[gmx-users] Make check error

[Shi Linyuan]

Hi,

I met some errors when running make check after compiling the Gromacs 2019. Really appreciate it if anyone could help me.

The Cmake info is listed as below:

cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON  -DGMX_SIMD=AVX2_256 -DCMAKE_INSTALL_PREFIX=/home/sly1993/sly1993/software/gromacs_run -DGMX_MPI=on -DMPIEXEC=srun

And  I used intel/2018 and openmpi/3.0.0 to compile it. The compiling is success and I can install it to my home path. Because the HPC uses SLURM system so I need to run the gromacs by the following command:

srun --mpi=pmix_v1 gmx_mpi

It works and output lots of normal information.

However, I met lots of errors when I run “make check” command because I want to check if the software works properly. The errors are listed as below:

Test project /home/sly1993/sly1993/software/gromacs/gromacs-2019.1/build
      Start  1: TestUtilsUnitTests
1/46 Test  #1: TestUtilsUnitTests ..................***Failed    0.15 sec
--------------------------------------------------------------------------
The application appears to have been direct launched using "srun",
but OMPI was not built with SLURM's PMI support and therefore cannot
execute. There are several options for building PMI support under
SLURM, depending upon the SLURM version you are using:

  version 16.05 or later: you can use SLURM's PMIx support. This
  requires that you configure and build SLURM --with-pmix.

  Versions earlier than 16.05: you must use either SLURM's PMI-1 or
  PMI-2 support. SLURM builds PMI-1 by default, or you can manually
  install PMI-2. You must then build Open MPI using --with-pmi pointing
  to the SLURM PMI library location.

Please configure as appropriate and try again.
--------------------------------------------------------------------------
*** An error occurred in MPI_Init_thread
*** on a NULL communicator
*** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,
***    and potentially your MPI job)
[i21a-s1.ufhpc:15257] Local abort before MPI_INIT completed completed successfully, but am not able to aggregate error messages, and not able to guarantee that all other processes were killed!

      Start  2: TestUtilsMpiUnitTests
2/46 Test  #2: TestUtilsMpiUnitTests ...............***Failed    2.01 sec
srun: error: Unable to create step for job 34989369: More processors requested than permitted

      Start  3: MdlibUnitTest
3/46 Test  #3: MdlibUnitTest .......................***Failed    0.03 sec

Abnormal return value for 'gmx_mpi grompp -f ./grompp.mdp -c ./conf -r ./conf -p ./topol -maxwarn 10  >grompp.out 2>grompp.err' was 1
No topol.tpr file in rb125. grompp failed
FAILED. Check grompp.err, grompp.out file(s) in rb125 for rb125
16 out of 16 simple tests FAILED

      Start 42: regressiontests/complex
^Cmake[3]: *** [CMakeFiles/run-ctest-nophys] Interrupt
make[2]: *** [CMakeFiles/run-ctest-nophys.dir/all] Interrupt
make[1]: *** [CMakeFiles/check.dir/rule] Interrupt
make: *** [check] Interrupt

I guess because the SLURM system adds the preflag “―mpi=pmix_v1”  in the run so I may need to adjust the CMAKE command. Anyone can tell me how to adjust the Cmake command?

Thank you very much in advance.

Regards,

Linyuan

------------------------------------------
Linyuan Shi
Ph.D. Candidate
Materials Science Engineering Department
University of Florida
Cell: 352-283-9950