I finally got it installed !
Next step is to add some codes and changes to the main C++ codes, mainly
relative entropy.
I will keep you posted if any question pops up.
Thanks again for your prompt responses.
Sincerely,
Hossein
On Tuesday, April 2, 2019 at 3:14:22 PM UTC-5, Christoph Junghans wrote:
>
> 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
> <h.mote...@gmail.com <javascript:>> 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
> >> <h.mote...@gmail.com> 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
> >> >>> <h.mote...@gmail.com> 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
> >> >>> >> <h.mote...@gmail.com> 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 <
> h.mote...@gmail.com> 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 vo...@googlegroups.com.
> >> >>> >> >>> To post to this group, send email to vo...@googlegroups.com.
>
> >> >>> >> >>> 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 vo...@googlegroups.com.
> >> >>> >> > To post to this group, send email to vo...@googlegroups.com.
> >> >>> >> > 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 vo...@googlegroups.com.
> >> >>> > To post to this group, send email to vo...@googlegroups.com.
> >> >>> > 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 vo...@googlegroups.com.
> >> > To post to this group, send email to vo...@googlegroups.com.
> >> > 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 vo...@googlegroups.com <javascript:>.
> > To post to this group, send email to vo...@googlegroups.com
> <javascript:>.
> > 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 votca+unsubscr...@googlegroups.com.
To post to this group, send email to votca@googlegroups.com.
Visit this group at https://groups.google.com/group/votca.
For more options, visit https://groups.google.com/d/optout.
