-------------------------------------------------------------------------------
-- Phase: setup
-------------------------------------------------------------------------------

Installing /packages/All/indexinfo-0.3.1.txz
Installing /packages/All/gettext-runtime-0.20.2.txz
Installing /packages/All/ncurses-6.1.20190525.txz
Installing /packages/All/bash-5.0.17.txz
Installing /packages/All/vim-console-8.2.0491_1.txz
Installing /packages/All/gmake-4.3.txz
Installing /packages/All/pkgconf-1.6.3,1.txz
Installing /packages/All/m4-1.4.18_1,1.txz
Installing /packages/All/autoconf-wrapper-20131203.txz
Installing /packages/All/perl5-5.30.2.txz
=====
Message from perl5-5.30.2:

--
The /usr/bin/perl symlink has been removed starting with Perl 5.20.
For shebangs, you should either use:

#!/usr/local/bin/perl

or

#!/usr/bin/env perl

The first one will only work if you have a /usr/local/bin/perl,
the second will work as long as perl is in PATH.
Installing /packages/All/autoconf-2.69_3.txz
Installing /packages/All/automake-1.16.2.txz

SUCCEEDED 00:00:13

-------------------------------------------------------------------------------
-- Phase: check-sanity
-------------------------------------------------------------------------------


SUCCEEDED 00:00:00

-------------------------------------------------------------------------------
-- Phase: pkg-depends
-------------------------------------------------------------------------------

===>   plumed-2.6.0 depends on file: /usr/local/sbin/pkg - found

SUCCEEDED 00:00:00

-------------------------------------------------------------------------------
-- Phase: fetch-depends
-------------------------------------------------------------------------------


SUCCEEDED 00:00:00

-------------------------------------------------------------------------------
-- Phase: fetch
-------------------------------------------------------------------------------

===>   plumed-2.6.0 depends on file: /usr/local/sbin/pkg - found
===> Fetching all distfiles required by plumed-2.6.0 for building

SUCCEEDED 00:00:00

-------------------------------------------------------------------------------
-- Phase: checksum
-------------------------------------------------------------------------------

===>   plumed-2.6.0 depends on file: /usr/local/sbin/pkg - found
===> Fetching all distfiles required by plumed-2.6.0 for building
=> SHA256 Checksum OK for plumed-plumed2-v2.6.0_GH0.tar.gz.

SUCCEEDED 00:00:02

-------------------------------------------------------------------------------
-- Phase: extract-depends
-------------------------------------------------------------------------------


SUCCEEDED 00:00:00

-------------------------------------------------------------------------------
-- Phase: extract
-------------------------------------------------------------------------------

===>   plumed-2.6.0 depends on file: /usr/local/sbin/pkg - found
===> Fetching all distfiles required by plumed-2.6.0 for building
===>  Extracting for plumed-2.6.0
===>   plumed-2.6.0 depends on file: /usr/local/sbin/pkg - found
===> Fetching all distfiles required by plumed-2.6.0 for building
=> SHA256 Checksum OK for plumed-plumed2-v2.6.0_GH0.tar.gz.

Extracted Memory Use: 320.66M
SUCCEEDED 00:00:05

-------------------------------------------------------------------------------
-- Phase: patch-depends
-------------------------------------------------------------------------------


SUCCEEDED 00:00:00

-------------------------------------------------------------------------------
-- Phase: patch
-------------------------------------------------------------------------------

===>  Patching for plumed-2.6.0
===>  Applying ports patches for plumed-2.6.0
===> Cleanly applied ports patch(es)  patch-configure.ac
/usr/bin/env WRKSRC=/construction/science/plumed/plumed2-2.6.0 REWARNFILE=/construction/science/plumed/reinplace_warnings.txt /xports/Tools/scripts/sed_checked.sh -e 's,FreeBSD,FreeBSD|DragonFly,g'  /construction/science/plumed/plumed2-2.6.0/configure.ac

SUCCEEDED 00:00:00

-------------------------------------------------------------------------------
-- Phase: build-depends
-------------------------------------------------------------------------------

===>   plumed-2.6.0 depends on executable: bash - found
===>   plumed-2.6.0 depends on executable: xxd - found
===>   plumed-2.6.0 depends on package: gmake>=4.3 - found
===>   plumed-2.6.0 depends on package: pkgconf>=1.3.0_1 - found
===>   plumed-2.6.0 depends on package: autoconf>=2.69 - found
===>   plumed-2.6.0 depends on package: automake>=1.16.1 - found

SUCCEEDED 00:00:00

-------------------------------------------------------------------------------
-- Phase: lib-depends
-------------------------------------------------------------------------------


SUCCEEDED 00:00:00

-------------------------------------------------------------------------------
-- Phase: configure
-------------------------------------------------------------------------------

===>   plumed-2.6.0 depends on executable: bash - found
===>   plumed-2.6.0 depends on executable: xxd - found
===>   plumed-2.6.0 depends on package: gmake>=4.3 - found
===>   plumed-2.6.0 depends on package: pkgconf>=1.3.0_1 - found
===>   plumed-2.6.0 depends on package: autoconf>=2.69 - found
===>   plumed-2.6.0 depends on package: automake>=1.16.1 - found
===>  Configuring for plumed-2.6.0
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 00:00:14

-------------------------------------------------------------------------------
-- Phase: build
-------------------------------------------------------------------------------

===>  Building for plumed-2.6.0
gmake[2]: Entering directory '/construction/science/plumed/plumed2-2.6.0'
gmake lib
gmake[3]: Entering directory '/construction/science/plumed/plumed2-2.6.0'
gmake	-C src
gmake[4]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src'
gmake -C lib
gmake[5]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/lib'
gmake dirslinks
gmake[6]: Entering directory '/construction/science/plumed/plumed2-2.6.0/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/plumed2-2.6.0/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/plumed2-2.6.0/src/blas'
gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/config'
Verify modules and create links in /construction/science/plumed/plumed2-2.6.0/src/blas
Nothing to do in /construction/science/plumed/plumed2-2.6.0/src/config
gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/config'
gmake -C ../gridtools links
gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/cltools'
gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/function'
Verify modules and create links in /construction/science/plumed/plumed2-2.6.0/src/cltools
Verify modules and create links in /construction/science/plumed/plumed2-2.6.0/src/function
gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/bias'
Verify modules and create links in /construction/science/plumed/plumed2-2.6.0/src/bias
gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/blas'
gmake -C ../isdb links
gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/core'
Verify modules and create links in /construction/science/plumed/plumed2-2.6.0/src/core
gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/gridtools'
Verify modules and create links in /construction/science/plumed/plumed2-2.6.0/src/gridtools
gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/isdb'
Verify modules and create links in /construction/science/plumed/plumed2-2.6.0/src/isdb
gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/asmjit'
Verify modules and create links in /construction/science/plumed/plumed2-2.6.0/src/asmjit
gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/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
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/colvar'
../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/plumed2-2.6.0/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
gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/generic'
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/analysis'
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: 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/plumed2-2.6.0/src/lapack'
../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/plumed2-2.6.0/src/generic
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../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/plumed2-2.6.0/src/analysis
Verify modules and create links in /construction/science/plumed/plumed2-2.6.0/src/lapack
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: 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/plumed2-2.6.0/src/lapack'
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
gmake -C ../lepton 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/plumed2-2.6.0/src/lepton'
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
Verify modules and create links in /construction/science/plumed/plumed2-2.6.0/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
gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/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
gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/main'
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
Verify modules and create links in /construction/science/plumed/plumed2-2.6.0/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
gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/main'
gmake -C ../mapping links
gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/mapping'
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
Verify modules and create links in /construction/science/plumed/plumed2-2.6.0/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
gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/bias'
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
gmake -C ../molfile 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/plumed2-2.6.0/src/molfile'
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
Verify modules and create links in /construction/science/plumed/plumed2-2.6.0/src/molfile
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/molfile'
gmake -C ../multicolvar 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
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: 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/plumed2-2.6.0/src/multicolvar'
Verify modules and create links in /construction/science/plumed/plumed2-2.6.0/src/multicolvar
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: 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/plumed2-2.6.0/src/gridtools'
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
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]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/cltools'
gmake -C ../secondarystructure 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]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/core'
gmake -C ../setup links
gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.0/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
gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/setup'
gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/secondarystructure'
../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/plumed2-2.6.0/src/setup
Verify modules and create links in /construction/science/plumed/plumed2-2.6.0/src/reference
Verify modules and create links in /construction/science/plumed/plumed2-2.6.0/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
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: 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/plumed2-2.6.0/src/generic'
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
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
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: 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/plumed2-2.6.0/src/tools'
../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/plumed2-2.6.0/src/tools
gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/colvar'
gmake -C ../vatom 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
gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/vatom'
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
Verify modules and create links in /construction/science/plumed/plumed2-2.6.0/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
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
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../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
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../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
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../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
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../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: 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/plumed2-2.6.0/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
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: 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/plumed2-2.6.0/src/vesselbase'
../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/plumed2-2.6.0/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
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
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gmake dirs
gmake[6]: Entering directory '/construction/science/plumed/plumed2-2.6.0/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/plumed2-2.6.0/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/plumed2-2.6.0/src/analysis'
gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/bias'
compiling  ABMD.cpp
gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/blas'
compiling  blas.cpp
gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/cltools'
compiling  CLTool.cpp
gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/asmjit'
gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/config'
gmake PLUMED_FORCE=yes ConfigInstall.inc Config.inc version.h config.txt
gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/core'
compiling  Action.cpp
compiling  arch.cpp
gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/config'
gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/colvar'
Updating ConfigInstall.inc
compiling  Angle.cpp
compiling  AnalysisBase.cpp
gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/function'
compiling  Combine.cpp
gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/generic'
compiling  Debug.cpp
cmp -s ConfigInstall.inc~ ConfigInstall.inc || cp ConfigInstall.inc~ ConfigInstall.inc
compiling  assembler.cpp
rm ConfigInstall.inc~
Updating Config.inc
cmp -s Config.inc~ Config.inc || cp Config.inc~ Config.inc
rm Config.inc~
Updating version.h
Updating config.txt file
compiling  codebuilder.cpp
compiling  codecompiler.cpp
compiling  codeemitter.cpp
compiling  codeholder.cpp
compiling  constpool.cpp
compiling  cpuinfo.cpp
gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/config'
gmake Config.o ConfigInstall.o compile_options.sh
gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.0/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  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
{ ../maketools/make-scripts-options.sh ; cat completion.sh ; }| xxd -i > completion.xxd
compiling  vmem.cpp
../../scripts/selector.sh: line 219: python: command not found
compiling  Driver.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  ConfigInstall.cpp
compiling  x86operand_regs.cpp
compiling  x86regalloc.cpp
compiling  zone.cpp
gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/asmjit'
compiling  DumpAtoms.cpp
compiling  Cell.cpp
compiling  DriverDouble.cpp
gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/config'
gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/config'
compiling  DumpDerivatives.cpp
compiling  Custom.cpp
compiling  DumpForces.cpp
gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/blas'
compiling  DumpMassCharge.cpp
compiling  Colvar.cpp
compiling  Average.cpp
compiling  ActionAnyorder.cpp
compiling  Bias.cpp
compiling  Constant.cpp
compiling  ContactMap.cpp
compiling  Ensemble.cpp
compiling  ActionAtomistic.cpp
compiling  FuncPathMSD.cpp
compiling  ActionPilot.cpp
compiling  AverageVessel.cpp
compiling  BiasValue.cpp
ActionAtomistic.cpp: In member function 'void PLMD::ActionAtomistic::requestAtoms(const std::vector<PLMD::AtomNumber>&, 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::__cxx11::basic_string<char> >&, std::vector<PLMD::AtomNumber>&)':
ActionAtomistic.cpp:181:28: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'const int' [-Wsign-compare]
         for(unsigned i=0; i<n; i++) t.push_back(AtomNumber::index(i));
                           ~^~
ActionAtomistic.cpp:186:28: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'const int' [-Wsign-compare]
         for(unsigned i=0; i<n; i++) t.push_back(AtomNumber::index(i));
                           ~^~
compiling  DumpProjections.cpp
compiling  EffectiveEnergyDrift.cpp
compiling  Committor.cpp
compiling  FuncSumHills.cpp
compiling  EndPlumed.cpp
compiling  ExtendedLagrangian.cpp
compiling  FitToTemplate.cpp
compiling  Function.cpp
compiling  ActionRegister.cpp
compiling  Coordination.cpp
compiling  DataCollectionObject.cpp
compiling  DriverFloat.cpp
compiling  Flush.cpp
compiling  External.cpp
compiling  EuclideanDissimilarityMatrix.cpp
compiling  FarthestPointSampling.cpp
compiling  LocalEnsemble.cpp
compiling  Piecewise.cpp
compiling  ActionSet.cpp
compiling  CoordinationBase.cpp
compiling  LWalls.cpp
compiling  ActionSetup.cpp
compiling  Group.cpp
compiling  Include.cpp
compiling  ActionShortcut.cpp
compiling  DHEnergy.cpp
compiling  Plumed.cpp
compiling  Print.cpp
compiling  ActionWithArguments.cpp
compiling  MaxEnt.cpp
compiling  Sort.cpp
Plumed.cpp: In member function 'virtual void PLMD::generic::Plumed::prepare()':
Plumed.cpp:324:26: warning: comparison of integer expressions of different signedness: 'std::vector<int>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
   bool redo=(index.size()!=n);
              ~~~~~~~~~~~~^~~
compiling  Histogram.cpp
Plumed.cpp: In member function 'virtual void PLMD::generic::Plumed::calculate()':
Plumed.cpp:365:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   for(int i=0; i<forces.size(); i++) forces[i]=0.0;
                ~^~~~~~~~~~~~~~
Plumed.cpp:366:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   for(int i=0; i<masses.size(); i++) masses[i]=getMass(i);
                ~^~~~~~~~~~~~~~
Plumed.cpp:367:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   for(int i=0; i<charges.size(); i++) charges[i]=getCharge(i);
                ~^~~~~~~~~~~~~~~
compiling  Stats.cpp
compiling  LandmarkSelectionBase.cpp
compiling  DRMSD.cpp
compiling  GenTemplate.cpp
compiling  LandmarkStaged.cpp
compiling  RandomExchanges.cpp
compiling  Target.cpp
compiling  Read.cpp
compiling  Info.cpp
compiling  OutputColvarFile.cpp
compiling  ActionWithValue.cpp
compiling  MetaD.cpp
compiling  OutputPDBFile.cpp
compiling  Manual.cpp
compiling  Dimer.cpp
compiling  Dipole.cpp
compiling  ResetCell.cpp
compiling  PdbRenumber.cpp
compiling  ActionWithVirtualAtom.cpp
gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/function'
compiling  Time.cpp
Dimer.cpp: In constructor 'PLMD::colvar::Dimer::Dimer(const PLMD::ActionOptions&)':
Dimer.cpp:222:28: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
     for(unsigned int i=0; i<isz1; i++)
                           ~^~~~~
Dimer.cpp:230:28: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
     for(unsigned int i=0; i<isz2; i++)
                           ~^~~~~
Dimer.cpp: In member function 'void PLMD::colvar::Dimer::consistencyCheck()':
Dimer.cpp:319:20: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
   if(dsigmas.size()!=nranks && dsigmas.size()!=1)
      ~~~~~~~~~~~~~~^~~~~~~~
compiling  Atoms.cpp
compiling  PrintDissimilarityMatrix.cpp
compiling  ReadAnalysisFrames.cpp
compiling  SimpleMD.cpp
compiling  UpdateIf.cpp
compiling  WholeMolecules.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<int>::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<std::allocator<int>, 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<int>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
   if(gatindex.size()<natoms) shuffledAtoms=1;
      ~~~~~~~~~~~~~~~^~~~~~~
Atoms.cpp: In member function 'void PLMD::Atoms::createFullList(int*)':
Atoms.cpp:464:24: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
     for(unsigned i=0; i<natoms; i++) fullList[i]=i;
                       ~^~~~~~~
compiling  WrapAround.cpp
compiling  Distance.cpp
compiling  CLTool.cpp
compiling  EEFSolv.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<std::vector<PLMD::AtomNumber> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
     for(int i=0; i<groups.size(); ++i) {
                  ~^~~~~~~~~~~~~~
compiling  ERMSD.cpp
compiling  SumHills.cpp
../maketools/makecmd map < CLToolMain.cpp > CLToolMainMap.inc
compiling  Energy.cpp
compiling  ReadDissimilarityMatrix.cpp
compiling  ReselectLandmarks.cpp
compiling  ExtraCV.cpp
../maketools/makecmd enum < CLToolMain.cpp > CLToolMainEnum.inc
compiling  CLToolRegister.cpp
gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/generic'
compiling  Fake.cpp
compiling  Colvar.cpp
compiling  MovingRestraint.cpp
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()) {
        ~~~^~~~~~~~~~~~~~~~~~
gmake -C ../gridtools obj
gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/gridtools'
compiling  ActionWithGrid.cpp
compiling  SelectRandomFrames.cpp
compiling  PBMetaD.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  SelectWithStride.cpp
compiling  WhamHistogram.cpp
compiling  ExchangePatterns.cpp
compiling  Gyration.cpp
compiling  ActionWithInputGrid.cpp
compiling  kT.cpp
compiling  FlexibleBin.cpp
compiling  ActionWithIntegral.cpp
compiling  WhamWeights.cpp
compiling  AverageOnGrid.cpp
In file included from core/../../core/tools/Tensor.h:1,
                 from core/../../core/ActionAtomistic.h:26,
                 from core/../../core/Colvar.h:25,
                 from core/Colvar.h:1,
                 from Colvar.h:24,
                 from Gyration.cpp:22:
core/../../core/tools/../../tools/Tensor.h: In instantiation of 'void PLMD::diagMatSym(const PLMD::TensorGeneric<n_, n_>&, PLMD::VectorGeneric<m_>&, PLMD::TensorGeneric<m_, n_>&) [with unsigned int n_ = 3; unsigned int m_ = 3; unsigned int n = 3; unsigned int m = 3]':
Gyration.cpp:252:43:   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; i<m; ++i) {
                ~^~
core/../../core/tools/../../tools/Tensor.h:559:15: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
     for(j=0; j<n; j++) if(evec(i,j)*evec(i,j)>1e-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<n) if(evec(i,j)<0.0) for(j=0; j<n; j++) evec(i,j)*=-1;
        ~^~
core/../../core/tools/../../tools/Tensor.h:560:41: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
     if(j<n) if(evec(i,j)<0.0) for(j=0; j<n; j++) evec(i,j)*=-1;
                                        ~^~
compiling  pesmd.cpp
compiling  ContourFindingBase.cpp
gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/analysis'
compiling  ConvertToFES.cpp
compiling  Restraint.cpp
compiling  MultiRMSD.cpp
compiling  DumpCube.cpp
compiling  ReweightBase.cpp
compiling  PCARMSD.cpp
compiling  DumpGrid.cpp
../maketools/makecmd map < GREX.cpp > GREXMap.inc
compiling  FindContour.cpp
compiling  Completion.cpp
compiling  FindContourSurface.cpp
compiling  FindSphericalContour.cpp
../maketools/makecmd enum < GREX.cpp > GREXEnum.inc
compiling  MDAtoms.cpp
compiling  ReweightBias.cpp
compiling  ReweightMetad.cpp
gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/cltools'
compiling  ReweightTemperaturePressure.cpp
compiling  PathMSD.cpp
gmake -C ../isdb obj
gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/isdb'
compiling  CS2Backbone.cpp
gmake -C ../lapack obj
gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/lapack'
compiling  lapack.cpp
compiling  Caliber.cpp
../maketools/makecmd map < PlumedMain.cpp > PlumedMainMap.inc
../maketools/makecmd enum < PlumedMain.cpp > PlumedMainEnum.inc
compiling  PlumedMainInitializer.cpp
In file included from tools/../../tools/RootFindingBase.h:26,
                 from tools/RootFindingBase.h:1,
                 from ContourFindingBase.h:26,
                 from FindSphericalContour.cpp:23:
tools/../../tools/Brent1DRootSearch.h: In member function 'double PLMD::Brent1DRootSearch<FCLASS>::search(PLMD::Brent1DRootSearch<FCLASS>::eng_pointer) [with FCLASS = PLMD::F1dim<PLMD::gridtools::ContourFindingBase>]':
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  EMMI.cpp
compiling  FretEfficiency.cpp
compiling  ReweightWham.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<FCLASS>::search(PLMD::Brent1DRootSearch<FCLASS>::eng_pointer) [with FCLASS = PLMD::F1dim<PLMD::gridtools::ContourFindingBase>]':
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);
                                                        ~^~
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<double>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   if(tindex+1<var[iarg].size()) end=tindex+2;
      ~~~~~~~~^~~~~~~~~~~~~~~~~
Caliber.cpp:286:14: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'const int' [-Wsign-compare]
     if(ipoint==tindex) x0=0;
        ~~~~~~^~~~~~~~
compiling  PathMSDBase.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<FCLASS>::search(PLMD::Brent1DRootSearch<FCLASS>::eng_pointer) [with FCLASS = PLMD::F1dim<PLMD::gridtools::ContourFindingBase>]':
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);
                                                        ~^~
EMMI.cpp: In member function 'void PLMD::isdb::EMMI::write_model_overlap(long int)':
EMMI.cpp:594:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   for(int i=0; i<ovmd_.size(); ++i) {
                ~^~~~~~~~~~~~~
EMMI.cpp: In member function 'std::vector<double> 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<nexp; ++i) {
                         ~^~~~~
EMMI.cpp: In member function 'void PLMD::isdb::EMMI::get_GMM_d(std::__cxx11::string)':
EMMI.cpp:942:22: warning: comparison of integer expressions of different signedness: '__gnu_cxx::__alloc_traits<std::allocator<int>, int>::value_type' {aka 'int'} and 'std::vector<std::vector<int> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
     if(GMM_d_beta_[i]>=GMM_d_grps_.size()) error("Check Beta values");
compiling  SetupMolInfo.cpp
compiling  Jcoupling.cpp
compiling  FourierTransform.cpp
compiling  UWalls.cpp
compiling  GridPrintingBase.cpp
compiling  Metainference.cpp
gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/bias'
compiling  MetainferenceBase.cpp
compiling  GridSearch.cpp
compiling  TargetDist.cpp
compiling  Position.cpp
compiling  GridToXYZ.cpp
compiling  NOE.cpp
compiling  GridVessel.cpp
compiling  PropertyMap.cpp
compiling  Value.cpp
compiling  Puckering.cpp
GridVessel.cpp: In member function 'void PLMD::gridtools::GridVessel::getNeighbors(const std::vector<unsigned int>&, const std::vector<unsigned int>&, unsigned int&, std::vector<unsigned int>&) 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];
compiling  RMSD.cpp
compiling  PRE.cpp
compiling  WithCmd.cpp
compiling  CLToolMain.cpp
compiling  HistogramOnGrid.cpp
compiling  IntegrateGrid.cpp
gmake -C ../lepton obj
gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/lepton'
compiling  CompiledExpression.cpp
gmake -C ../main obj
gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/main'
compiling  main.cpp
CompiledExpression.cpp: In member function 'void PLMD::lepton::CompiledExpression::compileExpression(const PLMD::lepton::ExpressionTreeNode&, std::vector<std::pair<PLMD::lepton::ExpressionTreeNode, int> >&)':
CompiledExpression.cpp:157:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<PLMD::lepton::ExpressionTreeNode>::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<int>::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<std::pair<double*, double*> >::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<PLMD::lepton::Operation*>::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<int>::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  Template.cpp
gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/main'
compiling  InterpolateGrid.cpp
gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/lapack'
compiling  ExpressionProgram.cpp
GridVessel.cpp: In member function 'unsigned int PLMD::gridtools::GridVessel::getFibonacciIndex(const std::vector<double>&) const':
GridVessel.cpp:251:10: warning: 'outind' may be used uninitialized in this function [-Wmaybe-uninitialized]
   return outind;
          ^~~~~~
compiling  GREX.cpp
gmake -C ../mapping obj
gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/mapping'
compiling  AdaptivePath.cpp
compiling  ExpressionTreeNode.cpp
compiling  Mapping.cpp
compiling  PCAVars.cpp
compiling  RDC.cpp
compiling  Torsion.cpp
ExpressionTreeNode.cpp: In constructor 'PLMD::lepton::ExpressionTreeNode::ExpressionTreeNode(PLMD::lepton::Operation*, const std::vector<PLMD::lepton::ExpressionTreeNode>&)':
ExpressionTreeNode.cpp:73:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<PLMD::lepton::ExpressionTreeNode>::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<PLMD::lepton::ExpressionTreeNode>::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<PLMD::lepton::ExpressionTreeNode>::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<PLMD::lepton::ExpressionTreeNode>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
     if (operation->getNumArguments() != children.size())
         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
compiling  Path.cpp
compiling  PathBase.cpp
AdaptivePath.cpp: In constructor 'PLMD::mapping::AdaptivePath::AdaptivePath(const PLMD::ActionOptions&)':
AdaptivePath.cpp:154:17: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
   for(int i=0; i<getNumberOfReferencePoints(); ++i) {
                ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compiling  Operation.cpp
compiling  PlumedMain.cpp
compiling  Volume.cpp
gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/gridtools'
compiling  ParsedExpression.cpp
compiling  Parser.cpp
compiling  Rescale.cpp
gmake -C ../molfile obj
gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/molfile'
compiling  crdplugin.cpp
compiling  dcdplugin.cpp
gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/colvar'
compiling  PathReparameterization.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  SAXS.cpp
Parser.cpp: In static member function 'static PLMD::lepton::ParsedExpression PLMD::lepton::Parser::parse(const string&, const std::map<std::__cxx11::basic_string<char>, PLMD::lepton::CustomFunction*>&)':
Parser.cpp:238:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<PLMD::lepton::ParseToken>::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<PLMD::lepton::ParseToken>::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<PLMD::lepton::ParseToken>&, int&, const std::map<std::__cxx11::basic_string<char>, PLMD::lepton::CustomFunction*>&, const std::map<std::__cxx11::basic_string<char>, PLMD::lepton::ExpressionTreeNode>&, int)':
Parser.cpp:258:13: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<PLMD::lepton::ParseToken>::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<PLMD::lepton::ParseToken>::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<PLMD::lepton::ParseToken>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
         if (pos == tokens.size() || tokens[pos].getType() != ParseToken::RightParen)
             ~~~~^~~~~~~~~~~~~~~~
compiling  PathTools.cpp
compiling  PropertyMap.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);
     ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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; ++i) sfrac[i] = target*(i-istart);
                              ~^~~~~~~
PathReparameterization.cpp:94:31: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'const int' [-Wsign-compare]
       for(unsigned i=istart; i<iend; ++i) sfrac[i] = dr*(i-istart);
                              ~^~~~~
PathReparameterization.cpp:102:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'const int' [-Wsign-compare]
         if( cfin==iend && k>= 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<std::unique_ptr<PLMD::ReferenceConfiguration> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   if( ifix2<(mypath.size()-1) ) reparameterizePart( ifix2, mypath.size()-1, target, TOL );
       ~~~~~^~~~~~~~~~~~~~~~~~
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);
   ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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<nbefore; ++i) {
                ~^~~~~~~~
compiling  Select.cpp
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)
            ^~~~~~~~~~~
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/plumed2-2.6.0/src/molfile'
compiling  SpathVessel.cpp
gmake -C ../multicolvar obj
gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/multicolvar'
compiling  ActionVolume.cpp
compiling  Selector.cpp
gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/lepton'
compiling  TrigonometricPathVessel.cpp
compiling  ZpathVessel.cpp
gmake -C ../reference obj
gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/reference'
compiling  ArgumentOnlyDistance.cpp
gmake -C ../secondarystructure obj
gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/secondarystructure'
compiling  AlphaRMSD.cpp
compiling  AntibetaRMSD.cpp
compiling  ParabetaRMSD.cpp
compiling  AlphaBeta.cpp
TrigonometricPathVessel.cpp: In member function 'virtual void PLMD::mapping::TrigonometricPathVessel::finish(const std::vector<double>&)':
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  SecondaryStructureRMSD.cpp
gmake -C ../setup obj
gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/setup'
compiling  Load.cpp
compiling  DRMSD.cpp
compiling  MolInfo.cpp
gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/core'
compiling  Restart.cpp
gmake -C ../tools obj
gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/tools'
compiling  Angle.cpp
compiling  Direction.cpp
compiling  Units.cpp
compiling  Angles.cpp
compiling  AtomNumber.cpp
gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/mapping'
compiling  BiasRepresentation.cpp
compiling  DotProductDistance.cpp
gmake -C ../vatom obj
gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/vatom'
compiling  ActionWithVirtualAtom.cpp
compiling  Brent1DRootSearch.cpp
compiling  AtomValuePack.cpp
gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/isdb'
compiling  Citations.cpp
compiling  Bridge.cpp
compiling  Communicator.cpp
compiling  Center.cpp
gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/setup'
compiling  ConjugateGradient.cpp
gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/secondarystructure'
compiling  DLLoader.cpp
compiling  DynamicList.cpp
compiling  EuclideanDistance.cpp
compiling  BridgedMultiColvarFunction.cpp
compiling  FixedAtom.cpp
compiling  CatomPack.cpp
compiling  Ghost.cpp
compiling  FakeFrame.cpp
compiling  ERMSD.cpp
compiling  Exception.cpp
compiling  FileBase.cpp
compiling  ForwardDecl.cpp
compiling  CenterOfMultiColvar.cpp
compiling  IntermolecularDRMSD.cpp
compiling  Grid.cpp
compiling  IntramolecularDRMSD.cpp
compiling  MahalanobisDistance.cpp
gmake -C ../vesselbase obj
gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/vesselbase'
compiling  ActionWithAveraging.cpp
compiling  HistogramBead.cpp
gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/vatom'
compiling  IFile.cpp
compiling  KernelFunctions.cpp
compiling  Keywords.cpp
compiling  MetricRegister.cpp
compiling  CoordinationNumbers.cpp
compiling  LatticeReduction.cpp
compiling  MultiDomainRMSD.cpp
compiling  NormalizedEuclideanDistance.cpp
compiling  OptimalRMSD.cpp
compiling  ActionWithInputVessel.cpp
compiling  RMSDBase.cpp
compiling  ReferenceArguments.cpp
compiling  Density.cpp
In file included from RootFindingBase.h:26,
                 from Grid.cpp:29:
Brent1DRootSearch.h: In member function 'double PLMD::Brent1DRootSearch<FCLASS>::search(PLMD::Brent1DRootSearch<FCLASS>::eng_pointer) [with FCLASS = PLMD::F1dim<PLMD::Grid>]':
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  ActionWithVessel.cpp
compiling  DihedralCorrelation.cpp
compiling  DistanceFromContour.cpp
compiling  LinkCells.cpp
compiling  ReferenceAtoms.cpp
compiling  Distances.cpp
compiling  Log.cpp
compiling  AltMin.cpp
compiling  AveragingVessel.cpp
compiling  Between.cpp
compiling  ReferenceConfiguration.cpp
compiling  LoopUnroller.cpp
compiling  Matrix.cpp
compiling  MatrixSquareBracketsAccess.cpp
gmake -C ../wrapper obj
gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.0/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:2421:49:
Plumed.h:2060:33: 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:2058:43: note: length computed here
     strlenpath=__PLUMED_WRAPPER_STD strlen(path);
                                           ^
compiling  Minimise1DBrent.cpp
compiling  Plumed.c
compiling  BridgeVessel.cpp
compiling  ReferenceValuePack.cpp
compiling  FunctionVessel.cpp
In file included from Plumed.c:44:
In function 'plumed_attempt_dlopen.part.1',
    inlined from 'plumed_attempt_dlopen' at Plumed.h:2031:7:
Plumed.h:2060:26: 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:2058:37: note: length computed here
     strlenpath=__PLUMED_WRAPPER_STD strlen(path);
                                     ^~~~~~~~~~~~
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<FCLASS>::search(PLMD::Brent1DRootSearch<FCLASS>::eng_pointer) [with FCLASS = PLMD::F1dim<PLMD::multicolvar::DistanceFromContour>]':
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  SimpleRMSD.cpp
compiling  SingleDomainRMSD.cpp
gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/wrapper'
compiling  DumpMultiColvar.cpp
compiling  MinimiseBase.cpp
compiling  Highest.cpp
compiling  Histogram.cpp
compiling  MolDataClass.cpp
compiling  MultiValue.cpp
compiling  FilterBetween.cpp
compiling  NeighborList.cpp
compiling  OFile.cpp
gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/reference'
compiling  FilterLessThan.cpp
compiling  OpenMP.cpp
compiling  FilterMoreThan.cpp
compiling  InPlaneDistances.cpp
compiling  LessThan.cpp
compiling  LocalAverage.cpp
compiling  MultiColvarBase.cpp
compiling  MultiColvarCombine.cpp
compiling  Lowest.cpp
InPlaneDistances.cpp: In constructor 'PLMD::multicolvar::InPlaneDistances::InPlaneDistances(const PLMD::ActionOptions&)':
InPlaneDistances.cpp:110:7: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
       if( bt ) use_link=true; rcut=bt->getCutoff();
       ^~
InPlaneDistances.cpp:110:31: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
       if( bt ) use_link=true; rcut=bt->getCutoff();
                               ^~~~
compiling  Max.cpp
MultiColvarBase.cpp: In member function 'void PLMD::multicolvar::MultiColvarBase::setupActiveTaskSet(std::vector<unsigned int>&, 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  MultiColvarDensity.cpp
compiling  PDB.cpp
compiling  MultiColvarFilter.cpp
compiling  Mean.cpp
compiling  Min.cpp
compiling  Pbc.cpp
compiling  PlumedHandle.cpp
compiling  MultiColvarProduct.cpp
compiling  RMSD.cpp
compiling  Moments.cpp
compiling  Random.cpp
compiling  RootFindingBase.cpp
compiling  MoreThan.cpp
In file included from RMSD.h:27,
                 from RMSD.cpp:22:
Tensor.h: In instantiation of 'void PLMD::diagMatSym(const PLMD::TensorGeneric<n_, n_>&, PLMD::VectorGeneric<m_>&, PLMD::TensorGeneric<m_, n_>&) [with unsigned int n_ = 4; unsigned int m_ = 4; unsigned int n = 3; unsigned int m = 3]':
RMSD.cpp:1028:40:   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; i<m; ++i) {
                ~^~
Tensor.h:559:15: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
     for(j=0; j<n; j++) if(evec(i,j)*evec(i,j)>1e-14) break;
              ~^~
Tensor.h:560:9: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
     if(j<n) if(evec(i,j)<0.0) for(j=0; j<n; j++) evec(i,j)*=-1;
        ~^~
Tensor.h:560:41: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
     if(j<n) if(evec(i,j)<0.0) for(j=0; j<n; j++) evec(i,j)*=-1;
                                        ~^~
compiling  OrderingVessel.cpp
Tensor.h: In instantiation of 'void PLMD::diagMatSym(const PLMD::TensorGeneric<n_, n_>&, PLMD::VectorGeneric<m_>&, PLMD::TensorGeneric<m_, n_>&) [with unsigned int n_ = 4; unsigned int m_ = 1; unsigned int n = 3; unsigned int m = 3]':
RMSD.cpp:1048:50:   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; i<m; ++i) {
                ~^~
Tensor.h:559:15: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
     for(j=0; j<n; j++) if(evec(i,j)*evec(i,j)>1e-14) break;
              ~^~
Tensor.h:560:9: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
     if(j<n) if(evec(i,j)<0.0) for(j=0; j<n; j++) evec(i,j)*=-1;
        ~^~
Tensor.h:560:41: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
     if(j<n) if(evec(i,j)<0.0) for(j=0; j<n; j++) evec(i,j)*=-1;
                                        ~^~
compiling  NumberOfLinks.cpp
compiling  ShortcutVessel.cpp
compiling  Torsions.cpp
compiling  Stopwatch.cpp
compiling  Subprocess.cpp
compiling  SwitchingFunction.cpp
compiling  Tensor.cpp
compiling  VolumeAround.cpp
compiling  Tools.cpp
compiling  VolumeBetweenContours.cpp
compiling  StoreDataVessel.cpp
compiling  Sum.cpp
compiling  Torsion.cpp
compiling  Units.cpp
compiling  VolumeCavity.cpp
compiling  VolumeGradientBase.cpp
compiling  ValueVessel.cpp
compiling  Vessel.cpp
compiling  Vector.cpp
compiling  VesselRegister.cpp
compiling  h36.cpp
compiling  VolumeInCylinder.cpp
compiling  VolumeInSphere.cpp
h36.cpp: In function 'const char* PLMD::h36::decode_pure(const int*, unsigned int, const char*, unsigned int, int*)':
h36.cpp:154:24: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
       if (dv < 0 || dv >= digits_size) {
                     ~~~^~~~~~~~~~~~~~
compiling  VolumeTetrapore.cpp
compiling  XAngle.cpp
gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/tools'
compiling  XDistances.cpp
compiling  XYDistances.cpp
compiling  XYTorsion.cpp
gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/vesselbase'
gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/multicolvar'
gmake[7]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/lib'
gmake[6]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/lib'
gmake lib
gmake[6]: Entering directory '/construction/science/plumed/plumed2-2.6.0/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/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/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/MDAtoms.o ../core/PlumedMain.o ../core/PlumedMainInitializer.o ../core/SetupMolInfo.o ../core/TargetDist.o ../core/Value.o ../core/WithCmd.o ../function/Combine.o ../function/Custom.o ../function/Ensemble.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/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/MolInfo.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/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/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/MDAtoms.o ../core/PlumedMain.o ../core/PlumedMainInitializer.o ../core/SetupMolInfo.o ../core/TargetDist.o ../core/Value.o ../core/WithCmd.o ../function/Combine.o ../function/Custom.o ../function/Ensemble.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/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/MolInfo.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
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-patch
ar cr libplumedWrapper.a ../wrapper/Plumed.o
chmod a+x plumed-mklib
Building Plumed.inc, runtime-linking version
chmod a+x plumed-selector
Building Plumed.inc, shared version
chmod a+x plumed-config
chmod a+x plumed-partial_tempering
Building Plumed.cmake
chmod a+x plumed-newcv
Building Plumed.inc, static version
Building Plumed.cmake, static version
Building Plumed.cmake, shared version
Building Plumed.cmake, runtime-linking version
chmod a+x plumed-vim2html
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/plumed2-2.6.0/src/lib'
gmake install-build
gmake[6]: Entering directory '/construction/science/plumed/plumed2-2.6.0/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/plumed2-2.6.0/src/lib'
gmake dirslinks
gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.0/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/plumed2-2.6.0/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/plumed2-2.6.0/src/analysis'
gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/asmjit'
gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/blas'
gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/bias'
gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/cltools'
Verify modules and create links in /construction/science/plumed/plumed2-2.6.0/src/blas
gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/generic'
gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/config'
Nothing to do in /construction/science/plumed/plumed2-2.6.0/src/config
gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/config'
gmake -C ../gridtools links
gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/colvar'
gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/function'
gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/gridtools'
Verify modules and create links in /construction/science/plumed/plumed2-2.6.0/src/function
Verify modules and create links in /construction/science/plumed/plumed2-2.6.0/src/gridtools
gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/blas'
gmake -C ../isdb links
Verify modules and create links in /construction/science/plumed/plumed2-2.6.0/src/cltools
gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/core'
Verify modules and create links in /construction/science/plumed/plumed2-2.6.0/src/colvar
Verify modules and create links in /construction/science/plumed/plumed2-2.6.0/src/core
gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/isdb'
Verify modules and create links in /construction/science/plumed/plumed2-2.6.0/src/asmjit
Verify modules and create links in /construction/science/plumed/plumed2-2.6.0/src/bias
gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/asmjit'
gmake -C ../lapack links
gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/lapack'
Verify modules and create links in /construction/science/plumed/plumed2-2.6.0/src/generic
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
Verify modules and create links in /construction/science/plumed/plumed2-2.6.0/src/analysis
Verify modules and create links in /construction/science/plumed/plumed2-2.6.0/src/isdb
Verify modules and create links in /construction/science/plumed/plumed2-2.6.0/src/lapack
gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/lapack'
gmake -C ../lepton links
gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/lepton'
Verify modules and create links in /construction/science/plumed/plumed2-2.6.0/src/lepton
../maketools/makelinks.sh: line 24: echo: write error: Broken pipe
gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/generic'
gmake -C ../main links
gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/main'
Verify modules and create links in /construction/science/plumed/plumed2-2.6.0/src/main
gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/gridtools'
gmake -C ../mapping links
gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/mapping'
Verify modules and create links in /construction/science/plumed/plumed2-2.6.0/src/mapping
gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/lepton'
gmake -C ../molfile links
gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/cltools'
gmake -C ../multicolvar links
gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/molfile'
Verify modules and create links in /construction/science/plumed/plumed2-2.6.0/src/molfile
gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/molfile'
gmake -C ../reference links
gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/reference'
Verify modules and create links in /construction/science/plumed/plumed2-2.6.0/src/reference
gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/main'
gmake -C ../secondarystructure links
gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/multicolvar'
gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/secondarystructure'
Verify modules and create links in /construction/science/plumed/plumed2-2.6.0/src/multicolvar
Verify modules and create links in /construction/science/plumed/plumed2-2.6.0/src/secondarystructure
gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/function'
gmake -C ../setup links
gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/setup'
Verify modules and create links in /construction/science/plumed/plumed2-2.6.0/src/setup
gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/bias'
gmake -C ../tools links
gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/core'
gmake -C ../vatom links
gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/tools'
Verify modules and create links in /construction/science/plumed/plumed2-2.6.0/src/tools
gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/vatom'
Verify modules and create links in /construction/science/plumed/plumed2-2.6.0/src/vatom
gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/isdb'
gmake -C ../vesselbase links
gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/vesselbase'
Verify modules and create links in /construction/science/plumed/plumed2-2.6.0/src/vesselbase
gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/analysis'
gmake -C ../wrapper links
gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/wrapper'
Nothing to do in /construction/science/plumed/plumed2-2.6.0/src/wrapper
gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/wrapper'
gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/colvar'
gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/tools'
gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/reference'
gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/mapping'
gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/vatom'
gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/secondarystructure'
gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/setup'
gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/multicolvar'
gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/vesselbase'
gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/lib'
gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/lib'
gmake dirs
gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.0/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/plumed2-2.6.0/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/plumed2-2.6.0/src/function'
gmake[10]: Nothing to be done for 'obj'.
gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/function'
gmake -C ../gridtools obj
gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/core'
gmake[10]: Nothing to be done for 'obj'.
gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/core'
gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/generic'
gmake[10]: Nothing to be done for 'obj'.
gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/generic'
gmake -C ../isdb obj
gmake -C ../lapack obj
gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/isdb'
gmake[10]: Nothing to be done for 'obj'.
gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/isdb'
gmake -C ../lepton obj
gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/bias'
gmake[10]: Nothing to be done for 'obj'.
gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/bias'
gmake -C ../main obj
gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/main'
gmake[10]: Nothing to be done for 'obj'.
gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/blas'
gmake[10]: Nothing to be done for 'obj'.
gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/blas'
gmake -C ../mapping obj
gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/asmjit'
gmake[10]: Nothing to be done for 'obj'.
gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/asmjit'
gmake -C ../molfile obj
gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/cltools'
gmake[10]: Nothing to be done for 'obj'.
gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/cltools'
gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/main'
gmake -C ../multicolvar obj
gmake -C ../reference obj
gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/lapack'
gmake[10]: Nothing to be done for 'obj'.
gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/lapack'
gmake -C ../secondarystructure obj
gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/gridtools'
gmake[10]: Nothing to be done for 'obj'.
gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/gridtools'
gmake -C ../setup obj
gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/secondarystructure'
gmake[10]: Nothing to be done for 'obj'.
gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/secondarystructure'
gmake -C ../tools obj
gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/setup'
gmake[10]: Nothing to be done for 'obj'.
gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/setup'
gmake -C ../vatom obj
gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/molfile'
gmake[10]: Nothing to be done for 'obj'.
gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/molfile'
gmake -C ../vesselbase obj
gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/lepton'
gmake[10]: Nothing to be done for 'obj'.
gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/lepton'
gmake -C ../wrapper obj
gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/multicolvar'
gmake[10]: Nothing to be done for 'obj'.
gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/multicolvar'
gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/tools'
gmake[10]: Nothing to be done for 'obj'.
gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/tools'
gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/mapping'
gmake[10]: Nothing to be done for 'obj'.
gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/mapping'
gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/config'
gmake PLUMED_FORCE=yes ConfigInstall.inc Config.inc version.h config.txt
gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/wrapper'
gmake[10]: Nothing to be done for 'obj'.
gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/wrapper'
gmake[11]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/config'
gmake[11]: 'config.txt' is up to date.
Updating ConfigInstall.inc
Updating version.h
Updating Config.inc
gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/colvar'
gmake[10]: Nothing to be done for 'obj'.
gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/colvar'
gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/vatom'
gmake[10]: Nothing to be done for 'obj'.
gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/vatom'
gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/reference'
gmake[10]: Nothing to be done for 'obj'.
gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/reference'
gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/analysis'
gmake[10]: Nothing to be done for 'obj'.
gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/analysis'
gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/vesselbase'
gmake[10]: Nothing to be done for 'obj'.
gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/vesselbase'
cmp -s Config.inc~ Config.inc || cp Config.inc~ Config.inc
cmp -s ConfigInstall.inc~ ConfigInstall.inc || cp ConfigInstall.inc~ ConfigInstall.inc
rm Config.inc~
rm ConfigInstall.inc~
gmake[11]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/config'
gmake Config.o ConfigInstall.o compile_options.sh
gmake[11]: Entering directory '/construction/science/plumed/plumed2-2.6.0/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/plumed2-2.6.0/src/config'
gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/config'
gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/lib'
gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/lib'
gmake lib
gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.0/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/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/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/MDAtoms.o ../core/PlumedMain.o ../core/PlumedMainInitializer.o ../core/SetupMolInfo.o ../core/TargetDist.o ../core/Value.o ../core/WithCmd.o ../function/Combine.o ../function/Custom.o ../function/Ensemble.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/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/MolInfo.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
mkdir -p install
Building Plumed.inc
chmod a+x install/plumed-config
c++  -pipe -O2 -fno-strict-aliasing  -fPIC -Wall -pedantic -std=c++11  ../main/main.o ../wrapper/Plumed.o -o install/plumed-runtime -ldl 
c++ -shared -o install/libplumedKernel.so ../analysis/AnalysisBase.o ../analysis/Average.o ../analysis/AverageVessel.o ../analysis/Committor.o ../analysis/DataCollectionObject.o ../analysis/EuclideanDissimilarityMatrix.o ../analysis/FarthestPointSampling.o ../analysis/Histogram.o ../analysis/LandmarkSelectionBase.o ../analysis/LandmarkStaged.o ../analysis/OutputColvarFile.o ../analysis/OutputPDBFile.o ../analysis/PrintDissimilarityMatrix.o ../analysis/ReadAnalysisFrames.o ../analysis/ReadDissimilarityMatrix.o ../analysis/ReselectLandmarks.o ../analysis/SelectRandomFrames.o ../analysis/SelectWithStride.o ../analysis/WhamHistogram.o ../analysis/WhamWeights.o ../asmjit/arch.o ../asmjit/assembler.o ../asmjit/codebuilder.o ../asmjit/codecompiler.o ../asmjit/codeemitter.o ../asmjit/codeholder.o ../asmjit/constpool.o ../asmjit/cpuinfo.o ../asmjit/func.o ../asmjit/globals.o ../asmjit/inst.o ../asmjit/logging.o ../asmjit/operand.o ../asmjit/osutils.o ../asmjit/regalloc.o ../asmjit/runtime.o ../asmjit/string.o ../asmjit/utils.o ../asmjit/vmem.o ../asmjit/x86assembler.o ../asmjit/x86builder.o ../asmjit/x86compiler.o ../asmjit/x86inst.o ../asmjit/x86instimpl.o ../asmjit/x86internal.o ../asmjit/x86logging.o ../asmjit/x86operand.o ../asmjit/x86operand_regs.o ../asmjit/x86regalloc.o ../asmjit/zone.o ../bias/ABMD.o ../bias/Bias.o ../bias/BiasValue.o ../bias/ExtendedLagrangian.o ../bias/External.o ../bias/LWalls.o ../bias/MaxEnt.o ../bias/MetaD.o ../bias/MovingRestraint.o ../bias/PBMetaD.o ../bias/Restraint.o ../bias/ReweightBase.o ../bias/ReweightBias.o ../bias/ReweightMetad.o ../bias/ReweightTemperaturePressure.o ../bias/ReweightWham.o ../bias/UWalls.o ../blas/blas.o ../cltools/CLTool.o ../cltools/Completion.o ../cltools/Driver.o ../cltools/DriverDouble.o ../cltools/DriverFloat.o ../cltools/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/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/MDAtoms.o ../core/PlumedMain.o ../core/PlumedMainInitializer.o ../core/SetupMolInfo.o ../core/TargetDist.o ../core/Value.o ../core/WithCmd.o ../function/Combine.o ../function/Custom.o ../function/Ensemble.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/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/MolInfo.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
mkdir -p install
ar cr install/libplumedWrapper.a ../wrapper/Plumed.o
Building Plumed.inc, runtime-linking version
chmod a+x install/plumed-partial_tempering
chmod a+x install/plumed-mklib
chmod a+x install/plumed-newcv
Building Plumed.inc, shared version
Building Plumed.inc, static version
Building Plumed.cmake
Building Plumed.cmake, runtime-linking version
chmod a+x install/plumed-vim2html
Building Plumed.cmake, shared version
Building Plumed.cmake, static version
chmod a+x install/plumed-patch
chmod a+x install/plumed-selector
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/plumed2-2.6.0/src/lib'
gmake[7]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/lib'
gmake PLUMED_INSTALL=Install install/kernel.o
gmake[7]: Entering directory '/construction/science/plumed/plumed2-2.6.0/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/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/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/MDAtoms.o ../core/PlumedMain.o ../core/PlumedMainInitializer.o ../core/SetupMolInfo.o ../core/TargetDist.o ../core/Value.o ../core/WithCmd.o ../function/Combine.o ../function/Custom.o ../function/Ensemble.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/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/MolInfo.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/plumed2-2.6.0/src/lib'
gmake PLUMED_INSTALL=Install install/libplumed.a
gmake[7]: Entering directory '/construction/science/plumed/plumed2-2.6.0/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/plumed2-2.6.0/src/lib'
gmake[6]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/lib'
gmake[5]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/lib'
gmake[4]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src'
gmake[3]: Leaving directory '/construction/science/plumed/plumed2-2.6.0'
gmake -C vim
gmake[3]: Entering directory '/construction/science/plumed/plumed2-2.6.0/vim'
./vimsyntax.sh
gmake[3]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/vim'
gmake -C python
gmake[3]: Entering directory '/construction/science/plumed/plumed2-2.6.0/python'
Python support was not configure
gmake[3]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/python'
gmake[2]: Leaving directory '/construction/science/plumed/plumed2-2.6.0'

SUCCEEDED 00:04:04

-------------------------------------------------------------------------------
-- Phase: run-depends
-------------------------------------------------------------------------------

===>   plumed-2.6.0 depends on executable: bash - found

SUCCEEDED 00:00:00

-------------------------------------------------------------------------------
-- Phase: stage
-------------------------------------------------------------------------------

===>  Staging for plumed-2.6.0
===>   plumed-2.6.0 depends on executable: bash - found
===>   Generating temporary packing list
gmake[2]: Entering directory '/construction/science/plumed/plumed2-2.6.0'
gmake -C src install
gmake[3]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src'
gmake -C lib install
gmake[4]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/lib'
cd ../config ; gmake
gmake[5]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/config'
gmake PLUMED_FORCE=yes ConfigInstall.inc Config.inc version.h config.txt
gmake[6]: Entering directory '/construction/science/plumed/plumed2-2.6.0/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/plumed2-2.6.0/src/config'
gmake Config.o ConfigInstall.o compile_options.sh
gmake[6]: Entering directory '/construction/science/plumed/plumed2-2.6.0/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/plumed2-2.6.0/src/config'
gmake[5]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/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/plumed2-2.6.0/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/plumed2-2.6.0/src/lib'
gmake dirslinks
gmake[7]: Entering directory '/construction/science/plumed/plumed2-2.6.0/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/plumed2-2.6.0/src/lib'
gmake -C ../analysis links
gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/analysis'
Verify modules and create links in /construction/science/plumed/plumed2-2.6.0/src/analysis
gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/analysis'
gmake -C ../asmjit links
gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/asmjit'
Verify modules and create links in /construction/science/plumed/plumed2-2.6.0/src/asmjit
gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/asmjit'
gmake -C ../bias links
gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/bias'
Verify modules and create links in /construction/science/plumed/plumed2-2.6.0/src/bias
gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/bias'
gmake -C ../blas links
gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/blas'
Verify modules and create links in /construction/science/plumed/plumed2-2.6.0/src/blas
gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/blas'
gmake -C ../cltools links
gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/cltools'
Verify modules and create links in /construction/science/plumed/plumed2-2.6.0/src/cltools
gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/cltools'
gmake -C ../colvar links
gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/colvar'
Verify modules and create links in /construction/science/plumed/plumed2-2.6.0/src/colvar
gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/colvar'
gmake -C ../config links
gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/config'
Nothing to do in /construction/science/plumed/plumed2-2.6.0/src/config
gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/config'
gmake -C ../core links
gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/core'
Verify modules and create links in /construction/science/plumed/plumed2-2.6.0/src/core
gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/core'
gmake -C ../function links
gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/function'
Verify modules and create links in /construction/science/plumed/plumed2-2.6.0/src/function
gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/function'
gmake -C ../generic links
gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/generic'
Verify modules and create links in /construction/science/plumed/plumed2-2.6.0/src/generic
gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/generic'
gmake -C ../gridtools links
gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/gridtools'
Verify modules and create links in /construction/science/plumed/plumed2-2.6.0/src/gridtools
gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/gridtools'
gmake -C ../isdb links
gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/isdb'
Verify modules and create links in /construction/science/plumed/plumed2-2.6.0/src/isdb
gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/isdb'
gmake -C ../lapack links
gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/lapack'
Verify modules and create links in /construction/science/plumed/plumed2-2.6.0/src/lapack
gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/lapack'
gmake -C ../lepton links
gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/lepton'
Verify modules and create links in /construction/science/plumed/plumed2-2.6.0/src/lepton
gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/lepton'
gmake -C ../main links
gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/main'
Verify modules and create links in /construction/science/plumed/plumed2-2.6.0/src/main
gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/main'
gmake -C ../mapping links
gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/mapping'
Verify modules and create links in /construction/science/plumed/plumed2-2.6.0/src/mapping
gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/mapping'
gmake -C ../molfile links
gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/molfile'
Verify modules and create links in /construction/science/plumed/plumed2-2.6.0/src/molfile
gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/molfile'
gmake -C ../multicolvar links
gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/multicolvar'
Verify modules and create links in /construction/science/plumed/plumed2-2.6.0/src/multicolvar
gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/multicolvar'
gmake -C ../reference links
gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/reference'
Verify modules and create links in /construction/science/plumed/plumed2-2.6.0/src/reference
gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/reference'
gmake -C ../secondarystructure links
gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/secondarystructure'
Verify modules and create links in /construction/science/plumed/plumed2-2.6.0/src/secondarystructure
gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/secondarystructure'
gmake -C ../setup links
gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/setup'
Verify modules and create links in /construction/science/plumed/plumed2-2.6.0/src/setup
gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/setup'
gmake -C ../tools links
gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/tools'
Verify modules and create links in /construction/science/plumed/plumed2-2.6.0/src/tools
gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/tools'
gmake -C ../vatom links
gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/vatom'
Verify modules and create links in /construction/science/plumed/plumed2-2.6.0/src/vatom
gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/vatom'
gmake -C ../vesselbase links
gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/vesselbase'
Verify modules and create links in /construction/science/plumed/plumed2-2.6.0/src/vesselbase
gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/vesselbase'
gmake -C ../wrapper links
gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/wrapper'
Nothing to do in /construction/science/plumed/plumed2-2.6.0/src/wrapper
gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/wrapper'
gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/lib'
gmake[7]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/lib'
gmake dirs
gmake[7]: Entering directory '/construction/science/plumed/plumed2-2.6.0/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/plumed2-2.6.0/src/lib'
gmake -C ../analysis obj
gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/analysis'
gmake[9]: Nothing to be done for 'obj'.
gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/analysis'
gmake -C ../asmjit obj
gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/asmjit'
gmake[9]: Nothing to be done for 'obj'.
gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/asmjit'
gmake -C ../bias obj
gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/bias'
gmake[9]: Nothing to be done for 'obj'.
gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/bias'
gmake -C ../blas obj
gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/blas'
gmake[9]: Nothing to be done for 'obj'.
gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/blas'
gmake -C ../cltools obj
gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/cltools'
gmake[9]: Nothing to be done for 'obj'.
gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/cltools'
gmake -C ../colvar obj
gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/colvar'
gmake[9]: Nothing to be done for 'obj'.
gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/colvar'
gmake -C ../config obj
gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/config'
gmake PLUMED_FORCE=yes ConfigInstall.inc Config.inc version.h config.txt
gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.0/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/plumed2-2.6.0/src/config'
gmake Config.o ConfigInstall.o compile_options.sh
gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.0/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/plumed2-2.6.0/src/config'
gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/config'
gmake -C ../core obj
gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/core'
gmake[9]: Nothing to be done for 'obj'.
gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/core'
gmake -C ../function obj
gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/function'
gmake[9]: Nothing to be done for 'obj'.
gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/function'
gmake -C ../generic obj
gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/generic'
gmake[9]: Nothing to be done for 'obj'.
gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/generic'
gmake -C ../gridtools obj
gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/gridtools'
gmake[9]: Nothing to be done for 'obj'.
gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/gridtools'
gmake -C ../isdb obj
gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/isdb'
gmake[9]: Nothing to be done for 'obj'.
gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/isdb'
gmake -C ../lapack obj
gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/lapack'
gmake[9]: Nothing to be done for 'obj'.
gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/lapack'
gmake -C ../lepton obj
gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/lepton'
gmake[9]: Nothing to be done for 'obj'.
gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/lepton'
gmake -C ../main obj
gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/main'
gmake[9]: Nothing to be done for 'obj'.
gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/main'
gmake -C ../mapping obj
gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/mapping'
gmake[9]: Nothing to be done for 'obj'.
gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/mapping'
gmake -C ../molfile obj
gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/molfile'
gmake[9]: Nothing to be done for 'obj'.
gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/molfile'
gmake -C ../multicolvar obj
gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/multicolvar'
gmake[9]: Nothing to be done for 'obj'.
gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/multicolvar'
gmake -C ../reference obj
gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/reference'
gmake[9]: Nothing to be done for 'obj'.
gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/reference'
gmake -C ../secondarystructure obj
gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/secondarystructure'
gmake[9]: Nothing to be done for 'obj'.
gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/secondarystructure'
gmake -C ../setup obj
gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/setup'
gmake[9]: Nothing to be done for 'obj'.
gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/setup'
gmake -C ../tools obj
gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/tools'
gmake[9]: Nothing to be done for 'obj'.
gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/tools'
gmake -C ../vatom obj
gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/vatom'
gmake[9]: Nothing to be done for 'obj'.
gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/vatom'
gmake -C ../vesselbase obj
gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/vesselbase'
gmake[9]: Nothing to be done for 'obj'.
gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/vesselbase'
gmake -C ../wrapper obj
gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/wrapper'
gmake[9]: Nothing to be done for 'obj'.
gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/wrapper'
gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/lib'
gmake[7]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/lib'
gmake lib
gmake[7]: Entering directory '/construction/science/plumed/plumed2-2.6.0/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/plumed2-2.6.0/src/lib'
gmake[6]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/lib'
gmake PLUMED_INSTALL=Install install/kernel.o
gmake[6]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/lib'
gmake[6]: 'install/kernel.o' is up to date.
gmake[6]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/lib'
gmake PLUMED_INSTALL=Install install/libplumed.a
gmake[6]: Entering directory '/construction/science/plumed/plumed2-2.6.0/src/lib'
gmake[6]: 'install/libplumed.a' is up to date.
gmake[6]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/lib'
gmake[5]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src/lib'
gmake install-html
gmake[5]: Entering directory '/construction/science/plumed/plumed2-2.6.0/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/plumed2-2.6.0/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/plumed2-2.6.0/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/plumed2-2.6.0/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/plumed2-2.6.0/src/lib'
gmake[3]: Leaving directory '/construction/science/plumed/plumed2-2.6.0/src'
gmake[2]: Leaving directory '/construction/science/plumed/plumed2-2.6.0'
====> 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 00:00:26

-------------------------------------------------------------------------------
-- Phase: package
-------------------------------------------------------------------------------

===>  Building package for plumed-2.6.0
file sizes/checksums   [491]:   0%
file sizes/checksums   [491]:  20%
file sizes/checksums   [491]:  40%
file sizes/checksums   [491]:  61%
file sizes/checksums   [491]:  81%
file sizes/checksums   [491]: 100%
packing files          [491]:   0%
packing files          [491]:  20%
packing files          [491]:  40%
packing files          [491]:  61%
packing files          [491]:  81%
packing files          [491]: 100%
packing directories      [0]:   0%
packing directories      [0]: 100%

SUCCEEDED 00:01:08
TOTAL TIME 00:06:12