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 ?
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] <javascript:>> 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] <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
>
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