[gmx-users] Fwd: make check error
Anna Vernon
lappala.anna at gmail.com
Fri Oct 21 11:35:18 CEST 2016
Let us try this again.
I run these commands from the build directory:
cmake .. -DMPIEXEC=mpirun -DMPIEXEC_NUMPROC_FLAG=-np -DNUMPROC=2,
-DNUMPROC=3, -DNUMPROC=4, -DNUMPROC=5, -DNUMPROC=6, -DNUMPROC=7,-DNUMPROC=8
make -j 4
make check -j 4
if I locate openmpi , I can see that it exists and openmpi is something I
want to use, because it had no problems with other MD software packages
that I have compiled in the past.
/etc/openmpi
/etc/openmpi/openmpi-default-hostfile
/etc/openmpi/openmpi-mca-params.conf
/etc/openmpi/openmpi-totalview.tcl
/usr/bin/mdrun_mpi.openmpi
/usr/bin/mdrun_mpi_d.openmpi
/usr/bin/mpiexec.openmpi
/usr/bin/mpirun.openmpi
/usr/lib/openmpi
Anyhow, after implementing make check, this is still what I get. Is there
some sort of flag that I am missing or is this something that is a bug?
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
On 21 October 2016 at 03:24, Mark Abraham <mark.j.abraham at gmail.com> wrote:
> Hi,
>
> On Fri, Oct 21, 2016 at 10:26 AM Anna Lappala <lappala.anna at gmail.com>
> wrote:
>
> >
> > > Hi,
> > >
> > > please decrypt what you said- it was obvious from my earlier steps that
> > i am making gromacs with mpi support.
>
>
> I haven't seen your original cmake call, so I can't tell. These tests all
> run whether you've configured with MPI or not. I've been forced to make
> educated guesses all along, which makes it frustrating for everyone :-)
>
>
> > Again, what is it if not mpirun? How do i check all this?
> >
>
> You're trying to run on a compute cluster - it has documentation about what
> it supports for running MPI. You might have to use srun, or mpiexec, or
> aprun or poe or something else, and each of those have a different way of
> expressing "run this program on n ranks." So all we have implemented is a
> way for the problem to be solved, and a default that will often work.
>
> >> "it wants you to choose multiple ranks, before you can use the
> > >> aforementioned CMake options to describe to ctest how to use it."
> > > No, all it "wants" is to locate mpirun in any of the aforementioned
> > folders. The tests run successfully if i put mpirun executable in the
> > folder it wants to.
> > > This does not however change the situation when i rerun the cmake
> > command.
> > > So let me be more clear. What do i do to make mpirun and which one of
> > the steps that i am doing is wrong? See the commands in previous emails.
> >
>
> mpirun isn't something we are building. It's infrastructure provided by
> your MPI installation for taking GROMACS and running it across multiple
> nodes. But depending on your MPI flavour, it could be named anything else,
> so for now the only want to get the tests to run for some of the MPI
> flavours is for you to consult your local documentation and work out how to
> use it. You'll need to do this anyway to learn how to run the equivalent of
>
> mpirun -np 16 gmx_mpi mdrun -s your-simulation
>
> Mark
>
>
> > >
> > >> On Oct 21, 2016, at 01:47, Mark Abraham <mark.j.abraham at gmail.com>
> > wrote:
> > >>
> > >> 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
> > --
> > Gromacs Users mailing list
> >
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