On Sun, Dec 20, 2020 at 9:03 AM nancyfor <[email protected]> wrote:
>
> Hi Christoph,
>
> In the gromacs installation(in
> /mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/share/cmake/gromacs/libgromacs_static.cmake)
> I found the libfftw3 that was used (I assume is the one in the following
> line)
> INTERFACE_LINK_LIBRARIES
> "\$<LINK_ONLY:>;\$<LINK_ONLY:rt>;/mpcdf/soft/SLE_12/packages/skylake/fftw/gcc_8-8.4.0-impi_2019.7-2019.7.217/3.3.7/lib/libfftw3f.a;\$<LINK_ONLY:-lpthread>;m;\$<LINK_ONLY:lmfit>"
The library is called libfftw3f.a, mind the f as the end, f stands for
single precision, while libfftw3.a (no f) is for double precision.
So you will need to do something like:
-DGROMACS_LIBRARY="/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a;/mpcdf/soft/SLE_12/packages/skylake/fftw/gcc_8-8.4.0-impi_2019.7-2019.7.217/3.3.7/lib/libfftw3f.a"
and you try to leave -DFFTW3 alone for now as the detecting work previously.
Are you planning to use gromacs for the cg runs or lammps? Otherwise
you could also build without gromacs (-DWITH_GMX=OFF
-DCMAKE_DISABLE_FIND_PACKAGE_GROMACS=ON
>
> So I tried two different things with the fftw, first the following where I
> list the gromacs dependencies
>
> cmake -Bbuilddir -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++
> -DBUILD_SHARED_LIBS=OFF -DBUILD_CSGAPPS=ON -DBUILD_XTP=OFF
> -DGROMACS_INCLUDE_DIR=/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/include/
>
> -DGROMACS_LIBRARY="/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a;/mpcdf/soft/SLE_12/packages/skylake/fftw/gcc_8-8.4.0-impi_2019.7-2019.7.217/3.3.7/lib/libfftw3.a"
> -DCMAKE_DISABLE_FIND_PACKAGE_MKL=ON -DCMAKE_INSTALL_PREFIX=${prefix} ../votca
>
> This is part of the output, the configuration was not complete:(attached
> CMakeOutput_1.log)
>
> -- Found FFTW3:
> /mpcdf/soft/SLE_12/packages/skylake/fftw/gcc_8-8.4.0-impi_2019.7-2019.7.217/3.3.7/lib/libfftw3.so
> -- Looking for fftw_plan_r2r_1d in
> /mpcdf/soft/SLE_12/packages/skylake/fftw/gcc_8-8.4.0-impi_2019.7-2019.7.217/3.3.7/lib/libfftw3.so;
> -- Looking for fftw_plan_r2r_1d in
> /mpcdf/soft/SLE_12/packages/skylake/fftw/gcc_8-8.4.0-impi_2019.7-2019.7.217/3.3.7/lib/libfftw3.so;
> - found
>
> and then explicitly using -DFFTW3_LIBRARY
>
> cmake -Bbuilddir -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++
> -DBUILD_SHARED_LIBS=OFF -DBUILD_CSGAPPS=ON -DBUILD_XTP=OFF
> -DFFTW3_INCLUDE_DIR=/mpcdf/soft/SLE_12/packages/skylake/fftw/gcc_8-8.4.0-impi_2019.7-2019.7.217/3.3.7/include
>
> -DFFTW3_LIBRARY=/mpcdf/soft/SLE_12/packages/skylake/fftw/gcc_8-8.4.0-impi_2019.7-2019.7.217/3.3.7/lib/libfftw3.a
>
> -DGROMACS_INCLUDE_DIR=/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/include/
>
> -DGROMACS_LIBRARY=/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a
> -DCMAKE_DISABLE_FIND_PACKAGE_MKL=ON -DCMAKE_INSTALL_PREFIX=${prefix}
> ../votca
>
> Here is the output (attached CMakeOutput_2.log)
>
> -- Found FFTW3:
> /mpcdf/soft/SLE_12/packages/skylake/fftw/gcc_8-8.4.0-impi_2019.7-2019.7.217/3.3.7/lib/libfftw3.a
> -- Looking for fftw_plan_r2r_1d in
> /mpcdf/soft/SLE_12/packages/skylake/fftw/gcc_8-8.4.0-impi_2019.7-2019.7.217/3.3.7/lib/libfftw3.a;
> -- Looking for fftw_plan_r2r_1d in
> /mpcdf/soft/SLE_12/packages/skylake/fftw/gcc_8-8.4.0-impi_2019.7-2019.7.217/3.3.7/lib/libfftw3.a;
> - not found
>
>
> So I gave up with this and tried votca building building gromacs but also got
> an error
>
> cmake -Bbuilddir -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++
> -DBUILD_SHARED_LIBS=OFF -DBUILD_CSGAPPS=ON -DBUILD_XTP=OFF
> -DBUILD_OWN_GROMACS=ON -DCMAKE_DISABLE_FIND_PACKAGE_MKL=ON
> -DCMAKE_INSTALL_PREFIX=${prefix} ../votca
>
> and
> cmake --build builddir gives me an error: (attached the output with --verbose)
>
> Scanning dependencies of target csg_gmxtopol
> [ 67%] Building CXX object
> csg/src/tools/CMakeFiles/csg_gmxtopol.dir/csg_gmxtopol.cc.o
> gmake[2]: *** No rule to make target 'gromacs/install/lib64/libgromacs.so',
> needed by 'csg/src/tools/csg_gmxtopol'. Stop.
> CMakeFiles/Makefile2:675: recipe for target
> 'csg/src/tools/CMakeFiles/csg_gmxtopol.dir/all' failed
> gmake[1]: *** [csg/src/tools/CMakeFiles/csg_gmxtopol.dir/all] Error 2
> Makefile:129: recipe for target 'all' failed
> gmake: *** [all] Error 2
Looking at the log, somehow Gromacs didn't get build, try to start
from a fresh checkout and try to run "cmake --build builddir --verbose
--target=Gromacs_build" first.
Christoph
>
> I also tried spack, there were too many errors.
>
> Perhaps it is a bad combination of the modules I am uploading.
> Cheers,
> Nancy
>
> On Sunday, 20 December 2020 at 01:27:52 UTC+1 Christoph Junghans wrote:
>>
>> On Sat, Dec 19, 2020 at 4:02 PM nancyfor <[email protected]> wrote:
>> >
>> >
>> > Hi Christoph,
>> >
>> > I really appreciate your input.
>> >
>> > Indeed, there was a problem with the boost. I loaded the wrong one. I also
>> > unloaded the modules. Now, I have used the one compiled with gcc-8. I
>> > overcame the preview error, but now I am getting one when linking the
>> > executable csg_gmxtopol. I thought it was related to the fftw libraries, I
>> > build it with both fftw-serial(which I think is the one prefered in VOTCA
>> > (?)) and fftw-mpi (this is the one it is used in the gromacs installation
>> > of the supercomputer), but I got the same error message. Below is the last
>> > part of the output for
>>
>> fftwf_version() is part of the single-precession version of fftw.
>> VOTCA only depends on the double precision version of fftw.
>> So my guess is that this is a dependency from libgromacs.a, which is
>> most likely single precision.
>> When doing a build with static libraries, you will have to list
>> libgromacs' dependencies in GROMACS_LIBRARY as well, e.g.
>> -DGROMACS_LIBRARY="/path/to/libgromacs.a;/path/to/libfftwf.a"
>> If you are linking against a mpi-enabled version of libgromacs, you
>> might need to add libmpi in there, too.
>> When using shared libraries all the dependency handling is automatic,
>> as dependencies are embedded in the .so files.
>>
>> As a sidenote, VOTCA doesn't really benefit from an mpi-enabled
>> libgromacs as we only use libgromacs to read gromacs file formats.
>> So using a serial version is preferred.
>>
>> Christoph
>>
>> >
>> > cmake --build builddir --verbose
>> > in both cases:
>> >
>> > fftw-serial
>> > ......
>> > [ 66%] Linking CXX executable csg_gmxtopol
>> > cd /u/forero/src/votca/builddir/csg/src/tools &&
>> > /u/system/soft/SLE_12/packages/x86_64/cmake/3.15.2/bin/cmake -E
>> > cmake_link_script CMakeFiles/csg_gmxtopol.dir/link.txt --verbose=1
>> > /mpcdf/soft/SLE_12/packages/x86_64/gcc/8.4.0/bin/g++ -Wall -Wextra
>> > -Wpedantic -Wshadow -Wconversion -O3 -DNDEBUG
>> > CMakeFiles/csg_gmxtopol.dir/csg_gmxtopol.cc.o -o csg_gmxtopol
>> > -Wl,-rpath,/mpcdf/soft/SLE_12/packages/skylake/hdf5/gcc_8-8.4.0/1.8.21/lib:/mpcdf/soft/SLE_12/packages/skylake/boost/gcc_8-8.4.0/1.74.0/lib64:/mpcdf/soft/SLE_12/packages/skylake/fftw/gcc_8-8.4.0/3.3.8/lib:
>> > ../libcsg/libvotca_csg.a
>> > /mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a
>> >
>> > /mpcdf/soft/SLE_12/packages/skylake/hdf5/gcc_8-8.4.0/1.8.21/lib/libhdf5.so
>> > /usr/lib64/libz.so /usr/lib64/libdl.so -lm
>> > ../../../tools/src/libtools/libvotca_tools.a
>> > /mpcdf/soft/SLE_12/packages/skylake/boost/gcc_8-8.4.0/1.74.0/lib64/libboost_program_options.so.1.74.0
>> >
>> > /mpcdf/soft/SLE_12/packages/skylake/boost/gcc_8-8.4.0/1.74.0/lib64/libboost_filesystem.so.1.74.0
>> >
>> > /mpcdf/soft/SLE_12/packages/skylake/boost/gcc_8-8.4.0/1.74.0/lib64/libboost_system.so.1.74.0
>> > /usr/lib64/libexpat.so -lm
>> > /mpcdf/soft/SLE_12/packages/skylake/fftw/gcc_8-8.4.0/3.3.8/lib/libfftw3.so
>> > /mpcdf/soft/SLE_12/packages/skylake/boost/gcc_8-8.4.0/1.74.0/lib64/libboost_program_options.so.1.74.0
>> >
>> > /mpcdf/soft/SLE_12/packages/skylake/boost/gcc_8-8.4.0/1.74.0/lib64/libboost_filesystem.so.1.74.0
>> >
>> > /mpcdf/soft/SLE_12/packages/skylake/boost/gcc_8-8.4.0/1.74.0/lib64/libboost_system.so.1.74.0
>> > -lpthread
>> > /usr/bin/ld:
>> > /mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(binaryinformation.cpp.o):
>> > in function `gmx::printBinaryInformation(gmx::TextWriter*,
>> > gmx::IProgramContext const&, gmx::BinaryInformationSettings const&)':
>> > binaryinformation.cpp:(.text+0x706): undefined reference to `fftwf_version'
>> > collect2: error: ld returned 1 exit status
>> > csg/src/tools/CMakeFiles/csg_gmxtopol.dir/build.make:98: recipe for target
>> > 'csg/src/tools/csg_gmxtopol' failed
>> > gmake[2]: *** [csg/src/tools/csg_gmxtopol] Error 1
>> > gmake[2]: Leaving directory '/cobra/u/forero/src/votca/builddir'
>> > CMakeFiles/Makefile2:644: recipe for target
>> > 'csg/src/tools/CMakeFiles/csg_gmxtopol.dir/all' failed
>> > gmake[1]: *** [csg/src/tools/CMakeFiles/csg_gmxtopol.dir/all] Error 2
>> > gmake[1]: Leaving directory '/cobra/u/forero/src/votca/builddir'
>> > Makefile:129: recipe for target 'all' failed
>> > gmake: *** [all] Error 2
>> >
>> >
>> > fftw-mpi
>> > .....
>> > [ 66%] Linking CXX executable csg_gmxtopol
>> > cd /u/forero/src/votca/builddir/csg/src/tools &&
>> > /u/system/soft/SLE_12/packages/x86_64/cmake/3.15.2/bin/cmake -E
>> > cmake_link_script CMakeFiles/csg_gmxtopol.dir/link.txt --verbose=1
>> > /mpcdf/soft/SLE_12/packages/x86_64/gcc/8.4.0/bin/g++ -Wall -Wextra
>> > -Wpedantic -Wshadow -Wconversion -O3 -DNDEBUG
>> > CMakeFiles/csg_gmxtopol.dir/csg_gmxtopol.cc.o -o csg_gmxtopol
>> > -Wl,-rpath,/mpcdf/soft/SLE_12/packages/skylake/hdf5/gcc_8-8.4.0/1.8.21/lib:/mpcdf/soft/SLE_12/packages/skylake/boost/gcc_8-8.4.0/1.74.0/lib64:/mpcdf/soft/SLE_12/packages/skylake/fftw/gcc_8-8.4.0-impi_2019.7-2019.7.217/3.3.7/lib:
>> > ../libcsg/libvotca_csg.a
>> > /mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a
>> >
>> > /mpcdf/soft/SLE_12/packages/skylake/hdf5/gcc_8-8.4.0/1.8.21/lib/libhdf5.so
>> > /usr/lib64/libz.so /usr/lib64/libdl.so -lm
>> > ../../../tools/src/libtools/libvotca_tools.a
>> > /mpcdf/soft/SLE_12/packages/skylake/boost/gcc_8-8.4.0/1.74.0/lib64/libboost_program_options.so.1.74.0
>> >
>> > /mpcdf/soft/SLE_12/packages/skylake/boost/gcc_8-8.4.0/1.74.0/lib64/libboost_filesystem.so.1.74.0
>> >
>> > /mpcdf/soft/SLE_12/packages/skylake/boost/gcc_8-8.4.0/1.74.0/lib64/libboost_system.so.1.74.0
>> > /usr/lib64/libexpat.so -lm
>> > /mpcdf/soft/SLE_12/packages/skylake/fftw/gcc_8-8.4.0-impi_2019.7-2019.7.217/3.3.7/lib/libfftw3.so
>> >
>> > /mpcdf/soft/SLE_12/packages/skylake/boost/gcc_8-8.4.0/1.74.0/lib64/libboost_program_options.so.1.74.0
>> >
>> > /mpcdf/soft/SLE_12/packages/skylake/boost/gcc_8-8.4.0/1.74.0/lib64/libboost_filesystem.so.1.74.0
>> >
>> > /mpcdf/soft/SLE_12/packages/skylake/boost/gcc_8-8.4.0/1.74.0/lib64/libboost_system.so.1.74.0
>> > -lpthread
>> > /usr/bin/ld:
>> > /mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(binaryinformation.cpp.o):
>> > in function `gmx::printBinaryInformation(gmx::TextWriter*,
>> > gmx::IProgramContext const&, gmx::BinaryInformationSettings const&)':
>> > binaryinformation.cpp:(.text+0x706): undefined reference to `fftwf_version'
>> > collect2: error: ld returned 1 exit status
>> > csg/src/tools/CMakeFiles/csg_gmxtopol.dir/build.make:98: recipe for target
>> > 'csg/src/tools/csg_gmxtopol' failed
>> > gmake[2]: *** [csg/src/tools/csg_gmxtopol] Error 1
>> > gmake[2]: Leaving directory '/cobra/u/forero/src/votca/builddir'
>> > CMakeFiles/Makefile2:644: recipe for target
>> > 'csg/src/tools/CMakeFiles/csg_gmxtopol.dir/all' failed
>> > gmake[1]: *** [csg/src/tools/CMakeFiles/csg_gmxtopol.dir/all] Error 2
>> > gmake[1]: Leaving directory '/cobra/u/forero/src/votca/builddir'
>> > Makefile:129: recipe for target 'all' failed
>> > gmake: *** [all] Error 2
>> >
>> >
>> > I do not know what else to check.
>> > Cheers,
>> > Nancy
>> >
>> >
>> >
>> > On Saturday, 19 December 2020 at 21:26:16 UTC+1 Christoph Junghans wrote:
>> >>
>> >> On Sat, Dec 19, 2020 at 9:41 AM nancyfor <[email protected]> wrote:
>> >> >
>> >> > Thanks Christoph,
>> >> >
>> >> > I have added -DBUILD_SHARED_LIBS=OFF -DBUILD_CSGAPPS=ON
>> >> > -DBUILD_XTP=OFF, since I want to use the gromacs in the supercomputer.
>> >> Hmm, I tried the same locally and it worked.
>> >>
>> >> The error below usually means your boost was compiled with a compiler
>> >> that has a different cxx abi.
>> >> Looking at the path of the boost package you are using, it looks like
>> >> it was compiled with intel_19.1.1, but you are compiling votca with
>> >> gcc-8.4.0.
>> >>
>> >> I have no good solution, except you could try to not load intel/19.1.1
>> >> impi/2019.7 mkl/2020.1 as you aren't really using any of these.
>> >>
>> >> Christoph
>> >>
>> >> > Now the output error for
>> >> >
>> >> > cmake --build builddir
>> >> >
>> >> > occurs when linking CXX executable votca_property
>> >> >
>> >> > here the last lines: (whole --verbose output attached)
>> >> > ...
>> >> > cESaIcEEESA_ERKSA_EE[_ZN5boost15program_options25basic_command_line_parserIcE12extra_parserENS_9function1ISt4pairINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESA_ERKSA_EE]+0x3e):
>> >> > undefined reference to
>> >> > `boost::program_options::detail::cmdline::set_additional_parser(boost::function1<std::pair<std::__cxx11::basic_string<char,
>> >> > std::char_traits<char>, std::allocator<char> >,
>> >> > std::__cxx11::basic_string<char, std::char_traits<char>,
>> >> > std::allocator<char> > >, std::__cxx11::basic_string<char,
>> >> > std::char_traits<char>, std::allocator<char> > const&>)'
>> >> > /usr/bin/ld: ../libtools/libvotca_tools.a(application.cc.o): in
>> >> > function
>> >> > `boost::program_options::basic_command_line_parser<char>::basic_command_line_parser(int,
>> >> > char const* const*)':
>> >> > application.cc:(.text._ZN5boost15program_options25basic_command_line_parserIcEC2EiPKPKc[_ZN5boost15program_options25basic_command_line_parserIcEC5EiPKPKc]+0x1b8):
>> >> > undefined reference to
>> >> > `boost::program_options::to_internal(std::__cxx11::basic_string<char,
>> >> > std::char_traits<char>, std::allocator<char> > const&)'
>> >> > /usr/bin/ld:
>> >> > application.cc:(.text._ZN5boost15program_options25basic_command_line_parserIcEC2EiPKPKc[_ZN5boost15program_options25basic_command_line_parserIcEC5EiPKPKc]+0x277):
>> >> > undefined reference to
>> >> > `boost::program_options::detail::cmdline::cmdline(std::vector<std::__cxx11::basic_string<char,
>> >> > std::char_traits<char>, std::allocator<char> >,
>> >> > std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>,
>> >> > std::allocator<char> > > > const&)'
>> >> > collect2: error: ld returned 1 exit status
>> >> > tools/src/tools/CMakeFiles/votca_property.dir/build.make:89: recipe for
>> >> > target 'tools/src/tools/votca_property' failed
>> >> > gmake[2]: *** [tools/src/tools/votca_property] Error 1
>> >> > CMakeFiles/Makefile2:317: recipe for target
>> >> > 'tools/src/tools/CMakeFiles/votca_property.dir/all' failed
>> >> > gmake[1]: *** [tools/src/tools/CMakeFiles/votca_property.dir/all] Error
>> >> > 2
>> >> > Makefile:129: recipe for target 'all' failed
>> >> > gmake: *** [all] Error 2
>> >> >
>> >> > Cheers,
>> >> > Nancy
>> >> > On Saturday, 19 December 2020 at 16:22:11 UTC+1 Christoph Junghans
>> >> > wrote:
>> >> >>
>> >> >> On Sat, Dec 19, 2020 at 8:05 AM nancyfor <[email protected]> wrote:
>> >> >> >
>> >> >> > Hi Christoph,
>> >> >> >
>> >> >> > I am using the following command,
>> >> >> >
>> >> >> > cmake -Bbuilddir -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++
>> >> >> > -DBUILD_CSGAPPS=ON -DBUILD_XTP=ON
>> >> >> > -DGROMACS_INCLUDE_DIR=/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/include/
>> >> >> >
>> >> >> > -DGROMACS_LIBRARY=/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a
>> >> >> >
>> >> >> > -DLIBXC_INCLUDE_DIR=/mpcdf/soft/SLE_12/packages/skylake/libxc/gcc_8-8.4.0/4.3.4/include/
>> >> >> >
>> >> >> > -DLIBXC_LIBRARY=/mpcdf/soft/SLE_12/packages/skylake/libxc/gcc_8-8.4.0/4.3.4/lib/libxc.a
>> >> >> > -DCMAKE_DISABLE_FIND_PACKAGE_MKL=ON
>> >> >> > -DCMAKE_INSTALL_PREFIX=${prefix} ../votca
>> >> >> >
>> >> >> > and the configuration show no problems. But when building it, I have
>> >> >> > a problem with the linking of the libraries for gromacs, which are
>> >> >> > in this cases static, there is not .so libraries available.
>> >> >> >
>> >> >> > Below is the last part of the output of
>> >> >> > cmake --build builddir --verbose
>> >> >> >
>> >> >> > I have attached the complete output in:
>> >> >> > output_verbose_votca_19_12_2020.txt
>> >> >> >
>> >> >> > I tried to pass the -fPIC option when compiling but I think I am
>> >> >> > doing it wrong. How this should be done?
>> >> >> >
>> >> >> > Best regards,
>> >> >> > Nancy
>> >> >> >
>> >> >> > ...
>> >> >> > /usr/bin/ld:
>> >> >> > /mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(merge_sort.c.o):
>> >> >> > relocation R_X86_64_PC32 against symbol `memcpy@@GLIBC_2.14' can
>> >> >> > not be used when making a shared object; recompile with -fPIC
>> >> >> > /usr/bin/ld: final link failed: nonrepresentable section on output
>> >> >> > collect2: error: ld returned 1 exit status
>> >> >> > csg/src/libcsg/CMakeFiles/votca_csg.dir/build.make:798: recipe for
>> >> >> > target 'csg/src/libcsg/libvotca_csg.so.6' failed
>> >> >> > gmake[2]: *** [csg/src/libcsg/libvotca_csg.so.6] Error 1
>> >> >> > gmake[2]: Leaving directory '/cobra/u/forero/src/votca/builddir'
>> >> >> > CMakeFiles/Makefile2:590: recipe for target
>> >> >> > 'csg/src/libcsg/CMakeFiles/votca_csg.dir/all' failed
>> >> >> > gmake[1]: *** [csg/src/libcsg/CMakeFiles/votca_csg.dir/all] Error 2
>> >> >> > gmake[1]: Leaving directory '/cobra/u/forero/src/votca/builddir'
>> >> >> > Makefile:129: recipe for target 'all' failed
>> >> >> > gmake: *** [all] Error 2
>> >> >> This error just means you cannot mix shared (.so) and static (.a)
>> >> >> libraries.
>> >> >>
>> >> >> You have three options:
>> >> >> - rebuild gromacs shared: using -DBUILD_SHARED_LIBS=ON when you build
>> >> >> gromacs
>> >> >> - have VOTCA builds its own gromacs: -DBUILD_OWN_GROMACS=ON when
>> >> >> building votca
>> >> >> - build VOTCA with static libs: -DBUILD_SHARED_LIBS=OFF when building
>> >> >> votca
>> >> >>
>> >> >> I see libxc is static, too, so you will have the same issue later when
>> >> >> building votca xtp.
>> >> >> Options here:
>> >> >> - rebuild libxc shared: using --enable-shared when building libxc
>> >> >> - build VOTCA with static libs: -DBUILD_SHARED_LIBS=OFF when building
>> >> >> votca
>> >> >> - don't build the xtp module (not sure if you need it):
>> >> >> -DBUILD_XTP=OFF when building votca
>> >> >>
>> >> >> Alternatively, you could use spack to install everything, see
>> >> >> https://github.com/votca/votca/blob/master/share/doc/INSTALL.rst#spack
>> >> >>
>> >> >> Christoph
>> >> >> >
>> >> >> > On Tuesday, 1 December 2020 at 15:20:46 UTC+1 nancyfor wrote:
>> >> >> >>
>> >> >> >> I think the issue with MKL is related to the gcc version, there is
>> >> >> >> not module of MKL for gcc-8.
>> >> >> >> When I succed, I will let you know.
>> >> >> >> Thank you!
>> >> >> >> Cheers
>> >> >> >> Nancy
>> >> >> >>
>> >> >> >> On Tuesday, 1 December 2020 at 15:15:11 UTC+1 Christoph Junghans
>> >> >> >> wrote:
>> >> >> >>>
>> >> >> >>> On Tue, Dec 1, 2020 at 7:11 AM nancyfor <[email protected]> wrote:
>> >> >> >>> >
>> >> >> >>> > Hi Christoph
>> >> >> >>> > Few minutes ago I was using,
>> >> >> >>> >
>> >> >> >>> > -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++
>> >> >> >>> >
>> >> >> >>> > and correctly use GNU 8.4.0
>> >> >> >>> >
>> >> >> >>> > However, now there is something related to the
>> >> >> >>> > 'MKL_ThreadingLibrary_LINK_LIBRARY-NOTFOUND'
>> >> >> >>> Try to compile without MKL for now:
>> >> >> >>> -DCMAKE_DISABLE_FIND_PACKAGE_MKL=ON, if you aren't using xtp, mkl
>> >> >> >>> doesn't gain you much anyhow.
>> >> >> >>>
>> >> >> >>> Christoph
>> >> >> >>>
>> >> >> >>> >
>> >> >> >>> > this is the output for cmake --build builddir
>> >> >> >>> >
>> >> >> >>> > Scanning dependencies of target gitversion-xtp
>> >> >> >>> > Current git revision is 9b6bbd0
>> >> >> >>> > [ 0%] Built target gitversion-xtp
>> >> >> >>> > Scanning dependencies of target gitversion
>> >> >> >>> > Current git revision is 9b6bbd0
>> >> >> >>> > [ 0%] Built target gitversion
>> >> >> >>> > Scanning dependencies of target votca_tools
>> >> >> >>> > [ 1%] Building CXX object
>> >> >> >>> > tools/src/libtools/CMakeFiles/votca_tools.dir/akimaspline.cc.o
>> >> >> >>> > [ 1%] Building CXX object
>> >> >> >>> > tools/src/libtools/CMakeFiles/votca_tools.dir/application.cc.o
>> >> >> >>> > [ 1%] Building CXX object
>> >> >> >>> > tools/src/libtools/CMakeFiles/votca_tools.dir/calculator.cc.o
>> >> >> >>> > [ 2%] Building CXX object
>> >> >> >>> > tools/src/libtools/CMakeFiles/votca_tools.dir/colors.cc.o
>> >> >> >>> > [ 2%] Building CXX object
>> >> >> >>> > tools/src/libtools/CMakeFiles/votca_tools.dir/correlate.cc.o
>> >> >> >>> > [ 2%] Building CXX object
>> >> >> >>> > tools/src/libtools/CMakeFiles/votca_tools.dir/crosscorrelate.cc.o
>> >> >> >>> > [ 3%] Building CXX object
>> >> >> >>> > tools/src/libtools/CMakeFiles/votca_tools.dir/cubicspline.cc.o
>> >> >> >>> > [ 3%] Building CXX object
>> >> >> >>> > tools/src/libtools/CMakeFiles/votca_tools.dir/datacollection.cc.o
>> >> >> >>> > [ 3%] Building CXX object
>> >> >> >>> > tools/src/libtools/CMakeFiles/votca_tools.dir/edge.cc.o
>> >> >> >>> > [ 4%] Building CXX object
>> >> >> >>> > tools/src/libtools/CMakeFiles/votca_tools.dir/edgecontainer.cc.o
>> >> >> >>> > [ 4%] Building CXX object
>> >> >> >>> > tools/src/libtools/CMakeFiles/votca_tools.dir/elements.cc.o
>> >> >> >>> > [ 4%] Building CXX object
>> >> >> >>> > tools/src/libtools/CMakeFiles/votca_tools.dir/filesystem.cc.o
>> >> >> >>> > [ 5%] Building CXX object
>> >> >> >>> > tools/src/libtools/CMakeFiles/votca_tools.dir/globals.cc.o
>> >> >> >>> > [ 5%] Building CXX object
>> >> >> >>> > tools/src/libtools/CMakeFiles/votca_tools.dir/graph.cc.o
>> >> >> >>> > [ 5%] Building CXX object
>> >> >> >>> > tools/src/libtools/CMakeFiles/votca_tools.dir/graph_bf_visitor.cc.o
>> >> >> >>> > [ 6%] Building CXX object
>> >> >> >>> > tools/src/libtools/CMakeFiles/votca_tools.dir/graph_df_visitor.cc.o
>> >> >> >>> > [ 6%] Building CXX object
>> >> >> >>> > tools/src/libtools/CMakeFiles/votca_tools.dir/graphalgorithm.cc.o
>> >> >> >>> > [ 6%] Building CXX object
>> >> >> >>> > tools/src/libtools/CMakeFiles/votca_tools.dir/graphdistvisitor.cc.o
>> >> >> >>> > [ 7%] Building CXX object
>> >> >> >>> > tools/src/libtools/CMakeFiles/votca_tools.dir/graphnode.cc.o
>> >> >> >>> > [ 7%] Building CXX object
>> >> >> >>> > tools/src/libtools/CMakeFiles/votca_tools.dir/graphvisitor.cc.o
>> >> >> >>> > [ 8%] Building CXX object
>> >> >> >>> > tools/src/libtools/CMakeFiles/votca_tools.dir/histogram.cc.o
>> >> >> >>> > [ 8%] Building CXX object
>> >> >> >>> > tools/src/libtools/CMakeFiles/votca_tools.dir/histogramnew.cc.o
>> >> >> >>> > [ 8%] Building CXX object
>> >> >> >>> > tools/src/libtools/CMakeFiles/votca_tools.dir/linalg.cc.o
>> >> >> >>> > [ 9%] Building CXX object
>> >> >> >>> > tools/src/libtools/CMakeFiles/votca_tools.dir/linspline.cc.o
>> >> >> >>> > [ 9%] Building CXX object
>> >> >> >>> > tools/src/libtools/CMakeFiles/votca_tools.dir/mutex.cc.o
>> >> >> >>> > [ 9%] Building CXX object
>> >> >> >>> > tools/src/libtools/CMakeFiles/votca_tools.dir/parcer.cc.o
>> >> >> >>> > [ 10%] Building CXX object
>> >> >> >>> > tools/src/libtools/CMakeFiles/votca_tools.dir/property.cc.o
>> >> >> >>> > [ 10%] Building CXX object
>> >> >> >>> > tools/src/libtools/CMakeFiles/votca_tools.dir/propertyiomanipulator.cc.o
>> >> >> >>> > [ 10%] Building CXX object
>> >> >> >>> > tools/src/libtools/CMakeFiles/votca_tools.dir/rangeparser.cc.o
>> >> >> >>> > [ 11%] Building CXX object
>> >> >> >>> > tools/src/libtools/CMakeFiles/votca_tools.dir/reducededge.cc.o
>> >> >> >>> > [ 11%] Building CXX object
>> >> >> >>> > tools/src/libtools/CMakeFiles/votca_tools.dir/reducedgraph.cc.o
>> >> >> >>> > [ 11%] Building CXX object
>> >> >> >>> > tools/src/libtools/CMakeFiles/votca_tools.dir/spline.cc.o
>> >> >> >>> > [ 12%] Building CXX object
>> >> >> >>> > tools/src/libtools/CMakeFiles/votca_tools.dir/table.cc.o
>> >> >> >>> > [ 12%] Building CXX object
>> >> >> >>> > tools/src/libtools/CMakeFiles/votca_tools.dir/thread.cc.o
>> >> >> >>> > [ 12%] Building CXX object
>> >> >> >>> > tools/src/libtools/CMakeFiles/votca_tools.dir/tokenizer.cc.o
>> >> >> >>> > [ 13%] Building CXX object
>> >> >> >>> > tools/src/libtools/CMakeFiles/votca_tools.dir/version.cc.o
>> >> >> >>> > gmake[2]: *** No rule to make target
>> >> >> >>> > 'MKL_ThreadingLibrary_LINK_LIBRARY-NOTFOUND', needed by
>> >> >> >>> > 'tools/src/libtools/libvotca_tools.so.6'. Stop.
>> >> >> >>> > CMakeFiles/Makefile2:256: recipe for target
>> >> >> >>> > 'tools/src/libtools/CMakeFiles/votca_tools.dir/all' failed
>> >> >> >>> > gmake[1]: ***
>> >> >> >>> > [tools/src/libtools/CMakeFiles/votca_tools.dir/all] Error 2
>> >> >> >>> > Makefile:129: recipe for target 'all' failed
>> >> >> >>> > gmake: *** [all] Error 2
>> >> >> >>> >
>> >> >> >>> > I have attached the output for cmake --build builddir --verbose
>> >> >> >>> >
>> >> >> >>> > Thanks
>> >> >> >>> > Nancy
>> >> >> >>> >
>> >> >> >>> > On Tuesday, 1 December 2020 at 14:46:11 UTC+1 Christoph Junghans
>> >> >> >>> > wrote:
>> >> >> >>> >>
>> >> >> >>> >> On Tue, Dec 1, 2020 at 3:00 AM nancyfor <[email protected]>
>> >> >> >>> >> wrote:
>> >> >> >>> >> >
>> >> >> >>> >> > Hi Christoph,
>> >> >> >>> >> >
>> >> >> >>> >> > I thought I was using gcc. I did not change anything on
>> >> >> >>> >> > purpose. So, to be a little bit more consistent, I checked
>> >> >> >>> >> > again the gcc and the boost version that worked together, and
>> >> >> >>> >> > include the flag -DCMAKE_CXX_COMPILER_ID=GNU (is this
>> >> >> >>> >> > alright?) Currently I have the following modules uploaded:
>> >> >> >>> >> >
>> >> >> >>> >> > mkl/2020.1
>> >> >> >>> >> > gromacs/2019.4
>> >> >> >>> >> > doxygen/1.8
>> >> >> >>> >> > cmake/3.15
>> >> >> >>> >> > clang/10.0
>> >> >> >>> >> > gcc/8
>> >> >> >>> >> > boost/1.66
>> >> >> >>> >> > libxc/4.3.4
>> >> >> >>> >> > fftw-serial/3.3.8
>> >> >> >>> >> > hdf5-serial/1.8.21
>> >> >> >>> >> >
>> >> >> >>> >> > Un run the following with the new library paths (I have
>> >> >> >>> >> > attached the CMakeOutput.log and the output from "cmake
>> >> >> >>> >> > -Bbuilddir ../votca" output_cmake_Bbuildir.txt)
>> >> >> >>> >> >
>> >> >> >>> >> > cmake -Bbuilddir -DCMAKE_CXX_COMPILER_ID=GNU
>> >> >> >>> >> > -DBUILD_CSGAPPS=ON -DBUILD_XTP=ON
>> >> >> >>> >> > -DGROMACS_INCLUDE_DIR=/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/include/
>> >> >> >>> >> >
>> >> >> >>> >> > -DGROMACS_LIBRARY=/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a
>> >> >> >>> >> >
>> >> >> >>> >> > -DLIBXC_INCLUDE_DIR=/mpcdf/soft/SLE_12/packages/skylake/libxc/gcc_8-8.4.0/4.3.4/include/
>> >> >> >>> >> >
>> >> >> >>> >> > -DLIBXC_LIBRARY=/mpcdf/soft/SLE_12/packages/skylake/libxc/gcc_8-8.4.0/4.3.4/lib/libxc.a
>> >> >> >>> >> > -DCMAKE_INSTALL_PREFIX=${prefix} ../votca
>> >> >> >>> >> >
>> >> >> >>> >> > and again when doing
>> >> >> >>> >> > cmake --build builddir --verbose
>> >> >> >>> >> > I get an error, different from the origina one I mentioned.
>> >> >> >>> >> > The full output is in cmake_verbose.txt
>> >> >> >>> >> Thanks, the cmake log says:
>> >> >> >>> >>
>> >> >> >>> >> The C compiler identification is GNU 4.8.5
>> >> >> >>> >>
>> >> >> >>> >> GCC 4.8.5 is unfortunately too old as it misses some C++-11
>> >> >> >>> >> features,
>> >> >> >>> >> you mentioned a "gcc/8" in your first email, maybe you can try
>> >> >> >>> >> to use
>> >> >> >>> >> that one instead. I guess something like
>> >> >> >>> >> "-DCMAKE_CXX_COMPILER=g++-8"
>> >> >> >>> >>
>> >> >> >>> >> Christoph
>> >> >> >>> >>
>> >> >> >>> >>
>> >> >> >>> >> >
>> >> >> >>> >> > Thanks
>> >> >> >>> >> > Nancy
>> >> >> >>> >> > On Monday, 30 November 2020 at 17:08:19 UTC+1 Christoph
>> >> >> >>> >> > Junghans wrote:
>> >> >> >>> >> >>
>> >> >> >>> >> >> Nancy,
>> >> >> >>> >> >>
>> >> >> >>> >> >> Are you trying to compile with gcc or icc?
>> >> >> >>> >> >>
>> >> >> >>> >> >> Could you attach the full output of "cmake -Bbuilddir
>> >> >> >>> >> >> ../votca" and
>> >> >> >>> >> >> "cmake --build builddir --verbose" (mind the extra
>> >> >> >>> >> >> "--verbose" here)?
>> >> >> >>> >> >>
>> >> >> >>> >> >> Thanks,
>> >> >> >>> >> >>
>> >> >> >>> >> >> Christoph
>> >> >> >>> >> >>
>> >> >> >>> >> >> On Mon, Nov 30, 2020 at 8:18 AM nancyfor <[email protected]>
>> >> >> >>> >> >> wrote:
>> >> >> >>> >> >> >
>> >> >> >>> >> >> > Hello everybody,
>> >> >> >>> >> >> >
>> >> >> >>> >> >> > I am trying to install votca version 1.6.2 in a
>> >> >> >>> >> >> > supercomputer. After succesffully configure using the
>> >> >> >>> >> >> > following modules:
>> >> >> >>> >> >> >
>> >> >> >>> >> >> > intel/19.1.1
>> >> >> >>> >> >> > impi/2019.7
>> >> >> >>> >> >> > mkl/2020.1
>> >> >> >>> >> >> > gromacs/2019.4
>> >> >> >>> >> >> > libxc/4.3.4
>> >> >> >>> >> >> > doxygen/1.8
>> >> >> >>> >> >> > cmake/3.15 (version 3.13 incompatible with doxygen 1.8)
>> >> >> >>> >> >> > clang/10.0
>> >> >> >>> >> >> > hdf5-serial/1.8.21
>> >> >> >>> >> >> > fftw-serial/3.3.8
>> >> >> >>> >> >> > boost/1.73
>> >> >> >>> >> >> > with gcc version 9.3.0
>> >> >> >>> >> >> >
>> >> >> >>> >> >> > and
>> >> >> >>> >> >> >
>> >> >> >>> >> >> > cmake -Bbuilddir -DBUILD_CSGAPPS=ON -DBUILD_XTP=ON
>> >> >> >>> >> >> > -DGROMACS_INCLUDE_DIR=/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/include/
>> >> >> >>> >> >> >
>> >> >> >>> >> >> > -DGROMACS_LIBRARY=/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a
>> >> >> >>> >> >> >
>> >> >> >>> >> >> > -DLIBXC_INCLUDE_DIR=/mpcdf/soft/SLE_12/packages/skylake/libxc/gcc_10-10.2.0/4.3.4/
>> >> >> >>> >> >> >
>> >> >> >>> >> >> > -DLIBXC_LIBRARY=/mpcdf/soft/SLE_12/packages/skylake/libxc/gcc_10-10.2.0/4.3.4/lib/libxc.a
>> >> >> >>> >> >> > -DCMAKE_INSTALL_PREFIX=${prefix} ../votca
>> >> >> >>> >> >> >
>> >> >> >>> >> >> > However when I try to run
>> >> >> >>> >> >> >
>> >> >> >>> >> >> > cmake --build builddir
>> >> >> >>> >> >> >
>> >> >> >>> >> >> > I got the following:
>> >> >> >>> >> >> >
>> >> >> >>> >> >> > Current git revision is 9b6bbd0
>> >> >> >>> >> >> > [ 0%] Built target gitversion-xtp
>> >> >> >>> >> >> > Current git revision is 9b6bbd0
>> >> >> >>> >> >> > [ 0%] Built target gitversion
>> >> >> >>> >> >> > [ 0%] Building CXX object
>> >> >> >>> >> >> > tools/src/libtools/CMakeFiles/votca_tools.dir/application.cc.o
>> >> >> >>> >> >> > In file included from
>> >> >> >>> >> >> > /u/forero/src/votca/tools/include/votca/tools/property.h:23:0,
>> >> >> >>> >> >> > from
>> >> >> >>> >> >> > /u/forero/src/votca/tools/include/votca/tools/application.h:21,
>> >> >> >>> >> >> > from
>> >> >> >>> >> >> > /u/forero/src/votca/tools/src/libtools/application.cc:19:
>> >> >> >>> >> >> > /u/forero/src/votca/tools/include/votca/tools/tokenizer.h:107:3:
>> >> >> >>> >> >> > error: ‘unique_ptr’ in namespace ‘std’ does not name a
>> >> >> >>> >> >> > type
>> >> >> >>> >> >> > std::unique_ptr<boost::tokenizer<boost::char_separator<char>>>
>> >> >> >>> >> >> > tok;
>> >> >> >>> >> >> > ^
>> >> >> >>> >> >> > /u/forero/src/votca/tools/include/votca/tools/tokenizer.h:
>> >> >> >>> >> >> > In constructor ‘votca::tools::Tokenizer::Tokenizer(const
>> >> >> >>> >> >> > string&, const char*)’:
>> >> >> >>> >> >> > /u/forero/src/votca/tools/include/votca/tools/tokenizer.h:50:5:
>> >> >> >>> >> >> > error: ‘tok’ was not declared in this scope
>> >> >> >>> >> >> > tok =
>> >> >> >>> >> >> > std::make_unique<boost::tokenizer<boost::char_separator<char>>>(_str,
>> >> >> >>> >> >> > ^
>> >> >> >>> >> >> > /u/forero/src/votca/tools/include/votca/tools/tokenizer.h:50:11:
>> >> >> >>> >> >> > error: ‘make_unique’ is not a member of ‘std’
>> >> >> >>> >> >> > tok =
>> >> >> >>> >> >> > std::make_unique<boost::tokenizer<boost::char_separator<char>>>(_str,
>> >> >> >>> >> >> > ^
>> >> >> >>> >> >> > /u/forero/src/votca/tools/include/votca/tools/tokenizer.h:50:73:
>> >> >> >>> >> >> > error: expected primary-expression before ‘>’ token
>> >> >> >>> >> >> > tok =
>> >> >> >>> >> >> > std::make_unique<boost::tokenizer<boost::char_separator<char>>>(_str,
>> >> >> >>> >> >> > ^
>> >> >> >>> >> >> > /u/forero/src/votca/tools/include/votca/tools/tokenizer.h:51:75:
>> >> >> >>> >> >> > warning: left operand of comma operator has no effect
>> >> >> >>> >> >> > [-Wunused-value]
>> >> >> >>> >> >> > sep);
>> >> >> >>> >> >> > ^
>> >> >> >>> >> >> > /u/forero/src/votca/tools/include/votca/tools/tokenizer.h:
>> >> >> >>> >> >> > In member function ‘votca::tools::Tokenizer::iterator
>> >> >> >>> >> >> > votca::tools::Tokenizer::begin()’:
>> >> >> >>> >> >> > /u/forero/src/votca/tools/include/votca/tools/tokenizer.h:60:29:
>> >> >> >>> >> >> > error: ‘tok’ was not declared in this scope
>> >> >> >>> >> >> > iterator begin() { return tok->begin(); }
>> >> >> >>> >> >> > ^
>> >> >> >>> >> >> > /u/forero/src/votca/tools/include/votca/tools/tokenizer.h:
>> >> >> >>> >> >> > In member function ‘votca::tools::Tokenizer::iterator
>> >> >> >>> >> >> > votca::tools::Tokenizer::end()’:
>> >> >> >>> >> >> > /u/forero/src/votca/tools/include/votca/tools/tokenizer.h:65:27:
>> >> >> >>> >> >> > error: ‘tok’ was not declared in this scope
>> >> >> >>> >> >> > iterator end() { return tok->end(); }
>> >> >> >>> >> >> > ^
>> >> >> >>> >> >> > In file included from
>> >> >> >>> >> >> > /u/forero/src/votca/tools/include/votca/tools/application.h:21:0,
>> >> >> >>> >> >> > from
>> >> >> >>> >> >> > /u/forero/src/votca/tools/src/libtools/application.cc:19:
>> >> >> >>> >> >> > /u/forero/src/votca/tools/include/votca/tools/property.h:
>> >> >> >>> >> >> > In constructor ‘votca::tools::Property::Property(const
>> >> >> >>> >> >> > string&, const string&, const string&)’:
>> >> >> >>> >> >> > /u/forero/src/votca/tools/include/votca/tools/property.h:59:7:
>> >> >> >>> >> >> > warning: declaration of ‘path’ shadows a member of 'this'
>> >> >> >>> >> >> > [-Wshadow]
>> >> >> >>> >> >> > : _name(name), _value(value), _path(path) {}
>> >> >> >>> >> >> > ^
>> >> >> >>> >> >> > /u/forero/src/votca/tools/include/votca/tools/property.h:59:7:
>> >> >> >>> >> >> > warning: declaration of ‘value’ shadows a member of
>> >> >> >>> >> >> > 'this' [-Wshadow]
>> >> >> >>> >> >> > /u/forero/src/votca/tools/include/votca/tools/property.h:59:7:
>> >> >> >>> >> >> > warning: declaration of ‘name’ shadows a member of 'this'
>> >> >> >>> >> >> > [-Wshadow]
>> >> >> >>> >> >> > /u/forero/src/votca/tools/include/votca/tools/property.h:
>> >> >> >>> >> >> > In member function ‘votca::tools::Property&
>> >> >> >>> >> >> > votca::tools::Property::set(const string&, const string&)’:
>> >> >> >>> >> >> > /u/forero/src/votca/tools/include/votca/tools/property.h:248:56:
>> >> >> >>> >> >> > warning: declaration of ‘value’ shadows a member of
>> >> >> >>> >> >> > 'this' [-Wshadow]
>> >> >> >>> >> >> > const std::string &value) {
>> >> >> >>> >> >> > ^
>> >> >> >>> >> >> > /u/forero/src/votca/tools/include/votca/tools/property.h:
>> >> >> >>> >> >> > In member function ‘votca::tools::Property&
>> >> >> >>> >> >> > votca::tools::Property::add(const string&, const string&)’:
>> >> >> >>> >> >> > /u/forero/src/votca/tools/include/votca/tools/property.h:255:56:
>> >> >> >>> >> >> > warning: declaration of ‘value’ shadows a member of
>> >> >> >>> >> >> > 'this' [-Wshadow]
>> >> >> >>> >> >> > const std::string &value) {
>> >> >> >>> >> >> > ^
>> >> >> >>> >> >> > /u/forero/src/votca/tools/include/votca/tools/property.h:256:15:
>> >> >> >>> >> >> > warning: declaration of ‘path’ shadows a member of 'this'
>> >> >> >>> >> >> > [-Wshadow]
>> >> >> >>> >> >> > std::string path = _path;
>> >> >> >>> >> >> > ^
>> >> >> >>> >> >> > /u/forero/src/votca/tools/include/votca/tools/property.h:
>> >> >> >>> >> >> > In member function ‘void
>> >> >> >>> >> >> > votca::tools::Property::setAttribute(const string&, const
>> >> >> >>> >> >> > T&)’:
>> >> >> >>> >> >> > /u/forero/src/votca/tools/include/votca/tools/property.h:420:50:
>> >> >> >>> >> >> > warning: declaration of ‘value’ shadows a member of
>> >> >> >>> >> >> > 'this' [-Wshadow]
>> >> >> >>> >> >> > const T &value) {
>> >> >> >>> >> >> > ^
>> >> >> >>> >> >> > tools/src/libtools/CMakeFiles/votca_tools.dir/build.make:75:
>> >> >> >>> >> >> > recipe for target
>> >> >> >>> >> >> > 'tools/src/libtools/CMakeFiles/votca_tools.dir/application.cc.o'
>> >> >> >>> >> >> > failed
>> >> >> >>> >> >> > gmake[2]: ***
>> >> >> >>> >> >> > [tools/src/libtools/CMakeFiles/votca_tools.dir/application.cc.o]
>> >> >> >>> >> >> > Error 1
>> >> >> >>> >> >> > CMakeFiles/Makefile2:256: recipe for target
>> >> >> >>> >> >> > 'tools/src/libtools/CMakeFiles/votca_tools.dir/all' failed
>> >> >> >>> >> >> > gmake[1]: ***
>> >> >> >>> >> >> > [tools/src/libtools/CMakeFiles/votca_tools.dir/all] Error 2
>> >> >> >>> >> >> > Makefile:129: recipe for target 'all' failed
>> >> >> >>> >> >> > gmake: *** [all] Error 2
>> >> >> >>> >> >> >
>> >> >> >>> >> >> > Does anyone have an idea of what might be the problem. I
>> >> >> >>> >> >> > tried different combinations of the gcc version and the
>> >> >> >>> >> >> > boost without success.
>> >> >> >>> >> >> >
>> >> >> >>> >> >> > Best regards,
>> >> >> >>> >> >> > Nancy
>> >> >> >>> >> >> >
>> >> >> >>> >> >> >
>> >> >> >>> >> >> >
>> >> >> >>> >> >> >
>> >> >> >>> >> >> >
>> >> >> >>> >> >> >
>> >> >> >>> >> >> >
>> >> >> >>> >> >> > --
>> >> >> >>> >> >> > Join us on Slack: https://join.slack.com/t/votca/signup
>> >> >> >>> >> >> > ---
>> >> >> >>> >> >> > 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 view this discussion on the web visit
>> >> >> >>> >> >> > https://groups.google.com/d/msgid/votca/41e71c8f-bef2-4df9-85ae-dcdc81474176n%40googlegroups.com.
>> >> >> >>> >> >>
>> >> >> >>> >> >>
>> >> >> >>> >> >>
>> >> >> >>> >> >> --
>> >> >> >>> >> >> Christoph Junghans
>> >> >> >>> >> >> Web: http://www.compphys.de
>> >> >> >>> >> >
>> >> >> >>> >> > --
>> >> >> >>> >> > Join us on Slack: https://join.slack.com/t/votca/signup
>> >> >> >>> >> > ---
>> >> >> >>> >> > 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 view this discussion on the web visit
>> >> >> >>> >> > https://groups.google.com/d/msgid/votca/27db68be-a714-4e69-92e0-a990dc90014en%40googlegroups.com.
>> >> >> >>> >>
>> >> >> >>> >>
>> >> >> >>> >>
>> >> >> >>> >> --
>> >> >> >>> >> Christoph Junghans
>> >> >> >>> >> Web: http://www.compphys.de
>> >> >> >>> >
>> >> >> >>> > --
>> >> >> >>> > Join us on Slack: https://join.slack.com/t/votca/signup
>> >> >> >>> > ---
>> >> >> >>> > 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 view this discussion on the web visit
>> >> >> >>> > https://groups.google.com/d/msgid/votca/6815a3c7-fefc-4d92-b3f5-7703a3e8cbc4n%40googlegroups.com.
>> >> >> >>>
>> >> >> >>>
>> >> >> >>>
>> >> >> >>> --
>> >> >> >>> Christoph Junghans
>> >> >> >>> Web: http://www.compphys.de
>> >> >> >
>> >> >> > --
>> >> >> > Join us on Slack: https://join.slack.com/t/votca/signup
>> >> >> > ---
>> >> >> > 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 view this discussion on the web visit
>> >> >> > https://groups.google.com/d/msgid/votca/61130d5f-ea2c-4326-9e05-c9ee9186863bn%40googlegroups.com.
>> >> >>
>> >> >>
>> >> >>
>> >> >> --
>> >> >> Christoph Junghans
>> >> >> Web: http://www.compphys.de
>> >> >
>> >> > --
>> >> > Join us on Slack: https://join.slack.com/t/votca/signup
>> >> > ---
>> >> > 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 view this discussion on the web visit
>> >> > https://groups.google.com/d/msgid/votca/f12d1177-3ac0-493c-b40b-0561c51aa00bn%40googlegroups.com.
>> >>
>> >>
>> >>
>> >> --
>> >> Christoph Junghans
>> >> Web: http://www.compphys.de
>> >
>> > --
>> > Join us on Slack: https://join.slack.com/t/votca/signup
>> > ---
>> > 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 view this discussion on the web visit
>> > https://groups.google.com/d/msgid/votca/c8c2483f-beac-434e-a33c-877618704c70n%40googlegroups.com.
>>
>>
>>
>> --
>> Christoph Junghans
>> Web: http://www.compphys.de
>
> --
> Join us on Slack: https://join.slack.com/t/votca/signup
> ---
> 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 view this discussion on the web visit
> https://groups.google.com/d/msgid/votca/6d745ebd-8dbc-4d6a-8949-81504846a3can%40googlegroups.com.
--
Christoph Junghans
Web: http://www.compphys.de
--
Join us on Slack: https://join.slack.com/t/votca/signup
---
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To view this discussion on the web visit
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