Hi Christoph: Adding /usr/lib/libpthread.so to GROMACS_DEP_LIBRARY, however, I find the same error mentioned above . Does it need more dependencies?
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] <javascript:>>: > > 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] <javascript:>. > > To post to this group, send email to [email protected]<javascript:>. > > > 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. 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