[gmx-users] regression test errors

Wed Oct 23 13:40:14 CEST 2019

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
> >>>>>>
> >>>>>>
> >>>>> --
> >>>>> Gromacs Users mailing list
> >>>>>
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> >>>>> posting!
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> >>>>>
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>
> --
> Paul Bauer, PhD
> GROMACS Release Manager
> KTH Stockholm, SciLifeLab
> 0046737308594
>
> --
> Gromacs Users mailing list
>
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