I installed Gromacs via:
./build.sh --prefix ${prefix} gromacs
I had previously installed the Gromacs and the development packages via the
standard Ubuntu repository & apt-get but then got an error message that my
Gromacs version was to old so I removed those packages and installed them via
buld.sh instead.
No, I didn't use any special options, just plain "build.sh --prefix
${prefix} tools csg". Eventually I also would like to install ctp but I was
trying to do this first.
Thanks,
Martijn
On Wednesday, 10 January 2018 14:08:35 UTC, Christoph Junghans wrote:
>
> On Wed, Jan 10, 2018 at 5:31 AM, Martijn Zwijnenburg
> <[email protected] <javascript:>> wrote:
> > Hi,
> >
> > I'm trying to build votca but I consistently get the error below when
> > running; ./build.sh --prefix ${prefix} tools csg, in the csg part of the
> > build:
> >
> > [ 45%] Building CXX object
> > src/libcsg/CMakeFiles/votca_csg.dir/modules/io/xyzwriter.cc.o
> >
> /home/martijn/bin/votca/src/csg/src/libcsg/modules/io/gmxtopologyreader.cc:
> > In member function ‘virtual bool
> > votca::csg::GMXTopologyReader::ReadTopology(std::__cxx11::string,
> > votca::csg::Topology&)’:
> >
> /home/martijn/bin/votca/src/csg/src/libcsg/modules/io/gmxtopologyreader.cc:52:16:
>
>
> > error: aggregate ‘t_inputrec ir’ has incomplete type and cannot be
> defined
> > t_inputrec ir;
> > ^
> > [ 46%] Building CXX object
> > src/libcsg/CMakeFiles/votca_csg.dir/modules/io/pdbreader.cc.o
> > [ 47%] Building CXX object
> > src/libcsg/CMakeFiles/votca_csg.dir/modules/io/groreader.cc.o
> > [ 48%] Building CXX object
> > src/libcsg/CMakeFiles/votca_csg.dir/modules/io/pdbwriter.cc.o
> > src/libcsg/CMakeFiles/votca_csg.dir/build.make:662: recipe for target
> > 'src/libcsg/CMakeFiles/votca_csg.dir/modules/io/gmxtopologyreader.cc.o'
> > failed
> > make[2]: ***
> > [src/libcsg/CMakeFiles/votca_csg.dir/modules/io/gmxtopologyreader.cc.o]
> > Error 1
> > make[2]: *** Waiting for unfinished jobs....
> > [ 50%] Building CXX object
> >
> src/libcsg/CMakeFiles/votca_csg.dir/modules/io/dlpolytrajectoryreader.cc.o
> >
> /home/martijn/bin/votca/src/csg/src/libcsg/modules/io/gmxtrajectoryreader.cc:
>
> > In member function ‘virtual bool
> > votca::csg::GMXTrajectoryReader::FirstFrame(votca::csg::Topology&)’:
> >
> /home/martijn/bin/votca/src/csg/src/libcsg/modules/io/gmxtrajectoryreader.cc:43:5:
>
>
> > error: ‘output_env_t’ was not declared in this scope
> > output_env_t oenv;
> > ^
> >
> /home/martijn/bin/votca/src/csg/src/libcsg/modules/io/gmxtrajectoryreader.cc:45:31:
>
>
> > error: ‘oenv’ was not declared in this scope
> > output_env_init_default (&oenv);
> > ^
> >
> /home/martijn/bin/votca/src/csg/src/libcsg/modules/io/gmxtrajectoryreader.cc:45:35:
>
>
> > error: ‘output_env_init_default’ was not declared in this scope
> > output_env_init_default (&oenv);
> > ^
> >
> /home/martijn/bin/votca/src/csg/src/libcsg/modules/io/gmxtrajectoryreader.cc:
>
> > In member function ‘virtual bool
> > votca::csg::GMXTrajectoryReader::NextFrame(votca::csg::Topology&)’:
> >
> /home/martijn/bin/votca/src/csg/src/libcsg/modules/io/gmxtrajectoryreader.cc:89:5:
>
>
> > error: ‘output_env_t’ was not declared in this scope
> > output_env_t oenv;
> > ^
> >
> /home/martijn/bin/votca/src/csg/src/libcsg/modules/io/gmxtrajectoryreader.cc:91:31:
>
>
> > error: ‘oenv’ was not declared in this scope
> > output_env_init_default (&oenv);
> > ^
> >
> /home/martijn/bin/votca/src/csg/src/libcsg/modules/io/gmxtrajectoryreader.cc:91:35:
>
>
> > error: ‘output_env_init_default’ was not declared in this scope
> > output_env_init_default (&oenv);
> > ^
> > src/libcsg/CMakeFiles/votca_csg.dir/build.make:710: recipe for target
> >
> 'src/libcsg/CMakeFiles/votca_csg.dir/modules/io/gmxtrajectoryreader.cc.o'
> > failed
> > make[2]: ***
> >
> [src/libcsg/CMakeFiles/votca_csg.dir/modules/io/gmxtrajectoryreader.cc.o]
> > Error 1
> > CMakeFiles/Makefile2:450: recipe for target
> > 'src/libcsg/CMakeFiles/votca_csg.dir/all' failed
> > make[1]: *** [src/libcsg/CMakeFiles/votca_csg.dir/all] Error 2
> > Makefile:127: recipe for target 'all' failed
> > make: *** [all] Error 2
> >
> > What could be the problem? I'm building on an Ubuntu machine and before
> > commencing the build it mentions all required packages are there.
> What version of Gromacs do you have installed?
> Did you use any special options or just plain "./build.sh --prefix
> ${prefix} tools csg" ?
>
> Christoph
> >
> > Thanks in advance,
> >
> > Martijn
> >
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>
>
>
> --
> Christoph Junghans
> Web: http://www.compphys.de
>
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