[gmx-users] make check error

[Mark Abraham]

Hi,

Assuming you are actually building GROMACS to run with MPI support, you
have a command that will be used to run an MPI program. Often that is
called mpirun, but not always. You need to find out what that is, and how
it wants you to choose multiple ranks, before you can use the
aforementioned CMake options to describe to ctest how to use it.

Mark

On Fri, Oct 21, 2016 at 1:25 AM Anna Vernon <lappala.anna at gmail.com> wrote:

> err, it does not find mpirun? I am confused
>
> Test project /home/anna/Downloads/gromacs-2016/build
>     Start 21: MdrunMpiTests
> Could not find executable /home/anna/Downloads/gromacs-2016/build/mpirun
> Looked in the following places:
> /home/anna/Downloads/gromacs-2016/build/mpirun
> /home/anna/Downloads/gromacs-2016/build/mpirun
> /home/anna/Downloads/gromacs-2016/build/Release/mpirun
> /home/anna/Downloads/gromacs-2016/build/Release/mpirun
> /home/anna/Downloads/gromacs-2016/build/Debug/mpirun
> /home/anna/Downloads/gromacs-2016/build/Debug/mpirun
> /home/anna/Downloads/gromacs-2016/build/MinSizeRel/mpirun
> /home/anna/Downloads/gromacs-2016/build/MinSizeRel/mpirun
> /home/anna/Downloads/gromacs-2016/build/RelWithDebInfo/mpirun
> /home/anna/Downloads/gromacs-2016/build/RelWithDebInfo/mpirun
> /home/anna/Downloads/gromacs-2016/build/Deployment/mpirun
> /home/anna/Downloads/gromacs-2016/build/Deployment/mpirun
> /home/anna/Downloads/gromacs-2016/build/Development/mpirun
> /home/anna/Downloads/gromacs-2016/build/Development/mpirun
> home/anna/Downloads/gromacs-2016/build/mpirun
> home/anna/Downloads/gromacs-2016/build/mpirun
> home/anna/Downloads/gromacs-2016/build/Release/mpirun
> home/anna/Downloads/gromacs-2016/build/Release/mpirun
> home/anna/Downloads/gromacs-2016/build/Debug/mpirun
> home/anna/Downloads/gromacs-2016/build/Debug/mpirun
> home/anna/Downloads/gromacs-2016/build/MinSizeRel/mpirun
> home/anna/Downloads/gromacs-2016/build/MinSizeRel/mpirun
> home/anna/Downloads/gromacs-2016/build/RelWithDebInfo/mpirun
> home/anna/Downloads/gromacs-2016/build/RelWithDebInfo/mpirun
> home/anna/Downloads/gromacs-2016/build/Deployment/mpirun
> home/anna/Downloads/gromacs-2016/build/Deployment/mpirun
> home/anna/Downloads/gromacs-2016/build/Development/mpirun
> home/anna/Downloads/gromacs-2016/build/Development/mpirun
> Unable to find executable: /home/anna/Downloads/gromacs-2016/build/mpirun
> 1/1 Test #21: MdrunMpiTests ....................***Not Run   0.00 sec
>
> 0% tests passed, 1 tests failed out of 1
>
> Label Time Summary:
> MpiIntegrationTest    =   0.00 sec
>
> Total Test time (real) =   0.00 sec
>
> The following tests FAILED:
>      21 - MdrunMpiTests (Not Run)
> Errors while running CTest
>
>
> On 20 October 2016 at 16:27, Anna Vernon <lappala.anna at gmail.com> wrote:
>
> > after doing this:
> > cmake .. -DMPIEXEC=mpirun -DMPIEXEC_NUMPROC_FLAG=-np -DNUMPROC=2,
> > -DNUMPROC=3, -DNUMPROC=4, -DNUMPROC=5, -DNUMPROC=6,
> -DNUMPROC=7,-DNUMPROC=8
> > make
> > make check
> > I get this:
> > The following tests FAILED:
> >      21 - MdrunMpiTests (Not Run)
> >      26 - regressiontests/pdb2gmx (Failed)
> > Errors while running CTest
> > CMakeFiles/run-ctest.dir/build.make:49: recipe for target
> > 'CMakeFiles/run-ctest' failed
> > make[3]: *** [CMakeFiles/run-ctest] Error 8
> > CMakeFiles/Makefile2:960: recipe for target
> 'CMakeFiles/run-ctest.dir/all'
> > failed
> > make[2]: *** [CMakeFiles/run-ctest.dir/all] Error 2
> > CMakeFiles/Makefile2:936: recipe for target 'CMakeFiles/check.dir/rule'
> > failed
> > make[1]: *** [CMakeFiles/check.dir/rule] Error 2
> > Makefile:544: recipe for target 'check' failed
> > make: *** [check] Error 2
> >
> >
> > On 20 October 2016 at 15:40, Mark Abraham <mark.j.abraham at gmail.com>
> > wrote:
> >
> >> Hi,
> >>
> >> It'd be great to be able to make all things clear to all people, but one
> >> person's clarity is another's verbosity :-( But do see
> >> http://manual.gromacs.org/documentation/2016/install-guide/
> >> index.html#using-cmake-command-line-options
> >> .
> >>
> >> Is an example of "cmake -DMPIEXEC=mpirun -DMPIEXEC_NUMPROC_FLAG=-np
> >> -DNUMPROC=6..." more clear, given that many people will want to
> customise
> >> at least one value?
> >>
> >> Mark
> >>
> >> On Thu, 20 Oct 2016 23:29 Anna Vernon <lappala.anna at gmail.com> wrote:
> >>
> >> > hi
> >> >
> >> > This passage (the one of interest in my case) of documentation is
> >> cryptic:
> >> >
> >> >
> >> > The make check target also runs integration-style tests that may run
> >> with
> >> > MPI if GMX_MPI=ON was set. To make these work, you may need to set the
> >> > CMake variables MPIEXEC, MPIEXEC_NUMPROC_FLAG, NUMPROC,
> MPIEXEC_PREFLAGS
> >> > and MPIEXEC_POSTFLAGS so that mdrun-mpi-test_mpi would run on multiple
> >> > ranks via the shell command
> >> >
> >> > ${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} ${NUMPROC} ${MPIEXEC_PREFLAGS} \
> >> >       mdrun-mpi-test_mpi ${MPIEXEC_POSTFLAGS} -otherflags
> >> >
> >> > Typically, one might use variable values mpirun, -np, 2, '', ''
> >> > respectively, in order to run on two ranks.
> >> > Is it possible to explain this more clearly? there are gazillions of
> >> files
> >> > in the cmake folder; where do I actually add the bit of code that sets
> >> the
> >> > variables?
> >> >
> >> > On 20 October 2016 at 07:56, Mark Abraham <mark.j.abraham at gmail.com>
> >> > wrote:
> >> >
> >> > > Hi,
> >> > >
> >> > > "make check" runs ctest behind the scenes. You can get some more
> >> > > information by running ctest directly. From your build directory,
> try
> >> > >
> >> > > ctest --output-on-failure --tests-regex "MdrunMpiTests"
> >> > > However, I suspect your issues may be already covered at
> >> > > http://manual.gromacs.org/documentation/2016/install-
> >> > > guide/index.html#testing-gromacs-for-correctness
> >> > > e.g.
> >> > > that you have done an MPI build, but you need to customize how you
> >> start
> >> > > your MPI enabled binaries.
> >> > >
> >> > > Mark
> >> > >
> >> > > On Thu, Oct 20, 2016 at 9:59 AM Anna Vernon <lappala.anna at gmail.com
> >
> >> > > wrote:
> >> > >
> >> > > trying  to compile gromacs 2016, upon execution of make check i get
> >> this:
> >> > >
> >> > > The following tests FAILED:
> >> > >       21 - MdrunMpiTests (Failed)
> >> > >       26 - regressiontests/pdb2gmx (Failed)
> >> > > Errors while running CTest
> >> > > CMakeFiles/run-ctest.dir/build.make:49: recipe for target
> >> > > 'CMakeFiles/run-ctest' failed
> >> > > make[3]: *** [CMakeFiles/run-ctest] Error 8
> >> > > CMakeFiles/Makefile2:960: recipe for target
> >> > > 'CMakeFiles/run-ctest.dir/all' failed
> >> > > make[2]: *** [CMakeFiles/run-ctest.dir/all] Error 2
> >> > > CMakeFiles/Makefile2:936: recipe for target
> >> 'CMakeFiles/check.dir/rule'
> >> > > failed
> >> > > make[1]: *** [CMakeFiles/check.dir/rule] Error 2
> >> > > Makefile:544: recipe for target 'check' failed
> >> > > make: *** [check] Error 2
> >> > >
> >> > >
> >> > > Can someone help please
> >> > > --
> >> > > Gromacs Users mailing list
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