Dear developers and users,
I am trying to build the votca package following the instructions on
the web page. However, I have some problems which I am not able to
solve.
To do that I use the following script
>cat compiler.sh
source /home/nightrain/CODES/VOTCA/VOTCA_1.2/TMP/
gromacs-4.5.4_b/bin/GMXRC.bash
prefix=`pwd`
echo $prefix
mkdir -p ${prefix}/src
cd ${prefix}/src
wget http://votca.googlecode.com/hg/build.sh
chmod +x build.sh
./build.sh --prefix ${prefix} -j 1 --log build.log tools csg
The tools are compiled without problem but in the case of the csg
package, after sometime, I get the following error:
===================================================
(...)
Scanning dependencies of target csg_property
[ 55%] Building CXX object src/tools/CMakeFiles/csg_property.dir/
csg_property.cc.o
Linking CXX executable csg_property
[ 55%] Built target csg_property
Scanning dependencies of target csg_property_manpage
[ 55%] Generating csg_property.man
[ 57%] Built target csg_property_manpage
Scanning dependencies of target csg_call
Current revision is 400a0374775a
[ 57%] Built target csg_call
Scanning dependencies of target csg_call_manpage
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: *** [all] Error 2
===================================================
Please, can someone help me to address this error?
Thanks in advance. Best regards
--------------------------------------------------------------
Dr. Javier Ramos
Molecular Structure and Properties of Polymers
Department of Macromolecular Physics
Instituto de Estructura de la Materia (CSIC)
C/ Serrano 113 bis 28006 Madrid (Spain)
Voice +34 91 561 68 00 (943112)
Fax +34 91 585 54 13
http://www.biophym.iem.csic.es/biophym
--------------------------------------------------------------
P.D. I paste here the content of the build.log file:
>cat build.log
Log of './build.sh --prefix /home/nightrain/CODES/VOTCA/VOTCA_1.2/
TMP4 -j 1 tools csg'
This is VOTCA build.sh, version 1.6.1
prefix is '/home/nightrain/CODES/VOTCA/VOTCA_1.2/TMP4'
Using 1 jobs for make
Working on tools
Doing checkout for tools from https://tools.votca.googlecode.com/hg/
(CTRL-C to stop) 5 4 3 2 1
requesting all changes
adding changesets
adding manifests
adding file changes
added 474 changesets with 2604 changes to 1678 files (+2 heads)
updating to branch default
1460 files updated, 0 files merged, 0 files removed, 0 files
unresolved
Switching to stable branch add --dev option to prevent that
7 files updated, 0 files merged, 0 files removed, 0 files unresolved
cmake -DCMAKE_INSTALL_PREFIX=/home/nightrain/CODES/VOTCA/VOTCA_1.2/
TMP4 .
-- 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
-- Looking for include files CMAKE_HAVE_PTHREAD_H
-- Looking for include files CMAKE_HAVE_PTHREAD_H - found
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Found TXT2TAGS: /usr/bin/txt2tags
-- Looking for assert.h
-- Looking for assert.h - found
-- Looking for math.h
-- Looking for math.h - found
-- Looking for stdio.h
-- Looking for stdio.h - found-- Looking for C++ include cmath
-- Looking for C++ include cmath - found
-- Looking for C++ include fstream
-- Looking for C++ include fstream - found
-- Looking for C++ include functional
-- Looking for C++ include functional - found
-- Looking for C++ include iostream
-- Looking for C++ include iostream - found
-- Looking for C++ include limits
-- Looking for C++ include limits - 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 ostream
-- Looking for C++ include ostream - found
-- Looking for C++ include sstream
-- Looking for C++ include sstream - found
-- Looking for C++ include stack
-- Looking for C++ include stack - 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 sqrt in m
-- Looking for sqrt in m - found
-- Boost version: 1.40.0
-- Found the following Boost libraries:
-- program_options
-- Found EXPAT: /usr/lib/libexpat.so
-- checking for module 'fftw3'
-- found fftw3, version 3.2.2
-- Found FFTW3: /usr/lib/libfftw3.so
-- Looking for fftw_plan_r2r_1d in /usr/lib/libfftw3.so
-- Looking for fftw_plan_r2r_1d in /usr/lib/libfftw3.so - found
-- Found CBLAS: /usr/lib/libcblas.so
-- Looking for cblas_dsyrk in /usr/lib/libcblas.so
-- Looking for cblas_dsyrk in /usr/lib/libcblas.so - found
-- checking for module 'gsl'
-- found gsl, version 1.13
-- Found GSL: /usr/lib/libgsl.so
-- Looking for gsl_linalg_QR_decomp in /usr/lib/libgsl.so;/usr/lib/
libcblas.so
-- Looking for gsl_linalg_QR_decomp in /usr/lib/libgsl.so;/usr/lib/
libcblas.so - found
-- checking for module 'sqlite3'
-- found sqlite3, version 3.6.22
-- Found SQLITE3: /usr/lib/libsqlite3.so
-- Found Doxygen: /usr/bin/doxygen
-- Configuring done
-- Generating done
-- Build files have been written to: /home/nightrain/CODES/VOTCA/
VOTCA_1.2/TMP4/src/tools
buidling tools
Scanning dependencies of target changelog
[ 0%] Building CHANGELOG using txt2tags
[ 3%] Built target changelog
Scanning dependencies of target hgversion
[ 3%] Built target hgversion
Scanning dependencies of target manpages
[ 3%] Building votca_tools manpage
[ 7%] Built target manpages
Scanning dependencies of target votca_tools
[ 11%] Building CXX object src/libtools/CMakeFiles/votca_tools.dir/
linalg.cc.o
[ 14%] Building CXX object src/libtools/CMakeFiles/votca_tools.dir/
matrix.cc.o
[ 18%] Building CXX object src/libtools/CMakeFiles/votca_tools.dir/
histogramnew.cc.o
[ 22%] Building CXX object src/libtools/CMakeFiles/votca_tools.dir/
spline.cc.o
[ 25%] Building CXX object src/libtools/CMakeFiles/votca_tools.dir/
random.cc.o
[ 29%] Building CXX object src/libtools/CMakeFiles/votca_tools.dir/
mutex.cc.o
[ 33%] Building CXX object src/libtools/CMakeFiles/votca_tools.dir/
rangeparser.cc.o
[ 37%] Building CXX object src/libtools/CMakeFiles/votca_tools.dir/
crosscorrelate.cc.o
[ 40%] Building CXX object src/libtools/CMakeFiles/votca_tools.dir/
tokenizer.cc.o
[ 44%] Building CXX object src/libtools/CMakeFiles/votca_tools.dir/
akimaspline.cc.o
[ 48%] Building CXX object src/libtools/CMakeFiles/votca_tools.dir/
parcer.cc.o
[ 51%] Building CXX object src/libtools/CMakeFiles/votca_tools.dir/
parsexml.cc.o
[ 55%] Building CXX object src/libtools/CMakeFiles/votca_tools.dir/
correlate.cc.o
[ 59%] Building CXX object src/libtools/CMakeFiles/votca_tools.dir/
linspline.cc.o
[ 62%] Building CXX object src/libtools/CMakeFiles/votca_tools.dir/
table.cc.o
[ 66%] Building CXX object src/libtools/CMakeFiles/votca_tools.dir/
cubicspline.cc.o
[ 70%] Building CXX object src/libtools/CMakeFiles/votca_tools.dir/
histogram.cc.o
[ 74%] Building CXX object src/libtools/CMakeFiles/votca_tools.dir/
thread.cc.o
[ 77%] Building CXX object src/libtools/CMakeFiles/votca_tools.dir/
datacollection.cc.o
[ 81%] Building CXX object src/libtools/CMakeFiles/votca_tools.dir/
property.cc.o
[ 85%] Building CXX object src/libtools/CMakeFiles/votca_tools.dir/
application.cc.o
[ 88%] Building CXX object src/libtools/CMakeFiles/votca_tools.dir/
version.cc.o
[ 92%] Building CXX object src/libtools/CMakeFiles/votca_tools.dir/
database.cc.o
[ 96%] Building CXX object src/libtools/CMakeFiles/votca_tools.dir/
statement.cc.o
Linking CXX shared library libvotca_tools.so
[ 96%] Built target votca_tools
Scanning dependencies of target linktest
[100%] Building CXX object src/libtools/CMakeFiles/linktest.dir/
linktest.cc.o
Linking CXX executable linktest
[100%] Built target linktest
installing tools
[ 3%] Built target changelog
[ 3%] Built target hgversion
[ 7%] Built target manpages
[ 96%] Built target votca_tools
[100%] Built target linktest
Install the project...
-- Install configuration: "Release"
-- Installing: /home/nightrain/CODES/VOTCA/VOTCA_1.2/TMP4/lib/
libvotca_tools.so.2
-- Installing: /home/nightrain/CODES/VOTCA/VOTCA_1.2/TMP4/lib/
libvotca_tools.so
-- Installing: /home/nightrain/CODES/VOTCA/VOTCA_1.2/TMP4/lib/
pkgconfig/libvotca_tools.pc
-- Installing: /home/nightrain/CODES/VOTCA/VOTCA_1.2/TMP4/include/
votca/tools/rangeparser.h
-- Installing: /home/nightrain/CODES/VOTCA/VOTCA_1.2/TMP4/include/
votca/tools/spline.h
-- Installing: /home/nightrain/CODES/VOTCA/VOTCA_1.2/TMP4/include/
votca/tools/random.h
-- Installing: /home/nightrain/CODES/VOTCA/VOTCA_1.2/TMP4/include/
votca/tools/parsexml.h
-- Installing: /home/nightrain/CODES/VOTCA/VOTCA_1.2/TMP4/include/
votca/tools/histogram.h
-- Installing: /home/nightrain/CODES/VOTCA/VOTCA_1.2/TMP4/include/
votca/tools/version.h
-- Installing: /home/nightrain/CODES/VOTCA/VOTCA_1.2/TMP4/include/
votca/tools/histogramnew.h
-- Installing: /home/nightrain/CODES/VOTCA/VOTCA_1.2/TMP4/include/
votca/tools/cubicspline.h
-- Installing: /home/nightrain/CODES/VOTCA/VOTCA_1.2/TMP4/include/
votca/tools/statement.h
-- Installing: /home/nightrain/CODES/VOTCA/VOTCA_1.2/TMP4/include/
votca/tools/table.h
-- Installing: /home/nightrain/CODES/VOTCA/VOTCA_1.2/TMP4/include/
votca/tools/database.h
-- Installing: /home/nightrain/CODES/VOTCA/VOTCA_1.2/TMP4/include/
votca/tools/akimaspline.h
-- Installing: /home/nightrain/CODES/VOTCA/VOTCA_1.2/TMP4/include/
votca/tools/lexical_cast.h
-- Installing: /home/nightrain/CODES/VOTCA/VOTCA_1.2/TMP4/include/
votca/tools/vec.h
-- Installing: /home/nightrain/CODES/VOTCA/VOTCA_1.2/TMP4/include/
votca/tools/mutex.h
-- Installing: /home/nightrain/CODES/VOTCA/VOTCA_1.2/TMP4/include/
votca/tools/property.h
-- Installing: /home/nightrain/CODES/VOTCA/VOTCA_1.2/TMP4/include/
votca/tools/thread.h
-- Installing: /home/nightrain/CODES/VOTCA/VOTCA_1.2/TMP4/include/
votca/tools/correlate.h
-- Installing: /home/nightrain/CODES/VOTCA/VOTCA_1.2/TMP4/include/
votca/tools/crosscorrelate.h
-- Installing: /home/nightrain/CODES/VOTCA/VOTCA_1.2/TMP4/include/
votca/tools/datacollection.h
-- Installing: /home/nightrain/CODES/VOTCA/VOTCA_1.2/TMP4/include/
votca/tools/matrix.h
-- Installing: /home/nightrain/CODES/VOTCA/VOTCA_1.2/TMP4/include/
votca/tools/application.h
-- Installing: /home/nightrain/CODES/VOTCA/VOTCA_1.2/TMP4/include/
votca/tools/linspline.h
-- Installing: /home/nightrain/CODES/VOTCA/VOTCA_1.2/TMP4/include/
votca/tools/objectfactory.h
-- Installing: /home/nightrain/CODES/VOTCA/VOTCA_1.2/TMP4/include/
votca/tools/linalg.h
-- Installing: /home/nightrain/CODES/VOTCA/VOTCA_1.2/TMP4/include/
votca/tools/types.h
-- Installing: /home/nightrain/CODES/VOTCA/VOTCA_1.2/TMP4/include/
votca/tools/average.h
-- Installing: /home/nightrain/CODES/VOTCA/VOTCA_1.2/TMP4/include/
votca/tools/tokenizer.h
-- Installing: /home/nightrain/CODES/VOTCA/VOTCA_1.2/TMP4/bin/
VOTCARC.csh
-- Installing: /home/nightrain/CODES/VOTCA/VOTCA_1.2/TMP4/bin/
VOTCARC.bash
-- Installing: /home/nightrain/CODES/VOTCA/VOTCA_1.2/TMP4/share/man/
man7/votca-tools.7
done with tools
Working on csg
Doing checkout for csg from https://csg.votca.googlecode.com/hg/
(CTRL-C to stop) 5 4 3 2 1
requesting all changes
adding changesets
adding manifests
adding file changes
added 1420 changesets with 4973 changes to 615 files (+7 heads)
updating to branch default
304 files updated, 0 files merged, 0 files removed, 0 files unresolved
Switching to stable branch add --dev option to prevent that
13 files updated, 0 files merged, 4 files removed, 0 files unresolved
cmake -DCMAKE_INSTALL_PREFIX=/home/nightrain/CODES/VOTCA/VOTCA_1.2/
TMP4 .
-- 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
-- Boost version: 1.40.0
-- Found the following Boost libraries:
-- program_options
-- checking for module 'libvotca_tools'
-- found libvotca_tools, version
-- Found VOTCA_TOOLS: /home/nightrain/CODES/VOTCA/VOTCA_1.2/TMP4/lib/
libvotca_tools.so
-- Looking for ToolsVersionStr in /home/nightrain/CODES/VOTCA/
VOTCA_1.2/TMP4/lib/libvotca_tools.so
-- Looking for ToolsVersionStr in /home/nightrain/CODES/VOTCA/
VOTCA_1.2/TMP4/lib/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 sqrt in m
-- Looking for sqrt in m - found
-- checking for module 'libgmx_d'
-- package 'libgmx_d' not found
-- Could NOT find GMX_D (missing: GMX_D_LIBRARY GMX_D_INCLUDE_DIR)
-- checking for module 'libgmx'
-- found libgmx, version 4.5.4
-- Found GMX: /home/nightrain/CODES/VOTCA/src/gromacs-4.5.4_b/lib/
libgmx.so
-- Looking for GromacsVersion in /home/nightrain/CODES/VOTCA/src/
gromacs-4.5.4_b/lib/libgmx.so
-- Looking for GromacsVersion in /home/nightrain/CODES/VOTCA/src/
gromacs-4.5.4_b/lib/libgmx.so - found
-- Looking for init_mtop in /home/nightrain/CODES/VOTCA/src/
gromacs-4.5.4_b/lib/libgmx.so
-- Looking for init_mtop in /home/nightrain/CODES/VOTCA/src/
gromacs-4.5.4_b/lib/libgmx.so - found
-- Found Doxygen: /usr/bin/doxygen
-- Configuring done
-- Generating done
-- Build files have been written to: /home/nightrain/CODES/VOTCA/
VOTCA_1.2/TMP4/src/csg
buidling csg
Scanning dependencies of target changelog
[ 0%] Building CHANGELOG using txt2tags
[ 1%] Built target changelog
Scanning dependencies of target gmx_print_version
[ 2%] Building CXX object src/libcsg/CMakeFiles/gmx_print_version.dir/
modules/io/gmx_print_version.cc.o
Linking CXX executable gmx_print_version
[ 2%] Built target gmx_print_version
Scanning dependencies of target hgversion
[ 2%] Built target hgversion
[ 3%] Generating gmx_libs_version.h
Scanning dependencies of target votca_csg
[ 5%] Building CXX object src/libcsg/CMakeFiles/votca_csg.dir/
boundarycondition.cc.o
[ 6%] Building CXX object src/libcsg/CMakeFiles/votca_csg.dir/
csgapplication.cc.o
[ 7%] Building CXX object src/libcsg/CMakeFiles/votca_csg.dir/
nblistgrid.cc.o
[ 9%] Building CXX object src/libcsg/CMakeFiles/votca_csg.dir/
openbox.cc.o
[ 10%] Building CXX object src/libcsg/CMakeFiles/votca_csg.dir/
nblist.cc.o
[ 11%] Building CXX object src/libcsg/CMakeFiles/votca_csg.dir/
trajectoryreader.cc.o
[ 12%] Building CXX object src/libcsg/CMakeFiles/votca_csg.dir/
topology.cc.o
[ 14%] Building CXX object src/libcsg/CMakeFiles/votca_csg.dir/
exclusionlist.cc.o
[ 15%] Building CXX object src/libcsg/CMakeFiles/votca_csg.dir/
triclinicbox.cc.o
[ 16%] Building CXX object src/libcsg/CMakeFiles/votca_csg.dir/
imcio.cc.o
[ 18%] Building CXX object src/libcsg/CMakeFiles/votca_csg.dir/
trajectorywriter.cc.o
[ 19%] Building CXX object src/libcsg/CMakeFiles/votca_csg.dir/
orthorhombicbox.cc.o
[ 20%] Building CXX object src/libcsg/CMakeFiles/votca_csg.dir/
topologyreader.cc.o
[ 22%] Building CXX object src/libcsg/CMakeFiles/votca_csg.dir/
map.cc.o
[ 23%] Building CXX object src/libcsg/CMakeFiles/votca_csg.dir/
cgmoleculedef.cc.o
[ 24%] Building CXX object src/libcsg/CMakeFiles/votca_csg.dir/
cgengine.cc.o
[ 25%] Building CXX object src/libcsg/CMakeFiles/votca_csg.dir/
molecule.cc.o
[ 27%] Building CXX object src/libcsg/CMakeFiles/votca_csg.dir/
topologymap.cc.o
[ 28%] Building CXX object src/libcsg/CMakeFiles/votca_csg.dir/
nematicorder.cc.o
[ 29%] Building CXX object src/libcsg/CMakeFiles/votca_csg.dir/
beadlist.cc.o
[ 31%] Building CXX object src/libcsg/CMakeFiles/votca_csg.dir/
version.cc.o
[ 32%] Building CXX object src/libcsg/CMakeFiles/votca_csg.dir/modules/
io/gmx_version_check.cc.o
[ 33%] Building CXX object src/libcsg/CMakeFiles/votca_csg.dir/modules/
io/gmxtrajectorywriter.cc.o
[ 35%] Building CXX object src/libcsg/CMakeFiles/votca_csg.dir/modules/
io/gmxtrajectoryreader.cc.o
[ 36%] Building CXX object src/libcsg/CMakeFiles/votca_csg.dir/modules/
io/gmx_version.cc.o
[ 37%] Building CXX object src/libcsg/CMakeFiles/votca_csg.dir/modules/
io/gmxtopologyreader.cc.o
[ 38%] Building CXX object src/libcsg/CMakeFiles/votca_csg.dir/modules/
io/growriter.cc.o
[ 40%] Building CXX object src/libcsg/CMakeFiles/votca_csg.dir/modules/
io/grotopologyreader.cc.o
[ 41%] Building CXX object src/libcsg/CMakeFiles/votca_csg.dir/modules/
io/pdbtopologyreader.cc.o
[ 42%] Building CXX object src/libcsg/CMakeFiles/votca_csg.dir/modules/
io/pdbwriter.cc.o
[ 44%] Building CXX object src/libcsg/CMakeFiles/votca_csg.dir/modules/
io/xyzwriter.cc.o
[ 45%] Building CXX object src/libcsg/CMakeFiles/votca_csg.dir/modules/
io/esptrajectoryreader.cc.o
[ 46%] Building CXX object src/libcsg/CMakeFiles/votca_csg.dir/modules/
io/esptopologyreader.cc.o
[ 48%] Building CXX object src/libcsg/CMakeFiles/votca_csg.dir/modules/
io/xmltopologyreader.cc.o
[ 49%] Building CXX object src/libcsg/CMakeFiles/votca_csg.dir/modules/
io/lammpsreader.cc.o
Linking CXX shared library libvotca_csg.so
[ 49%] Built target votca_csg
Scanning dependencies of target csg_fmatch
[ 50%] Building CXX object src/tools/CMakeFiles/csg_fmatch.dir/
csg_fmatch.cc.o
Linking CXX executable csg_fmatch
[ 50%] Built target csg_fmatch
Scanning dependencies of target help2t2t
[ 50%] Built target help2t2t
Scanning dependencies of target csg_fmatch_manpage
[ 50%] Generating csg_fmatch.man
[ 51%] Built target csg_fmatch_manpage
Scanning dependencies of target csg_part_dist
[ 53%] Building CXX object src/tools/CMakeFiles/csg_part_dist.dir/
csg_part_dist.cc.o
Linking CXX executable csg_part_dist
[ 53%] Built target csg_part_dist
Scanning dependencies of target csg_part_dist_manpage
[ 53%] Generating csg_part_dist.man
[ 54%] Built target csg_part_dist_manpage
Scanning dependencies of target csg_property
[ 55%] Building CXX object src/tools/CMakeFiles/csg_property.dir/
csg_property.cc.o
Linking CXX executable csg_property
[ 55%] Built target csg_property
Scanning dependencies of target csg_property_manpage
[ 55%] Generating csg_property.man
[ 57%] Built target csg_property_manpage
Scanning dependencies of target csg_call
[ 57%] Built target csg_call
Scanning dependencies of target csg_call_manpage
-- Looking for stdlib.h
-- Looking for stdlib.h - found
-- Looking for string.h
-- Looking for string.h - found
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