2013/11/17 Zhicheng <[email protected]>: > Hi Christoph: > Adding /usr/lib/libpthread.so to GROMACS_DEP_LIBRARY, however, I find the > same error mentioned above . Does it need more dependencies? Can you post the end of the new CMakeEtror.log again?
> > 在 2013年11月16日星期六UTC+8上午12时28分01秒，Christoph Junghans写道： >> >> 2013/11/14 Zhicheng <[email protected]>: >> > Hi Christoph: >> > >> > This is my CMakeEroor.log file : >> > >> > Determining if the function GromacsVersion exists in the >> > /gpfs/home/lsd001/gromacs/lib/libgmx_mpi_d.so; failed with the following >> > output: >> > >> > Change Dir: /gpfs/home/lsd001/votca_csg/src/csg/CMakeFiles/CMakeTmp >> > >> > >> > Run Build Command:/usr/bin/gmake "cmTryCompileExec3300959071/fast" >> > >> > /usr/bin/gmake -f CMakeFiles/cmTryCompileExec3300959071.dir/build.make >> > CMakeFiles/cmTryCompileExec3300959071.dir/build >> > >> > gmake[1]: Entering directory >> > `/gpfs/home/lsd001/votca_csg/src/csg/CMakeFiles/CMakeTmp' >> > >> > /usr/local/bin/cmake -E cmake_progress_report >> > /gpfs/home/lsd001/votca_csg/src/csg/CMakeFiles/CMakeTmp/CMakeFiles 1 >> > >> > Building C object >> > CMakeFiles/cmTryCompileExec3300959071.dir/CheckFunctionExists.c.o >> > >> > /usr/bin/cc -DCHECK_FUNCTION_EXISTS=GromacsVersion -o >> > CMakeFiles/cmTryCompileExec3300959071.dir/CheckFunctionExists.c.o -c >> > /usr/local/share/cmake-2.8/Modules/CheckFunctionExists.c >> > >> > Linking C executable cmTryCompileExec3300959071 >> > >> > /usr/local/bin/cmake -E cmake_link_script >> > CMakeFiles/cmTryCompileExec3300959071.dir/link.txt --verbose=1 >> > >> > /usr/bin/cc -DCHECK_FUNCTION_EXISTS=GromacsVersion >> > CMakeFiles/cmTryCompileExec3300959071.dir/CheckFunctionExists.c.o -o >> > cmTryCompileExec3300959071 -rdynamic >> > /gpfs/home/lsd001/gromacs/lib/libgmx_mpi_d.so >> > -Wl,-rpath,/gpfs/home/lsd001/gromacs/lib >> > >> > /gpfs/hpc/intel/Compiler/11.1/064/lib/intel64/libimf.so: warning: >> > warning: >> > feupdateenv is not implemented and will always fail >> > >> > /gpfs/hpc/intel/mkl/10.2.3.029/lib/em64t/libguide.so: undefined >> > reference to >> > `pthread_atfork' >> > >> > collect2: ld returned 1 exit status >> Here is the problem, you need to add /usr/lib/libpthread.so to >> GROMACS_DEP_LIBRARY, too! >> >> Linking VOTCA with an mpi version of gromacs is not necessary nor >> useful as VOTCA doesn't use any part of the mpi parallelization. >> (also see my previous posting on this topic). In short, a mpi version >> of libgmx just pulls in more dependencies! >> >> Christoph >> > >> > gmake[1]: *** [cmTryCompileExec3300959071] Error 1 >> > >> > gmake[1]: Leaving directory >> > `/gpfs/home/lsd001/votca_csg/src/csg/CMakeFiles/CMakeTmp' >> > >> > gmake: *** [cmTryCompileExec3300959071/fast] Error 2 >> > >> > 在 2013年11月15日星期五UTC+8上午12时11分54秒，Christoph Junghans写道： >> >> >> >> 2013/11/14 郭志成 <[email protected]>: >> >> > Hi: >> >> > >> >> > I get the error message as described below using build.sh to install >> >> > votca_csg on cluster. >> >> > -- checking for module 'libgmx' >> >> > >> >> > -- package 'libgmx' not found >> >> > >> >> > -- Looking for GromacsVersion in >> >> > /gpfs/home/lsd001/gromacs/lib/libgmx_mpi_d.so; >> >> > >> >> > -- Looking for GromacsVersion in >> >> > /gpfs/home/lsd001/gromacs/lib/libgmx_mpi_d.so; - not found >> >> > >> >> > CMake Error at CMakeModules/FindGROMACS.cmake:81 (message): >> >> > >> >> > Could not find GromacsVersion in >> >> > >> >> > /gpfs/home/lsd001/gromacs/lib/libgmx_mpi_d.so;, take look at the >> >> > error >> >> > >> >> > message in >> >> > /gpfs/home/lsd001/votca_csg/src/csg/CMakeFiles/CMakeError.log >> >> > to >> >> Can you have a look in the CMakeError.log and post the last 50 lines? >> >> >> >> Christoph >> >> >> >> > >> >> > find out what was going wrong. If you don't have pkg-config >> >> > installed >> >> > you >> >> > >> >> > will most likely have to set GROMACS_LIBRARY and >> >> > GROMACS_DEP_LIBRARY >> >> > by >> >> > >> >> > hand which sets the gromacs lib and it's depencies (i.e. >> >> > >> >> > -DGROMACS_LIBRARY='/path/to/libgmx.so' >> >> > >> >> > -DGROMACS_DEP_LIBRARIES='/path/to/libblas.so;/path/to/libm.so') ! >> >> > >> >> > Call Stack (most recent call first): >> >> > >> >> > src/libcsg/CMakeLists.txt:23 (find_package) >> >> > >> >> > I have specified the information about GROMACS: >> >> > >> >> > >> >> > >> >> > -DGROMACS_INCLUDE_DIR=/gpfs/home/lsd001/gromacs/include >> >> > >> >> > -DGROMACS_LIBRARY=/gpfs/home/lsd001/gromacs/lib/libgmx_mpi_d.so >> >> > >> >> > >> >> > >> >> > -DGROMACS_DEP_LIBARIES="/gpfs/home/lsd001/gsl-1.16/lib/libgslcblas.so;/gpfs/home/lsd001/gsl-1.16/lib/libgsl.so" >> >> > >> >> > >> >> > >> >> > Detailed infromation about GROMACS described below: >> >> > >> >> > >> >> > >> >> > Gromacs version: VERSION 4.6.3 >> >> > >> >> > Precision: double >> >> > >> >> > Memory model: 64 bit >> >> > >> >> > MPI library: MPI >> >> > >> >> > OpenMP support: disabled >> >> > >> >> > GPU support: disabled >> >> > >> >> > invsqrt routine: gmx_software_invsqrt(x) >> >> > >> >> > CPU acceleration: SSE2 >> >> > >> >> > FFT library: fftw-3.3.3-sse2 >> >> > >> >> > Large file support: enabled >> >> > >> >> > RDTSCP usage: enabled >> >> > >> >> > Built on: Mon Oct 28 15:45:17 CST 2013 >> >> > >> >> > Built by: lsd001@lnode [CMAKE] >> >> > >> >> > Build OS/arch: Linux 2.6.16.60-0.54.5-smp x86_64 >> >> > >> >> > Build CPU vendor: GenuineIntel >> >> > >> >> > Build CPU brand: Intel(R) Xeon(R) CPU E5630 @ 2.53GHz >> >> > >> >> > Build CPU family: 6 Model: 44 Stepping: 2 >> >> > >> >> > Build CPU features: apic clfsh cmov cx8 cx16 htt lahf_lm mmx msr >> >> > nonstop_tsc >> >> > pcid pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 >> >> > >> >> > C compiler: /usr/bin/cc GNU cc (GCC) 4.1.2 20070115 (SUSE >> >> > Linux) >> >> > >> >> > C compiler flags: -msse2 -Wextra -Wno-missing-field-initializers >> >> > -Wno-sign-compare -Wall -Wno-unused -Wunus >> >> > >> >> > >> >> > >> >> > What's wrong with this? How can I fix it? >> >> > >> >> > >> >> > -- >> >> > You received this message because you are subscribed to the Google >> >> > Groups >> >> > "votca" group. >> >> > To unsubscribe from this group and stop receiving emails from it, >> >> > send >> >> > an >> >> > email to [email protected]. >> >> > To post to this group, send email to [email protected]. >> >> > Visit this group at http://groups.google.com/group/votca. >> >> > For more options, visit https://groups.google.com/groups/opt_out. >> >> >> >> >> >> >> >> -- >> >> Christoph Junghans >> >> Web: http://www.compphys.de >> > >> > -- >> > You received this message because you are subscribed to the Google >> > Groups >> > "votca" group. >> > To unsubscribe from this group and stop receiving emails from it, send >> > an >> > email to [email protected]. >> > To post to this group, send email to [email protected]. >> > Visit this group at http://groups.google.com/group/votca. >> > For more options, visit https://groups.google.com/groups/opt_out. >> >> >> >> -- >> Christoph Junghans >> Web: http://www.compphys.de > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To post to this group, send email to [email protected]. > Visit this group at http://groups.google.com/group/votca. > For more options, visit https://groups.google.com/groups/opt_out. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/votca. For more options, visit https://groups.google.com/groups/opt_out.
