Hi Christoph: This is the new CMakeError.log: Determining if the function GromacsVersion exists in the /gpfs/home/lsd001/GROMACS/lib/libgmx_d.so; failed with the following output: Change Dir: /gpfs/home/lsd001/votca_csg/src/csg/CMakeFiles/CMakeTmp Run Build Command:/usr/bin/gmake "cmTryCompileExec3655553290/fast" /usr/bin/gmake -f CMakeFiles/cmTryCompileExec3655553290.dir/build.make CMakeFiles/cmTryCompileExec3655553290.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/cmTryCompileExec3655553290.dir/CheckFunctionExists.c.o /usr/bin/cc -DCHECK_FUNCTION_EXISTS=GromacsVersion -o CMakeFiles/cmTryCompileExec3655553290.dir/CheckFunctionExists.c.o -c /usr/local/share/cmake-2.8/Modules/CheckFunctionExists.c gmake[1]: *** No rule to make target `/gpfs/home/lsd001/GROMACS/lib/libgmx_d.so', needed by `cmTryCompileExec3655553290'. Stop. gmake[1]: Leaving directory `/gpfs/home/lsd001/votca_csg/src/csg/CMakeFiles/CMakeTmp' gmake: *** [cmTryCompileExec3655553290/fast] Error 2 在 2013年11月19日星期二UTC+8上午6时45分05秒，Christoph Junghans写道：
> 2013/11/17 Zhicheng <[email protected] <javascript:>>: > > 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] <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. 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.
