On Tue, Apr 2, 2019 at 1:48 PM Mohammad Motevaselian <[email protected]> wrote: > > Dear Christoph, > Update on installing VOTCA master branch on Blue Waters cluster: > > So I have manged to make the cmake working and figured out the BOOST library > error from "make -j 32" by manually specifying it to the cmake command ( > which is strange because cmake automatically was able to find the Boost > Package). Sorry, can you give some details on how exactly you fixed it? Which cmake option did you use?
> But I am getting the following error while doing "make -j 32": libacml.so is the AMD math library, I am not sure why this gets pulled. My guess is libgromacs needs it, can you do a $ ldd /path/to/libgromacs.so to see if libacml show up. A fix could be to find libacml.so and at its path to LD_LIBRARY_PATH. Christoph > > [ 37%] Building CXX object > csg/src/libcsg/CMakeFiles/votca_csg.dir/version.cc.o > [ 38%] Linking CXX shared library libvotca_moo.so > [ 38%] Building CXX object > csg/src/libcsg/CMakeFiles/votca_csg.dir/potentialfunctions/potentialfunction.cc.o > [ 39%] Building CXX object > csg/src/libcsg/CMakeFiles/votca_csg.dir/potentialfunctions/potentialfunctioncbspl.cc.o > [ 39%] Building CXX object > csg/src/libcsg/CMakeFiles/votca_csg.dir/potentialfunctions/potentialfunctionlj126.cc.o > [ 39%] Built target votca_property > [ 39%] Building CXX object > csg/src/libcsg/CMakeFiles/votca_csg.dir/potentialfunctions/potentialfunctionljg.cc.o > [ 39%] Built target votca_moo > [ 40%] Building CXX object > csg/src/libcsg/CMakeFiles/votca_csg.dir/modules/io/gmxtopologyreader.cc.o > [ 40%] Linking CXX shared library libvotca_kmc.so > [ 40%] Building CXX object > csg/src/libcsg/CMakeFiles/votca_csg.dir/modules/io/gmxtrajectoryreader.cc.o > [ 41%] Building CXX object > csg/src/libcsg/CMakeFiles/votca_csg.dir/modules/io/gmxtrajectorywriter.cc.o > Scanning dependencies of target votca_property_manpage > [ 41%] Building votca_property manpage > ./votca_property: error while loading shared libraries: libacml.so: cannot > open shared object file: No such file or directory > make[2]: *** [tools/src/tools/votca_property.man] Error 127 > make[2]: *** Deleting file `tools/src/tools/votca_property.man' > make[1]: *** [tools/src/tools/CMakeFiles/votca_property_manpage.dir/all] > Error 2 > make[1]: *** Waiting for unfinished jobs.... > [ 41%] Building CXX object > csg/src/libcsg/CMakeFiles/votca_csg.dir/modules/io/dlpolytopologyreader.cc.o > [ 41%] Built target votca_kmc > [ 41%] Building CXX object > csg/src/libcsg/CMakeFiles/votca_csg.dir/modules/io/dlpolytrajectoryreader.cc.o > [ 42%] Building CXX object > csg/src/libcsg/CMakeFiles/votca_csg.dir/modules/io/dlpolytrajectorywriter.cc.o > [ 42%] Building CXX object > csg/src/libcsg/CMakeFiles/votca_csg.dir/modules/io/groreader.cc.o > [ 43%] Building CXX object > csg/src/libcsg/CMakeFiles/votca_csg.dir/modules/io/growriter.cc.o > [ 43%] Building CXX object > csg/src/libcsg/CMakeFiles/votca_csg.dir/modules/io/lammpsdatareader.cc.o > [ 43%] Building CXX object > csg/src/libcsg/CMakeFiles/votca_csg.dir/modules/io/lammpsdumpreader.cc.o > [ 44%] Building CXX object > csg/src/libcsg/CMakeFiles/votca_csg.dir/modules/io/lammpsdumpwriter.cc.o > [ 44%] Building CXX object > csg/src/libcsg/CMakeFiles/votca_csg.dir/modules/io/pdbreader.cc.o > [ 45%] Building CXX object > csg/src/libcsg/CMakeFiles/votca_csg.dir/modules/io/pdbwriter.cc.o > [ 45%] Building CXX object > csg/src/libcsg/CMakeFiles/votca_csg.dir/modules/io/xmltopologyreader.cc.o > [ 46%] Building CXX object > csg/src/libcsg/CMakeFiles/votca_csg.dir/modules/io/xyzreader.cc.o > [ 46%] Building CXX object > csg/src/libcsg/CMakeFiles/votca_csg.dir/modules/io/xyzwriter.cc.o > [ 46%] Linking CXX shared library libvotca_csg.so > [ 46%] Built target votca_csg > make: *** [all] Error 2 > > I have no idea how to fix this. I would really appreciate any help on this. > Sincerely, > Hossein > > On Sunday, March 31, 2019 at 6:50:11 PM UTC-5, Mohammad Motevaselian wrote: >> >> By looking at the output of the cmake process, the Boost libraries were >> found. Only during the make command the error appears. >> I will try to do cmake again by manually specifying the boost_root and see >> if it works. Also I did do make VERBOSE=1, here is the output: >> >> /mnt/a/sw/xe/cmake/3.9.4/sles11.3_gnu4.9.3/bin/cmake >> -H/u/sciteam/motevase/application/install/votca >> -B/u/sciteam/motevase/application/install/votca/build --check-build-system >> CMakeFiles/Makefile.cmake 0 >> /mnt/a/sw/xe/cmake/3.9.4/sles11.3_gnu4.9.3/bin/cmake -E cmake_progress_start >> /u/sciteam/motevase/application/install/votca/build/CMakeFiles >> /u/sciteam/motevase/application/install/votca/build/CMakeFiles/progress.marks >> make -f CMakeFiles/Makefile2 all >> make[1]: Entering directory >> `/mnt/a/u/sciteam/motevase/application/install/votca/build' >> make -f ctp/src/libkmc/CMakeFiles/gitversion-kmc.dir/build.make >> ctp/src/libkmc/CMakeFiles/gitversion-kmc.dir/depend >> make[2]: Entering directory >> `/mnt/a/u/sciteam/motevase/application/install/votca/build' >> cd /u/sciteam/motevase/application/install/votca/build && >> /mnt/a/sw/xe/cmake/3.9.4/sles11.3_gnu4.9.3/bin/cmake -E cmake_depends "Unix >> Makefiles" /u/sciteam/motevase/application/install/votca >> /u/sciteam/motevase/application/install/votca/ctp/src/libkmc >> /u/sciteam/motevase/application/install/votca/build >> /u/sciteam/motevase/application/install/votca/build/ctp/src/libkmc >> /u/sciteam/motevase/application/install/votca/build/ctp/src/libkmc/CMakeFiles/gitversion-kmc.dir/DependInfo.cmake >> --color= >> make[2]: Leaving directory >> `/mnt/a/u/sciteam/motevase/application/install/votca/build' >> make -f ctp/src/libkmc/CMakeFiles/gitversion-kmc.dir/build.make >> ctp/src/libkmc/CMakeFiles/gitversion-kmc.dir/build >> make[2]: Entering directory >> `/mnt/a/u/sciteam/motevase/application/install/votca/build' >> cd /u/sciteam/motevase/application/install/votca/build/ctp/src/libkmc && >> /mnt/a/sw/xe/cmake/3.9.4/sles11.3_gnu4.9.3/bin/cmake >> -DTOP_SOURCE_DIR="/u/sciteam/motevase/application/install/votca" >> -DGIT_EXECUTABLE="/sw/EasyBuild/software/git/2.17.0/bin/git" -P >> /u/sciteam/motevase/application/install/votca/ctp/CMakeModules/gitversion.cmake >> Current git revision is b2da0c7 >> make[2]: Leaving directory >> `/mnt/a/u/sciteam/motevase/application/install/votca/build' >> [ 0%] Built target gitversion-kmc >> make -f tools/src/libtools/CMakeFiles/gitversion.dir/build.make >> tools/src/libtools/CMakeFiles/gitversion.dir/depend >> make[2]: Entering directory >> `/mnt/a/u/sciteam/motevase/application/install/votca/build' >> cd /u/sciteam/motevase/application/install/votca/build && >> /mnt/a/sw/xe/cmake/3.9.4/sles11.3_gnu4.9.3/bin/cmake -E cmake_depends "Unix >> Makefiles" /u/sciteam/motevase/application/install/votca >> /u/sciteam/motevase/application/install/votca/tools/src/libtools >> /u/sciteam/motevase/application/install/votca/build >> /u/sciteam/motevase/application/install/votca/build/tools/src/libtools >> /u/sciteam/motevase/application/install/votca/build/tools/src/libtools/CMakeFiles/gitversion.dir/DependInfo.cmake >> --color= >> make[2]: Leaving directory >> `/mnt/a/u/sciteam/motevase/application/install/votca/build' >> make -f tools/src/libtools/CMakeFiles/gitversion.dir/build.make >> tools/src/libtools/CMakeFiles/gitversion.dir/build >> make[2]: Entering directory >> `/mnt/a/u/sciteam/motevase/application/install/votca/build' >> cd /u/sciteam/motevase/application/install/votca/build/tools/src/libtools && >> /mnt/a/sw/xe/cmake/3.9.4/sles11.3_gnu4.9.3/bin/cmake >> -DTOP_SOURCE_DIR="/u/sciteam/motevase/application/install/votca" >> -DGIT_EXECUTABLE="/sw/EasyBuild/software/git/2.17.0/bin/git" >> -DMERCURIAL_EXECUTABLE="" -P >> /u/sciteam/motevase/application/install/votca/tools/CMakeModules/gitversion.cmake >> Current git revision is b2da0c7 >> make[2]: Leaving directory >> `/mnt/a/u/sciteam/motevase/application/install/votca/build' >> [ 0%] Built target gitversion >> make -f tools/src/libtools/CMakeFiles/votca_tools.dir/build.make >> tools/src/libtools/CMakeFiles/votca_tools.dir/depend >> make[2]: Entering directory >> `/mnt/a/u/sciteam/motevase/application/install/votca/build' >> cd /u/sciteam/motevase/application/install/votca/build && >> /mnt/a/sw/xe/cmake/3.9.4/sles11.3_gnu4.9.3/bin/cmake -E cmake_depends "Unix >> Makefiles" /u/sciteam/motevase/application/install/votca >> /u/sciteam/motevase/application/install/votca/tools/src/libtools >> /u/sciteam/motevase/application/install/votca/build >> /u/sciteam/motevase/application/install/votca/build/tools/src/libtools >> /u/sciteam/motevase/application/install/votca/build/tools/src/libtools/CMakeFiles/votca_tools.dir/DependInfo.cmake >> --color= >> make[2]: Leaving directory >> `/mnt/a/u/sciteam/motevase/application/install/votca/build' >> make -f tools/src/libtools/CMakeFiles/votca_tools.dir/build.make >> tools/src/libtools/CMakeFiles/votca_tools.dir/build >> make[2]: Entering directory >> `/mnt/a/u/sciteam/motevase/application/install/votca/build' >> [ 1%] Linking CXX shared library libvotca_tools.so >> cd /u/sciteam/motevase/application/install/votca/build/tools/src/libtools && >> /mnt/a/sw/xe/cmake/3.9.4/sles11.3_gnu4.9.3/bin/cmake -E cmake_link_script >> CMakeFiles/votca_tools.dir/link.txt --verbose=1 >> /opt/cray/craype/2.5.8/bin/CC -O3 -DNDEBUG -shared >> -Wl,-soname,libvotca_tools.so.6 -o libvotca_tools.so.6 >> CMakeFiles/votca_tools.dir/akimaspline.cc.o >> CMakeFiles/votca_tools.dir/application.cc.o >> CMakeFiles/votca_tools.dir/colors.cc.o >> CMakeFiles/votca_tools.dir/correlate.cc.o >> CMakeFiles/votca_tools.dir/crosscorrelate.cc.o >> CMakeFiles/votca_tools.dir/cubicspline.cc.o >> CMakeFiles/votca_tools.dir/datacollection.cc.o >> CMakeFiles/votca_tools.dir/edge.cc.o >> CMakeFiles/votca_tools.dir/edgecontainer.cc.o >> CMakeFiles/votca_tools.dir/elements.cc.o >> CMakeFiles/votca_tools.dir/globals.cc.o >> CMakeFiles/votca_tools.dir/graph.cc.o >> CMakeFiles/votca_tools.dir/graph_bf_visitor.cc.o >> CMakeFiles/votca_tools.dir/graph_df_visitor.cc.o >> CMakeFiles/votca_tools.dir/graphalgorithm.cc.o >> CMakeFiles/votca_tools.dir/graphdistvisitor.cc.o >> CMakeFiles/votca_tools.dir/graphnode.cc.o >> CMakeFiles/votca_tools.dir/graphvisitor.cc.o >> CMakeFiles/votca_tools.dir/histogram.cc.o >> CMakeFiles/votca_tools.dir/histogramnew.cc.o >> CMakeFiles/votca_tools.dir/linalg.cc.o >> CMakeFiles/votca_tools.dir/linspline.cc.o >> CMakeFiles/votca_tools.dir/matrix.cc.o CMakeFiles/votca_tools.dir/mutex.cc.o >> CMakeFiles/votca_tools.dir/parcer.cc.o >> CMakeFiles/votca_tools.dir/parsexml.cc.o >> CMakeFiles/votca_tools.dir/property.cc.o >> CMakeFiles/votca_tools.dir/propertyiomanipulator.cc.o >> CMakeFiles/votca_tools.dir/random2.cc.o >> CMakeFiles/votca_tools.dir/rangeparser.cc.o >> CMakeFiles/votca_tools.dir/reducededge.cc.o >> CMakeFiles/votca_tools.dir/reducedgraph.cc.o >> CMakeFiles/votca_tools.dir/spline.cc.o CMakeFiles/votca_tools.dir/table.cc.o >> CMakeFiles/votca_tools.dir/thread.cc.o >> CMakeFiles/votca_tools.dir/tokenizer.cc.o >> CMakeFiles/votca_tools.dir/version.cc.o >> CMakeFiles/votca_tools.dir/database.cc.o >> CMakeFiles/votca_tools.dir/statement.cc.o -lboost_program_options >> -lboost_filesystem -lboost_system -lmkl_rt >> /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 >> -lsqlite3 -lfftw3f -lexpat -lm >> /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[2]: Leaving directory >> `/mnt/a/u/sciteam/motevase/application/install/votca/build' >> make[1]: *** [tools/src/libtools/CMakeFiles/votca_tools.dir/all] Error 2 >> make[1]: Leaving directory >> `/mnt/a/u/sciteam/motevase/application/install/votca/build' >> make: *** [all] Error 2 >> >> Regards, >> Hossein >> >> >> On Sunday, March 31, 2019 at 5:59:04 PM UTC-5, Christoph Junghans wrote: >>> >>> 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. -- 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.
