------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/indexinfo-0.3.1.txz Installing /packages/All/gettext-runtime-0.21.txz Installing /packages/All/ncurses-6.2.20210116.txz Installing /packages/All/readline-8.0.4_1.txz Installing /packages/All/bash-5.1.4_1.txz Installing /packages/All/vim-console-8.2.2263_1.txz Installing /packages/All/gmake-4.3_2.txz Installing /packages/All/pkgconf-1.7.3,1.txz Installing /packages/All/m4-1.4.18_1,1.txz Installing /packages/All/autoconf-wrapper-20131203.txz Installing /packages/All/perl5-5.32.0_1.txz Installing /packages/All/autoconf-2.69_3.txz Installing /packages/All/automake-1.16.3.txz SUCCEEDED 00:00:28 ------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- ===> plumed-2.7.0 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> plumed-2.7.0 depends on file: /usr/local/sbin/pkg - found => plumed-plumed2-v2.7.0_GH0.tar.gz doesn't seem to exist in /distfiles/. => Attempting to fetch https://codeload.github.com/plumed/plumed2/tar.gz/v2.7.0?dummy=/plumed-plumed2-v2.7.0_GH0.tar.gz fetch: https://codeload.github.com/plumed/plumed2/tar.gz/v2.7.0?dummy=/plumed-plumed2-v2.7.0_GH0.tar.gz: size unknown fetch: https://codeload.github.com/plumed/plumed2/tar.gz/v2.7.0?dummy=/plumed-plumed2-v2.7.0_GH0.tar.gz: size of remote file is not known plumed-plumed2-v2.7.0_GH0.tar.gz 0 B 0 Bps plumed-plumed2-v2.7.0_GH0.tar.gz 208 kB 2140 kBps plumed-plumed2-v2.7.0_GH0.tar.gz 6112 kB 5954 kBps plumed-plumed2-v2.7.0_GH0.tar.gz 11 MB 5696 kBps plumed-plumed2-v2.7.0_GH0.tar.gz 15 MB 4093 kBps plumed-plumed2-v2.7.0_GH0.tar.gz 20 MB 4981 kBps plumed-plumed2-v2.7.0_GH0.tar.gz 24 MB 4470 kBps plumed-plumed2-v2.7.0_GH0.tar.gz 31 MB 6324 kBps plumed-plumed2-v2.7.0_GH0.tar.gz 37 MB 6493 kBps plumed-plumed2-v2.7.0_GH0.tar.gz 43 MB 6557 kBps plumed-plumed2-v2.7.0_GH0.tar.gz 51 MB 7505 kBps plumed-plumed2-v2.7.0_GH0.tar.gz 55 MB 4131 kBps plumed-plumed2-v2.7.0_GH0.tar.gz 60 MB 5170 kBps plumed-plumed2-v2.7.0_GH0.tar.gz 64 MB 4716 kBps plumed-plumed2-v2.7.0_GH0.tar.gz 69 MB 5276 kBps plumed-plumed2-v2.7.0_GH0.tar.gz 81 MB 11 MBps plumed-plumed2-v2.7.0_GH0.tar.gz 87 MB 5774 kBps plumed-plumed2-v2.7.0_GH0.tar.gz 94 MB 6033 kBps 16s ===> Fetching all distfiles required by plumed-2.7.0 for building SUCCEEDED 00:00:16 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> plumed-2.7.0 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by plumed-2.7.0 for building => SHA256 Checksum OK for plumed-plumed2-v2.7.0_GH0.tar.gz. SUCCEEDED 00:00:03 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> plumed-2.7.0 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by plumed-2.7.0 for building ===> Extracting for plumed-2.7.0 ===> plumed-2.7.0 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by plumed-2.7.0 for building => SHA256 Checksum OK for plumed-plumed2-v2.7.0_GH0.tar.gz. Extracted Memory Use: 420.46M SUCCEEDED 00:00:07 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for plumed-2.7.0 ===> Applying ports patches for plumed-2.7.0 from /xports/science/plumed/files /usr/bin/env WRKSRC=/construction/science/plumed/plumed2-2.7.0 REWARNFILE=/construction/science/plumed/reinplace_warnings.txt /xports/Mk/Scripts/sed_checked.sh -e 's,FreeBSD,FreeBSD|DragonFly,g' /construction/science/plumed/plumed2-2.7.0/configure.ac SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> plumed-2.7.0 depends on executable: bash - found ===> plumed-2.7.0 depends on executable: xxd - found ===> plumed-2.7.0 depends on package: gmake>=4.3 - found ===> plumed-2.7.0 depends on package: pkgconf>=1.3.0_1 - found ===> plumed-2.7.0 depends on package: autoconf>=2.69 - found ===> plumed-2.7.0 depends on package: automake>=1.16.1 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> plumed-2.7.0 depends on executable: bash - found ===> plumed-2.7.0 depends on executable: xxd - found ===> plumed-2.7.0 depends on package: gmake>=4.3 - found ===> plumed-2.7.0 depends on package: pkgconf>=1.3.0_1 - found ===> plumed-2.7.0 depends on package: autoconf>=2.69 - found ===> plumed-2.7.0 depends on package: automake>=1.16.1 - found ===> Configuring for plumed-2.7.0 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 we are using the GNU C++ compiler... yes checking whether c++ accepts -g... yes checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ISO C89... 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 we are using the GNU Fortran compiler... no checking whether accepts -g... no configure: Initial CXX: c++ configure: Initial CXXFLAGS: -pipe -O2 -fno-strict-aliasing configure: Initial CPPFLAGS: configure: Initial CFLAGS: -pipe -O2 -fno-strict-aliasing configure: Initial LDFLAGS: configure: Initial LIBS: 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 how to run the C++ preprocessor... c++ -E checking for grep that handles long lines and -e... (cached) /usr/bin/grep checking for egrep... (cached) /usr/bin/egrep checking for ANSI C header files... (cached) yes checking for sys/types.h... (cached) yes checking for sys/stat.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for memory.h... (cached) yes checking for strings.h... (cached) yes checking for inttypes.h... (cached) yes checking for stdint.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_... no configure: WARNING: using internal lapack and blas, could be inefficient configure: Now we will check for optional headers and libraries checking libmolfile_plugin.h usability... no checking libmolfile_plugin.h presence... no 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 mpi.h usability... no checking mpi.h presence... no checking for mpi.h... no configure: WARNING: cannot enable __PLUMED_HAS_MPI checking for c++ option to support OpenMP... -fopenmp checking regex.h usability... yes checking regex.h presence... yes 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 execinfo.h usability... yes checking execinfo.h presence... yes 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... no configure: WARNING: cannot enable __PLUMED_HAS_GSL checking xdrfile/xdrfile_xtc.h usability... no checking xdrfile/xdrfile_xtc.h presence... no checking for xdrfile/xdrfile_xtc.h... no configure: WARNING: cannot enable __PLUMED_HAS_XDRFILE checking fftw3.h usability... no checking fftw3.h presence... no checking for fftw3.h... no configure: WARNING: cannot enable __PLUMED_HAS_FFTW 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 for xxd... found 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 00:00:20 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for plumed-2.7.0 gmake[2]: Entering directory '/construction/science/plumed/plumed2-2.7.0' gmake lib gmake[3]: Entering directory '/construction/science/plumed/plumed2-2.7.0' gmake -C src gmake[4]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src' gmake -C lib gmake[5]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/lib' gmake dirslinks gmake[6]: Entering directory '/construction/science/plumed/plumed2-2.7.0/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 gmake[7]: Entering directory '/construction/science/plumed/plumed2-2.7.0/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[8]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/blas' Verify modules and create links in /construction/science/plumed/plumed2-2.7.0/src/blas gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/blas' gmake -C ../gridtools links gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/analysis' gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/generic' Verify modules and create links in /construction/science/plumed/plumed2-2.7.0/src/analysis Verify modules and create links in /construction/science/plumed/plumed2-2.7.0/src/generic gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/core' gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/gridtools' Verify modules and create links in /construction/science/plumed/plumed2-2.7.0/src/gridtools gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/bias' Verify modules and create links in /construction/science/plumed/plumed2-2.7.0/src/core Verify modules and create links in /construction/science/plumed/plumed2-2.7.0/src/bias gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/asmjit' ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/cltools' Verify modules and create links in /construction/science/plumed/plumed2-2.7.0/src/cltools ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/function' ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe Verify modules and create links in /construction/science/plumed/plumed2-2.7.0/src/function ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/config' ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe Verify modules and create links in /construction/science/plumed/plumed2-2.7.0/src/asmjit Nothing to do in /construction/science/plumed/plumed2-2.7.0/src/config ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/config' gmake -C ../isdb links gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/asmjit' gmake -C ../lapack links ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/lapack' ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/isdb' ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe Verify modules and create links in /construction/science/plumed/plumed2-2.7.0/src/isdb ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/colvar' ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe Verify modules and create links in /construction/science/plumed/plumed2-2.7.0/src/lapack ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe Verify modules and create links in /construction/science/plumed/plumed2-2.7.0/src/colvar ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/lapack' gmake -C ../lepton links ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/lepton' Verify modules and create links in /construction/science/plumed/plumed2-2.7.0/src/lepton ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/lepton' ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe gmake -C ../main links ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/main' ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe Verify modules and create links in /construction/science/plumed/plumed2-2.7.0/src/main ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/main' gmake -C ../mapping links ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/mapping' Verify modules and create links in /construction/science/plumed/plumed2-2.7.0/src/mapping ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/generic' gmake -C ../molfile links ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/bias' gmake -C ../multicolvar links ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/molfile' ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe Verify modules and create links in /construction/science/plumed/plumed2-2.7.0/src/molfile ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/molfile' gmake -C ../reference links ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/multicolvar' ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/reference' ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe Verify modules and create links in /construction/science/plumed/plumed2-2.7.0/src/multicolvar ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe Verify modules and create links in /construction/science/plumed/plumed2-2.7.0/src/reference ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/colvar' gmake -C ../secondarystructure links ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/secondarystructure' ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe Verify modules and create links in /construction/science/plumed/plumed2-2.7.0/src/secondarystructure ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/core' gmake -C ../setup links ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/setup' ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe Verify modules and create links in /construction/science/plumed/plumed2-2.7.0/src/setup ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/function' gmake -C ../tools links ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/tools' Verify modules and create links in /construction/science/plumed/plumed2-2.7.0/src/tools gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/gridtools' gmake -C ../vatom links gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/vatom' Verify modules and create links in /construction/science/plumed/plumed2-2.7.0/src/vatom ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/isdb' gmake -C ../vesselbase links ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/vesselbase' ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe Verify modules and create links in /construction/science/plumed/plumed2-2.7.0/src/vesselbase ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/analysis' ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe gmake -C ../wrapper links ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/wrapper' Nothing to do in /construction/science/plumed/plumed2-2.7.0/src/wrapper gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/wrapper' ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/cltools' ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/tools' ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/reference' ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/setup' ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/vatom' ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/mapping' ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/secondarystructure' ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/vesselbase' ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/multicolvar' gmake[7]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/lib' gmake[6]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/lib' gmake dirs gmake[6]: Entering directory '/construction/science/plumed/plumed2-2.7.0/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 gmake[7]: Entering directory '/construction/science/plumed/plumed2-2.7.0/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[8]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/function' compiling Combine.cpp gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/analysis' compiling AnalysisBase.cpp gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/asmjit' compiling arch.cpp gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/blas' compiling blas.cpp gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/cltools' gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/colvar' compiling Angle.cpp gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/config' gmake PLUMED_FORCE=yes ConfigInstall.inc Config.inc version.h config.txt gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/config' Updating ConfigInstall.inc cmp -s ConfigInstall.inc~ ConfigInstall.inc || cp ConfigInstall.inc~ ConfigInstall.inc gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/bias' gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/core' compiling ABMD.cpp rm ConfigInstall.inc~ gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/generic' compiling Action.cpp Updating Config.inc compiling CLTool.cpp cmp -s Config.inc~ Config.inc || cp Config.inc~ Config.inc rm Config.inc~ Updating version.h compiling assembler.cpp Updating config.txt file compiling codebuilder.cpp compiling Debug.cpp compiling codecompiler.cpp compiling codeemitter.cpp compiling codeholder.cpp compiling constpool.cpp gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/config' gmake Config.o ConfigInstall.o compile_options.sh gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/config' cat ../../Makefile.conf | xxd -i > Makefile.conf.xxd Building compile_options.sh, a sourceable bash script with some compilation options compiling Config.cpp compiling cpuinfo.cpp compiling func.cpp compiling globals.cpp compiling inst.cpp compiling logging.cpp compiling operand.cpp compiling osutils.cpp compiling regalloc.cpp compiling runtime.cpp compiling string.cpp compiling utils.cpp compiling vmem.cpp compiling x86assembler.cpp compiling x86builder.cpp compiling x86compiler.cpp compiling x86inst.cpp compiling x86instimpl.cpp compiling x86internal.cpp compiling x86logging.cpp compiling x86operand.cpp compiling x86operand_regs.cpp compiling x86regalloc.cpp compiling zone.cpp gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/asmjit' compiling ConfigInstall.cpp compiling Bias.cpp { ../maketools/make-scripts-options.sh ; cat completion.sh ; }| xxd -i > completion.xxd ../../scripts/selector.sh: line 219: python: command not found compiling Driver.cpp gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/config' gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/config' compiling BiasValue.cpp compiling Cell.cpp compiling Custom.cpp compiling DumpAtoms.cpp compiling DumpDerivatives.cpp compiling DriverDouble.cpp compiling Average.cpp compiling ExtendedLagrangian.cpp gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/blas' compiling DumpForces.cpp compiling DriverFloat.cpp compiling Colvar.cpp compiling ActionAnyorder.cpp compiling External.cpp compiling Constant.cpp compiling ActionAtomistic.cpp compiling AverageVessel.cpp compiling Ensemble.cpp compiling DumpMassCharge.cpp compiling DumpProjections.cpp compiling LWalls.cpp compiling EffectiveEnergyDrift.cpp ActionAtomistic.cpp: In member function 'void PLMD::ActionAtomistic::requestAtoms(const std::vector&, bool)': ActionAtomistic.cpp:73:26: 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::interpretAtomList(std::vector >&, std::vector&)': ActionAtomistic.cpp:181:28: 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'} and 'int' [-Wsign-compare] bool redo=(index.size()!=n); ~~~~~~~~~~~~^~~ Plumed.cpp: In member function 'virtual void PLMD::generic::Plumed::calculate()': Plumed.cpp:366:17: 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(dsigmas.size()!=nranks && dsigmas.size()!=1) ~~~~~~~~~~~~~~^~~~~~~~ compiling Function.cpp compiling Time.cpp compiling ReweightMetad.cpp compiling Dipole.cpp compiling UpdateIf.cpp compiling LandmarkStaged.cpp compiling pesmd.cpp compiling ActionWithVirtualAtom.cpp compiling Distance.cpp compiling ReweightTemperaturePressure.cpp compiling EEFSolv.cpp compiling ERMSD.cpp compiling LocalEnsemble.cpp compiling Atoms.cpp compiling Completion.cpp compiling WholeMolecules.cpp compiling OutputColvarFile.cpp compiling ReweightWham.cpp compiling CLTool.cpp WholeMolecules.cpp: In constructor 'PLMD::generic::WholeMolecules::WholeMolecules(const PLMD::ActionOptions&)': WholeMolecules.cpp:156:19: 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 CLToolMainMap.inc compiling UWalls.cpp Atoms.cpp: In member function 'void PLMD::Atoms::setAtomsGatindex(int*, bool)': Atoms.cpp:391:22: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if( gatindex.size()==natoms ) { ~~~~~~~~~~~~~~~^~~~~~~~ Atoms.cpp:394:22: 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:416:21: 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 OutputPDBFile.cpp compiling Piecewise.cpp compiling PrintDissimilarityMatrix.cpp compiling ReadAnalysisFrames.cpp compiling WrapAround.cpp compiling Sort.cpp compiling ReadDissimilarityMatrix.cpp gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/bias' compiling CLToolRegister.cpp compiling Colvar.cpp compiling Stats.cpp compiling ReselectLandmarks.cpp gmake -C ../gridtools obj gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/gridtools' compiling ActionWithGrid.cpp gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/generic' compiling DataFetchingObject.cpp Colvar.cpp: In member function 'virtual void PLMD::Colvar::apply()': Colvar.cpp:63:9: warning: comparison of integer expressions of different signedness: 'const unsigned int' and 'int' [-Wsign-compare] if(ncp>4*comm.Get_size()) { ~~~^~~~~~~~~~~~~~~~~~ Colvar.cpp:103:11: warning: comparison of integer expressions of different signedness: 'const unsigned int' and 'int' [-Wsign-compare] if(ncp>4*comm.Get_size()) { ~~~^~~~~~~~~~~~~~~~~~ compiling Energy.cpp compiling ActionWithInputGrid.cpp DataFetchingObject.cpp: In static member function 'static void PLMD::DataFetchingObject::get_rank(const PLMD::ActionSet&, const string&, const string&, long int*)': DataFetchingObject.cpp:77:10: 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&, long int*)': DataFetchingObject.cpp:98:10: warning: unused variable 'val' [-Wunused-variable] Value* val = myv->copyOutput( key ); ^~~ compiling Target.cpp compiling ActionWithIntegral.cpp compiling SelectRandomFrames.cpp compiling AverageOnGrid.cpp compiling ExchangePatterns.cpp compiling FlexibleBin.cpp compiling ContourFindingBase.cpp compiling ExtraCV.cpp compiling SelectWithStride.cpp compiling ConvertToFES.cpp ../maketools/makecmd map < GREX.cpp > GREXMap.inc gmake -C ../isdb obj gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/isdb' compiling CS2Backbone.cpp ../maketools/makecmd enum < GREX.cpp > GREXEnum.inc compiling Fake.cpp gmake -C ../lapack obj gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/lapack' compiling lapack.cpp compiling DumpCube.cpp compiling GenericMolInfo.cpp gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/function' compiling MDAtoms.cpp compiling WhamHistogram.cpp ../maketools/makecmd map < PlumedMain.cpp > PlumedMainMap.inc compiling DumpGrid.cpp compiling Caliber.cpp compiling Gyration.cpp ../maketools/makecmd enum < PlumedMain.cpp > PlumedMainEnum.inc compiling FindContour.cpp compiling EMMI.cpp compiling PlumedMainInitializer.cpp Caliber.cpp: In member function 'double PLMD::isdb::Caliber::getSpline(unsigned int)': Caliber.cpp:275:14: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] if(tindex+1&, PLMD::VectorGeneric&, PLMD::TensorGeneric&) [with unsigned int n_ = 3; unsigned int m_ = 3; unsigned int n = 3; unsigned int m = 3]': Gyration.cpp:249:43: required from here core/../../core/tools/../../tools/Tensor.h:557:17: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] for(int i=0; i1e-14) break; ~^~ core/../../core/tools/../../tools/Tensor.h:560:9: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] if(j::size_type' {aka 'long unsigned int'} [-Wsign-compare] for(int i=0; i PLMD::isdb::EMMI::read_exp_errors(std::__cxx11::string)': EMMI.cpp:775:26: 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 TargetDist.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 FourierTransform.cpp compiling MultiRMSD.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); ~^~ 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 FretEfficiency.cpp compiling Value.cpp compiling Jcoupling.cpp gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/analysis' compiling Metainference.cpp compiling PCARMSD.cpp compiling GridPrintingBase.cpp gmake -C ../lepton obj gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/lepton' compiling CompiledExpression.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++) ~~^~~~~~~~~~~~~ CompiledExpression.cpp:236:23: warning: unused variable 'asmjit' [-Wunused-variable] static const bool asmjit=useAsmJit(); ^~~~~~ compiling WithCmd.cpp compiling GridSearch.cpp compiling GridToXYZ.cpp compiling CLToolMain.cpp compiling PathMSD.cpp compiling ExpressionProgram.cpp compiling MetainferenceBase.cpp gmake -C ../main obj gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/main' compiling main.cpp gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/main' compiling PathMSDBase.cpp compiling ExpressionTreeNode.cpp compiling Operation.cpp compiling GREX.cpp compiling PlumedMain.cpp ExpressionTreeNode.cpp: In constructor 'PLMD::lepton::ExpressionTreeNode::ExpressionTreeNode(PLMD::lepton::Operation*, const std::vector&)': ExpressionTreeNode.cpp:73:38: 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:80:38: 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:86:38: 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:91:38: 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()) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ compiling GridVessel.cpp gmake -C ../mapping obj gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/mapping' compiling AdaptivePath.cpp GridVessel.cpp: In member function 'void PLMD::gridtools::GridVessel::getNeighbors(const std::vector&, const std::vector&, unsigned int&, std::vector&) const': GridVessel.cpp:415:23: 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:417:23: 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]; 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(&children[1].getOperation())->getValue()), children[1].getChildren()[0]); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ParsedExpression.cpp:67: Operation.h:975:44: warning: 'second' may be used uninitialized in this function [-Wmaybe-uninitialized] AddConstant(double value) : value(value) { ^ ParsedExpression.cpp:161:19: note: 'second' was declared here double first, second; // if yes, value of first and second child ^~~~~~ GridVessel.cpp: In member function 'unsigned int PLMD::gridtools::GridVessel::getFibonacciIndex(const std::vector&) const': GridVessel.cpp:251:10: warning: 'outind' may be used uninitialized in this function [-Wmaybe-uninitialized] return outind; ^~~~~~ gmake -C ../molfile obj gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/molfile' compiling crdplugin.cpp compiling dcdplugin.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 HistogramOnGrid.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) ~~~~^~~~~~~~~~~~~~~~ compiling PathBase.cpp compiling IntegrateGrid.cpp compiling gromacsplugin.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 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) ^~~~~~~~~~~ compiling InterpolateGrid.cpp 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/plumed2-2.7.0/src/molfile' compiling PathReparameterization.cpp compiling RDC.cpp gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/lepton' compiling PathTools.cpp gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/core' compiling PropertyMap.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 Position.cpp gmake -C ../multicolvar obj gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/multicolvar' compiling ActionVolume.cpp compiling SpathVessel.cpp compiling Rescale.cpp PathTools.cpp: In member function 'virtual int PLMD::mapping::PathTools::main(FILE*, FILE*, PLMD::Communicator&)': PathTools.cpp:268:17: 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 PropertyMap.cpp compiling Puckering.cpp compiling RMSD.cpp compiling AtomValuePack.cpp gmake -C ../reference obj gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/reference' compiling ArgumentOnlyDistance.cpp gmake -C ../secondarystructure obj gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/secondarystructure' compiling AlphaRMSD.cpp compiling DRMSD.cpp gmake -C ../setup obj gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/setup' compiling Load.cpp compiling Direction.cpp compiling AntibetaRMSD.cpp compiling Restart.cpp gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/mapping' compiling ParabetaRMSD.cpp compiling Bridge.cpp compiling SecondaryStructureRMSD.cpp compiling BridgedMultiColvarFunction.cpp compiling Units.cpp compiling DotProductDistance.cpp compiling Template.cpp compiling CatomPack.cpp compiling EuclideanDistance.cpp compiling Torsion.cpp compiling CenterOfMultiColvar.cpp gmake -C ../tools obj gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/tools' compiling Angle.cpp gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/setup' compiling FakeFrame.cpp gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/isdb' compiling CoordinationNumbers.cpp compiling Density.cpp compiling AtomNumber.cpp compiling Volume.cpp compiling IntermolecularDRMSD.cpp compiling BiasRepresentation.cpp compiling IntramolecularDRMSD.cpp compiling DihedralCorrelation.cpp compiling MahalanobisDistance.cpp gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/secondarystructure' compiling MetricRegister.cpp gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/colvar' compiling MultiDomainRMSD.cpp compiling Brent1DRootSearch.cpp gmake -C ../vatom obj gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/vatom' compiling ActionWithVirtualAtom.cpp compiling NormalizedEuclideanDistance.cpp compiling DistanceFromContour.cpp gmake -C ../vesselbase obj gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/vesselbase' compiling ActionWithAveraging.cpp compiling Distances.cpp compiling ActionWithInputVessel.cpp compiling Center.cpp compiling Citations.cpp compiling Communicator.cpp compiling ActionWithVessel.cpp compiling AltMin.cpp compiling AveragingVessel.cpp compiling ConjugateGradient.cpp compiling OptimalRMSD.cpp compiling FixedAtom.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 Between.cpp compiling DLLoader.cpp compiling DynamicList.cpp compiling BridgeVessel.cpp compiling RMSDBase.cpp compiling ERMSD.cpp compiling Ghost.cpp compiling DumpMultiColvar.cpp compiling FunctionVessel.cpp compiling Highest.cpp compiling FilterBetween.cpp gmake -C ../wrapper obj gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/wrapper' compiling PlumedStatic.cpp 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:2445:49: Plumed.h:2084:33: 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:2082:43: note: length computed here strlenpath=__PLUMED_WRAPPER_STD strlen(path); ^ compiling ReferenceArguments.cpp compiling FilterLessThan.cpp compiling Plumed.c In file included from Plumed.c:44: In function 'plumed_attempt_dlopen.part.1', inlined from 'plumed_attempt_dlopen' at Plumed.h:2055:7: Plumed.h:2084:26: 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:2082:37: note: length computed here strlenpath=__PLUMED_WRAPPER_STD strlen(path); ^~~~~~~~~~~~ gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/wrapper' compiling Histogram.cpp compiling FilterMoreThan.cpp compiling InPlaneDistances.cpp compiling Exception.cpp gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/vatom' compiling LessThan.cpp compiling ReferenceAtoms.cpp compiling FileBase.cpp compiling ReferenceConfiguration.cpp compiling Lowest.cpp compiling Max.cpp compiling Mean.cpp compiling Min.cpp compiling Moments.cpp compiling ForwardDecl.cpp compiling ReferenceValuePack.cpp compiling Grid.cpp compiling SimpleRMSD.cpp compiling LocalAverage.cpp compiling MoreThan.cpp compiling OrderingVessel.cpp compiling SingleDomainRMSD.cpp compiling HistogramBead.cpp compiling ShortcutVessel.cpp compiling StoreDataVessel.cpp compiling IFile.cpp gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/reference' compiling KernelFunctions.cpp compiling MultiColvarBase.cpp compiling MultiColvarCombine.cpp compiling Keywords.cpp compiling LatticeReduction.cpp compiling LinkCells.cpp compiling Sum.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); ~^~ compiling ValueVessel.cpp MultiColvarBase.cpp: In member function 'void PLMD::multicolvar::MultiColvarBase::setupActiveTaskSet(std::vector&, const string&)': MultiColvarBase.cpp:743:34: 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 Log.cpp compiling LoopUnroller.cpp compiling Vessel.cpp compiling Matrix.cpp compiling VesselRegister.cpp compiling MatrixSquareBracketsAccess.cpp compiling Minimise1DBrent.cpp compiling MultiColvarDensity.cpp compiling MinimiseBase.cpp compiling MultiColvarFilter.cpp compiling MultiColvarProduct.cpp compiling NumberOfLinks.cpp compiling MolDataClass.cpp compiling Torsions.cpp compiling MultiValue.cpp compiling VolumeAround.cpp compiling VolumeBetweenContours.cpp compiling NeighborList.cpp compiling OFile.cpp gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/vesselbase' compiling VolumeCavity.cpp compiling OpenMP.cpp NeighborList.cpp: In member function 'void PLMD::NeighborList::update(const std::vector >&)': NeighborList.cpp:159:22: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] for(unsigned i=0; i&, PLMD::VectorGeneric&, PLMD::TensorGeneric&) [with unsigned int n_ = 4; unsigned int m_ = 4; unsigned int n = 3; unsigned int m = 3]': RMSD.cpp:1038:40: required from here Tensor.h:557:17: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] for(int i=0; i1e-14) break; ~^~ Tensor.h:560:9: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] if(j&, PLMD::VectorGeneric&, PLMD::TensorGeneric&) [with unsigned int n_ = 4; unsigned int m_ = 1; unsigned int n = 3; unsigned int m = 3]': RMSD.cpp:1058:50: required from here Tensor.h:557:17: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] for(int i=0; i1e-14) break; ~^~ Tensor.h:560:9: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] if(j= digits_size) { ~~~^~~~~~~~~~~~~~ gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/tools' gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/multicolvar' gmake[7]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/lib' gmake[6]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/lib' gmake lib gmake[6]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/lib' c++ -pipe -O2 -fno-strict-aliasing -fPIC -Wall -pedantic -std=c++11 ../main/main.o ../analysis/AnalysisBase.o ../analysis/Average.o ../analysis/AverageVessel.o ../analysis/Committor.o ../analysis/DataCollectionObject.o ../analysis/EuclideanDissimilarityMatrix.o ../analysis/FarthestPointSampling.o ../analysis/Histogram.o ../analysis/LandmarkSelectionBase.o ../analysis/LandmarkStaged.o ../analysis/OutputColvarFile.o ../analysis/OutputPDBFile.o ../analysis/PrintDissimilarityMatrix.o ../analysis/ReadAnalysisFrames.o ../analysis/ReadDissimilarityMatrix.o ../analysis/ReselectLandmarks.o ../analysis/SelectRandomFrames.o ../analysis/SelectWithStride.o ../analysis/WhamHistogram.o ../analysis/WhamWeights.o ../asmjit/arch.o ../asmjit/assembler.o ../asmjit/codebuilder.o ../asmjit/codecompiler.o ../asmjit/codeemitter.o ../asmjit/codeholder.o ../asmjit/constpool.o ../asmjit/cpuinfo.o ../asmjit/func.o ../asmjit/globals.o ../asmjit/inst.o ../asmjit/logging.o ../asmjit/operand.o ../asmjit/osutils.o ../asmjit/regalloc.o ../asmjit/runtime.o ../asmjit/string.o ../asmjit/utils.o ../asmjit/vmem.o ../asmjit/x86assembler.o ../asmjit/x86builder.o ../asmjit/x86compiler.o ../asmjit/x86inst.o ../asmjit/x86instimpl.o ../asmjit/x86internal.o ../asmjit/x86logging.o ../asmjit/x86operand.o ../asmjit/x86operand_regs.o ../asmjit/x86regalloc.o ../asmjit/zone.o ../bias/ABMD.o ../bias/Bias.o ../bias/BiasValue.o ../bias/ExtendedLagrangian.o ../bias/External.o ../bias/LWalls.o ../bias/MaxEnt.o ../bias/MetaD.o ../bias/MovingRestraint.o ../bias/PBMetaD.o ../bias/Restraint.o ../bias/ReweightBase.o ../bias/ReweightBias.o ../bias/ReweightMetad.o ../bias/ReweightTemperaturePressure.o ../bias/ReweightWham.o ../bias/UWalls.o ../blas/blas.o ../cltools/CLTool.o ../cltools/Completion.o ../cltools/Driver.o ../cltools/DriverDouble.o ../cltools/DriverFloat.o ../cltools/GenExample.o ../cltools/GenTemplate.o ../cltools/Info.o ../cltools/Manual.o ../cltools/PdbRenumber.o ../cltools/SimpleMD.o ../cltools/SumHills.o ../cltools/kT.o ../cltools/pesmd.o ../colvar/Angle.o ../colvar/Cell.o ../colvar/Colvar.o ../colvar/Constant.o ../colvar/ContactMap.o ../colvar/Coordination.o ../colvar/CoordinationBase.o ../colvar/DHEnergy.o ../colvar/DRMSD.o ../colvar/Dimer.o ../colvar/Dipole.o ../colvar/Distance.o ../colvar/EEFSolv.o ../colvar/ERMSD.o ../colvar/Energy.o ../colvar/ExtraCV.o ../colvar/Fake.o ../colvar/Gyration.o ../colvar/MultiRMSD.o ../colvar/PCARMSD.o ../colvar/PathMSD.o ../colvar/PathMSDBase.o ../colvar/Position.o ../colvar/ProjectionOnAxis.o ../colvar/PropertyMap.o ../colvar/Puckering.o ../colvar/RMSD.o ../colvar/Template.o ../colvar/Torsion.o ../colvar/Volume.o ../core/Action.o ../core/ActionAnyorder.o ../core/ActionAtomistic.o ../core/ActionPilot.o ../core/ActionRegister.o ../core/ActionSet.o ../core/ActionSetup.o ../core/ActionShortcut.o ../core/ActionWithArguments.o ../core/ActionWithValue.o ../core/ActionWithVirtualAtom.o ../core/Atoms.o ../core/CLTool.o ../core/CLToolMain.o ../core/CLToolRegister.o ../core/Colvar.o ../core/DataFetchingObject.o ../core/ExchangePatterns.o ../core/FlexibleBin.o ../core/GREX.o ../core/GenericMolInfo.o ../core/MDAtoms.o ../core/PlumedMain.o ../core/PlumedMainInitializer.o ../core/TargetDist.o ../core/Value.o ../core/WithCmd.o ../function/Combine.o ../function/Custom.o ../function/Ensemble.o ../function/FuncPathGeneral.o ../function/FuncPathMSD.o ../function/FuncSumHills.o ../function/Function.o ../function/LocalEnsemble.o ../function/Piecewise.o ../function/Sort.o ../function/Stats.o ../function/Target.o ../generic/Debug.o ../generic/DumpAtoms.o ../generic/DumpDerivatives.o ../generic/DumpForces.o ../generic/DumpMassCharge.o ../generic/DumpProjections.o ../generic/EffectiveEnergyDrift.o ../generic/EndPlumed.o ../generic/FitToTemplate.o ../generic/Flush.o ../generic/Group.o ../generic/Include.o ../generic/MolInfo.o ../generic/Plumed.o ../generic/Print.o ../generic/RandomExchanges.o ../generic/Read.o ../generic/ResetCell.o ../generic/Time.o ../generic/UpdateIf.o ../generic/WholeMolecules.o ../generic/WrapAround.o ../gridtools/ActionWithGrid.o ../gridtools/ActionWithInputGrid.o ../gridtools/ActionWithIntegral.o ../gridtools/AverageOnGrid.o ../gridtools/ContourFindingBase.o ../gridtools/ConvertToFES.o ../gridtools/DumpCube.o ../gridtools/DumpGrid.o ../gridtools/FindContour.o ../gridtools/FindContourSurface.o ../gridtools/FindSphericalContour.o ../gridtools/FourierTransform.o ../gridtools/GridPrintingBase.o ../gridtools/GridSearch.o ../gridtools/GridToXYZ.o ../gridtools/GridVessel.o ../gridtools/HistogramOnGrid.o ../gridtools/IntegrateGrid.o ../gridtools/InterpolateGrid.o ../isdb/CS2Backbone.o ../isdb/Caliber.o ../isdb/EMMI.o ../isdb/FretEfficiency.o ../isdb/Jcoupling.o ../isdb/Metainference.o ../isdb/MetainferenceBase.o ../isdb/NOE.o ../isdb/PRE.o ../isdb/RDC.o ../isdb/Rescale.o ../isdb/SAXS.o ../isdb/Select.o ../isdb/Selector.o ../lapack/lapack.o ../lepton/CompiledExpression.o ../lepton/ExpressionProgram.o ../lepton/ExpressionTreeNode.o ../lepton/Operation.o ../lepton/ParsedExpression.o ../lepton/Parser.o ../mapping/AdaptivePath.o ../mapping/Mapping.o ../mapping/PCAVars.o ../mapping/Path.o ../mapping/PathBase.o ../mapping/PathReparameterization.o ../mapping/PathTools.o ../mapping/PropertyMap.o ../mapping/SpathVessel.o ../mapping/TrigonometricPathVessel.o ../mapping/ZpathVessel.o ../molfile/crdplugin.o ../molfile/dcdplugin.o ../molfile/gromacsplugin.o ../molfile/pdbplugin.o ../multicolvar/ActionVolume.o ../multicolvar/AlphaBeta.o ../multicolvar/Angles.o ../multicolvar/AtomValuePack.o ../multicolvar/Bridge.o ../multicolvar/BridgedMultiColvarFunction.o ../multicolvar/CatomPack.o ../multicolvar/CenterOfMultiColvar.o ../multicolvar/CoordinationNumbers.o ../multicolvar/Density.o ../multicolvar/DihedralCorrelation.o ../multicolvar/DistanceFromContour.o ../multicolvar/Distances.o ../multicolvar/DumpMultiColvar.o ../multicolvar/FilterBetween.o ../multicolvar/FilterLessThan.o ../multicolvar/FilterMoreThan.o ../multicolvar/InPlaneDistances.o ../multicolvar/LocalAverage.o ../multicolvar/MultiColvarBase.o ../multicolvar/MultiColvarCombine.o ../multicolvar/MultiColvarDensity.o ../multicolvar/MultiColvarFilter.o ../multicolvar/MultiColvarProduct.o ../multicolvar/NumberOfLinks.o ../multicolvar/Torsions.o ../multicolvar/VolumeAround.o ../multicolvar/VolumeBetweenContours.o ../multicolvar/VolumeCavity.o ../multicolvar/VolumeGradientBase.o ../multicolvar/VolumeInCylinder.o ../multicolvar/VolumeInSphere.o ../multicolvar/VolumeTetrapore.o ../multicolvar/XAngle.o ../multicolvar/XDistances.o ../multicolvar/XYDistances.o ../multicolvar/XYTorsion.o ../reference/ArgumentOnlyDistance.o ../reference/DRMSD.o ../reference/Direction.o ../reference/DotProductDistance.o ../reference/EuclideanDistance.o ../reference/FakeFrame.o ../reference/IntermolecularDRMSD.o ../reference/IntramolecularDRMSD.o ../reference/MahalanobisDistance.o ../reference/MetricRegister.o ../reference/MultiDomainRMSD.o ../reference/NormalizedEuclideanDistance.o ../reference/OptimalRMSD.o ../reference/RMSDBase.o ../reference/ReferenceArguments.o ../reference/ReferenceAtoms.o ../reference/ReferenceConfiguration.o ../reference/ReferenceValuePack.o ../reference/SimpleRMSD.o ../reference/SingleDomainRMSD.o ../secondarystructure/AlphaRMSD.o ../secondarystructure/AntibetaRMSD.o ../secondarystructure/ParabetaRMSD.o ../secondarystructure/SecondaryStructureRMSD.o ../setup/Load.o ../setup/Restart.o ../setup/Units.o ../tools/Angle.o ../tools/AtomNumber.o ../tools/BiasRepresentation.o ../tools/Brent1DRootSearch.o ../tools/Citations.o ../tools/Communicator.o ../tools/ConjugateGradient.o ../tools/DLLoader.o ../tools/DynamicList.o ../tools/ERMSD.o ../tools/Exception.o ../tools/FileBase.o ../tools/ForwardDecl.o ../tools/Grid.o ../tools/HistogramBead.o ../tools/IFile.o ../tools/KernelFunctions.o ../tools/Keywords.o ../tools/LatticeReduction.o ../tools/LinkCells.o ../tools/Log.o ../tools/LoopUnroller.o ../tools/Matrix.o ../tools/MatrixSquareBracketsAccess.o ../tools/Minimise1DBrent.o ../tools/MinimiseBase.o ../tools/MolDataClass.o ../tools/MultiValue.o ../tools/NeighborList.o ../tools/OFile.o ../tools/OpenMP.o ../tools/PDB.o ../tools/Pbc.o ../tools/PlumedHandle.o ../tools/RMSD.o ../tools/Random.o ../tools/RootFindingBase.o ../tools/Stopwatch.o ../tools/Subprocess.o ../tools/SwitchingFunction.o ../tools/Tensor.o ../tools/Tools.o ../tools/Torsion.o ../tools/Units.o ../tools/Vector.o ../tools/h36.o ../vatom/ActionWithVirtualAtom.o ../vatom/Center.o ../vatom/FixedAtom.o ../vatom/Ghost.o ../vesselbase/ActionWithAveraging.o ../vesselbase/ActionWithInputVessel.o ../vesselbase/ActionWithVessel.o ../vesselbase/AltMin.o ../vesselbase/AveragingVessel.o ../vesselbase/Between.o ../vesselbase/BridgeVessel.o ../vesselbase/FunctionVessel.o ../vesselbase/Highest.o ../vesselbase/Histogram.o ../vesselbase/LessThan.o ../vesselbase/Lowest.o ../vesselbase/Max.o ../vesselbase/Mean.o ../vesselbase/Min.o ../vesselbase/Moments.o ../vesselbase/MoreThan.o ../vesselbase/OrderingVessel.o ../vesselbase/ShortcutVessel.o ../vesselbase/StoreDataVessel.o ../vesselbase/Sum.o ../vesselbase/ValueVessel.o ../vesselbase/Vessel.o ../vesselbase/VesselRegister.o ../config/Config.o ../wrapper/PlumedStatic.o -o plumed-static -ldl -lstdc++ -lz -ldl -rdynamic -Wl,-Bsymbolic -fopenmp Building Plumed.inc c++ -shared -o libplumedKernel.so ../analysis/AnalysisBase.o ../analysis/Average.o ../analysis/AverageVessel.o ../analysis/Committor.o ../analysis/DataCollectionObject.o ../analysis/EuclideanDissimilarityMatrix.o ../analysis/FarthestPointSampling.o ../analysis/Histogram.o ../analysis/LandmarkSelectionBase.o ../analysis/LandmarkStaged.o ../analysis/OutputColvarFile.o ../analysis/OutputPDBFile.o ../analysis/PrintDissimilarityMatrix.o ../analysis/ReadAnalysisFrames.o ../analysis/ReadDissimilarityMatrix.o ../analysis/ReselectLandmarks.o ../analysis/SelectRandomFrames.o ../analysis/SelectWithStride.o ../analysis/WhamHistogram.o ../analysis/WhamWeights.o ../asmjit/arch.o ../asmjit/assembler.o ../asmjit/codebuilder.o ../asmjit/codecompiler.o ../asmjit/codeemitter.o ../asmjit/codeholder.o ../asmjit/constpool.o ../asmjit/cpuinfo.o ../asmjit/func.o ../asmjit/globals.o ../asmjit/inst.o ../asmjit/logging.o ../asmjit/operand.o ../asmjit/osutils.o ../asmjit/regalloc.o ../asmjit/runtime.o ../asmjit/string.o ../asmjit/utils.o ../asmjit/vmem.o ../asmjit/x86assembler.o ../asmjit/x86builder.o ../asmjit/x86compiler.o ../asmjit/x86inst.o ../asmjit/x86instimpl.o ../asmjit/x86internal.o ../asmjit/x86logging.o ../asmjit/x86operand.o ../asmjit/x86operand_regs.o ../asmjit/x86regalloc.o ../asmjit/zone.o ../bias/ABMD.o ../bias/Bias.o ../bias/BiasValue.o ../bias/ExtendedLagrangian.o ../bias/External.o ../bias/LWalls.o ../bias/MaxEnt.o ../bias/MetaD.o ../bias/MovingRestraint.o ../bias/PBMetaD.o ../bias/Restraint.o ../bias/ReweightBase.o ../bias/ReweightBias.o ../bias/ReweightMetad.o ../bias/ReweightTemperaturePressure.o ../bias/ReweightWham.o ../bias/UWalls.o ../blas/blas.o ../cltools/CLTool.o ../cltools/Completion.o ../cltools/Driver.o ../cltools/DriverDouble.o ../cltools/DriverFloat.o ../cltools/GenExample.o ../cltools/GenTemplate.o ../cltools/Info.o ../cltools/Manual.o ../cltools/PdbRenumber.o ../cltools/SimpleMD.o ../cltools/SumHills.o ../cltools/kT.o ../cltools/pesmd.o ../colvar/Angle.o ../colvar/Cell.o ../colvar/Colvar.o ../colvar/Constant.o ../colvar/ContactMap.o ../colvar/Coordination.o ../colvar/CoordinationBase.o ../colvar/DHEnergy.o ../colvar/DRMSD.o ../colvar/Dimer.o ../colvar/Dipole.o ../colvar/Distance.o ../colvar/EEFSolv.o ../colvar/ERMSD.o ../colvar/Energy.o ../colvar/ExtraCV.o ../colvar/Fake.o ../colvar/Gyration.o ../colvar/MultiRMSD.o ../colvar/PCARMSD.o ../colvar/PathMSD.o ../colvar/PathMSDBase.o ../colvar/Position.o ../colvar/ProjectionOnAxis.o ../colvar/PropertyMap.o ../colvar/Puckering.o ../colvar/RMSD.o ../colvar/Template.o ../colvar/Torsion.o ../colvar/Volume.o ../core/Action.o ../core/ActionAnyorder.o ../core/ActionAtomistic.o ../core/ActionPilot.o ../core/ActionRegister.o ../core/ActionSet.o ../core/ActionSetup.o ../core/ActionShortcut.o ../core/ActionWithArguments.o ../core/ActionWithValue.o ../core/ActionWithVirtualAtom.o ../core/Atoms.o ../core/CLTool.o ../core/CLToolMain.o ../core/CLToolRegister.o ../core/Colvar.o ../core/DataFetchingObject.o ../core/ExchangePatterns.o ../core/FlexibleBin.o ../core/GREX.o ../core/GenericMolInfo.o ../core/MDAtoms.o ../core/PlumedMain.o ../core/PlumedMainInitializer.o ../core/TargetDist.o ../core/Value.o ../core/WithCmd.o ../function/Combine.o ../function/Custom.o ../function/Ensemble.o ../function/FuncPathGeneral.o ../function/FuncPathMSD.o ../function/FuncSumHills.o ../function/Function.o ../function/LocalEnsemble.o ../function/Piecewise.o ../function/Sort.o ../function/Stats.o ../function/Target.o ../generic/Debug.o ../generic/DumpAtoms.o ../generic/DumpDerivatives.o ../generic/DumpForces.o ../generic/DumpMassCharge.o ../generic/DumpProjections.o ../generic/EffectiveEnergyDrift.o ../generic/EndPlumed.o ../generic/FitToTemplate.o ../generic/Flush.o ../generic/Group.o ../generic/Include.o ../generic/MolInfo.o ../generic/Plumed.o ../generic/Print.o ../generic/RandomExchanges.o ../generic/Read.o ../generic/ResetCell.o ../generic/Time.o ../generic/UpdateIf.o ../generic/WholeMolecules.o ../generic/WrapAround.o ../gridtools/ActionWithGrid.o ../gridtools/ActionWithInputGrid.o ../gridtools/ActionWithIntegral.o ../gridtools/AverageOnGrid.o ../gridtools/ContourFindingBase.o ../gridtools/ConvertToFES.o ../gridtools/DumpCube.o ../gridtools/DumpGrid.o ../gridtools/FindContour.o ../gridtools/FindContourSurface.o ../gridtools/FindSphericalContour.o ../gridtools/FourierTransform.o ../gridtools/GridPrintingBase.o ../gridtools/GridSearch.o ../gridtools/GridToXYZ.o ../gridtools/GridVessel.o ../gridtools/HistogramOnGrid.o ../gridtools/IntegrateGrid.o ../gridtools/InterpolateGrid.o ../isdb/CS2Backbone.o ../isdb/Caliber.o ../isdb/EMMI.o ../isdb/FretEfficiency.o ../isdb/Jcoupling.o ../isdb/Metainference.o ../isdb/MetainferenceBase.o ../isdb/NOE.o ../isdb/PRE.o ../isdb/RDC.o ../isdb/Rescale.o ../isdb/SAXS.o ../isdb/Select.o ../isdb/Selector.o ../lapack/lapack.o ../lepton/CompiledExpression.o ../lepton/ExpressionProgram.o ../lepton/ExpressionTreeNode.o ../lepton/Operation.o ../lepton/ParsedExpression.o ../lepton/Parser.o ../mapping/AdaptivePath.o ../mapping/Mapping.o ../mapping/PCAVars.o ../mapping/Path.o ../mapping/PathBase.o ../mapping/PathReparameterization.o ../mapping/PathTools.o ../mapping/PropertyMap.o ../mapping/SpathVessel.o ../mapping/TrigonometricPathVessel.o ../mapping/ZpathVessel.o ../molfile/crdplugin.o ../molfile/dcdplugin.o ../molfile/gromacsplugin.o ../molfile/pdbplugin.o ../multicolvar/ActionVolume.o ../multicolvar/AlphaBeta.o ../multicolvar/Angles.o ../multicolvar/AtomValuePack.o ../multicolvar/Bridge.o ../multicolvar/BridgedMultiColvarFunction.o ../multicolvar/CatomPack.o ../multicolvar/CenterOfMultiColvar.o ../multicolvar/CoordinationNumbers.o ../multicolvar/Density.o ../multicolvar/DihedralCorrelation.o ../multicolvar/DistanceFromContour.o ../multicolvar/Distances.o ../multicolvar/DumpMultiColvar.o ../multicolvar/FilterBetween.o ../multicolvar/FilterLessThan.o ../multicolvar/FilterMoreThan.o ../multicolvar/InPlaneDistances.o ../multicolvar/LocalAverage.o ../multicolvar/MultiColvarBase.o ../multicolvar/MultiColvarCombine.o ../multicolvar/MultiColvarDensity.o ../multicolvar/MultiColvarFilter.o ../multicolvar/MultiColvarProduct.o ../multicolvar/NumberOfLinks.o ../multicolvar/Torsions.o ../multicolvar/VolumeAround.o ../multicolvar/VolumeBetweenContours.o ../multicolvar/VolumeCavity.o ../multicolvar/VolumeGradientBase.o ../multicolvar/VolumeInCylinder.o ../multicolvar/VolumeInSphere.o ../multicolvar/VolumeTetrapore.o ../multicolvar/XAngle.o ../multicolvar/XDistances.o ../multicolvar/XYDistances.o ../multicolvar/XYTorsion.o ../reference/ArgumentOnlyDistance.o ../reference/DRMSD.o ../reference/Direction.o ../reference/DotProductDistance.o ../reference/EuclideanDistance.o ../reference/FakeFrame.o ../reference/IntermolecularDRMSD.o ../reference/IntramolecularDRMSD.o ../reference/MahalanobisDistance.o ../reference/MetricRegister.o ../reference/MultiDomainRMSD.o ../reference/NormalizedEuclideanDistance.o ../reference/OptimalRMSD.o ../reference/RMSDBase.o ../reference/ReferenceArguments.o ../reference/ReferenceAtoms.o ../reference/ReferenceConfiguration.o ../reference/ReferenceValuePack.o ../reference/SimpleRMSD.o ../reference/SingleDomainRMSD.o ../secondarystructure/AlphaRMSD.o ../secondarystructure/AntibetaRMSD.o ../secondarystructure/ParabetaRMSD.o ../secondarystructure/SecondaryStructureRMSD.o ../setup/Load.o ../setup/Restart.o ../setup/Units.o ../tools/Angle.o ../tools/AtomNumber.o ../tools/BiasRepresentation.o ../tools/Brent1DRootSearch.o ../tools/Citations.o ../tools/Communicator.o ../tools/ConjugateGradient.o ../tools/DLLoader.o ../tools/DynamicList.o ../tools/ERMSD.o ../tools/Exception.o ../tools/FileBase.o ../tools/ForwardDecl.o ../tools/Grid.o ../tools/HistogramBead.o ../tools/IFile.o ../tools/KernelFunctions.o ../tools/Keywords.o ../tools/LatticeReduction.o ../tools/LinkCells.o ../tools/Log.o ../tools/LoopUnroller.o ../tools/Matrix.o ../tools/MatrixSquareBracketsAccess.o ../tools/Minimise1DBrent.o ../tools/MinimiseBase.o ../tools/MolDataClass.o ../tools/MultiValue.o ../tools/NeighborList.o ../tools/OFile.o ../tools/OpenMP.o ../tools/PDB.o ../tools/Pbc.o ../tools/PlumedHandle.o ../tools/RMSD.o ../tools/Random.o ../tools/RootFindingBase.o ../tools/Stopwatch.o ../tools/Subprocess.o ../tools/SwitchingFunction.o ../tools/Tensor.o ../tools/Tools.o ../tools/Torsion.o ../tools/Units.o ../tools/Vector.o ../tools/h36.o ../vatom/ActionWithVirtualAtom.o ../vatom/Center.o ../vatom/FixedAtom.o ../vatom/Ghost.o ../vesselbase/ActionWithAveraging.o ../vesselbase/ActionWithInputVessel.o ../vesselbase/ActionWithVessel.o ../vesselbase/AltMin.o ../vesselbase/AveragingVessel.o ../vesselbase/Between.o ../vesselbase/BridgeVessel.o ../vesselbase/FunctionVessel.o ../vesselbase/Highest.o ../vesselbase/Histogram.o ../vesselbase/LessThan.o ../vesselbase/Lowest.o ../vesselbase/Max.o ../vesselbase/Mean.o ../vesselbase/Min.o ../vesselbase/Moments.o ../vesselbase/MoreThan.o ../vesselbase/OrderingVessel.o ../vesselbase/ShortcutVessel.o ../vesselbase/StoreDataVessel.o ../vesselbase/Sum.o ../vesselbase/ValueVessel.o ../vesselbase/Vessel.o ../vesselbase/VesselRegister.o ../config/Config.o -Wl,-soname,"libplumedKernel.so" -lstdc++ -lz -ldl -rdynamic -Wl,-Bsymbolic -fopenmp chmod a+x plumed-newcv c++ -pipe -O2 -fno-strict-aliasing -fPIC -Wall -pedantic -std=c++11 ../main/main.o ../wrapper/Plumed.o -o plumed-runtime -ldl chmod a+x plumed-selector chmod a+x plumed-config ar cr libplumedWrapper.a ../wrapper/Plumed.o chmod a+x plumed-patch Building Plumed.inc, static version Building Plumed.cmake Building Plumed.inc, runtime-linking version Building Plumed.inc, shared version chmod a+x plumed-vim2html Building Plumed.cmake, static version Building Plumed.cmake, runtime-linking version Building Plumed.cmake, shared version chmod a+x plumed-mklib chmod a+x plumed-partial_tempering ../core/PlumedMain.o:PlumedMain.cpp:function PLMD::PlumedMain::readInputLines(std::__cxx11::basic_string, std::allocator > const&): warning: warning: tmpnam() possibly used unsafely; consider using mkstemp() ../core/PlumedMain.o:PlumedMain.cpp:function PLMD::PlumedMain::readInputLines(std::__cxx11::basic_string, std::allocator > const&): warning: warning: tmpnam() possibly used unsafely; consider using mkstemp() c++ -shared -o libplumed.so ../wrapper/PlumedStatic.o libplumedKernel.so -Wl,-soname,"libplumed.so" c++ -pipe -O2 -fno-strict-aliasing -fPIC -Wall -pedantic -std=c++11 ../main/main.o ../wrapper/PlumedStatic.o libplumedKernel.so -o plumed -ldl gmake[6]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/lib' gmake install-build gmake[6]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/lib' gmake[6]: ../maketools/purge-d: No such file or directory mkdir -p install/ gmake PLUMED_INSTALL=Install all gmake[7]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/lib' gmake dirslinks gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.7.0/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 gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.7.0/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[10]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/function' Verify modules and create links in /construction/science/plumed/plumed2-2.7.0/src/function gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/bias' gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/config' gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/blas' gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/core' gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/cltools' Nothing to do in /construction/science/plumed/plumed2-2.7.0/src/config gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/config' gmake -C ../gridtools links Verify modules and create links in /construction/science/plumed/plumed2-2.7.0/src/blas Verify modules and create links in /construction/science/plumed/plumed2-2.7.0/src/bias gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/colvar' Verify modules and create links in /construction/science/plumed/plumed2-2.7.0/src/core gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/generic' gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/analysis' Verify modules and create links in /construction/science/plumed/plumed2-2.7.0/src/analysis gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/blas' gmake -C ../isdb links Verify modules and create links in /construction/science/plumed/plumed2-2.7.0/src/colvar gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/asmjit' gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/gridtools' gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/isdb' Verify modules and create links in /construction/science/plumed/plumed2-2.7.0/src/isdb Verify modules and create links in /construction/science/plumed/plumed2-2.7.0/src/asmjit Verify modules and create links in /construction/science/plumed/plumed2-2.7.0/src/cltools Verify modules and create links in /construction/science/plumed/plumed2-2.7.0/src/generic Verify modules and create links in /construction/science/plumed/plumed2-2.7.0/src/gridtools gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/asmjit' gmake -C ../lapack links gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/lapack' Verify modules and create links in /construction/science/plumed/plumed2-2.7.0/src/lapack gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/lapack' gmake -C ../lepton links gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/lepton' Verify modules and create links in /construction/science/plumed/plumed2-2.7.0/src/lepton gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/lepton' gmake -C ../main links gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/main' Verify modules and create links in /construction/science/plumed/plumed2-2.7.0/src/main gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/main' gmake -C ../mapping links gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/mapping' Verify modules and create links in /construction/science/plumed/plumed2-2.7.0/src/mapping gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/core' gmake -C ../molfile links gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/bias' gmake -C ../multicolvar links gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/molfile' Verify modules and create links in /construction/science/plumed/plumed2-2.7.0/src/molfile gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/molfile' gmake -C ../reference links gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/reference' gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/gridtools' gmake -C ../secondarystructure links gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/multicolvar' Verify modules and create links in /construction/science/plumed/plumed2-2.7.0/src/reference gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/secondarystructure' Verify modules and create links in /construction/science/plumed/plumed2-2.7.0/src/secondarystructure Verify modules and create links in /construction/science/plumed/plumed2-2.7.0/src/multicolvar gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/isdb' gmake -C ../setup links gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/setup' Verify modules and create links in /construction/science/plumed/plumed2-2.7.0/src/setup gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/generic' gmake -C ../tools links gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/tools' Verify modules and create links in /construction/science/plumed/plumed2-2.7.0/src/tools gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/function' gmake -C ../vatom links gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/vatom' Verify modules and create links in /construction/science/plumed/plumed2-2.7.0/src/vatom gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/colvar' gmake -C ../vesselbase links gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/vesselbase' Verify modules and create links in /construction/science/plumed/plumed2-2.7.0/src/vesselbase gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/cltools' gmake -C ../wrapper links gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/wrapper' Nothing to do in /construction/science/plumed/plumed2-2.7.0/src/wrapper gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/wrapper' gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/analysis' gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/reference' gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/tools' gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/vatom' gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/secondarystructure' gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/vesselbase' gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/setup' gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/multicolvar' gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/mapping' gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/lib' gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/lib' gmake dirs gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.7.0/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 gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.7.0/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[10]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/function' gmake[10]: Nothing to be done for 'obj'. gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/function' gmake -C ../gridtools obj gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/generic' gmake[10]: Nothing to be done for 'obj'. gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/generic' gmake -C ../isdb obj gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/isdb' gmake[10]: Nothing to be done for 'obj'. gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/isdb' gmake -C ../lapack obj gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/bias' gmake[10]: Nothing to be done for 'obj'. gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/bias' gmake -C ../lepton obj gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/gridtools' gmake[10]: Nothing to be done for 'obj'. gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/gridtools' gmake -C ../main obj gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/main' gmake[10]: Nothing to be done for 'obj'. gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/main' gmake -C ../mapping obj gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/asmjit' gmake[10]: Nothing to be done for 'obj'. gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/asmjit' gmake -C ../molfile obj gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/blas' gmake[10]: Nothing to be done for 'obj'. gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/blas' gmake -C ../multicolvar obj gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/mapping' gmake[10]: Nothing to be done for 'obj'. gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/mapping' gmake -C ../reference obj gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/core' gmake[10]: Nothing to be done for 'obj'. gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/core' gmake -C ../secondarystructure obj gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/cltools' gmake[10]: Nothing to be done for 'obj'. gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/cltools' gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/molfile' gmake[10]: Nothing to be done for 'obj'. gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/molfile' gmake -C ../setup obj gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/colvar' gmake[10]: Nothing to be done for 'obj'. gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/colvar' gmake -C ../tools obj gmake -C ../vatom obj gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/lepton' gmake[10]: Nothing to be done for 'obj'. gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/lepton' gmake -C ../vesselbase obj gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/setup' gmake[10]: Nothing to be done for 'obj'. gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/setup' gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/vatom' gmake[10]: Nothing to be done for 'obj'. gmake -C ../wrapper obj gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/vatom' gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/config' gmake PLUMED_FORCE=yes ConfigInstall.inc Config.inc version.h config.txt gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/lapack' gmake[10]: Nothing to be done for 'obj'. gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/lapack' gmake[11]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/config' gmake[11]: 'config.txt' is up to date. gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/analysis' gmake[10]: Nothing to be done for 'obj'. gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/analysis' Updating ConfigInstall.inc Updating Config.inc Updating version.h cmp -s Config.inc~ Config.inc || cp Config.inc~ Config.inc rm Config.inc~ cmp -s ConfigInstall.inc~ ConfigInstall.inc || cp ConfigInstall.inc~ ConfigInstall.inc gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/wrapper' gmake[10]: Nothing to be done for 'obj'. gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/wrapper' rm ConfigInstall.inc~ gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/vesselbase' gmake[10]: Nothing to be done for 'obj'. gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/vesselbase' gmake[11]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/config' gmake Config.o ConfigInstall.o compile_options.sh gmake[11]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/config' gmake[11]: 'Config.o' is up to date. gmake[11]: 'ConfigInstall.o' is up to date. gmake[11]: 'compile_options.sh' is up to date. gmake[11]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/config' gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/config' gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/secondarystructure' gmake[10]: Nothing to be done for 'obj'. gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/secondarystructure' gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/reference' gmake[10]: Nothing to be done for 'obj'. gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/reference' gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/tools' gmake[10]: Nothing to be done for 'obj'. gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/tools' gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/multicolvar' gmake[10]: Nothing to be done for 'obj'. gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/multicolvar' gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/lib' gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/lib' gmake lib gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/lib' c++ -pipe -O2 -fno-strict-aliasing -fPIC -Wall -pedantic -std=c++11 ../main/main.o ../analysis/AnalysisBase.o ../analysis/Average.o ../analysis/AverageVessel.o ../analysis/Committor.o ../analysis/DataCollectionObject.o ../analysis/EuclideanDissimilarityMatrix.o ../analysis/FarthestPointSampling.o ../analysis/Histogram.o ../analysis/LandmarkSelectionBase.o ../analysis/LandmarkStaged.o ../analysis/OutputColvarFile.o ../analysis/OutputPDBFile.o ../analysis/PrintDissimilarityMatrix.o ../analysis/ReadAnalysisFrames.o ../analysis/ReadDissimilarityMatrix.o ../analysis/ReselectLandmarks.o ../analysis/SelectRandomFrames.o ../analysis/SelectWithStride.o ../analysis/WhamHistogram.o ../analysis/WhamWeights.o ../asmjit/arch.o ../asmjit/assembler.o ../asmjit/codebuilder.o ../asmjit/codecompiler.o ../asmjit/codeemitter.o ../asmjit/codeholder.o ../asmjit/constpool.o ../asmjit/cpuinfo.o ../asmjit/func.o ../asmjit/globals.o ../asmjit/inst.o ../asmjit/logging.o ../asmjit/operand.o ../asmjit/osutils.o ../asmjit/regalloc.o ../asmjit/runtime.o ../asmjit/string.o ../asmjit/utils.o ../asmjit/vmem.o ../asmjit/x86assembler.o ../asmjit/x86builder.o ../asmjit/x86compiler.o ../asmjit/x86inst.o ../asmjit/x86instimpl.o ../asmjit/x86internal.o ../asmjit/x86logging.o ../asmjit/x86operand.o ../asmjit/x86operand_regs.o ../asmjit/x86regalloc.o ../asmjit/zone.o ../bias/ABMD.o ../bias/Bias.o ../bias/BiasValue.o ../bias/ExtendedLagrangian.o ../bias/External.o ../bias/LWalls.o ../bias/MaxEnt.o ../bias/MetaD.o ../bias/MovingRestraint.o ../bias/PBMetaD.o ../bias/Restraint.o ../bias/ReweightBase.o ../bias/ReweightBias.o ../bias/ReweightMetad.o ../bias/ReweightTemperaturePressure.o ../bias/ReweightWham.o ../bias/UWalls.o ../blas/blas.o ../cltools/CLTool.o ../cltools/Completion.o ../cltools/Driver.o ../cltools/DriverDouble.o ../cltools/DriverFloat.o ../cltools/GenExample.o ../cltools/GenTemplate.o ../cltools/Info.o ../cltools/Manual.o ../cltools/PdbRenumber.o ../cltools/SimpleMD.o ../cltools/SumHills.o ../cltools/kT.o ../cltools/pesmd.o ../colvar/Angle.o ../colvar/Cell.o ../colvar/Colvar.o ../colvar/Constant.o ../colvar/ContactMap.o ../colvar/Coordination.o ../colvar/CoordinationBase.o ../colvar/DHEnergy.o ../colvar/DRMSD.o ../colvar/Dimer.o ../colvar/Dipole.o ../colvar/Distance.o ../colvar/EEFSolv.o ../colvar/ERMSD.o ../colvar/Energy.o ../colvar/ExtraCV.o ../colvar/Fake.o ../colvar/Gyration.o ../colvar/MultiRMSD.o ../colvar/PCARMSD.o ../colvar/PathMSD.o ../colvar/PathMSDBase.o ../colvar/Position.o ../colvar/ProjectionOnAxis.o ../colvar/PropertyMap.o ../colvar/Puckering.o ../colvar/RMSD.o ../colvar/Template.o ../colvar/Torsion.o ../colvar/Volume.o ../core/Action.o ../core/ActionAnyorder.o ../core/ActionAtomistic.o ../core/ActionPilot.o ../core/ActionRegister.o ../core/ActionSet.o ../core/ActionSetup.o ../core/ActionShortcut.o ../core/ActionWithArguments.o ../core/ActionWithValue.o ../core/ActionWithVirtualAtom.o ../core/Atoms.o ../core/CLTool.o ../core/CLToolMain.o ../core/CLToolRegister.o ../core/Colvar.o ../core/DataFetchingObject.o ../core/ExchangePatterns.o ../core/FlexibleBin.o ../core/GREX.o ../core/GenericMolInfo.o ../core/MDAtoms.o ../core/PlumedMain.o ../core/PlumedMainInitializer.o ../core/TargetDist.o ../core/Value.o ../core/WithCmd.o ../function/Combine.o ../function/Custom.o ../function/Ensemble.o ../function/FuncPathGeneral.o ../function/FuncPathMSD.o ../function/FuncSumHills.o ../function/Function.o ../function/LocalEnsemble.o ../function/Piecewise.o ../function/Sort.o ../function/Stats.o ../function/Target.o ../generic/Debug.o ../generic/DumpAtoms.o ../generic/DumpDerivatives.o ../generic/DumpForces.o ../generic/DumpMassCharge.o ../generic/DumpProjections.o ../generic/EffectiveEnergyDrift.o ../generic/EndPlumed.o ../generic/FitToTemplate.o ../generic/Flush.o ../generic/Group.o ../generic/Include.o ../generic/MolInfo.o ../generic/Plumed.o ../generic/Print.o ../generic/RandomExchanges.o ../generic/Read.o ../generic/ResetCell.o ../generic/Time.o ../generic/UpdateIf.o ../generic/WholeMolecules.o ../generic/WrapAround.o ../gridtools/ActionWithGrid.o ../gridtools/ActionWithInputGrid.o ../gridtools/ActionWithIntegral.o ../gridtools/AverageOnGrid.o ../gridtools/ContourFindingBase.o ../gridtools/ConvertToFES.o ../gridtools/DumpCube.o ../gridtools/DumpGrid.o ../gridtools/FindContour.o ../gridtools/FindContourSurface.o ../gridtools/FindSphericalContour.o ../gridtools/FourierTransform.o ../gridtools/GridPrintingBase.o ../gridtools/GridSearch.o ../gridtools/GridToXYZ.o ../gridtools/GridVessel.o ../gridtools/HistogramOnGrid.o ../gridtools/IntegrateGrid.o ../gridtools/InterpolateGrid.o ../isdb/CS2Backbone.o ../isdb/Caliber.o ../isdb/EMMI.o ../isdb/FretEfficiency.o ../isdb/Jcoupling.o ../isdb/Metainference.o ../isdb/MetainferenceBase.o ../isdb/NOE.o ../isdb/PRE.o ../isdb/RDC.o ../isdb/Rescale.o ../isdb/SAXS.o ../isdb/Select.o ../isdb/Selector.o ../lapack/lapack.o ../lepton/CompiledExpression.o ../lepton/ExpressionProgram.o ../lepton/ExpressionTreeNode.o ../lepton/Operation.o ../lepton/ParsedExpression.o ../lepton/Parser.o ../mapping/AdaptivePath.o ../mapping/Mapping.o ../mapping/PCAVars.o ../mapping/Path.o ../mapping/PathBase.o ../mapping/PathReparameterization.o ../mapping/PathTools.o ../mapping/PropertyMap.o ../mapping/SpathVessel.o ../mapping/TrigonometricPathVessel.o ../mapping/ZpathVessel.o ../molfile/crdplugin.o ../molfile/dcdplugin.o ../molfile/gromacsplugin.o ../molfile/pdbplugin.o ../multicolvar/ActionVolume.o ../multicolvar/AlphaBeta.o ../multicolvar/Angles.o ../multicolvar/AtomValuePack.o ../multicolvar/Bridge.o ../multicolvar/BridgedMultiColvarFunction.o ../multicolvar/CatomPack.o ../multicolvar/CenterOfMultiColvar.o ../multicolvar/CoordinationNumbers.o ../multicolvar/Density.o ../multicolvar/DihedralCorrelation.o ../multicolvar/DistanceFromContour.o ../multicolvar/Distances.o ../multicolvar/DumpMultiColvar.o ../multicolvar/FilterBetween.o ../multicolvar/FilterLessThan.o ../multicolvar/FilterMoreThan.o ../multicolvar/InPlaneDistances.o ../multicolvar/LocalAverage.o ../multicolvar/MultiColvarBase.o ../multicolvar/MultiColvarCombine.o ../multicolvar/MultiColvarDensity.o ../multicolvar/MultiColvarFilter.o ../multicolvar/MultiColvarProduct.o ../multicolvar/NumberOfLinks.o ../multicolvar/Torsions.o ../multicolvar/VolumeAround.o ../multicolvar/VolumeBetweenContours.o ../multicolvar/VolumeCavity.o ../multicolvar/VolumeGradientBase.o ../multicolvar/VolumeInCylinder.o ../multicolvar/VolumeInSphere.o ../multicolvar/VolumeTetrapore.o ../multicolvar/XAngle.o ../multicolvar/XDistances.o ../multicolvar/XYDistances.o ../multicolvar/XYTorsion.o ../reference/ArgumentOnlyDistance.o ../reference/DRMSD.o ../reference/Direction.o ../reference/DotProductDistance.o ../reference/EuclideanDistance.o ../reference/FakeFrame.o ../reference/IntermolecularDRMSD.o ../reference/IntramolecularDRMSD.o ../reference/MahalanobisDistance.o ../reference/MetricRegister.o ../reference/MultiDomainRMSD.o ../reference/NormalizedEuclideanDistance.o ../reference/OptimalRMSD.o ../reference/RMSDBase.o ../reference/ReferenceArguments.o ../reference/ReferenceAtoms.o ../reference/ReferenceConfiguration.o ../reference/ReferenceValuePack.o ../reference/SimpleRMSD.o ../reference/SingleDomainRMSD.o ../secondarystructure/AlphaRMSD.o ../secondarystructure/AntibetaRMSD.o ../secondarystructure/ParabetaRMSD.o ../secondarystructure/SecondaryStructureRMSD.o ../setup/Load.o ../setup/Restart.o ../setup/Units.o ../tools/Angle.o ../tools/AtomNumber.o ../tools/BiasRepresentation.o ../tools/Brent1DRootSearch.o ../tools/Citations.o ../tools/Communicator.o ../tools/ConjugateGradient.o ../tools/DLLoader.o ../tools/DynamicList.o ../tools/ERMSD.o ../tools/Exception.o ../tools/FileBase.o ../tools/ForwardDecl.o ../tools/Grid.o ../tools/HistogramBead.o ../tools/IFile.o ../tools/KernelFunctions.o ../tools/Keywords.o ../tools/LatticeReduction.o ../tools/LinkCells.o ../tools/Log.o ../tools/LoopUnroller.o ../tools/Matrix.o ../tools/MatrixSquareBracketsAccess.o ../tools/Minimise1DBrent.o ../tools/MinimiseBase.o ../tools/MolDataClass.o ../tools/MultiValue.o ../tools/NeighborList.o ../tools/OFile.o ../tools/OpenMP.o ../tools/PDB.o ../tools/Pbc.o ../tools/PlumedHandle.o ../tools/RMSD.o ../tools/Random.o ../tools/RootFindingBase.o ../tools/Stopwatch.o ../tools/Subprocess.o ../tools/SwitchingFunction.o ../tools/Tensor.o ../tools/Tools.o ../tools/Torsion.o ../tools/Units.o ../tools/Vector.o ../tools/h36.o ../vatom/ActionWithVirtualAtom.o ../vatom/Center.o ../vatom/FixedAtom.o ../vatom/Ghost.o ../vesselbase/ActionWithAveraging.o ../vesselbase/ActionWithInputVessel.o ../vesselbase/ActionWithVessel.o ../vesselbase/AltMin.o ../vesselbase/AveragingVessel.o ../vesselbase/Between.o ../vesselbase/BridgeVessel.o ../vesselbase/FunctionVessel.o ../vesselbase/Highest.o ../vesselbase/Histogram.o ../vesselbase/LessThan.o ../vesselbase/Lowest.o ../vesselbase/Max.o ../vesselbase/Mean.o ../vesselbase/Min.o ../vesselbase/Moments.o ../vesselbase/MoreThan.o ../vesselbase/OrderingVessel.o ../vesselbase/ShortcutVessel.o ../vesselbase/StoreDataVessel.o ../vesselbase/Sum.o ../vesselbase/ValueVessel.o ../vesselbase/Vessel.o ../vesselbase/VesselRegister.o ../config/ConfigInstall.o ../wrapper/PlumedStatic.o -o install/plumed-static -ldl -lstdc++ -lz -ldl -rdynamic -Wl,-Bsymbolic -fopenmp Building Plumed.inc mkdir -p install c++ -shared -o install/libplumedKernel.so ../analysis/AnalysisBase.o ../analysis/Average.o ../analysis/AverageVessel.o ../analysis/Committor.o ../analysis/DataCollectionObject.o ../analysis/EuclideanDissimilarityMatrix.o ../analysis/FarthestPointSampling.o ../analysis/Histogram.o ../analysis/LandmarkSelectionBase.o ../analysis/LandmarkStaged.o ../analysis/OutputColvarFile.o ../analysis/OutputPDBFile.o ../analysis/PrintDissimilarityMatrix.o ../analysis/ReadAnalysisFrames.o ../analysis/ReadDissimilarityMatrix.o ../analysis/ReselectLandmarks.o ../analysis/SelectRandomFrames.o ../analysis/SelectWithStride.o ../analysis/WhamHistogram.o ../analysis/WhamWeights.o ../asmjit/arch.o ../asmjit/assembler.o ../asmjit/codebuilder.o ../asmjit/codecompiler.o ../asmjit/codeemitter.o ../asmjit/codeholder.o ../asmjit/constpool.o ../asmjit/cpuinfo.o ../asmjit/func.o ../asmjit/globals.o ../asmjit/inst.o ../asmjit/logging.o ../asmjit/operand.o ../asmjit/osutils.o ../asmjit/regalloc.o ../asmjit/runtime.o ../asmjit/string.o ../asmjit/utils.o ../asmjit/vmem.o ../asmjit/x86assembler.o ../asmjit/x86builder.o ../asmjit/x86compiler.o ../asmjit/x86inst.o ../asmjit/x86instimpl.o ../asmjit/x86internal.o ../asmjit/x86logging.o ../asmjit/x86operand.o ../asmjit/x86operand_regs.o ../asmjit/x86regalloc.o ../asmjit/zone.o ../bias/ABMD.o ../bias/Bias.o ../bias/BiasValue.o ../bias/ExtendedLagrangian.o ../bias/External.o ../bias/LWalls.o ../bias/MaxEnt.o ../bias/MetaD.o ../bias/MovingRestraint.o ../bias/PBMetaD.o ../bias/Restraint.o ../bias/ReweightBase.o ../bias/ReweightBias.o ../bias/ReweightMetad.o ../bias/ReweightTemperaturePressure.o ../bias/ReweightWham.o ../bias/UWalls.o ../blas/blas.o ../cltools/CLTool.o ../cltools/Completion.o ../cltools/Driver.o ../cltools/DriverDouble.o ../cltools/DriverFloat.o ../cltools/GenExample.o ../cltools/GenTemplate.o ../cltools/Info.o ../cltools/Manual.o ../cltools/PdbRenumber.o ../cltools/SimpleMD.o ../cltools/SumHills.o ../cltools/kT.o ../cltools/pesmd.o ../colvar/Angle.o ../colvar/Cell.o ../colvar/Colvar.o ../colvar/Constant.o ../colvar/ContactMap.o ../colvar/Coordination.o ../colvar/CoordinationBase.o ../colvar/DHEnergy.o ../colvar/DRMSD.o ../colvar/Dimer.o ../colvar/Dipole.o ../colvar/Distance.o ../colvar/EEFSolv.o ../colvar/ERMSD.o ../colvar/Energy.o ../colvar/ExtraCV.o ../colvar/Fake.o ../colvar/Gyration.o ../colvar/MultiRMSD.o ../colvar/PCARMSD.o ../colvar/PathMSD.o ../colvar/PathMSDBase.o ../colvar/Position.o ../colvar/ProjectionOnAxis.o ../colvar/PropertyMap.o ../colvar/Puckering.o ../colvar/RMSD.o ../colvar/Template.o ../colvar/Torsion.o ../colvar/Volume.o ../core/Action.o ../core/ActionAnyorder.o ../core/ActionAtomistic.o ../core/ActionPilot.o ../core/ActionRegister.o ../core/ActionSet.o ../core/ActionSetup.o ../core/ActionShortcut.o ../core/ActionWithArguments.o ../core/ActionWithValue.o ../core/ActionWithVirtualAtom.o ../core/Atoms.o ../core/CLTool.o ../core/CLToolMain.o ../core/CLToolRegister.o ../core/Colvar.o ../core/DataFetchingObject.o ../core/ExchangePatterns.o ../core/FlexibleBin.o ../core/GREX.o ../core/GenericMolInfo.o ../core/MDAtoms.o ../core/PlumedMain.o ../core/PlumedMainInitializer.o ../core/TargetDist.o ../core/Value.o ../core/WithCmd.o ../function/Combine.o ../function/Custom.o ../function/Ensemble.o ../function/FuncPathGeneral.o ../function/FuncPathMSD.o ../function/FuncSumHills.o ../function/Function.o ../function/LocalEnsemble.o ../function/Piecewise.o ../function/Sort.o ../function/Stats.o ../function/Target.o ../generic/Debug.o ../generic/DumpAtoms.o ../generic/DumpDerivatives.o ../generic/DumpForces.o ../generic/DumpMassCharge.o ../generic/DumpProjections.o ../generic/EffectiveEnergyDrift.o ../generic/EndPlumed.o ../generic/FitToTemplate.o ../generic/Flush.o ../generic/Group.o ../generic/Include.o ../generic/MolInfo.o ../generic/Plumed.o ../generic/Print.o ../generic/RandomExchanges.o ../generic/Read.o ../generic/ResetCell.o ../generic/Time.o ../generic/UpdateIf.o ../generic/WholeMolecules.o ../generic/WrapAround.o ../gridtools/ActionWithGrid.o ../gridtools/ActionWithInputGrid.o ../gridtools/ActionWithIntegral.o ../gridtools/AverageOnGrid.o ../gridtools/ContourFindingBase.o ../gridtools/ConvertToFES.o ../gridtools/DumpCube.o ../gridtools/DumpGrid.o ../gridtools/FindContour.o ../gridtools/FindContourSurface.o ../gridtools/FindSphericalContour.o ../gridtools/FourierTransform.o ../gridtools/GridPrintingBase.o ../gridtools/GridSearch.o ../gridtools/GridToXYZ.o ../gridtools/GridVessel.o ../gridtools/HistogramOnGrid.o ../gridtools/IntegrateGrid.o ../gridtools/InterpolateGrid.o ../isdb/CS2Backbone.o ../isdb/Caliber.o ../isdb/EMMI.o ../isdb/FretEfficiency.o ../isdb/Jcoupling.o ../isdb/Metainference.o ../isdb/MetainferenceBase.o ../isdb/NOE.o ../isdb/PRE.o ../isdb/RDC.o ../isdb/Rescale.o ../isdb/SAXS.o ../isdb/Select.o ../isdb/Selector.o ../lapack/lapack.o ../lepton/CompiledExpression.o ../lepton/ExpressionProgram.o ../lepton/ExpressionTreeNode.o ../lepton/Operation.o ../lepton/ParsedExpression.o ../lepton/Parser.o ../mapping/AdaptivePath.o ../mapping/Mapping.o ../mapping/PCAVars.o ../mapping/Path.o ../mapping/PathBase.o ../mapping/PathReparameterization.o ../mapping/PathTools.o ../mapping/PropertyMap.o ../mapping/SpathVessel.o ../mapping/TrigonometricPathVessel.o ../mapping/ZpathVessel.o ../molfile/crdplugin.o ../molfile/dcdplugin.o ../molfile/gromacsplugin.o ../molfile/pdbplugin.o ../multicolvar/ActionVolume.o ../multicolvar/AlphaBeta.o ../multicolvar/Angles.o ../multicolvar/AtomValuePack.o ../multicolvar/Bridge.o ../multicolvar/BridgedMultiColvarFunction.o ../multicolvar/CatomPack.o ../multicolvar/CenterOfMultiColvar.o ../multicolvar/CoordinationNumbers.o ../multicolvar/Density.o ../multicolvar/DihedralCorrelation.o ../multicolvar/DistanceFromContour.o ../multicolvar/Distances.o ../multicolvar/DumpMultiColvar.o ../multicolvar/FilterBetween.o ../multicolvar/FilterLessThan.o ../multicolvar/FilterMoreThan.o ../multicolvar/InPlaneDistances.o ../multicolvar/LocalAverage.o ../multicolvar/MultiColvarBase.o ../multicolvar/MultiColvarCombine.o ../multicolvar/MultiColvarDensity.o ../multicolvar/MultiColvarFilter.o ../multicolvar/MultiColvarProduct.o ../multicolvar/NumberOfLinks.o ../multicolvar/Torsions.o ../multicolvar/VolumeAround.o ../multicolvar/VolumeBetweenContours.o ../multicolvar/VolumeCavity.o ../multicolvar/VolumeGradientBase.o ../multicolvar/VolumeInCylinder.o ../multicolvar/VolumeInSphere.o ../multicolvar/VolumeTetrapore.o ../multicolvar/XAngle.o ../multicolvar/XDistances.o ../multicolvar/XYDistances.o ../multicolvar/XYTorsion.o ../reference/ArgumentOnlyDistance.o ../reference/DRMSD.o ../reference/Direction.o ../reference/DotProductDistance.o ../reference/EuclideanDistance.o ../reference/FakeFrame.o ../reference/IntermolecularDRMSD.o ../reference/IntramolecularDRMSD.o ../reference/MahalanobisDistance.o ../reference/MetricRegister.o ../reference/MultiDomainRMSD.o ../reference/NormalizedEuclideanDistance.o ../reference/OptimalRMSD.o ../reference/RMSDBase.o ../reference/ReferenceArguments.o ../reference/ReferenceAtoms.o ../reference/ReferenceConfiguration.o ../reference/ReferenceValuePack.o ../reference/SimpleRMSD.o ../reference/SingleDomainRMSD.o ../secondarystructure/AlphaRMSD.o ../secondarystructure/AntibetaRMSD.o ../secondarystructure/ParabetaRMSD.o ../secondarystructure/SecondaryStructureRMSD.o ../setup/Load.o ../setup/Restart.o ../setup/Units.o ../tools/Angle.o ../tools/AtomNumber.o ../tools/BiasRepresentation.o ../tools/Brent1DRootSearch.o ../tools/Citations.o ../tools/Communicator.o ../tools/ConjugateGradient.o ../tools/DLLoader.o ../tools/DynamicList.o ../tools/ERMSD.o ../tools/Exception.o ../tools/FileBase.o ../tools/ForwardDecl.o ../tools/Grid.o ../tools/HistogramBead.o ../tools/IFile.o ../tools/KernelFunctions.o ../tools/Keywords.o ../tools/LatticeReduction.o ../tools/LinkCells.o ../tools/Log.o ../tools/LoopUnroller.o ../tools/Matrix.o ../tools/MatrixSquareBracketsAccess.o ../tools/Minimise1DBrent.o ../tools/MinimiseBase.o ../tools/MolDataClass.o ../tools/MultiValue.o ../tools/NeighborList.o ../tools/OFile.o ../tools/OpenMP.o ../tools/PDB.o ../tools/Pbc.o ../tools/PlumedHandle.o ../tools/RMSD.o ../tools/Random.o ../tools/RootFindingBase.o ../tools/Stopwatch.o ../tools/Subprocess.o ../tools/SwitchingFunction.o ../tools/Tensor.o ../tools/Tools.o ../tools/Torsion.o ../tools/Units.o ../tools/Vector.o ../tools/h36.o ../vatom/ActionWithVirtualAtom.o ../vatom/Center.o ../vatom/FixedAtom.o ../vatom/Ghost.o ../vesselbase/ActionWithAveraging.o ../vesselbase/ActionWithInputVessel.o ../vesselbase/ActionWithVessel.o ../vesselbase/AltMin.o ../vesselbase/AveragingVessel.o ../vesselbase/Between.o ../vesselbase/BridgeVessel.o ../vesselbase/FunctionVessel.o ../vesselbase/Highest.o ../vesselbase/Histogram.o ../vesselbase/LessThan.o ../vesselbase/Lowest.o ../vesselbase/Max.o ../vesselbase/Mean.o ../vesselbase/Min.o ../vesselbase/Moments.o ../vesselbase/MoreThan.o ../vesselbase/OrderingVessel.o ../vesselbase/ShortcutVessel.o ../vesselbase/StoreDataVessel.o ../vesselbase/Sum.o ../vesselbase/ValueVessel.o ../vesselbase/Vessel.o ../vesselbase/VesselRegister.o ../config/ConfigInstall.o -Wl,-soname,"libplumedKernel.so" -lstdc++ -lz -ldl -rdynamic -Wl,-Bsymbolic -fopenmp c++ -pipe -O2 -fno-strict-aliasing -fPIC -Wall -pedantic -std=c++11 ../main/main.o ../wrapper/Plumed.o -o install/plumed-runtime -ldl chmod a+x install/plumed-vim2html chmod a+x install/plumed-patch mkdir -p install ar cr install/libplumedWrapper.a ../wrapper/Plumed.o Building Plumed.inc, runtime-linking version chmod a+x install/plumed-mklib chmod a+x install/plumed-partial_tempering Building Plumed.inc, shared version Building Plumed.inc, static version chmod a+x install/plumed-selector Building Plumed.cmake chmod a+x install/plumed-newcv chmod a+x install/plumed-config Building Plumed.cmake, static version Building Plumed.cmake, shared version Building Plumed.cmake, runtime-linking version ../core/PlumedMain.o:PlumedMain.cpp:function PLMD::PlumedMain::readInputLines(std::__cxx11::basic_string, std::allocator > const&): warning: warning: tmpnam() possibly used unsafely; consider using mkstemp() ../core/PlumedMain.o:PlumedMain.cpp:function PLMD::PlumedMain::readInputLines(std::__cxx11::basic_string, std::allocator > const&): warning: warning: tmpnam() possibly used unsafely; consider using mkstemp() mkdir -p install c++ -pipe -O2 -fno-strict-aliasing -fPIC -Wall -pedantic -std=c++11 ../main/main.o ../wrapper/PlumedStatic.o install/libplumedKernel.so -o install/plumed -ldl c++ -shared -o install/libplumed.so ../wrapper/PlumedStatic.o install/libplumedKernel.so -Wl,-soname,"libplumed.so" gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/lib' gmake[7]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/lib' gmake PLUMED_INSTALL=Install install/kernel.o gmake[7]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/lib' ld -r -o install/kernel.o ../analysis/AnalysisBase.o ../analysis/Average.o ../analysis/AverageVessel.o ../analysis/Committor.o ../analysis/DataCollectionObject.o ../analysis/EuclideanDissimilarityMatrix.o ../analysis/FarthestPointSampling.o ../analysis/Histogram.o ../analysis/LandmarkSelectionBase.o ../analysis/LandmarkStaged.o ../analysis/OutputColvarFile.o ../analysis/OutputPDBFile.o ../analysis/PrintDissimilarityMatrix.o ../analysis/ReadAnalysisFrames.o ../analysis/ReadDissimilarityMatrix.o ../analysis/ReselectLandmarks.o ../analysis/SelectRandomFrames.o ../analysis/SelectWithStride.o ../analysis/WhamHistogram.o ../analysis/WhamWeights.o ../asmjit/arch.o ../asmjit/assembler.o ../asmjit/codebuilder.o ../asmjit/codecompiler.o ../asmjit/codeemitter.o ../asmjit/codeholder.o ../asmjit/constpool.o ../asmjit/cpuinfo.o ../asmjit/func.o ../asmjit/globals.o ../asmjit/inst.o ../asmjit/logging.o ../asmjit/operand.o ../asmjit/osutils.o ../asmjit/regalloc.o ../asmjit/runtime.o ../asmjit/string.o ../asmjit/utils.o ../asmjit/vmem.o ../asmjit/x86assembler.o ../asmjit/x86builder.o ../asmjit/x86compiler.o ../asmjit/x86inst.o ../asmjit/x86instimpl.o ../asmjit/x86internal.o ../asmjit/x86logging.o ../asmjit/x86operand.o ../asmjit/x86operand_regs.o ../asmjit/x86regalloc.o ../asmjit/zone.o ../bias/ABMD.o ../bias/Bias.o ../bias/BiasValue.o ../bias/ExtendedLagrangian.o ../bias/External.o ../bias/LWalls.o ../bias/MaxEnt.o ../bias/MetaD.o ../bias/MovingRestraint.o ../bias/PBMetaD.o ../bias/Restraint.o ../bias/ReweightBase.o ../bias/ReweightBias.o ../bias/ReweightMetad.o ../bias/ReweightTemperaturePressure.o ../bias/ReweightWham.o ../bias/UWalls.o ../blas/blas.o ../cltools/CLTool.o ../cltools/Completion.o ../cltools/Driver.o ../cltools/DriverDouble.o ../cltools/DriverFloat.o ../cltools/GenExample.o ../cltools/GenTemplate.o ../cltools/Info.o ../cltools/Manual.o ../cltools/PdbRenumber.o ../cltools/SimpleMD.o ../cltools/SumHills.o ../cltools/kT.o ../cltools/pesmd.o ../colvar/Angle.o ../colvar/Cell.o ../colvar/Colvar.o ../colvar/Constant.o ../colvar/ContactMap.o ../colvar/Coordination.o ../colvar/CoordinationBase.o ../colvar/DHEnergy.o ../colvar/DRMSD.o ../colvar/Dimer.o ../colvar/Dipole.o ../colvar/Distance.o ../colvar/EEFSolv.o ../colvar/ERMSD.o ../colvar/Energy.o ../colvar/ExtraCV.o ../colvar/Fake.o ../colvar/Gyration.o ../colvar/MultiRMSD.o ../colvar/PCARMSD.o ../colvar/PathMSD.o ../colvar/PathMSDBase.o ../colvar/Position.o ../colvar/ProjectionOnAxis.o ../colvar/PropertyMap.o ../colvar/Puckering.o ../colvar/RMSD.o ../colvar/Template.o ../colvar/Torsion.o ../colvar/Volume.o ../core/Action.o ../core/ActionAnyorder.o ../core/ActionAtomistic.o ../core/ActionPilot.o ../core/ActionRegister.o ../core/ActionSet.o ../core/ActionSetup.o ../core/ActionShortcut.o ../core/ActionWithArguments.o ../core/ActionWithValue.o ../core/ActionWithVirtualAtom.o ../core/Atoms.o ../core/CLTool.o ../core/CLToolMain.o ../core/CLToolRegister.o ../core/Colvar.o ../core/DataFetchingObject.o ../core/ExchangePatterns.o ../core/FlexibleBin.o ../core/GREX.o ../core/GenericMolInfo.o ../core/MDAtoms.o ../core/PlumedMain.o ../core/PlumedMainInitializer.o ../core/TargetDist.o ../core/Value.o ../core/WithCmd.o ../function/Combine.o ../function/Custom.o ../function/Ensemble.o ../function/FuncPathGeneral.o ../function/FuncPathMSD.o ../function/FuncSumHills.o ../function/Function.o ../function/LocalEnsemble.o ../function/Piecewise.o ../function/Sort.o ../function/Stats.o ../function/Target.o ../generic/Debug.o ../generic/DumpAtoms.o ../generic/DumpDerivatives.o ../generic/DumpForces.o ../generic/DumpMassCharge.o ../generic/DumpProjections.o ../generic/EffectiveEnergyDrift.o ../generic/EndPlumed.o ../generic/FitToTemplate.o ../generic/Flush.o ../generic/Group.o ../generic/Include.o ../generic/MolInfo.o ../generic/Plumed.o ../generic/Print.o ../generic/RandomExchanges.o ../generic/Read.o ../generic/ResetCell.o ../generic/Time.o ../generic/UpdateIf.o ../generic/WholeMolecules.o ../generic/WrapAround.o ../gridtools/ActionWithGrid.o ../gridtools/ActionWithInputGrid.o ../gridtools/ActionWithIntegral.o ../gridtools/AverageOnGrid.o ../gridtools/ContourFindingBase.o ../gridtools/ConvertToFES.o ../gridtools/DumpCube.o ../gridtools/DumpGrid.o ../gridtools/FindContour.o ../gridtools/FindContourSurface.o ../gridtools/FindSphericalContour.o ../gridtools/FourierTransform.o ../gridtools/GridPrintingBase.o ../gridtools/GridSearch.o ../gridtools/GridToXYZ.o ../gridtools/GridVessel.o ../gridtools/HistogramOnGrid.o ../gridtools/IntegrateGrid.o ../gridtools/InterpolateGrid.o ../isdb/CS2Backbone.o ../isdb/Caliber.o ../isdb/EMMI.o ../isdb/FretEfficiency.o ../isdb/Jcoupling.o ../isdb/Metainference.o ../isdb/MetainferenceBase.o ../isdb/NOE.o ../isdb/PRE.o ../isdb/RDC.o ../isdb/Rescale.o ../isdb/SAXS.o ../isdb/Select.o ../isdb/Selector.o ../lapack/lapack.o ../lepton/CompiledExpression.o ../lepton/ExpressionProgram.o ../lepton/ExpressionTreeNode.o ../lepton/Operation.o ../lepton/ParsedExpression.o ../lepton/Parser.o ../mapping/AdaptivePath.o ../mapping/Mapping.o ../mapping/PCAVars.o ../mapping/Path.o ../mapping/PathBase.o ../mapping/PathReparameterization.o ../mapping/PathTools.o ../mapping/PropertyMap.o ../mapping/SpathVessel.o ../mapping/TrigonometricPathVessel.o ../mapping/ZpathVessel.o ../molfile/crdplugin.o ../molfile/dcdplugin.o ../molfile/gromacsplugin.o ../molfile/pdbplugin.o ../multicolvar/ActionVolume.o ../multicolvar/AlphaBeta.o ../multicolvar/Angles.o ../multicolvar/AtomValuePack.o ../multicolvar/Bridge.o ../multicolvar/BridgedMultiColvarFunction.o ../multicolvar/CatomPack.o ../multicolvar/CenterOfMultiColvar.o ../multicolvar/CoordinationNumbers.o ../multicolvar/Density.o ../multicolvar/DihedralCorrelation.o ../multicolvar/DistanceFromContour.o ../multicolvar/Distances.o ../multicolvar/DumpMultiColvar.o ../multicolvar/FilterBetween.o ../multicolvar/FilterLessThan.o ../multicolvar/FilterMoreThan.o ../multicolvar/InPlaneDistances.o ../multicolvar/LocalAverage.o ../multicolvar/MultiColvarBase.o ../multicolvar/MultiColvarCombine.o ../multicolvar/MultiColvarDensity.o ../multicolvar/MultiColvarFilter.o ../multicolvar/MultiColvarProduct.o ../multicolvar/NumberOfLinks.o ../multicolvar/Torsions.o ../multicolvar/VolumeAround.o ../multicolvar/VolumeBetweenContours.o ../multicolvar/VolumeCavity.o ../multicolvar/VolumeGradientBase.o ../multicolvar/VolumeInCylinder.o ../multicolvar/VolumeInSphere.o ../multicolvar/VolumeTetrapore.o ../multicolvar/XAngle.o ../multicolvar/XDistances.o ../multicolvar/XYDistances.o ../multicolvar/XYTorsion.o ../reference/ArgumentOnlyDistance.o ../reference/DRMSD.o ../reference/Direction.o ../reference/DotProductDistance.o ../reference/EuclideanDistance.o ../reference/FakeFrame.o ../reference/IntermolecularDRMSD.o ../reference/IntramolecularDRMSD.o ../reference/MahalanobisDistance.o ../reference/MetricRegister.o ../reference/MultiDomainRMSD.o ../reference/NormalizedEuclideanDistance.o ../reference/OptimalRMSD.o ../reference/RMSDBase.o ../reference/ReferenceArguments.o ../reference/ReferenceAtoms.o ../reference/ReferenceConfiguration.o ../reference/ReferenceValuePack.o ../reference/SimpleRMSD.o ../reference/SingleDomainRMSD.o ../secondarystructure/AlphaRMSD.o ../secondarystructure/AntibetaRMSD.o ../secondarystructure/ParabetaRMSD.o ../secondarystructure/SecondaryStructureRMSD.o ../setup/Load.o ../setup/Restart.o ../setup/Units.o ../tools/Angle.o ../tools/AtomNumber.o ../tools/BiasRepresentation.o ../tools/Brent1DRootSearch.o ../tools/Citations.o ../tools/Communicator.o ../tools/ConjugateGradient.o ../tools/DLLoader.o ../tools/DynamicList.o ../tools/ERMSD.o ../tools/Exception.o ../tools/FileBase.o ../tools/ForwardDecl.o ../tools/Grid.o ../tools/HistogramBead.o ../tools/IFile.o ../tools/KernelFunctions.o ../tools/Keywords.o ../tools/LatticeReduction.o ../tools/LinkCells.o ../tools/Log.o ../tools/LoopUnroller.o ../tools/Matrix.o ../tools/MatrixSquareBracketsAccess.o ../tools/Minimise1DBrent.o ../tools/MinimiseBase.o ../tools/MolDataClass.o ../tools/MultiValue.o ../tools/NeighborList.o ../tools/OFile.o ../tools/OpenMP.o ../tools/PDB.o ../tools/Pbc.o ../tools/PlumedHandle.o ../tools/RMSD.o ../tools/Random.o ../tools/RootFindingBase.o ../tools/Stopwatch.o ../tools/Subprocess.o ../tools/SwitchingFunction.o ../tools/Tensor.o ../tools/Tools.o ../tools/Torsion.o ../tools/Units.o ../tools/Vector.o ../tools/h36.o ../vatom/ActionWithVirtualAtom.o ../vatom/Center.o ../vatom/FixedAtom.o ../vatom/Ghost.o ../vesselbase/ActionWithAveraging.o ../vesselbase/ActionWithInputVessel.o ../vesselbase/ActionWithVessel.o ../vesselbase/AltMin.o ../vesselbase/AveragingVessel.o ../vesselbase/Between.o ../vesselbase/BridgeVessel.o ../vesselbase/FunctionVessel.o ../vesselbase/Highest.o ../vesselbase/Histogram.o ../vesselbase/LessThan.o ../vesselbase/Lowest.o ../vesselbase/Max.o ../vesselbase/Mean.o ../vesselbase/Min.o ../vesselbase/Moments.o ../vesselbase/MoreThan.o ../vesselbase/OrderingVessel.o ../vesselbase/ShortcutVessel.o ../vesselbase/StoreDataVessel.o ../vesselbase/Sum.o ../vesselbase/ValueVessel.o ../vesselbase/Vessel.o ../vesselbase/VesselRegister.o ../config/ConfigInstall.o gmake[7]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/lib' gmake PLUMED_INSTALL=Install install/libplumed.a gmake[7]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/lib' rm -f install/libplumed.a ar cr install/libplumed.a install/kernel.o ../wrapper/PlumedStatic.o gmake[7]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/lib' gmake[6]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/lib' gmake[5]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/lib' gmake[4]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src' gmake[3]: Leaving directory '/construction/science/plumed/plumed2-2.7.0' gmake -C vim gmake[3]: Entering directory '/construction/science/plumed/plumed2-2.7.0/vim' ./vimsyntax.sh gmake[3]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/vim' gmake -C python gmake[3]: Entering directory '/construction/science/plumed/plumed2-2.7.0/python' Python support was not configure gmake[3]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/python' gmake[2]: Leaving directory '/construction/science/plumed/plumed2-2.7.0' SUCCEEDED 00:05:53 ------------------------------------------------------------------------------- -- Phase: run-depends ------------------------------------------------------------------------------- ===> plumed-2.7.0 depends on executable: bash - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: stage ------------------------------------------------------------------------------- ===> Staging for plumed-2.7.0 ===> plumed-2.7.0 depends on executable: bash - found ===> Generating temporary packing list gmake[2]: Entering directory '/construction/science/plumed/plumed2-2.7.0' gmake -C src install gmake[3]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src' gmake -C lib install gmake[4]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/lib' cd ../config ; gmake gmake[5]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/config' gmake PLUMED_FORCE=yes ConfigInstall.inc Config.inc version.h config.txt gmake[6]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/config' Updating ConfigInstall.inc cmp -s ConfigInstall.inc~ ConfigInstall.inc || cp ConfigInstall.inc~ ConfigInstall.inc rm ConfigInstall.inc~ Updating Config.inc cmp -s Config.inc~ Config.inc || cp Config.inc~ Config.inc rm Config.inc~ Updating version.h gmake[6]: 'config.txt' is up to date. gmake[6]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/config' gmake Config.o ConfigInstall.o compile_options.sh gmake[6]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/config' gmake[6]: 'Config.o' is up to date. gmake[6]: 'ConfigInstall.o' is up to date. gmake[6]: 'compile_options.sh' is up to date. gmake[6]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/config' gmake[5]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/config' # gmake uninstall mkdir -p "/construction/science/plumed/stage/usr/local/bin" mkdir -p "/construction/science/plumed/stage/usr/local/lib" mkdir -p "/construction/science/plumed/stage/usr/local/lib/pkgconfig" mkdir -p "/construction/science/plumed/stage/usr/local/include/plumed" mkdir -p "/construction/science/plumed/stage/usr/local/lib/plumed/obj" mkdir -p "/construction/science/plumed/stage/usr/local/lib/plumed/src/lib" mkdir -p "/construction/science/plumed/stage/usr/local/lib/plumed/src/config" mkdir -p "/construction/science/plumed/stage/usr/local/lib/plumed/src/colvar" gmake install-build gmake[5]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/lib' gmake[5]: ../maketools/purge-d: No such file or directory mkdir -p install/ gmake PLUMED_INSTALL=Install all gmake[6]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/lib' gmake dirslinks gmake[7]: Entering directory '/construction/science/plumed/plumed2-2.7.0/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 gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/lib' gmake -C ../analysis links gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/analysis' Verify modules and create links in /construction/science/plumed/plumed2-2.7.0/src/analysis gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/analysis' gmake -C ../asmjit links gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/asmjit' Verify modules and create links in /construction/science/plumed/plumed2-2.7.0/src/asmjit gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/asmjit' gmake -C ../bias links gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/bias' Verify modules and create links in /construction/science/plumed/plumed2-2.7.0/src/bias gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/bias' gmake -C ../blas links gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/blas' Verify modules and create links in /construction/science/plumed/plumed2-2.7.0/src/blas gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/blas' gmake -C ../cltools links gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/cltools' Verify modules and create links in /construction/science/plumed/plumed2-2.7.0/src/cltools gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/cltools' gmake -C ../colvar links gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/colvar' Verify modules and create links in /construction/science/plumed/plumed2-2.7.0/src/colvar gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/colvar' gmake -C ../config links gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/config' Nothing to do in /construction/science/plumed/plumed2-2.7.0/src/config gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/config' gmake -C ../core links gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/core' Verify modules and create links in /construction/science/plumed/plumed2-2.7.0/src/core gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/core' gmake -C ../function links gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/function' Verify modules and create links in /construction/science/plumed/plumed2-2.7.0/src/function gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/function' gmake -C ../generic links gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/generic' Verify modules and create links in /construction/science/plumed/plumed2-2.7.0/src/generic gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/generic' gmake -C ../gridtools links gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/gridtools' Verify modules and create links in /construction/science/plumed/plumed2-2.7.0/src/gridtools gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/gridtools' gmake -C ../isdb links gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/isdb' Verify modules and create links in /construction/science/plumed/plumed2-2.7.0/src/isdb gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/isdb' gmake -C ../lapack links gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/lapack' Verify modules and create links in /construction/science/plumed/plumed2-2.7.0/src/lapack gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/lapack' gmake -C ../lepton links gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/lepton' Verify modules and create links in /construction/science/plumed/plumed2-2.7.0/src/lepton gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/lepton' gmake -C ../main links gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/main' Verify modules and create links in /construction/science/plumed/plumed2-2.7.0/src/main gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/main' gmake -C ../mapping links gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/mapping' Verify modules and create links in /construction/science/plumed/plumed2-2.7.0/src/mapping gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/mapping' gmake -C ../molfile links gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/molfile' Verify modules and create links in /construction/science/plumed/plumed2-2.7.0/src/molfile gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/molfile' gmake -C ../multicolvar links gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/multicolvar' Verify modules and create links in /construction/science/plumed/plumed2-2.7.0/src/multicolvar gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/multicolvar' gmake -C ../reference links gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/reference' Verify modules and create links in /construction/science/plumed/plumed2-2.7.0/src/reference gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/reference' gmake -C ../secondarystructure links gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/secondarystructure' Verify modules and create links in /construction/science/plumed/plumed2-2.7.0/src/secondarystructure gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/secondarystructure' gmake -C ../setup links gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/setup' Verify modules and create links in /construction/science/plumed/plumed2-2.7.0/src/setup gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/setup' gmake -C ../tools links gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/tools' Verify modules and create links in /construction/science/plumed/plumed2-2.7.0/src/tools gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/tools' gmake -C ../vatom links gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/vatom' Verify modules and create links in /construction/science/plumed/plumed2-2.7.0/src/vatom gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/vatom' gmake -C ../vesselbase links gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/vesselbase' Verify modules and create links in /construction/science/plumed/plumed2-2.7.0/src/vesselbase gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/vesselbase' gmake -C ../wrapper links gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/wrapper' Nothing to do in /construction/science/plumed/plumed2-2.7.0/src/wrapper gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/wrapper' gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/lib' gmake[7]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/lib' gmake dirs gmake[7]: Entering directory '/construction/science/plumed/plumed2-2.7.0/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 gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/lib' gmake -C ../analysis obj gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/analysis' gmake[9]: Nothing to be done for 'obj'. gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/analysis' gmake -C ../asmjit obj gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/asmjit' gmake[9]: Nothing to be done for 'obj'. gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/asmjit' gmake -C ../bias obj gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/bias' gmake[9]: Nothing to be done for 'obj'. gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/bias' gmake -C ../blas obj gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/blas' gmake[9]: Nothing to be done for 'obj'. gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/blas' gmake -C ../cltools obj gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/cltools' gmake[9]: Nothing to be done for 'obj'. gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/cltools' gmake -C ../colvar obj gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/colvar' gmake[9]: Nothing to be done for 'obj'. gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/colvar' gmake -C ../config obj gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/config' gmake PLUMED_FORCE=yes ConfigInstall.inc Config.inc version.h config.txt gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/config' Updating ConfigInstall.inc cmp -s ConfigInstall.inc~ ConfigInstall.inc || cp ConfigInstall.inc~ ConfigInstall.inc rm ConfigInstall.inc~ Updating Config.inc cmp -s Config.inc~ Config.inc || cp Config.inc~ Config.inc rm Config.inc~ Updating version.h gmake[10]: 'config.txt' is up to date. gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/config' gmake Config.o ConfigInstall.o compile_options.sh gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/config' gmake[10]: 'Config.o' is up to date. gmake[10]: 'ConfigInstall.o' is up to date. gmake[10]: 'compile_options.sh' is up to date. gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/config' gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/config' gmake -C ../core obj gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/core' gmake[9]: Nothing to be done for 'obj'. gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/core' gmake -C ../function obj gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/function' gmake[9]: Nothing to be done for 'obj'. gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/function' gmake -C ../generic obj gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/generic' gmake[9]: Nothing to be done for 'obj'. gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/generic' gmake -C ../gridtools obj gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/gridtools' gmake[9]: Nothing to be done for 'obj'. gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/gridtools' gmake -C ../isdb obj gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/isdb' gmake[9]: Nothing to be done for 'obj'. gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/isdb' gmake -C ../lapack obj gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/lapack' gmake[9]: Nothing to be done for 'obj'. gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/lapack' gmake -C ../lepton obj gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/lepton' gmake[9]: Nothing to be done for 'obj'. gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/lepton' gmake -C ../main obj gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/main' gmake[9]: Nothing to be done for 'obj'. gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/main' gmake -C ../mapping obj gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/mapping' gmake[9]: Nothing to be done for 'obj'. gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/mapping' gmake -C ../molfile obj gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/molfile' gmake[9]: Nothing to be done for 'obj'. gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/molfile' gmake -C ../multicolvar obj gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/multicolvar' gmake[9]: Nothing to be done for 'obj'. gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/multicolvar' gmake -C ../reference obj gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/reference' gmake[9]: Nothing to be done for 'obj'. gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/reference' gmake -C ../secondarystructure obj gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/secondarystructure' gmake[9]: Nothing to be done for 'obj'. gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/secondarystructure' gmake -C ../setup obj gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/setup' gmake[9]: Nothing to be done for 'obj'. gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/setup' gmake -C ../tools obj gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/tools' gmake[9]: Nothing to be done for 'obj'. gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/tools' gmake -C ../vatom obj gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/vatom' gmake[9]: Nothing to be done for 'obj'. gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/vatom' gmake -C ../vesselbase obj gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/vesselbase' gmake[9]: Nothing to be done for 'obj'. gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/vesselbase' gmake -C ../wrapper obj gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/wrapper' gmake[9]: Nothing to be done for 'obj'. gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/wrapper' gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/lib' gmake[7]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/lib' gmake lib gmake[7]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/lib' Building Plumed.inc Building Plumed.inc, static version Building Plumed.cmake Building Plumed.cmake, static version chmod a+x install/plumed-config chmod a+x install/plumed-mklib chmod a+x install/plumed-newcv chmod a+x install/plumed-partial_tempering chmod a+x install/plumed-patch chmod a+x install/plumed-selector chmod a+x install/plumed-vim2html Building Plumed.inc, runtime-linking version Building Plumed.inc, shared version Building Plumed.cmake, runtime-linking version Building Plumed.cmake, shared version gmake[7]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/lib' gmake[6]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/lib' gmake PLUMED_INSTALL=Install install/kernel.o gmake[6]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/lib' gmake[6]: 'install/kernel.o' is up to date. gmake[6]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/lib' gmake PLUMED_INSTALL=Install install/libplumed.a gmake[6]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/lib' gmake[6]: 'install/libplumed.a' is up to date. gmake[6]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/lib' gmake[5]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/lib' gmake install-html gmake[5]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/lib' if test -d ../../user-doc/html ; then mkdir -p "/construction/science/plumed/stage/usr/local/share/doc/plumed" && cd ../../ && tar cf - user-doc/html | tar xf - -C "/construction/science/plumed/stage/usr/local/share/doc/plumed/" ; fi if test -d ../../developer-doc/html ; then mkdir -p "/construction/science/plumed/stage/usr/local/share/doc/plumed" && cd ../../ && tar cf - developer-doc/html | tar xf - -C "/construction/science/plumed/stage/usr/local/share/doc/plumed/" ; fi if test -d ../../developer-doc/coverage ; then mkdir -p "/construction/science/plumed/stage/usr/local/share/doc/plumed" && cd ../../ && tar cf - developer-doc/coverage | tar xf - -C "/construction/science/plumed/stage/usr/local/share/doc/plumed/" ; fi if test -f ../../user-doc/manual.pdf ; then mkdir -p "/construction/science/plumed/stage/usr/local/share/doc/plumed/user-doc" && cp ../../user-doc/manual.pdf "/construction/science/plumed/stage/usr/local/share/doc/plumed/user-doc/" ; fi gmake[5]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/lib' cd ../../ ; tar cf - patches scripts | tar xf - -C "/construction/science/plumed/stage/usr/local/lib/plumed/" cp ../colvar/Template.cpp "/construction/science/plumed/stage/usr/local/lib/plumed/src/colvar/" grep -v "^link_uninstalled=" ../config/compile_options.sh > "/construction/science/plumed/stage/usr/local/lib/plumed/src/config/compile_options.sh" cp ../config/config.txt "/construction/science/plumed/stage/usr/local/lib/plumed/src/config/config.txt" cp install/libplumed.a "/construction/science/plumed/stage/usr/local/lib/" gmake install-headers gmake[5]: Entering directory '/construction/science/plumed/plumed2-2.7.0/src/lib' bash ../maketools/install.headers "/construction/science/plumed/stage/usr/local/include/plumed/" analysis asmjit bias blas cltools colvar config core function generic gridtools isdb lapack lepton main mapping molfile multicolvar reference secondarystructure setup tools vatom vesselbase wrapper gmake[5]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/lib' cp install/"plumed" "/construction/science/plumed/stage/usr/local/bin/" cp install/plumed-patch "/construction/science/plumed/stage/usr/local/bin/plumed-patch" cp install/plumed-config "/construction/science/plumed/stage/usr/local/bin/plumed-config" cp install/Plumed.cmake* "/construction/science/plumed/stage/usr/local/lib/plumed/src/lib/" cp install/Plumed.inc* "/construction/science/plumed/stage/usr/local/lib/plumed/src/lib/" for file in config mklib newcv partial_tempering patch selector vim2html ; do cp install/plumed-$file "/construction/science/plumed/stage/usr/local/lib/plumed/plumed-$file" ; done cp install/lib"plumed".so "/construction/science/plumed/stage/usr/local/lib/" cp install/lib"plumed"Kernel.so "/construction/science/plumed/stage/usr/local/lib/" if test -e install/"plumed"-runtime ; then cp install/"plumed"-runtime "/construction/science/plumed/stage/usr/local/lib/plumed/plumed-runtime" ; fi cp install/libplumedWrapper.a "/construction/science/plumed/stage/usr/local/lib/" cp install/modulefile "/construction/science/plumed/stage/usr/local/lib/plumed/modulefile" cp install/pkgconfig "/construction/science/plumed/stage/usr/local/lib/pkgconfig/plumed.pc" cp install/pkgconfigWrapper "/construction/science/plumed/stage/usr/local/lib/pkgconfig/plumedWrapper.pc" cp install/pkgconfigInternals "/construction/science/plumed/stage/usr/local/lib/pkgconfig/plumedInternals.pc" if test -d ../../vim/syntax ; then mkdir -p "/construction/science/plumed/stage/usr/local/lib/plumed" && cd ../../ && tar cf - vim/syntax | tar xf - -C "/construction/science/plumed/stage/usr/local/lib/plumed/" ; fi if test -d ../../vim/help ; then mkdir -p "/construction/science/plumed/stage/usr/local/lib/plumed" && cd ../../ && tar cf - vim/help | tar xf - -C "/construction/science/plumed/stage/usr/local/lib/plumed/" ; fi if test -f ../../vim/scripts.vim ; then mkdir -p "/construction/science/plumed/stage/usr/local/lib/plumed/vim" && cp ../../vim/scripts.vim "/construction/science/plumed/stage/usr/local/lib/plumed/vim/" ; fi chmod -R go+rX,go-w "/construction/science/plumed/stage/usr/local/lib/plumed" chmod -R go+rX,go-w "/construction/science/plumed/stage/usr/local/include/plumed" chmod -R go+rX,go-w "/construction/science/plumed/stage/usr/local/bin/plumed" chmod -R go+rX,go-w "/construction/science/plumed/stage/usr/local/bin/plumed-patch" *** PLUMED has been installed *** WARNING: Staged install with DESTDIR = /construction/science/plumed/stage Install prefix : /usr/local Full name : plumed Setup your environment - Ensure this is in your execution path : /usr/local/bin - Ensure this is in your include path : /usr/local/include - Ensure this is in your library path : /usr/local/lib - Ensure this is in your PKG_CONFIG_PATH path : /usr/local/lib/pkgconfig For runtime binding: - Set this environment variable : PLUMED_KERNEL=/usr/local/lib/libplumedKernel.so To create a tcl module that sets all the variables above, use this one as a starting point: /usr/local/lib/plumed/modulefile To uninstall, remove the following files and directories: /usr/local/lib/plumed /usr/local/share/doc/plumed /usr/local/include/plumed /usr/local/bin/plumed /usr/local/bin/plumed-patch /usr/local/bin/plumed-config /usr/local/lib/pkgconfig/plumed.pc /usr/local/lib/libplumed.so /usr/local/lib/libplumedKernel.so A vim plugin can be found here: /usr/local/lib/plumed/vim/ Copy it to /construction/science/plumed/.vim/ directory Alternatively: - Set this environment variable : PLUMED_VIMPATH=/usr/local/lib/plumed/vim - Add the command 'let &runtimepath.=','.$PLUMED_VIMPATH' to your .vimrc file From vim, you can use :set syntax=plumed to enable it gmake[4]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src/lib' gmake[3]: Leaving directory '/construction/science/plumed/plumed2-2.7.0/src' gmake[2]: Leaving directory '/construction/science/plumed/plumed2-2.7.0' ====> Compressing man pages (compress-man) ====> Running Q/A tests (stage-qa) Warning: You have disabled the licenses framework with DISABLE_LICENSES, unable to run checks SUCCEEDED 00:00:31 ------------------------------------------------------------------------------- -- Phase: check-plist ------------------------------------------------------------------------------- ====> Checking for pkg-plist issues (check-plist) ===> Parsing plist ===> Checking for items in STAGEDIR missing from pkg-plist ===> Checking for items in pkg-plist which are not in STAGEDIR ===> No pkg-plist issues found (check-plist) SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: package ------------------------------------------------------------------------------- ===> Building package for plumed-2.7.0 file sizes/checksums [497]: 0% file sizes/checksums [497]: 20% file sizes/checksums [497]: 40% file sizes/checksums [497]: 60% file sizes/checksums [497]: 80% file sizes/checksums [497]: 100% packing files [497]: 0% packing files [497]: 20% packing files [497]: 40% packing files [497]: 60% packing files [497]: 80% packing files [497]: 100% packing directories [0]: 0% packing directories [0]: 100% SUCCEEDED 00:00:47 TOTAL TIME 00:08:28