I guess you don't need ctp, so add -DBUILD_CTP=OFF to your options. You could also try to compile with mkl, with -DCMAKE_DISABLE_FIND_PACKAGE_MKL=ON.
Christoph On Tue, Apr 2, 2019 at 2:10 PM Mohammad Motevaselian <[email protected]> wrote: > > I just specified the BOOST path to the cmake. Also I thought the error that I > just posted was due to the manpages so I set it's flag off and it seemed it > was working until I get the following error: > > /sw/xe/gsl/1.16-2015-04/cnl5.2_gnu4.8.2/include/gsl/gsl_blas_types.h:46:45: > error: invalid type in declaration before ';' token > typedef enum CBLAS_DIAG CBLAS_DIAG_t; > ^ > /sw/xe/gsl/1.16-2015-04/cnl5.2_gnu4.8.2/include/gsl/gsl_blas_types.h:47:15: > error: using typedef-name 'CBLAS_SIDE' after 'enum' > typedef enum CBLAS_SIDE CBLAS_SIDE_t; > ^ > In file included from > /opt/intel/compilers_and_libraries_2018.3.222/linux/mkl/include/mkl.h:31:0, > from > /u/sciteam/motevase/application/install/votca/tools/include/votca/tools/eigen.h:26, > from > /u/sciteam/motevase/application/install/votca/tools/include/votca/tools/vec.h:26, > from > /u/sciteam/motevase/application/install/votca/ctp/include/votca/ctp/qmatom.h:26, > from > /u/sciteam/motevase/application/install/votca/ctp/include/votca/ctp/orbitals.h:25, > from > /u/sciteam/motevase/application/install/votca/ctp/include/votca/ctp/overlap.h:21, > from > /u/sciteam/motevase/application/install/votca/ctp/src/libctp/overlap.cc:23: > /opt/intel/compilers_and_libraries_2018.3.222/linux/mkl/include/mkl_cblas.h:46:46: > note: 'CBLAS_SIDE' has a previous declaration here > typedef enum {CblasLeft=141, CblasRight=142} CBLAS_SIDE; > ^ > In file included from > /sw/xe/gsl/1.16-2015-04/cnl5.2_gnu4.8.2/include/gsl/gsl_blas.h:29:0, > from > /u/sciteam/motevase/application/install/votca/ctp/include/votca/ctp/eigen.h:32, > from > /u/sciteam/motevase/application/install/votca/ctp/include/votca/ctp/linalg.h:33, > from > /u/sciteam/motevase/application/install/votca/ctp/src/libctp/overlap.cc:24: > /sw/xe/gsl/1.16-2015-04/cnl5.2_gnu4.8.2/include/gsl/gsl_blas_types.h:47:45: > error: invalid type in declaration before ';' token > typedef enum CBLAS_SIDE CBLAS_SIDE_t; > ^ > [ 87%] Building CXX object > ctp/src/libctp/CMakeFiles/votca_ctp.dir/segment.cc.o > [ 87%] Building CXX object > ctp/src/libctp/CMakeFiles/votca_ctp.dir/sqlapplication.cc.o > make[2]: *** [ctp/src/libctp/CMakeFiles/votca_ctp.dir/overlap.cc.o] Error 1 > make[2]: *** Waiting for unfinished jobs.... > make[1]: *** [ctp/src/libctp/CMakeFiles/votca_ctp.dir/all] Error 2 > make: *** [all] Error 2 > > There is not enough description about the error. Any idea as what I can do to > fix this? Below is my cmake command: > > cmake -DBUILD_CSGAPPS=ON -DBUILD_CTP=ON -DBUILD_XTP=OFF -DBUILD_MANPAGES=OFF > -DEIGEN3_INCLUDE_DIR=${path_eigen3} -DFFTW3_INCLUDE_DIR=$FFTW_INC > -DFFTW3_LIBRARY=$FFTW_DIR/libfftw3f.so -DBOOST_ROOT=$BOOST_ROOT > -DGROMACS_LIBRARY=/u/sciteam/motevase/application/gromacs-2019.1/lib64/libgromacs_mpi.so > > -DGROMACS_INCLUDE_DIR=/u/sciteam/motevase/application/gromacs-2019.1/include/ > -DCMAKE_INSTALL_PREFIX=${prefix} .. > > By the way, this the output of ldd: > linux-vdso.so.1 => (0x00002aaaaaaab000) > libdl.so.2 => /lib64/libdl.so.2 (0x00002aaaac226000) > librt.so.1 => /lib64/librt.so.1 (0x00002aaaac42a000) > librca.so.0 => /opt/cray/rca/1.0.0-2.0502.60530.1.63.gem/lib64/librca.so.0 > (0x00002aaaac634000) > libz.so.1 => /lib64/libz.so.1 (0x00002aaaac838000) > libfftw3f_mpi.so.mpi31.3 => > /opt/cray/fftw/3.3.4.10/interlagos/lib/libfftw3f_mpi.so.mpi31.3 > (0x00002aaaaca4e000) > libfftw3f_threads.so.mpi31.3 => > /opt/cray/fftw/3.3.4.10/interlagos/lib/libfftw3f_threads.so.mpi31.3 > (0x00002aaaacc65000) > libfftw3f.so.mpi31.3 => > /opt/cray/fftw/3.3.4.10/interlagos/lib/libfftw3f.so.mpi31.3 > (0x00002aaaace6b000) > libfftw3_mpi.so.mpi31.3 => > /opt/cray/fftw/3.3.4.10/interlagos/lib/libfftw3_mpi.so.mpi31.3 > (0x00002aaaad28f000) > libfftw3_threads.so.mpi31.3 => > /opt/cray/fftw/3.3.4.10/interlagos/lib/libfftw3_threads.so.mpi31.3 > (0x00002aaaad4a6000) > libfftw3.so.mpi31.3 => > /opt/cray/fftw/3.3.4.10/interlagos/lib/libfftw3.so.mpi31.3 > (0x00002aaaad6ac000) > libmpich_gnu_49.so.3 => > /opt/cray/mpt/7.5.0/gni/mpich-gnu/4.9/lib/libmpich_gnu_49.so.3 > (0x00002aaaadaa9000) > libm.so.6 => /lib64/libm.so.6 (0x00002aaaae03d000) > libpthread.so.0 => /lib64/libpthread.so.0 (0x00002aaaae2b6000) > libstdc++.so.6 => /opt/gcc/4.9.3/snos/lib64/libstdc++.so.6 > (0x00002aaaae4d3000) > libgomp.so.1 => /opt/gcc/4.9.3/snos/lib64/libgomp.so.1 (0x00002aaaae7e4000) > libgcc_s.so.1 => /opt/gcc/4.9.3/snos/lib64/libgcc_s.so.1 (0x00002aaaae9fb000) > libc.so.6 => /lib64/libc.so.6 (0x00002aaaaec12000) > /lib64/ld-linux-x86-64.so.2 (0x0000555555554000) > libxpmem.so.0 => /opt/cray/xpmem/default/lib64/libxpmem.so.0 > (0x00002aaaaef8f000) > libugni.so.0 => /opt/cray/ugni/default/lib64/libugni.so.0 (0x00002aaaaf192000) > libudreg.so.0 => /opt/cray/udreg/default/lib64/libudreg.so.0 > (0x00002aaaaf3e8000) > libpmi.so.0 => /opt/cray/lib64/libpmi.so.0 (0x00002aaaaf5f1000) > > Regards, > Hossein > > On Tuesday, April 2, 2019 at 2:56:50 PM UTC-5, Christoph Junghans wrote: >> >> 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. -- 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.
