertToFES.cpp compiling DumpCube.cpp compiling PrintDissimilarityMatrix.cpp compiling PlumedMainInitializer.cpp compiling zone.cpp compiling TargetDist.cpp compiling DumpGrid.cpp compiling Value.cpp compiling MultiRMSD.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 { ^~~~~~~~~~~~~~~~~~~~~~~~ gmake[8]: Leaving directory '/construction/science/plumed/plumed-2.8.0/src/asmjit' compiling FindContour.cpp compiling ReadAnalysisFrames.cpp compiling ResetCell.cpp compiling FindContourSurface.cpp compiling Time.cpp compiling UpdateIf.cpp 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::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 ReselectLandmarks.cpp compiling SelectRandomFrames.cpp compiling GridPrintingBase.cpp compiling GridSearch.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 SelectWithStride.cpp compiling CLToolMain.cpp compiling WhamHistogram.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); ~^~ gmake -C ../isdb obj gmake[8]: Entering directory '/construction/science/plumed/plumed-2.8.0/src/isdb' compiling CS2Backbone.cpp compiling PCARMSD.cpp compiling PathMSD.cpp compiling PathMSDBase.cpp gmake -C ../lapack obj gmake[8]: Entering directory '/construction/science/plumed/plumed-2.8.0/src/lapack' compiling lapack.cpp gmake -C ../lepton obj gmake[8]: Entering directory '/construction/science/plumed/plumed-2.8.0/src/lepton' compiling CompiledExpression.cpp gmake[8]: Leaving directory '/construction/science/plumed/plumed-2.8.0/src/lapack' compiling Position.cpp compiling Caliber.cpp compiling WholeMolecules.cpp compiling ProjectionOnAxis.cpp compiling GridToXYZ.cpp compiling GridVessel.cpp compiling HistogramOnGrid.cpp compiling WhamWeights.cpp compiling IntegrateGrid.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 >&)': 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++) ~~^~~~~~~~~~~~~ compiling ExpressionProgram.cpp gmake -C ../main obj gmake[8]: Leaving directory '/construction/science/plumed/plumed-2.8.0/src/analysis' compiling Template.cpp gmake[8]: Entering directory '/construction/science/plumed/plumed-2.8.0/src/main' compiling main.cpp compiling FretEfficiency.cpp EMMI.cpp: In member function 'void PLMD::isdb::EMMI::write_model_overlap(long int)': EMMI.cpp:770:17: 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 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 Torsion.cpp compiling ExpressionTreeNode.cpp compiling Jcoupling.cpp GridVessel.cpp: In member function 'void PLMD::gridtools::GridVessel::getNeighbors(const std::vector&, 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 Metainference.cpp compiling MetainferenceBase.cpp gmake[8]: Leaving directory '/construction/science/plumed/plumed-2.8.0/src/main' compiling NOE.cpp compiling PRE.cpp gmake[8]: Leaving directory '/construction/science/plumed/plumed-2.8.0/src/generic' compiling Operation.cpp compiling ParsedExpression.cpp 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 RDC.cpp compiling Rescale.cpp gmake[8]: Leaving directory '/construction/science/plumed/plumed-2.8.0/src/gridtools' compiling Parser.cpp compiling Volume.cpp compiling SAXS.cpp gmake -C ../mapping obj gmake[8]: Entering directory '/construction/science/plumed/plumed-2.8.0/src/mapping' compiling AdaptivePath.cpp compiling Select.cpp gmake -C ../molfile obj gmake[8]: Entering directory '/construction/science/plumed/plumed-2.8.0/src/molfile' compiling crdplugin.cpp compiling dcdplugin.cpp gmake[8]: Leaving directory '/construction/science/plumed/plumed-2.8.0/src/colvar' 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 Selector.cpp compiling gromacsplugin.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 -C ../multicolvar obj compiling pdbplugin.cpp gmake[8]: Entering directory '/construction/science/plumed/plumed-2.8.0/src/multicolvar' compiling ActionVolume.cpp gmake -C ../reference obj 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); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gmake -C ../secondarystructure obj gmake[8]: Entering directory '/construction/science/plumed/plumed-2.8.0/src/secondarystructure' gmake[8]: Entering directory '/construction/science/plumed/plumed-2.8.0/src/reference' compiling AlphaRMSD.cpp compiling ArgumentOnlyDistance.cpp gmake -C ../setup obj gmake[8]: Entering directory '/construction/science/plumed/plumed-2.8.0/src/setup' compiling Load.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) ~~~~^~~~~~~~~~~~~~~~ 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/lepton' gmake -C ../tools obj gmake[8]: Leaving directory '/construction/science/plumed/plumed-2.8.0/src/molfile' gmake[8]: Entering directory '/construction/science/plumed/plumed-2.8.0/src/tools' compiling Restart.cpp compiling Angle.cpp AdaptivePath.cpp: In constructor 'PLMD::mapping::AdaptivePath::AdaptivePath(const PLMD::ActionOptions&)': AdaptivePath.cpp:154:17: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] for(int i=0; i= 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(version),xd) != (strlen(version)+1) ) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ compiling AveragingVessel.cpp compiling xdrfile_xtc.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; ^ gmake[8]: Leaving directory '/construction/science/plumed/plumed-2.8.0/src/xdrfile' compiling DLLoader.cpp compiling Direction.cpp compiling Between.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 DynamicList.cpp compiling BridgeVessel.cpp compiling FunctionVessel.cpp compiling DotProductDistance.cpp compiling ERMSD.cpp compiling Exception.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::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); ~^~ compiling Min.cpp compiling Moments.cpp compiling MoreThan.cpp compiling MahalanobisDistance.cpp TrigonometricPathVessel.cpp: In member function 'virtual void PLMD::mapping::TrigonometricPathVessel::finish(const std::vector&)': 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 MetricRegister.cpp compiling OrderingVessel.cpp compiling ShortcutVessel.cpp compiling MultiDomainRMSD.cpp gmake[8]: Leaving directory '/construction/science/plumed/plumed-2.8.0/src/mapping' compiling NormalizedEuclideanDistance.cpp compiling CoordinationNumbers.cpp compiling StoreDataVessel.cpp compiling OptimalRMSD.cpp compiling Sum.cpp compiling RMSDBase.cpp compiling ValueVessel.cpp compiling ReferenceArguments.cpp compiling LinkCells.cpp compiling ReferenceAtoms.cpp compiling Vessel.cpp compiling Log.cpp compiling Density.cpp compiling VesselRegister.cpp compiling LoopUnroller.cpp compiling Matrix.cpp compiling ReferenceConfiguration.cpp compiling DihedralCorrelation.cpp compiling MatrixSquareBracketsAccess.cpp compiling Minimise1DBrent.cpp compiling ReferenceValuePack.cpp compiling SimpleRMSD.cpp compiling DistanceFromContour.cpp compiling MinimiseBase.cpp compiling Distances.cpp compiling MolDataClass.cpp compiling MultiValue.cpp 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]: *** [../maketools/make.rules:21: CLToolMain.o] Error 1 gmake[8]: *** Waiting for unfinished jobs.... compiling SingleDomainRMSD.cpp compiling NeighborList.cpp compiling DumpMultiColvar.cpp compiling OFile.cpp gmake[8]: Leaving directory '/construction/science/plumed/plumed-2.8.0/src/vesselbase' compiling OpenMP.cpp compiling FilterBetween.cpp compiling FilterLessThan.cpp compiling FilterMoreThan.cpp compiling InPlaneDistances.cpp compiling LocalAverage.cpp gmake[8]: Leaving directory '/construction/science/plumed/plumed-2.8.0/src/reference' compiling MultiColvarBase.cpp compiling PDB.cpp compiling MultiColvarCombine.cpp compiling Pbc.cpp In file included from tools/../../tools/RootFindingBase.h:26, from tools/RootFindingBase.h:1, from DistanceFromContour.cpp:26: 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 MultiColvarDensity.cpp compiling MultiColvarFilter.cpp compiling PlumedHandle.cpp compiling RMSD.cpp compiling MultiColvarProduct.cpp compiling NumberOfLinks.cpp compiling Torsions.cpp compiling Random.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 VolumeAround.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 PlumedHandle.cpp:38: In function 'void* {anonymous}::plumed_attempt_dlopen(const char*, int)', inlined from 'plumed {anonymous}::plumed_create_dlopen2(const char*, int)' at ../wrapper/Plumed.h:3433:42, inlined from 'plumed {anonymous}::plumed_create_dlopen(const char*)' at ../wrapper/Plumed.h:3391:47, inlined from 'PLMD::PlumedHandle::PlumedHandle(const char*)' at PlumedHandle.cpp:52:20: ../wrapper/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); ^ ../wrapper/Plumed.h: In constructor 'PLMD::PlumedHandle::PlumedHandle(const char*)': ../wrapper/Plumed.h:3037:43: note: length computed here strlenpath=__PLUMED_WRAPPER_STD strlen(path); ^ 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/multicolvar' 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 00:00:19