building votca tools on supercomputer

[nancyfor]

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

[Christoph Junghans]

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

> --
> Join us on Slack: https://join.slack.com/t/votca/signup
> ---
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> To unsubscribe from this group and stop receiving emails from it, send an email to votca+un...@googlegroups.com.
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--
Christoph Junghans
Web: http://www.compphys.de

[nancyfor]

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

Nancy

[Christoph Junghans]

On Tue, Dec 1, 2020 at 3:00 AM nancyfor <nanc...@gmail.com> 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

> To view this discussion on the web visit https://groups.google.com/d/msgid/votca/27db68be-a714-4e69-92e0-a990dc90014en%40googlegroups.com.

[nancyfor]

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' 

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

[Christoph Junghans]

On Tue, Dec 1, 2020 at 7:11 AM nancyfor <nanc...@gmail.com> 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

> To view this discussion on the web visit https://groups.google.com/d/msgid/votca/6815a3c7-fefc-4d92-b3f5-7703a3e8cbc4n%40googlegroups.com.

[nancyfor]

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

[nancyfor]

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

[Christoph Junghans]

On Sat, Dec 19, 2020 at 8:05 AM nancyfor <nanc...@gmail.com> 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

> To view this discussion on the web visit https://groups.google.com/d/msgid/votca/61130d5f-ea2c-4326-9e05-c9ee9186863bn%40googlegroups.com.

[nancyfor]

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.

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

[Christoph Junghans]

On Sat, Dec 19, 2020 at 9:41 AM nancyfor <nanc...@gmail.com> 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

> To view this discussion on the web visit https://groups.google.com/d/msgid/votca/f12d1177-3ac0-493c-b40b-0561c51aa00bn%40googlegroups.com.

[nancyfor]

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 

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

[Christoph Junghans]

On Sat, Dec 19, 2020 at 4:02 PM nancyfor <nanc...@gmail.com> 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

> To view this discussion on the web visit https://groups.google.com/d/msgid/votca/c8c2483f-beac-434e-a33c-877618704c70n%40googlegroups.com.

[nancyfor]

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>"

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

I also tried spack, there were too many errors.

Perhaps it is a bad combination of the modules I am uploading.

Cheers, 

Nancy 

[Christoph Junghans]

On Sun, Dec 20, 2020 at 9:03 AM nancyfor <nanc...@gmail.com> 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

> To view this discussion on the web visit https://groups.google.com/d/msgid/votca/6d745ebd-8dbc-4d6a-8949-81504846a3can%40googlegroups.com.

[nancyfor]

Hi Christoph,

Thanks for your reply. Below my answers/comments

> 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.

I did not see the f.  However it did not past the configuration step. It seems it is looking  for gmx_is_double_precision. That is the line on the screen output, related to the error. 

Looking for c++ gmx_is_double_precision in /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 - not found

I tried then for VOTCA to build its own gromacs 

 

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

I use gromacs,  but it is useful to know it could be disable for lammps  

> 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.

if I used cmake --build builddir --verbose  --target=Gromacs_build

I get

Unknown argument --target=Gromacs_build

However, using only cmake --build builddir

It seems in fact the target exits

cmake --build builddir

Scanning dependencies of target Gromacs_build

[  1%] Creating directories for 'Gromacs_build'

[  1%] Performing download step (download, verify and extract) for 'Gromacs_build'

-- Downloading...

   dst='/u/forero/src/votca/builddir/gromacs/src/gromacs-2019.6.tar.gz'

Looking at the screen output it installed gromacs, the error appears because it is looking for libgromacs.so and because I used  -DBUILD_SHARED_LIBS=OFF so there was only  libgromacs.a.  I finally used

cmake -Bbuilddir -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ -DBUILD_CSGAPPS=ON -DBUILD_XTP=OFF -DBUILD_OWN_GROMACS=ON -DCMAKE_DISABLE_FIND_PACKAGE_MKL=ON -DCMAKE_INSTALL_PREFIX=${prefix} ../votca

 

and finally it was successfully installed :).  Is there a way to choose the gromacs version to be installed? I am running all my atomistic simulations in version 2019.4.  I believe this can be  changed  in the settings.xml file

Cheers, 

Nancy

[Christoph Junghans]

On Mon, Dec 21, 2020 at 6:32 AM nancyfor <nanc...@gmail.com> wrote:
>
> Hi Christoph,
>
> Thanks for your reply. Below my answers/comments
>
>>
>> > 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.
>
>
> I did not see the f. However it did not past the configuration step. It seems it is looking for gmx_is_double_precision. That is the line on the screen output, related to the error.
>
> Looking for c++ gmx_is_double_precision in /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 - not found

You can look in the CMake error log to see why this test is failing, I
assume you will need to list libmpi in GROMACS_LIBRARY as well to make
that work.

ok, yeah, I never thought about that combination.
I added a user error here: https://github.com/votca/votca/pull/552
Thanks for pointing that out!

>
> cmake -Bbuilddir -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ -DBUILD_CSGAPPS=ON -DBUILD_XTP=OFF -DBUILD_OWN_GROMACS=ON -DCMAKE_DISABLE_FIND_PACKAGE_MKL=ON -DCMAKE_INSTALL_PREFIX=${prefix} ../votca
>
> and finally it was successfully installed :). Is there a way to choose the gromacs version to be installed? I am running all my atomistic simulations in version 2019.4. I believe this can be changed in the settings.xml file

There is no option to select the gromacs version, that would be a case
of installing with spack.
VOTCA builds 2019.6 internally, as it is that last version that has
support for tabulated interactions.
When you install VOTCA the internally-built gromacs binaries will end
up in the same directory.

However you can tweak what gromacs version is used at runtime to run
the simulation with the
cg.inverse.gromacs.mdrun.command option in the xml files.
You could set it to something like "mpirun -np 16 mdrun_mpi".
To tweak the grompp binary use cg.inverse.gromacs.grompp.bin, the
default is "gmx grompp" for that.

Christoph
>
> Cheers,

> Nancy
>
> --
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[nancyfor]

On Monday, 21 December 2020 at 15:35:37 UTC+1 Christoph Junghans wrote:

> Looking for c++ gmx_is_double_precision in /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 - not found

You can look in the CMake error log to see why this test is failing, I
assume you will need to list libmpi in GROMACS_LIBRARY as well to make
that work.

I can not located libmpi.a or libm.a. I only  found a libmpx.a in /mpcdf/soft/SLE_12/packages/x86_64/gcc/8.4.0/lib64/libmpx.a  and used

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/libfftw3f.a;/mpcdf/soft/SLE_12/packages/x86_64/gcc/8.4.0/lib64/libmpx.a" -DCMAKE_DISABLE_FIND_PACKAGE_MKL=ON -DCMAKE_INSTALL_PREFIX=${prefix} ../votca

the configuration worked, but when building it I got the same error as before when linking csg_gmxtopol 

.....

[ 66%] Linking CXX executable csg_gmxtopol

cd /u/forero/src/votca-tmp/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-tmp/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-tmp/votca/builddir'

Makefile:129: recipe for target 'all' failed

gmake: *** [all] Error 2

> Looking at the screen output it installed gromacs, the error appears because it is looking for libgromacs.so and because I used -DBUILD_SHARED_LIBS=OFF so there was only libgromacs.a. I finally used

ok, yeah, I never thought about that combination.
I added a user error here: https://github.com/votca/votca/pull/552
Thanks for pointing that out!

Good! I am glad something useful came out of this long thread :) 

There is no option to select the gromacs version, that would be a case
of installing with spack.
VOTCA builds 2019.6 internally, as it is that last version that has
support for tabulated interactions.
When you install VOTCA the internally-built gromacs binaries will end
up in the same directory.

Oh, I was not aware this was the case in the new versions of GROMACS. 

 

However you can tweak what gromacs version is used at runtime to run
the simulation with the
cg.inverse.gromacs.mdrun.command option in the xml files.
You could set it to something like "mpirun -np 16 mdrun_mpi".
To tweak the grompp binary use cg.inverse.gromacs.grompp.bin, the
default is "gmx grompp" for that.

Thank you for your help!

Cheers, 

Nancy 

[Christoph Junghans]

On Mon, Dec 21, 2020 at 10:05 AM nancyfor <nanc...@gmail.com> wrote:
>
>
> On Monday, 21 December 2020 at 15:35:37 UTC+1 Christoph Junghans wrote:
>>
>>
>> > Looking for c++ gmx_is_double_precision in /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 - not found
>>
>> You can look in the CMake error log to see why this test is failing, I
>> assume you will need to list libmpi in GROMACS_LIBRARY as well to make
>> that work.
>>
>
> I can not located libmpi.a or libm.a. I only found a libmpx.a in /mpcdf/soft/SLE_12/packages/x86_64/gcc/8.4.0/lib64/libmpx.a and used
>
> 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/libfftw3f.a;/mpcdf/soft/SLE_12/packages/x86_64/gcc/8.4.0/lib64/libmpx.a" -DCMAKE_DISABLE_FIND_PACKAGE_MKL=ON -DCMAKE_INSTALL_PREFIX=${prefix} ../votca
>
> the configuration worked, but when building it I got the same error as before when linking csg_gmxtopol
> .....
> [ 66%] Linking CXX executable csg_gmxtopol
> cd /u/forero/src/votca-tmp/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'

I am running out of ideas....not sure why libfftw3f.a is missing here,
even though you had it in GROMACS_LIBRARY above.

> 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-tmp/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-tmp/votca/builddir'
> Makefile:129: recipe for target 'all' failed
> gmake: *** [all] Error 2
>
>
>>
>>
>> > Looking at the screen output it installed gromacs, the error appears because it is looking for libgromacs.so and because I used -DBUILD_SHARED_LIBS=OFF so there was only libgromacs.a. I finally used
>>
>> ok, yeah, I never thought about that combination.
>> I added a user error here: https://github.com/votca/votca/pull/552
>> Thanks for pointing that out!
>
>
> Good! I am glad something useful came out of this long thread :)
>
>>
>> There is no option to select the gromacs version, that would be a case
>> of installing with spack.
>> VOTCA builds 2019.6 internally, as it is that last version that has
>> support for tabulated interactions.
>> When you install VOTCA the internally-built gromacs binaries will end
>> up in the same directory.
>
>
> Oh, I was not aware this was the case in the new versions of GROMACS.

Yeah, gromacs-2020 and higher won't work for coarse-graining,
hopefully that feature will be back in gromacs-2022.

>
>>
>> However you can tweak what gromacs version is used at runtime to run
>> the simulation with the
>> cg.inverse.gromacs.mdrun.command option in the xml files.
>> You could set it to something like "mpirun -np 16 mdrun_mpi".
>> To tweak the grompp binary use cg.inverse.gromacs.grompp.bin, the
>> default is "gmx grompp" for that.
>
>
> Thank you for your help!
> Cheers,
> Nancy
>

> --
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