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<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt">So my guess would be that I should configure my version of OpenMPI to work with slurm?
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;mso-fareast-language:EN-US">Yes, your OpenMPI installation should be configured with PMI support (--with-pmi flag) to work with srun. That issue is not related to container, since both SLURM and
OpenMPI are on the host side.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
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<b><span style="font-size:12.0pt;color:black">From: </span></b><span style="font-size:12.0pt;color:black">cp2k@googlegroups.com <cp2k@googlegroups.com> on behalf of Ava Rajh <ava.rajh@gmail.com><br>
<b>Date: </b>Thursday, 19 October 2023 at 13:56<br>
<b>To: </b>cp2k@googlegroups.com <cp2k@googlegroups.com><br>
<b>Subject: </b>Re: [CP2K:19393] Help with running cp2k in parallel with Slurm<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt">Hi,
<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt">I tested the provided docker. When running in the container it again works great, outside the container starting the job with mpirun -n works and sets the number of processes, but
starting with srun (either through bash file or inline) produces the following error:
<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt">--------------------------------------------------------------------------<br>
The application appears to have been direct launched using "srun",<br>
but OMPI was not built with SLURM's PMI support and therefore cannot<br>
execute. There are several options for building PMI support under<br>
SLURM, depending upon the SLURM version you are using:<br>
<br>
version 16.05 or later: you can use SLURM's PMIx support. This<br>
requires that you configure and build SLURM --with-pmix.<br>
<br>
Versions earlier than 16.05: you must use either SLURM's PMI-1 or<br>
PMI-2 support. SLURM builds PMI-1 by default, or you can manually<br>
install PMI-2. You must then build Open MPI using --with-pmi pointing<br>
to the SLURM PMI library location.<br>
<br>
Please configure as appropriate and try again.<br>
--------------------------------------------------------------------------<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt">So my guess would be that I should configure my version of OpenMPI to work with slurm?
<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt">thanks for all the help, Ava<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt">V V čet., 19. okt. 2023 ob 12:46 je oseba Krack Matthias <<a href="mailto:matthias.krack@psi.ch">matthias.krack@psi.ch</a>> napisala:<o:p></o:p></span></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt">
<span lang="DE-CH" style="font-size:11.0pt">Hi Ava</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
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<span lang="DE-CH" style="font-size:11.0pt"> </span><span style="font-size:11.0pt"><o:p></o:p></span></p>
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<span lang="EN-US" style="font-size:11.0pt">Thanks for testing. Indeed, the .sif file does not seem to work with the host MPI properly. These .sif files were directly built with apptainer. This was a test and we will not provide such containers in the future
any longer. Instead, I suggest the download of a cp2k production docker container. Could you test such a docker container with apptainer? You can download it with the command </span><span style="font-size:11.0pt"><o:p></o:p></span></p>
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<span lang="EN-US" style="font-size:11.0pt">apptainer pull docker://mkrack/cp2k:2023.2_mpich_generic_psmp</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt">
<span lang="EN-US" style="font-size:11.0pt">or</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
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<span lang="EN-US" style="font-size:11.0pt">apptainer pull docker://mkrack/cp2k:2023.2_openmpi_generic_psmp</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
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<span lang="EN-US" style="font-size:11.0pt">depending on your host MPI version.</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
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<span lang="EN-US" style="font-size:11.0pt">A list of the available docker containers can be found
<a href="https://hub.docker.com/repository/docker/mkrack/cp2k/tags?page=1&ordering=last_updated" target="_blank">
here</a>.</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
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<span lang="EN-US" style="font-size:11.0pt"> </span><span style="font-size:11.0pt"><o:p></o:p></span></p>
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<span lang="EN-US" style="font-size:11.0pt">Best</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
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<span lang="EN-US" style="font-size:11.0pt"> </span><span style="font-size:11.0pt"><o:p></o:p></span></p>
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<span lang="EN-US" style="font-size:11.0pt">Matthias</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
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<span lang="EN-US" style="font-size:11.0pt"> </span><span style="font-size:11.0pt"><o:p></o:p></span></p>
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<b><span style="font-size:12.0pt;color:black">From: </span></b><span style="font-size:12.0pt;color:black"><a href="mailto:cp2k@googlegroups.com" target="_blank">cp2k@googlegroups.com</a> <<a href="mailto:cp2k@googlegroups.com" target="_blank">cp2k@googlegroups.com</a>>
on behalf of Ava Rajh <<a href="mailto:ava.rajh@gmail.com" target="_blank">ava.rajh@gmail.com</a>><br>
<b>Date: </b>Thursday, 19 October 2023 at 12:17<br>
<b>To: </b>cp2k <<a href="mailto:cp2k@googlegroups.com" target="_blank">cp2k@googlegroups.com</a>><br>
<b>Subject: </b>Re: [CP2K:19391] Help with running cp2k in parallel with Slurm</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
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<span style="font-size:11.0pt"> <o:p></o:p></span></p>
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<span style="font-size:11.0pt">Sorry for the confusion, I read the output wrong, <o:p>
</o:p></span></p>
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<span style="font-size:11.0pt">and if I put the ntasks in the header of the batch file I get the same result as running just with srun, so the number of tasks determines the number of programs running with one MPI rank each.
<o:p></o:p></span></p>
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<span style="font-size:11.0pt"> <o:p></o:p></span></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:72.0pt">
<span style="font-size:11.0pt">On Thursday, October 19, 2023 at 10:20:39 AM UTC+2 Ava Rajh wrote:<o:p></o:p></span></p>
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<span style="font-size:11.0pt"> <o:p></o:p></span></p>
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<span style="font-size:11.0pt">Hi Matthias, <o:p></o:p></span></p>
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<span style="font-size:11.0pt"> <o:p></o:p></span></p>
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<span style="font-size:11.0pt">Thank you for the reply<o:p></o:p></span></p>
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<span style="font-size:11.0pt"> <o:p></o:p></span></p>
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<span style="font-size:11.0pt">I tried both, first just with the srun command and as part of the #SBATCH file.
<o:p></o:p></span></p>
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<span style="font-size:11.0pt">If I run the "srun" command and specify the number of tasks I get the before mentioned multiple copies of the same program with 1 MPI rank each. The same happens if I run the command outside the container without the srun and
specify the number of tasks with just: mpiexec -n 4 <o:p></o:p></span></p>
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<span style="font-size:11.0pt"> <o:p></o:p></span></p>
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<span style="font-size:11.0pt">and if I put the ntasks in the header of the batch file, then I just get one copy of the program with 1 MPI rank, no matter how many -ntasks are defined.
<o:p></o:p></span></p>
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<span style="font-size:11.0pt"> <o:p></o:p></span></p>
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<span style="font-size:11.0pt">Any idea about how to start my calculation would be very helpful, thank you.
<o:p></o:p></span></p>
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<span style="font-size:11.0pt">kind regards, Ava<o:p></o:p></span></p>
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<span style="font-size:11.0pt"> <o:p></o:p></span></p>
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<span style="font-size:11.0pt"> <o:p></o:p></span></p>
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<span style="font-size:11.0pt">On Wednesday, October 18, 2023 at 7:21:22 PM UTC+2 Krack Matthias wrote:<o:p></o:p></span></p>
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<span lang="DE-CH" style="font-size:11.0pt">Hi Ava</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
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<span lang="DE-CH" style="font-size:11.0pt"> </span><span style="font-size:11.0pt"><o:p></o:p></span></p>
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<span lang="EN-US" style="font-size:11.0pt">Do you run the “srun” command as part of a SLURM batch job file with a #SBATCH header section or interactively?</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
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<span lang="EN-US" style="font-size:11.0pt">Your guess is right, the –ntasks flag defines the number of MPI ranks.</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
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<span lang="EN-US" style="font-size:11.0pt"> </span><span style="font-size:11.0pt"><o:p></o:p></span></p>
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<span lang="EN-US" style="font-size:11.0pt">Best</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
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<span lang="EN-US" style="font-size:11.0pt"> </span><span style="font-size:11.0pt"><o:p></o:p></span></p>
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<span lang="EN-US" style="font-size:11.0pt">Matthias</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
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<span lang="EN-US" style="font-size:11.0pt"> </span><span style="font-size:11.0pt"><o:p></o:p></span></p>
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<b><span style="font-size:12.0pt;color:black">From: </span></b><span style="font-size:12.0pt;color:black"><a href="mailto:cp...@googlegroups.com" target="_blank">cp...@googlegroups.com</a> <<a href="mailto:cp...@googlegroups.com" target="_blank">cp...@googlegroups.com</a>>
on behalf of Ava Rajh <<a href="mailto:ava....@gmail.com" target="_blank">ava....@gmail.com</a>><br>
<b>Date: </b>Wednesday, 18 October 2023 at 14:17<br>
<b>To: </b>cp2k <<a href="mailto:cp...@googlegroups.com" target="_blank">cp...@googlegroups.com</a>><br>
<b>Subject: </b>[CP2K:19379] Help with running cp2k in parallel with Slurm</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
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<span style="font-size:11.0pt">Dear all, <br>
<br>
I am trying to run cp2k on our HPC cluster and I am new in doing any kind of parallel computing and work on a cluster, so I would appreciate if some help and I apologize if I am missing something obvious.
<o:p></o:p></span></p>
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<span style="font-size:11.0pt">I am trying to use Cp2k in combination with apptainer and I followed instructions at
<a href="https://github.com/cp2k/cp2k/tree/master/tools/apptainer" target="_blank">
https://github.com/cp2k/cp2k/tree/master/tools/apptainer</a> <o:p></o:p></span></p>
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<span style="font-size:11.0pt"> <o:p></o:p></span></p>
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<span style="font-size:11.0pt">I have a .sif file in my work directory and if I work within it (Running MPI within the container), everything works perfectly and I can set the number of MPI threads.
<o:p></o:p></span></p>
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<span style="font-size:11.0pt"> <o:p></o:p></span></p>
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<span style="font-size:11.0pt">But when trying to run it through slurm, I can't seem to be able to set the number of MPI processes per node. If i start a command like:
<o:p></o:p></span></p>
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<span style="font-size:11.0pt">srun --ntasks=2 apptainer run -B $PWD cp2k-2023.2_mpich_generic_psmp.sif cp2k -i H2O-32.in<o:p></o:p></span></p>
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<span style="font-size:11.0pt">it just starts 2 instances of the program that run at the same time, and for each, the total number of message passing processes is 1. I am able to set and change the number of OpenMP threads though.
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<span style="font-size:11.0pt">So my question would be first, am I wrongly assuming that --ntasks X should correspond to the number of MPI threads? And if I am, how would I set it.
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<span style="font-size:11.0pt"> <o:p></o:p></span></p>
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<span style="font-size:11.0pt">Please let me know if I need to provide any more information to diagnose the issue.
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<span style="font-size:11.0pt">Thank you very much for the help and kind regards,
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<span style="font-size:11.0pt">Ava Rajh<o:p></o:p></span></p>
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