Hi Christoph,
I did a clean install using shared libraries and it worked. It seems
some of the libraries were compiled with static option, so I recompiled
them using the shared libraries and then installed votca 1.2.
I couldn't figure out the problem with the static building though.
Thanks,
Cahit
On 07/01/2011 01:15 PM, Christoph Junghans wrote:
Hi Cahit,
when building statically (BUILD_SHARED_LIBS=OFF, not recommended)
cmake needs to know what are the dependency libraries of libgmx.a.
Usually that is done by pkg-config (see
csg/CMakeModules/FindGMX.cmake) and that is where /usr/lib64/libm.so
in ccmake comes from.
However libgmx also depends on libpthread and libdl, but libpthread
and libdl don't show up in the output of pkg-config (run pkg-config
--libs libgmx). That is why the undefined reference appear. So this is
actually a bug in gromacs autotools build system.
To workaround that issue, just add libpthread and libdl by hand to
GMX_LIBRARY, e.g.
-DGMX_LIBRARY="$HOME/progs/gromacs-4.5.3/lib/libgmx.a;/usr/lib64/libpthread.so;/usr/lib64/libdl.so;/usr/lib64/libm.so"
Cheers,
Christoph
2011/7/1 cdalgicdir<[email protected]>:
Hi all,
I am trying to install Votca 1.2 using ccmake. I have managed to install
tools without problem. However while installing csg, I receive an error
concerning the gromacs library file. Is there any specific way I should
specify the gromacs library?
Thanks,
Cahit
My command is:
ccmake -DGSL_LIBRARY=/home/cdalgicdir/progs/gsl-1.14/lib/libgsl.so
-DCBLAS_LIBRARY=/home/cdalgicdir/progs/gsl-1.14/lib/libgslcblas.so
-DCMAKE_INSTALL_PREFIX=/home/cdalgicdir/progs/votca/votca-1.2/
-DBoost_INCLUDE_DIR=/home/cdalgicdir/progs/boost-1.46.1/include/
-DBoost_LIBRARY=/home/cdalgicdir/progs/boost-1.46.1/lib/libboost_filesystem.so
-DBoost_PROGRAM_OPTIONS_LIBRARY=/home/cdalgicdir/progs/boost-1.46.1/lib/libboost_program_options.so
-DBUILD_SHARED_LIBS=OFF -DWITH_SQLITE3=OFF
-DGMX_INCLUDE_DIR=$HOME/progs/gromacs-4.5.3/include
-DGMX_LIBRARY=$HOME/progs/gromacs-4.5.3/lib/libgmx.a .
GMX_LIBRARY in ccmake window is :
/home/cdalgicdir/progs/gromacs-4.5.3/lib/libgmx.a;/usr/lib64/libm.so
Error output:
txt2tags not found, help cmake to find it by setting TXT2TAGS_EXECUTABLE
CMake Warning at src/libcsg/CMakeLists.txt:41 (message):
gromacs-4.5 double precision not found failback to single precision
CMake Error at CMakeModules/FindGMX.cmake:63 (message):
Could not find GromacsVersion in
/home/cdalgicdir/progs/gromacs-4.5.3/lib/libgmx.a;/usr/lib64/libm.so, take
look at the error message in
/home/cdalgicdir/progs/tars/votca-csg-1.2/CMakeFiles/CMakeError.log to
find
out what was going wrong. If you don't have pkg-config installed you will
most likely have to set GMX_LIBRARY by hand and include all it's deps in
there (i.e.
-DGMX_LIBRARY='/path/to/libgmx.so;/path/to/libblas.so;/path/to/libm.so') !
Call Stack (most recent call first):
src/libcsg/CMakeLists.txt:42 (find_package)
Error log:
Determining if the function GromacsVersion exists in the
/home/cdalgicdir/progs/gromacs-4.5.3/lib/libgmx.a;/usr/lib64/libm.so failed
with the following output:
Change Dir: /home/cdalgicdir/progs/tars/votca-csg-1.2/CMakeFiles/CMakeTmp
Run Build Command:/usr/bin/gmake "cmTryCompileExec/fast"
/usr/bin/gmake -f CMakeFiles/cmTryCompileExec.dir/build.make
CMakeFiles/cmTryCompileExec.dir/build
gmake[1]: Entering directory
`/home/cdalgicdir/progs/tars/votca-csg-1.2/CMakeFiles/CMakeTmp'
/home/cdalgicdir/progs/cmake-2.8.4/bin/cmake -E cmake_progress_report
/home/cdalgicdir/progs/tars/votca-csg-1.2/CMakeFiles/CMakeTmp/CMakeFiles 1
Building C object CMakeFiles/cmTryCompileExec.dir/CheckFunctionExists.c.o
/usr/bin/gcc -DCHECK_FUNCTION_EXISTS=GromacsVersion -o
CMakeFiles/cmTryCompileExec.dir/CheckFunctionExists.c.o -c
/home/cdalgicdir/progs/cmake-2.8.4/share/cmake-2.8/Modules/CheckFunctionExists.c
Linking C executable cmTryCompileExec
/home/cdalgicdir/progs/cmake-2.8.4/bin/cmake -E cmake_link_script
CMakeFiles/cmTryCompileExec.dir/link.txt --verbose=1
/usr/bin/gcc -DCHECK_FUNCTION_EXISTS=GromacsVersion
CMakeFiles/cmTryCompileExec.dir/CheckFunctionExists.c.o -o cmTryCompileExec
-rdynamic /home/cdalgicdir/progs/gromacs-4.5.3/lib/libgmx.a -lm
gmake[1]: Leaving directory
`/home/cdalgicdir/progs/tars/votca-csg-1.2/CMakeFiles/CMakeTmp'
/home/cdalgicdir/progs/gromacs-4.5.3/lib/libgmx.a(pthreads.o): In function
`tMPI_Thread_key_delete':
pthreads.c:(.text+0x5b6): undefined reference to `pthread_key_delete'
/home/cdalgicdir/progs/gromacs-4.5.3/lib/libgmx.a(pthreads.o): In function
`tMPI_Thread_key_create':
pthreads.c:(.text+0x658): undefined reference to `pthread_key_create'
/home/cdalgicdir/progs/gromacs-4.5.3/lib/libgmx.a(pthreads.o): In function
`tMPI_Thread_join':
pthreads.c:(.text+0x790): undefined reference to `pthread_join'
/home/cdalgicdir/progs/gromacs-4.5.3/lib/libgmx.a(pthreads.o): In function
`tMPI_Thread_create':
pthreads.c:(.text+0x839): undefined reference to `pthread_create'
/home/cdalgicdir/progs/gromacs-4.5.3/lib/libgmx.a(pthreads.o): In function
`tMPI_Thread_cancel':
pthreads.c:(.text+0x164): undefined reference to `pthread_cancel'
/home/cdalgicdir/progs/gromacs-4.5.3/lib/libgmx.a(pthreads.o): In function
`tMPI_Thread_setspecific':
pthreads.c:(.text+0x1eb): undefined reference to `pthread_setspecific'
/home/cdalgicdir/progs/gromacs-4.5.3/lib/libgmx.a(pthreads.o): In function
`tMPI_Thread_getspecific':
pthreads.c:(.text+0x1f8): undefined reference to `pthread_getspecific'
/home/cdalgicdir/progs/gromacs-4.5.3/lib/libgmx.a(pthreads.o): In function
`tMPI_Thread_mutex_trylock':
pthreads.c:(.text+0x9b7): undefined reference to `pthread_mutex_trylock'
/home/cdalgicdir/progs/gromacs-4.5.3/lib/libgmx.a(vmddlopen.o): In function
`vmddlclose':
vmddlopen.c:(.text+0x1): undefined reference to `dlclose'
/home/cdalgicdir/progs/gromacs-4.5.3/lib/libgmx.a(vmddlopen.o): In function
`vmddlsym':
vmddlopen.c:(.text+0x11): undefined reference to `dlsym'
/home/cdalgicdir/progs/gromacs-4.5.3/lib/libgmx.a(vmddlopen.o): In function
`vmddlerror':
vmddlopen.c:(.text+0x21): undefined reference to `dlerror'
/home/cdalgicdir/progs/gromacs-4.5.3/lib/libgmx.a(vmddlopen.o): In function
`vmddlopen':
vmddlopen.c:(.text+0x36): undefined reference to `dlopen'
collect2: ld returned 1 exit status
gmake[1]: *** [cmTryCompileExec] Error 1
gmake: *** [cmTryCompileExec/fast] Error 2
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