[gmx-users] make check error

[Anna Vernon]

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
>> > >
>> > > * Please search the archive at
>> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> > > posting!
>> > >
>> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> > >
>> > > * For (un)subscribe requests visit
>> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> > send
>> > > a mail to gmx-users-request at gromacs.org.
>> > > --
>> > > Gromacs Users mailing list
>> > >
>> > > * Please search the archive at http://www.gromacs.org/
>> > > Support/Mailing_Lists/GMX-Users_List before posting!
>> > >
>> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> > >
>> > > * For (un)subscribe requests visit
>> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> > > send a mail to gmx-users-request at gromacs.org.
>> > >
>> > --
>> > Gromacs Users mailing list
>> >
>> > * Please search the archive at
>> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> > posting!
>> >
>> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> >
>> > * For (un)subscribe requests visit
>> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> > send a mail to gmx-users-request at gromacs.org.
>> >
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support
>> /Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>
>
>