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.
