[gmx-users] regression test errors
Dave M
dave.gromax at gmail.com
Wed Oct 23 14:04:27 CEST 2019
Thanks a lot Paul.
best regards,
D
On Wed, Oct 23, 2019 at 4:44 AM Paul bauer <paul.bauer.q at gmail.com> wrote:
> Hello Dave,
>
> I thought it was something like that.
> The error is harmless (just telling you that MPI is doing its job), and
> the testing script gets confused because of the extra message in the
> output file.
>
> So I think you are good to go (and we need to do something about the
> testing script).
>
> Happy simulating!
>
> Cheers
>
> Paul
>
> On 23/10/2019 13:39, Dave M wrote:
> > Hi Paul,
> >
> > I checked using this command for a specific folder, and I used '-mpirun
> > mdrun' rather '-mpirun mpirun':
> >
> >
> > ./gmxtest.pl -mpirun mdrun -np 2 -noverbose rotation
> >
> >
> >
> > I get lot of these errors:
> >
> >
> > topol.tpr file different from ./reference_s.tpr. Check files in flex for
> > flex
> >
> > FAILED. Check checktpr.out, checktpr.err file(s) in flex for flex
> >
> > topol.tpr file different from ./reference_s.tpr. Check files in flex-t
> for
> > flex-t
> >
> > FAILED. Check checktpr.out, checktpr.err file(s) in flex-t for flex-t
> >
> > topol.tpr file different from ./reference_s.tpr. Check files in flex2 for
> > flex2
> >
> > FAILED. Check checktpr.out, checktpr.err file(s) in flex2 for flex2
> >
> > topol.tpr file different from ./reference_s.tpr. Check files in flex2-t
> for
> > flex2-t
> >
> > FAILED. Check checktpr.out, checktpr.err file(s) in flex2-t for flex2-t
> >
> >
> > .... so on
> >
> >
> >
> > A) the only suspicious thing I see in checktpr.err is possibly different
> > software versions.
> >
> >
> > Command line:
> >
> > gmx_mpi check -s1 ./reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol
> > 0.001
> >
> >
> > Note: When comparing run input files, default tolerances are reduced.
> >
> > Reading file ./reference_s.tpr, VERSION 5.0-beta2-dev-20140130-02adca5
> > (single precision)
> >
> > Note: file tpx version 96, software tpx version 116
> >
> > Reading file topol.tpr, VERSION 2019.4 (single precision)
> >
> >
> >
> >
> > B) And Only suspicious thing I see in checktpr.out is pasted below (I
> have
> > removed the host ip number). Just to mention I use Amazon web services so
> > probably the following error is related to instance when it was created
> and
> > then stored as an image and then re-used with a different ip. May be am
> > just talking silly!
> >
> >
> > [[2115,1],0]: A high-performance Open MPI point-to-point messaging module
> >
> > was unable to find any relevant network interfaces:
> >
> >
> > Module: OpenFabrics (openib)
> >
> > Host: ip-xxx-xx-xx-xxx
> >
> >
> > Another transport will be used instead, although this may result in
> >
> > lower performance.
> >
> >
> > NOTE: You can disable this warning by setting the MCA parameter
> >
> > btl_base_warn_component_unused to 0.
> >
> >
> > On Wed, Oct 23, 2019 at 4:10 AM Paul bauer <paul.bauer.q at gmail.com>
> wrote:
> >
> >> Hello Dave,
> >>
> >> this is weird, no idea why it didn't work then.
> >> You can try running the test suite manually in the folder you found with
> >>
> >> perl gmxtest.pl -mpirun mpirun -np X -noverbose
> >>
> >> That will show if the test binary works and should report any failing
> >> tests.
> >> Don't forget to source the GMXRC file before trying, though!
> >>
> >> Cheers
> >>
> >> Paul
> >>
> >>
> >> On 23/10/2019 12:36, Dave M wrote:
> >>> Hi Paul,
> >>>
> >>> Thanks for the 'mpirun -n X gmx_mpi mdrun'. It works now.
> >>>
> >>> Regarding tests, I found the folder here build/tests/regressiontests
> >>> So I checked all the log using a simple script (searching keyword
> >>> 'Finished') and it shows that all the log files have Finished properly
> >> in
> >>> their corresponding folders. So log files do not say anything here.
> >>>
> >>> On Wed, Oct 23, 2019 at 3:07 AM Paul Bauer <paul.bauer.q at gmail.com>
> >> wrote:
> >>>> Hello Dave,
> >>>>
> >>>> You need to use mpirun -n (number of processes) gmx_mpi mdrun to use a
> >> MPI
> >>>> enabled build of GROMACS. This is what the error message tries to tell
> >> you,
> >>>> but we might need to improve on this.
> >>>>
> >>>> There should be a regressiontests folder somewhere in your build tree
> >> if it
> >>>> downloaded the tests correctly.
> >>>>
> >>>> Cheers
> >>>>
> >>>> Paul
> >>>>
> >>>> On Wed, 23 Oct 2019, 12:02 Dave M, <dave.gromax at gmail.com> wrote:
> >>>>
> >>>>> Hi Paul,
> >>>>>
> >>>>> Thanks for your reply.
> >>>>> a) I just checked there is no tests/regressiontests, some other
> folder
> >> is
> >>>>> there test/sphysicalvalidation
> >>>>> There is no log file.
> >>>>> b) Regarding thread-mpi I think it is not installed because when I
> use
> >>>> some
> >>>>> command like this:
> >>>>>
> >>>>>
> >>>>> gmx_mpi mdrun -v -deffnm 03-run -rdd 2.0 -nt 2
> >>>>>
> >>>>> I get an error:
> >>>>>
> >>>>>
> >>>>> Fatal error:
> >>>>>
> >>>>> Setting the total number of threads is only supported with thread-MPI
> >> and
> >>>>> GROMACS was compiled without thread-MPI
> >>>>>
> >>>>> I think (please correct me) gmx_mpi is for external MPI openMPI in
> my
> >>>> case
> >>>>> so I tried just 'gmx mdrun' (not gmx_mpi) but then it says command
> not
> >>>>> found. I am not sure what I missed in installation cmake flags.
> >>>>>
> >>>>> Dave
> >>>>>
> >>>>> On Wed, Oct 23, 2019 at 2:45 AM Paul Bauer <paul.bauer.q at gmail.com>
> >>>> wrote:
> >>>>>> Hello Dave,
> >>>>>>
> >>>>>> Did you have a look into the log files from the regression tests
> under
> >>>>>> tests/regressiontests?
> >>>>>> They might give us some insight into what is happening.
> >>>>>>
> >>>>>> The warning in respect to thread-MPI is harmless, it just tells you
> >>>> that
> >>>>>> you are using real MPI instead of thread-MPI.
> >>>>>>
> >>>>>> Cheers
> >>>>>> Paul
> >>>>>>
> >>>>>> On Wed, 23 Oct 2019, 07:36 Dave M, <dave.gromax at gmail.com> wrote:
> >>>>>>
> >>>>>>> Hi All,
> >>>>>>>
> >>>>>>> Any hints/help much appreciated why am getting regression tests
> >>>>> failure.
> >>>>>>> Also to mention I think thread-mpi was not installed as I got an
> >>>> error
> >>>>>>> saying "MPI is not compatible with thread-MPI. Disabling
> thread-MPI".
> >>>>> How
> >>>>>>> to check the compatibility?
> >>>>>>>
> >>>>>>> Thanks.
> >>>>>>>
> >>>>>>> best regards,
> >>>>>>> D
> >>>>>>>
> >>>>>>> On Sun, Oct 20, 2019 at 2:58 AM Dave M <dave.gromax at gmail.com>
> >>>> wrote:
> >>>>>>>> Hi All,
> >>>>>>>>
> >>>>>>>> I am trying to install gromacs2019.4 with:
> >>>>>>>> cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=on
> >>>>>>>> -DGMX_MPI=on -DGMX_GPU=on
> >>>>>>>> -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs/gromacs2019_4
> >>>>>>>> -DGMX_FFT_LIBRARY=fftw3 -DCMAKE_BUILD_TYPE=Debug
> >>>>>>>>
> >>>>>>>> But 5 tests (41 to 46) were failed copied below:
> >>>>>>>>
> >>>>>>>>
> >>>>>>>> The following tests FAILED:
> >>>>>>>>
> >>>>>>>> 41 - regressiontests/simple (Failed)
> >>>>>>>>
> >>>>>>>> 42 - regressiontests/complex (Failed)
> >>>>>>>>
> >>>>>>>> 43 - regressiontests/kernel (Failed)
> >>>>>>>>
> >>>>>>>> 44 - regressiontests/freeenergy (Failed)
> >>>>>>>>
> >>>>>>>> 45 - regressiontests/rotation (Failed)
> >>>>>>>>
> >>>>>>>> Errors while running CTest
> >>>>>>>>
> >>>>>>>> CMakeFiles/run-ctest-nophys.dir/build.make:57: recipe for target
> >>>>>>>> 'CMakeFiles/run-ctest-nophys' failed
> >>>>>>>>
> >>>>>>>> make[3]: *** [CMakeFiles/run-ctest-nophys] Error 8
> >>>>>>>>
> >>>>>>>> CMakeFiles/Makefile2:1392: recipe for target
> >>>>>>>> 'CMakeFiles/run-ctest-nophys.dir/all' failed
> >>>>>>>>
> >>>>>>>> make[2]: *** [CMakeFiles/run-ctest-nophys.dir/all] Error 2
> >>>>>>>>
> >>>>>>>> CMakeFiles/Makefile2:1172: recipe for target
> >>>>>> 'CMakeFiles/check.dir/rule'
> >>>>>>>> failed
> >>>>>>>>
> >>>>>>>> make[1]: *** [CMakeFiles/check.dir/rule] Error 2
> >>>>>>>>
> >>>>>>>> Makefile:626: recipe for target 'check' failed
> >>>>>>>> make: *** [check] Error 2
> >>>>>>>>
> >>>>>>>> Not sure what could be wrong. Just to add I get some error/warning
> >>>>>> during
> >>>>>>>> installation which says "MPI is not compatible with thread-MPI.
> >>>>>> Disabling
> >>>>>>>> thread-MPI". I am using -DGMX_MPI=on and to have openMPI on ubuntu
> >>>>>> 18.04
> >>>>>>> I
> >>>>>>>> used "sudo apt-get install openmpi-bin openmpi-common
> >>>> libopenmpi-dev"
> >>>>>>>> Please let me know how I can fix this.
> >>>>>>>>
> >>>>>>>> best regards,
> >>>>>>>> D
> >>>>>>>>
> >>>>>>>>
> >>>>>>> --
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> >>>>>>>
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> >>>>>>> posting!
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> >> --
> >> Paul Bauer, PhD
> >> GROMACS Release Manager
> >> KTH Stockholm, SciLifeLab
> >> 0046737308594
> >>
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at
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> >> posting!
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> >>
>
> --
> Paul Bauer, PhD
> GROMACS Release Manager
> KTH Stockholm, SciLifeLab
> 0046737308594
>
> --
> Gromacs Users mailing list
>
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