[gmx-users] regression test errors

[Paul bauer]

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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-- 
Paul Bauer, PhD
GROMACS Release Manager
KTH Stockholm, SciLifeLab
0046737308594