Facing problem with VOTCA installation in Ubuntu 16.04

[Souvik Chakraborty]

Dear members,

I am trying to install votca-csg for the first time. I found some error at the 'cmake' step. Please shed light on the issue and if I did something wrong.

I have Gromacs 16.03 installed and I am using cmake 3.14.5.

##############################################################################

$->  pkg-config --libs libgromacs

-L/usr/local/gromacs/lib -lgromacs -lm

$->  cmake -DBUILD_CSGAPPS=ON -DCMAKE_INSTALL_PREFIX=${prefix} -DWITH_GMX=ON -DGROMACS_INCLUDE_DIR=/usr/local/gromacs/include  -DGROMACS_LIBRARY=/usr/local/gromacs/lib/libgromacs.so ..

-- Boost version: 1.58.0
-- Found the following Boost libraries:
--   program_options
--   filesystem
--   system
-- Intel(R) MKL could not be found.
-- Found Eigen3: /usr/local/share/eigen3/cmake
-- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE)
-- Boost version: 1.58.0
-- Found the following Boost libraries:
--   program_options
--   filesystem
--   system
-- Found Eigen3: /usr/local/share/eigen3/cmake
-- Found VOTCA_TOOLS:
CMake Error at csg/CMakeModules/FindGROMACS.cmake:52 (message):
  Could not find a suitable gromacs library.  gmx_version is not defined in
  the gromacs library, that is very very strange, take a look at the error
  message in
  /home/souvik/Downloads/VOTKA/VOTKA-git/votca/build/CMakeFiles/CMakeError.log
  to find out what was going wrong.  This most likely means that your gromacs
  version is too old, we need at least gromacs 2016!
Call Stack (most recent call first):
  CMakeLists.txt:78 (_find_package)
  csg/CMakeLists.txt:73 (find_package)


-- Configuring incomplete, errors occurred!
See also "/home/souvik/Downloads/VOTKA/VOTKA-git/votca/build/CMakeFiles/CMakeOutput.log".
See also "/home/souvik/Downloads/VOTKA/VOTKA-git/votca/build/CMakeFiles/CMakeError.log".

#########################################################################################

The errors printed on CMakeError.log:

CMakeFiles/cmTC_6e721.dir/build.make:65: recipe for target 'CMakeFiles/cmTC_6e721.dir/src.c.o' failed
make[1]: *** [CMakeFiles/cmTC_6e721.dir/src.c.o] Error 1
make[1]: Leaving directory '/home/souvik/Downloads/VOTKA/VOTKA-git/votca/build/CMakeFiles/CMakeTmp'
Makefile:121: recipe for target 'cmTC_6e721/fast' failed
make: *** [cmTC_6e721/fast] Error 2

Source file was:
int main(void) {
      #ifndef _AIX
      #error
      #endif
      return 0;
      }
Determining if the function gmx_version exists in the /usr/lib/x86_64-linux-gnu/libgromacs_d.so failed with the following output:
Change Dir: /home/souvik/Downloads/VOTKA/VOTKA-git/votca/build/CMakeFiles/CMakeTmp

Run Build Command(s):/usr/bin/make cmTC_ba1cf/fast
/usr/bin/make -f CMakeFiles/cmTC_ba1cf.dir/build.make CMakeFiles/cmTC_ba1cf.dir/build
make[1]: Entering directory '/home/souvik/Downloads/VOTKA/VOTKA-git/votca/build/CMakeFiles/CMakeTmp'
Building CXX object CMakeFiles/cmTC_ba1cf.dir/CheckFunctionExists.cpp.o
/usr/bin/c++    -DCHECK_FUNCTION_EXISTS=gmx_version   -std=c++14 -o CMakeFiles/cmTC_ba1cf.dir/CheckFunctionExists.cpp.o -c /home/souvik/Downloads/VOTKA/VOTKA-git/votca/csg/CMakeModules/CheckFunctionExists.cpp
Linking CXX executable cmTC_ba1cf
/usr/local/bin/cmake -E cmake_link_script CMakeFiles/cmTC_ba1cf.dir/link.txt --verbose=1
/usr/bin/c++   -DCHECK_FUNCTION_EXISTS=gmx_version    CMakeFiles/cmTC_ba1cf.dir/CheckFunctionExists.cpp.o  -o cmTC_ba1cf /usr/lib/x86_64-linux-gnu/libgromacs_d.so
CMakeFiles/cmTC_ba1cf.dir/CheckFunctionExists.cpp.o: In function `main':
CheckFunctionExists.cpp:(.text+0x10): undefined reference to `gmx_version()'
collect2: error: ld returned 1 exit status
CMakeFiles/cmTC_ba1cf.dir/build.make:87: recipe for target 'cmTC_ba1cf' failed
make[1]: *** [cmTC_ba1cf] Error 1
make[1]: Leaving directory '/home/souvik/Downloads/VOTKA/VOTKA-git/votca/build/CMakeFiles/CMakeTmp'
Makefile:121: recipe for target 'cmTC_ba1cf/fast' failed
make: *** [cmTC_ba1cf/fast] Error 2

##########################################################################

Regards,

Souvik

[Christoph Junghans]

On Wed, Jun 5, 2019, 06:04 Souvik Chakraborty <souv...@gmail.com> wrote:

Dear members,

I am trying to install votca-csg for the first time. I found some error at the 'cmake' step. Please shed light on the issue and if I did something wrong.

I have Gromacs 16.03 installed and I am using cmake 3.14.5.

##############################################################################

$->  pkg-config --libs libgromacs

-L/usr/local/gromacs/lib -lgromacs -lm

If you look at the error message below VOTCA actually picked up a libgromacs_d.so from somewhere else. Setting GROMACS_LIBRARY should actually overwrite that finding. Please check another time you point CMake to the right place and start from a empty build directory again.

Otherwise, you can also have votca compile it's own gromacs by setting BUILD_OWN_GROMACS=ON.

Christoph

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[Souvik Chakraborty]

Thanks a lot, Christoph. It worked when started afresh. One thing to clarify: if Votca compiles its "own" gromacs, what will be its version? And will it be compatible with the all-atom trajectory generated by any gromacs version (2016 and beyond)?

Regards,

Souvik

To unsubscribe from this group and stop receiving emails from it, send an email to vo...@googlegroups.com.

[Christoph Junghans]

On Wed, Jun 5, 2019 at 10:01 PM Souvik Chakraborty <souv...@gmail.com> wrote:
>
> Thanks a lot, Christoph. It worked when started afresh. One thing to clarify: if Votca compiles its "own" gromacs, what will be its version? And will it be compatible with the all-atom trajectory generated by any gromacs version (2016 and beyond)?

Yeah, we just build gromacs-2018.6 internally.

Christoph

> To unsubscribe from this group and stop receiving emails from it, send an email to votca+un...@googlegroups.com.

> To post to this group, send email to vo...@googlegroups.com.
> Visit this group at https://groups.google.com/group/votca.

> To view this discussion on the web visit https://groups.google.com/d/msgid/votca/ce9212d2-9329-420a-a949-7a0bdbcf3660%40googlegroups.com.

> For more options, visit https://groups.google.com/d/optout.

--
Christoph Junghans
Web: http://www.compphys.de

[Souvik Chakraborty]

Thanks, Christoph.

Rgds.

Souvik