Dear all
I follow the installation procedure recommend on webpage, with a few
modifications on last line.
prefix=/home/marc/votca
mkdir -p ${prefix}/src
cd ${prefix}/src
wget http://votca.googlecode.com/hg/build.sh
chmod +x build.sh
sudo ./build.sh --prefix ${prefix} -DEXTERNAL_BOOST=OFF
-DWITH_SQLITE3=OFF gromacs tools csg
After gromacs and tools do fine , csg have problems, as below, any suggestion ?
Is an linux mint on 64 bit 4core machine.
Thanking your help
Marc
Working on csg
Source dir (csg) is already there - skipping checkout
Not trusting file /home/marc/votca/src/csg/.hg/hgrc from untrusted
user marc, group marc
Not trusting file .hg/hgrc from untrusted user marc, group marc
Not trusting file /home/marc/votca/src/csg/.hg/hgrc from untrusted
user marc, group marc
Not trusting file /home/marc/votca/src/csg/.hg/hgrc from untrusted
user marc, group marc
Not trusting file /home/marc/votca/src/csg/.hg/hgrc from untrusted
user marc, group marc
Not trusting file .hg/hgrc from untrusted user marc, group marc
Not trusting file /home/marc/votca/src/csg/.hg/hgrc from untrusted
user marc, group marc
Not trusting file /home/marc/votca/src/csg/.hg/hgrc from untrusted
user marc, group marc
Not trusting file /home/marc/votca/src/csg/.hg/hgrc from untrusted
user marc, group marc
Not trusting file .hg/hgrc from untrusted user marc, group marc
Not trusting file /home/marc/votca/src/csg/.hg/hgrc from untrusted
user marc, group marc
Not trusting file /home/marc/votca/src/csg/.hg/hgrc from untrusted
user marc, group marc
Not trusting file /home/marc/votca/src/csg/.hg/hgrc from untrusted
user marc, group marc
Not trusting file .hg/hgrc from untrusted user marc, group marc
Not trusting file /home/marc/votca/src/csg/.hg/hgrc from untrusted
user marc, group marc
Not trusting file /home/marc/votca/src/csg/.hg/hgrc from untrusted
user marc, group marc
cmake -DCMAKE_INSTALL_PREFIX=/home/marc/votca -DEXTERNAL_BOOST=OFF
-DWITH_SQLITE3=OFF -DCMAKE_INSTALL_RPATH_USE_LINK_PATH=ON .
-- The C compiler identification is GNU
-- The CXX compiler identification is GNU
-- Check for working C compiler: /usr/bin/gcc
-- Check for working C compiler: /usr/bin/gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Found TXT2TAGS: /usr/bin/txt2tags
-- checking for module 'libvotca_boost'
-- found libvotca_boost, version
-- Found VOTCA_BOOST: /home/marc/votca/lib64/libvotca_boost.so
-- checking for module 'libvotca_tools'
-- found libvotca_tools, version
-- Found VOTCA_TOOLS: /home/marc/votca/lib64/libvotca_tools.so
-- Looking for VotcaToolsFromC in /home/marc/votca/lib64/libvotca_tools.so;
-- Looking for VotcaToolsFromC in
/home/marc/votca/lib64/libvotca_tools.so; - found
-- Looking for assert.h
-- Looking for assert.h - found
-- Looking for C++ include algorithm
-- Looking for C++ include algorithm - found
-- Looking for C++ include fstream
-- Looking for C++ include fstream - found
-- Looking for C++ include iomanip
-- Looking for C++ include iomanip - found
-- Looking for C++ include iostream
-- Looking for C++ include iostream - found
-- Looking for C++ include list
-- Looking for C++ include list - found
-- Looking for C++ include map
-- Looking for C++ include map - found
-- Looking for C++ include numeric
-- Looking for C++ include numeric - found
-- Looking for C++ include sstream
-- Looking for C++ include sstream - found
-- Looking for C++ include stdexcept
-- Looking for C++ include stdexcept - found
-- Looking for C++ include string
-- Looking for C++ include string - found
-- Looking for C++ include vector
-- Looking for C++ include vector - found
-- Looking for C++ include cstdlib
-- Looking for C++ include cstdlib - found
-- Looking for sqrt in m
-- Looking for sqrt in m - found
-- checking for module 'libgmx'
-- found libgmx, version 4.5.3
-- Looking for GromacsVersion in /usr/lib/libgmx.so;
-- Looking for GromacsVersion in /usr/lib/libgmx.so; - found
-- Looking for init_mtop in /usr/lib/libgmx.so;
-- Looking for init_mtop in /usr/lib/libgmx.so; - found
-- Looking for output_env_init in /usr/lib/libgmx.so;
-- Looking for output_env_init in /usr/lib/libgmx.so; - found
-- Looking for init_domdec_vsites in /usr/lib/libgmx.so;
-- Looking for init_domdec_vsites in /usr/lib/libgmx.so; - not found
-- Found GROMACS: /usr/lib/libgmx.so
-- Found Doxygen: /usr/bin/doxygen
-- Configuring done
-- Generating done
-- Build files have been written to: /home/marc/votca/src/csg
cleaning csg
buidling csg
Scanning dependencies of target changelog
[ 1%] [ 1%] Building CXX object
src/libcsg/CMakeFiles/gmx_print_version.dir/modules/io/gmx_print_version.cc.o
Building CHANGELOG using txt2tags
[ 2%] Built target changelog
Current revision is 75b296de50f4
[ 2%] Built target help2t2t
Current revision is 75b296de50f4
Current revision is 75b296de50f4
Linking CXX executable gmx_print_version
[ 2%] Built target hgversion
[ 2%] Built target csg_call
[ 2%] Building votca-csg manpage
Current revision is 75b296de50f4
[ 2%] Built target gmx_print_version
[ 3%] [ 3%] Built target csg_include_links
Built target csg_inverse
make[2]: *** No rule to make target `help2t2t', needed by
`scripts/help2t2t'. Stop.
make[1]: *** [scripts/CMakeFiles/csg_call_manpage.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
[ 5%] Built target votca-csg_manpage
make[2]: *** No rule to make target `help2t2t', needed by
`scripts/help2t2t'. Stop.
make[1]: *** [scripts/CMakeFiles/csg_inverse_manpage.dir/all] Error 2
[ 6%] Generating gmx_libs_version.h
Current revision is 75b296de50f4
[ 6%] Built target multi_g_rdf
[ 9%] [ 10%] [ 9%] [ 11%] [ 12%] Building CXX object
src/libcsg/CMakeFiles/votca_csg.dir/trajectorywriter.cc.o
Building CXX object src/libcsg/CMakeFiles/votca_csg.dir/nblistgrid.cc.o
Building CXX object src/libcsg/CMakeFiles/votca_csg.dir/triclinicbox.cc.o
Building CXX object src/libcsg/CMakeFiles/votca_csg.dir/exclusionlist.cc.o
Building CXX object src/libcsg/CMakeFiles/votca_csg.dir/openbox.cc.o
[ 14%] [ 15%] Building CXX object
src/libcsg/CMakeFiles/votca_csg.dir/topologyreader.cc.o
Building CXX object src/libcsg/CMakeFiles/votca_csg.dir/trajectoryreader.cc.o
[ 16%] Building CXX object
src/libcsg/CMakeFiles/votca_csg.dir/boundarycondition.cc.o
[ 18%] Building CXX object src/libcsg/CMakeFiles/votca_csg.dir/map.cc.o
[ 19%] Building CXX object src/libcsg/CMakeFiles/votca_csg.dir/molecule.cc.o
[ 20%] Building CXX object src/libcsg/CMakeFiles/votca_csg.dir/topology.cc.o
[ 22%] Building CXX object src/libcsg/CMakeFiles/votca_csg.dir/cgengine.cc.o
[ 23%] Building CXX object src/libcsg/CMakeFiles/votca_csg.dir/nblist.cc.o
[ 24%] Building CXX object
src/libcsg/CMakeFiles/votca_csg.dir/cgmoleculedef.cc.o
[ 25%] Building CXX object src/libcsg/CMakeFiles/votca_csg.dir/topologymap.cc.o
[ 27%] [ 28%] Building CXX object
src/libcsg/CMakeFiles/votca_csg.dir/beadlist.cc.o
Building CXX object src/libcsg/CMakeFiles/votca_csg.dir/version.cc.o
[ 29%] Building CXX object src/libcsg/CMakeFiles/votca_csg.dir/imcio.cc.o
[ 31%] Building CXX object src/libcsg/CMakeFiles/votca_csg.dir/nematicorder.cc.o
[ 32%] Building CXX object
src/libcsg/CMakeFiles/votca_csg.dir/orthorhombicbox.cc.o
[ 33%] Building CXX object
src/libcsg/CMakeFiles/votca_csg.dir/csgapplication.cc.o
[ 35%] Building CXX object
src/libcsg/CMakeFiles/votca_csg.dir/modules/io/gmx_version_check.cc.o
[ 36%] Building CXX object
src/libcsg/CMakeFiles/votca_csg.dir/modules/io/gmxtrajectorywriter.cc.o
[ 37%] Building CXX object
src/libcsg/CMakeFiles/votca_csg.dir/modules/io/gmxtrajectoryreader.cc.o
[ 38%] Building CXX object
src/libcsg/CMakeFiles/votca_csg.dir/modules/io/gmx_version.cc.o
[ 40%] Building CXX object
src/libcsg/CMakeFiles/votca_csg.dir/modules/io/gmxtopologyreader.cc.o
[ 41%] Building CXX object
src/libcsg/CMakeFiles/votca_csg.dir/modules/io/growriter.cc.o
[ 42%] [ 44%] Building CXX object
src/libcsg/CMakeFiles/votca_csg.dir/modules/io/pdbtopologyreader.cc.o
Building CXX object
src/libcsg/CMakeFiles/votca_csg.dir/modules/io/grotopologyreader.cc.o
[ 45%] Building CXX object
src/libcsg/CMakeFiles/votca_csg.dir/modules/io/xmltopologyreader.cc.o
[ 46%] Building CXX object
src/libcsg/CMakeFiles/votca_csg.dir/modules/io/xyzwriter.cc.o
[ 48%] Building CXX object
src/libcsg/CMakeFiles/votca_csg.dir/modules/io/lammpsreader.cc.o
[ 49%] Building CXX object
src/libcsg/CMakeFiles/votca_csg.dir/modules/io/esptopologyreader.cc.o
/home/marc/votca/src/csg/src/libcsg/modules/io/xyzwriter.cc: In member
function ‘virtual void
votca::csg::XYZWriter::Write(votca::csg::Topology*)’:
/home/marc/votca/src/csg/src/libcsg/modules/io/xyzwriter.cc:40:46:
warning: format ‘%d’ expects type ‘int’, but argument 3 has type
‘std::vector<votca::csg::Bead*, std::allocator<votca::csg::Bead*>
>::size_type’
[ 50%] Building CXX object
src/libcsg/CMakeFiles/votca_csg.dir/modules/io/esptrajectoryreader.cc.o
[ 51%] Building CXX object
src/libcsg/CMakeFiles/votca_csg.dir/modules/io/pdbwriter.cc.o
Linking CXX shared library libvotca_csg.so
[ 51%] Built target votca_csg
make: *** [all] Error 2
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