On Sun, Mar 31, 2019 at 4:30 PM Mohammad Motevaselian <[email protected]> wrote: > > So with > -DGROMACS_INCLUDE_DIR=/u/sciteam/motevase/application/gromacs-2019.1/include/ > cmake is able to find the gromacs version, so that is good. > But it gives error for not finding LIB_XTP and the XTP related stuff. I > turned the flag off by using -DBUILD_XTP=OFF and the configuration is done. > But when I do make -j 12, the following error pops up: > [ 0%] Built target gitversion > [ 0%] Built target gitversion-kmc > [ 0%] Built target gitversion-moo > [ 0%] Built target gitversion-ctp > [ 0%] Built target gitversion-csg > [ 0%] Built target csg_inverse_build > [ 1%] Built target votca_compare_build > [ 1%] Built target votca_tools_manpages > [ 1%] Built target csg_call_build > Current git revision is b2da0c7 > Current git revision is b2da0c7 > [ 1%] Built target ctp_update > [ 1%] Built target ctp_testsuite > [ 2%] Linking CXX shared library libvotca_tools.so > /usr/bin/ld: cannot find -lboost_program_options > /usr/bin/ld: cannot find -lboost_filesystem > /usr/bin/ld: cannot find -lboost_system > /usr/bin/ld: cannot find -lmkl_rt > /usr/bin/sha1sum: libvotca_tools.so.6: No such file or directory > collect2: error: ld returned 1 exit status > make[2]: *** [tools/src/libtools/libvotca_tools.so.6] Error 1 > make[1]: *** [tools/src/libtools/CMakeFiles/votca_tools.dir/all] Error 2 > make: *** [all] Error 2 > > I have already specified an installation path for CMAKE via ${prefix} > variable. Is it trying to install VOTCA in /usr/bin ? This has nothing to do with the prefix, that is only used during "make install".
For relevant error is: > /usr/bin/ld: cannot find -lboost_program_options > /usr/bin/ld: cannot find -lboost_filesystem > /usr/bin/ld: cannot find -lboost_system > /usr/bin/ld: cannot find -lmkl_rt which means the linker (/usr/bin/ld) was not able to find your boost libraries. You can run "make VERBOSE=1" to see what command actually triggers the issue. Christoph > > Regards, > Hossein > > > > On Sunday, March 31, 2019 at 5:07:02 PM UTC-5, Christoph Junghans wrote: >> >> I looked at the original error message again >> Could NOT find GROMACS: Found unsuitable version "0", but required is at >> least "20160000" (found >> /u/sciteam/motevase/application/gromacs-2019.1/lib64/libgromacs_mpi.so) >> >> It seems the gromacs version could not be detected correctly? >> Can you try >> -DGROMACS_INCLUDE_DIR=/u/sciteam/motevase/application/gromacs-2019.1/include >> (with the /gromacs at the end)? >> >> Christoph >> >> On Sun, Mar 31, 2019 at 3:21 PM Mohammad Motevaselian >> <[email protected]> wrote: >> > >> > Thank for your prompt response. When I looked at the Blue Water's >> > compiling page (https://bluewaters.ncsa.illinois.edu/compiling), they >> > mentioned " ... do NOT use mpicc (for instance) to compile MPI codes, the >> > cc or CC wrapper already contains the proper compiler and library >> > invocations." >> > That's why I have the follwoing in my installation script: >> > export CC=cc >> > export CXX=CC >> > >> > I have also looked at the CMakeError.log, but I can't figured out what's >> > the problem. Below is the CMakeError.log content. >> > Any ideas how to fix the error? >> > >> > Performing C SOURCE FILE Test HAVE_AIX failed with the following output: >> > Change Dir: >> > /u/sciteam/motevase/application/install/votca/build/CMakeFiles/CMakeTmp >> > >> > Run Build Command:"/usr/bin/gmake" "cmTC_f612b/fast" >> > /usr/bin/gmake -f CMakeFiles/cmTC_f612b.dir/build.make >> > CMakeFiles/cmTC_f612b.dir/build >> > gmake[1]: Entering directory >> > `/mnt/a/u/sciteam/motevase/application/install/votca/build/CMakeFiles/CMakeTmp' >> > Building C object CMakeFiles/cmTC_f612b.dir/src.c.o >> > /opt/cray/craype/2.5.8/bin/cc -DHAVE_AIX -o >> > CMakeFiles/cmTC_f612b.dir/src.c.o -c >> > /u/sciteam/motevase/application/install/votca/build/CMakeFiles/CMakeTmp/src.c >> > /u/sciteam/motevase/application/install/votca/build/CMakeFiles/CMakeTmp/src.c: >> > In function 'main': >> > /u/sciteam/motevase/application/install/votca/build/CMakeFiles/CMakeTmp/src.c:3:8: >> > error: #error >> > #error >> > ^ >> > gmake[1]: *** [CMakeFiles/cmTC_f612b.dir/src.c.o] Error 1 >> > gmake[1]: Leaving directory >> > `/mnt/a/u/sciteam/motevase/application/install/votca/build/CMakeFiles/CMakeTmp' >> > gmake: *** [cmTC_f612b/fast] Error 2 >> > >> > Source file was: >> > int main(void) { >> > #ifndef _AIX >> > #error >> > #endif >> > return 0; >> > } >> > Determining if the function gmx_is_double_precision exists in the >> > /u/sciteam/motevase/application/gromacs-2019.1/lib64/libgromacs_mpi.so >> > failed with the following output: >> > Change Dir: >> > /u/sciteam/motevase/application/install/votca/build/CMakeFiles/CMakeTmp >> > >> > Run Build Command:"/usr/bin/gmake" "cmTC_7fa2f/fast" >> > /usr/bin/gmake -f CMakeFiles/cmTC_7fa2f.dir/build.make >> > CMakeFiles/cmTC_7fa2f.dir/build >> > gmake[1]: Entering directory >> > `/mnt/a/u/sciteam/motevase/application/install/votca/build/CMakeFiles/CMakeTmp' >> > Building CXX object CMakeFiles/cmTC_7fa2f.dir/CheckFunctionExists.cpp.o >> > /opt/cray/craype/2.5.8/bin/CC >> > -DCHECK_FUNCTION_EXISTS=gmx_is_double_precision -o >> > CMakeFiles/cmTC_7fa2f.dir/CheckFunctionExists.cpp.o -c >> > /u/sciteam/motevase/application/install/votca/csg/CMakeModules/CheckFunctionExists.cpp >> > Linking CXX executable cmTC_7fa2f >> > /mnt/a/sw/xe/cmake/3.9.4/sles11.3_gnu4.9.3/bin/cmake -E cmake_link_script >> > CMakeFiles/cmTC_7fa2f.dir/link.txt --verbose=1 >> > /opt/cray/craype/2.5.8/bin/CC >> > -DCHECK_FUNCTION_EXISTS=gmx_is_double_precision -dynamic >> > CMakeFiles/cmTC_7fa2f.dir/CheckFunctionExists.cpp.o -o cmTC_7fa2f >> > -Wl,-rpath,/u/sciteam/motevase/application/gromacs-2019.1/lib64 >> > /u/sciteam/motevase/application/gromacs-2019.1/lib64/libgromacs_mpi.so >> > CMakeFiles/cmTC_7fa2f.dir/CheckFunctionExists.cpp.o: In function `main': >> > CheckFunctionExists.cpp:(.text+0x10): undefined reference to >> > `gmx_is_double_precision()' >> > /usr/bin/ld: link errors found, deleting executable `cmTC_7fa2f' >> > /usr/bin/sha1sum: cmTC_7fa2f: No such file or directory >> > collect2: error: ld returned 1 exit status >> > gmake[1]: *** [cmTC_7fa2f] Error 1 >> > gmake[1]: Leaving directory >> > `/mnt/a/u/sciteam/motevase/application/install/votca/build/CMakeFiles/CMakeTmp' >> > gmake: *** [cmTC_7fa2f/fast] Error 2 >> > >> > Thanks again. >> > Hossein >> > >> > >> > On Sunday, March 31, 2019 at 4:06:09 PM UTC-5, Christoph Junghans wrote: >> >> >> >> >> >> >> >> On Sun, Mar 31, 2019 at 14:57 Mohammad Motevaselian <[email protected]> >> >> wrote: >> >>> >> >>> Hi, >> >>> >> >>> I am trying to install VOTCA software on Blue waters cluster. Below is >> >>> my installation script: >> >>> >> >>> module swap PrgEnv-cray PrgEnv-gnu >> >>> module add cmake/3.9.4 >> >>> module add fftw >> >>> module add boost/1.63.0 >> >>> module add intel/18.0.3.222 >> >>> module add cblas >> >>> export CRAYPE_LINK_TYPE=dynamic >> >>> export CRAY_ADD_RPATH=yes >> >>> export CC=cc >> >>> export CXX=CC >> >>> export FC=ftn >> >>> >> >>> prefix=/u/sciteam/motevase/application/install/votca-master/ >> >>> version=master >> >>> git clone -b ${version} --recursive https://github.com/votca/votca.git >> >>> cd votca >> >>> mkdir build >> >>> cd build >> >>> path_eigen3=/u/sciteam/motevase/application/eigen3.3.7/include/eigen3 >> >>> cmake -DBUILD_CSGAPPS=ON -DBUILD_CTP=ON -DBUILD_XTP=ON >> >>> -DEIGEN3_INCLUDE_DIR=${path_eigen3} -DFFTW3_INCLUDE_DIR=$FFTW_INC >> >>> -DFFTW3_LIBRARY=$FFTW_DIR/libfftw3f.so >> >>> -DGROMACS_LIBRARY=/u/sciteam/motevase/application/gromacs-2019.1/lib64/libgromacs_mpi.so >> >>> >> >>> -DGROMACS_INCLUDE_DIR=/u/sciteam/motevase/application/gromacs-2019.1/include/gromacs >> >>> -DCMAKE_INSTALL_PREFIX=${prefix} .. >> >>> >> >>> >> >>> But I am getting the following error: >> >>> >> >>> Fault line: DOTFILE_DIRS = >> >>> Call Stack (most recent call first): >> >>> tools/share/doc/CMakeLists.txt:1 (find_package) >> >>> This warning is for project developers. Use -Wno-dev to suppress it. >> >>> >> >>> -- Could NOT find TXT2TAGS (missing: TXT2TAGS_EXECUTABLE) >> >>> txt2tags not found, help cmake to find it by setting TXT2TAGS_EXECUTABLE >> >>> -- Boost version: 1.63.0 >> >>> -- Found the following Boost libraries: >> >>> -- program_options >> >>> -- filesystem >> >>> -- system >> >>> -- Checking for module 'libvotca_tools' >> >>> -- Package 'fftw3', required by 'libvotca_tools', not found >> >>> -- Intel(R) MKL was found: >> >>> MKL_INCLUDE_DIRS: >> >>> /opt/intel/compilers_and_libraries_2018.3.222/linux/mkl/include >> >>> MKL_LIBRARY_DIRS: >> >>> /opt/intel/compilers_and_libraries_2018.3.222/linux/mkl/lib/intel64;/opt/intel/compilers_and_libraries_2018.3.222/linux/compiler/lib/intel64 >> >>> MKL_LIBRARIES: >> >>> /opt/intel/compilers_and_libraries_2018.3.222/linux/mkl/lib/intel64/libmkl_rt.so;/opt/intel/compilers_and_libraries_2018.3.222/linux/compiler/lib/intel64/libiomp5.so;/opt/intel/compilers_and_libraries_2018.3.222/linux/compiler/lib/intel64/libimf.so >> >>> -- Checking for module 'sqlite3' >> >>> -- Found sqlite3, version 3.7.6.3 >> >>> -- Checking for module 'libgromacs_d' >> >>> -- No package 'libgromacs_d' found >> >>> -- Checking for module 'libgromacs' >> >>> -- No package 'libgromacs' found >> >>> CMake Error at >> >>> /mnt/a/sw/xe/cmake/3.9.4/sles11.3_gnu4.9.3/share/cmake-3.9/Modules/FindPackageHandleStandardArgs.cmake:137 >> >>> (message): >> >>> Could NOT find GROMACS: Found unsuitable version "0", but required is >> >>> at >> >>> least "20160000" (found >> >>> /u/sciteam/motevase/application/gromacs-2019.1/lib64/libgromacs_mpi.so) >> >>> Call Stack (most recent call first): >> >>> >> >>> /mnt/a/sw/xe/cmake/3.9.4/sles11.3_gnu4.9.3/share/cmake-3.9/Modules/FindPackageHandleStandardArgs.cmake:375 >> >>> (_FPHSA_FAILURE_MESSAGE) >> >>> csg/CMakeModules/FindGROMACS.cmake:76 >> >>> (find_package_handle_standard_args) >> >>> csg/CMakeLists.txt:85 (find_package) >> >>> >> >>> >> >>> -- Configuring incomplete, errors occurred! >> >>> See also >> >>> "/u/sciteam/motevase/application/install/votca/build/CMakeFiles/CMakeOutput.log". >> >>> See also >> >>> "/u/sciteam/motevase/application/install/votca/build/CMakeFiles/CMakeError.log". >> >>> >> >>> It seems the error is due to the version of gromacs, but I am using >> >>> Gromacs 2019.1. >> >>> I would appreciate you help on this. >> >> >> >> >> >> >> >> You should have a look at your CMakeError.log, but my guess is that if >> >> you want to use an mpi-enable libgromacs you need to use an mpi compiler. >> >> >> >> I would recommend using a serial libgromacs. >> >> >> >> Christoph >> >>> >> >>> >> >>> Sincerely, >> >>> Hossein >> >>> >> >>> -- >> >>> 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 https://groups.google.com/group/votca. >> >>> For more options, visit https://groups.google.com/d/optout. >> >> >> >> -- >> >> 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 https://groups.google.com/group/votca. >> > For more options, visit https://groups.google.com/d/optout. >> >> >> >> -- >> 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 https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- 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 https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
