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] <javascript:>> 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] <javascript:>.
> > To post to this group, send email to [email protected]
> <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 [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.
