<br /><div>Hi Matthias, <br /></div><div><br /></div><div>Thank you for the reply<br /></div><div><br /></div><div>I tried both, first just with the srun command and as part of the #SBATCH file. <br /></div><div>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: <span><span>mpiexec -n 4</span></span> </div><div><br /></div><div>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. <br /></div><div><br /></div><div>Any idea about how to start my calculation would be very helpful, thank you. <br /></div><div>kind regards, Ava<br /></div><div><br /></div><div><br /></div><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Wednesday, October 18, 2023 at 7:21:22 PM UTC+2 Krack Matthias wrote:<br/></div><blockquote class="gmail_quote" style="margin: 0 0 0 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"> <div lang="en-CH" link="blue" vlink="purple" style="word-wrap:break-word"> <div> <p class="MsoNormal"><span lang="DE-CH" style="font-size:11.0pt">Hi Ava<u></u><u></u></span></p> <p class="MsoNormal"><span lang="DE-CH" style="font-size:11.0pt"><u></u> <u></u></span></p> <p class="MsoNormal"><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?<u></u><u></u></span></p> <p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt">Your guess is right, the –ntasks flag defines the number of MPI ranks.<u></u><u></u></span></p> <p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt"><u></u> <u></u></span></p> <p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt">Best<u></u><u></u></span></p> <p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt"><u></u> <u></u></span></p> <p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt">Matthias<u></u><u></u></span></p> <p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt"><u></u> <u></u></span></p> <div> <div></div></div></div></div><div lang="en-CH" link="blue" vlink="purple" style="word-wrap:break-word"><div><div><div> <div style="border:none;border-top:solid #b5c4df 1.0pt;padding:3.0pt 0cm 0cm 0cm"> <p class="MsoNormal" style="margin-right:0cm;margin-bottom:12.0pt;margin-left:36.0pt"> <b><span style="font-size:12.0pt;color:black">From: </span></b><span style="font-size:12.0pt;color:black"><a href data-email-masked rel="nofollow">cp...@googlegroups.com</a> <<a href data-email-masked rel="nofollow">cp...@googlegroups.com</a>> on behalf of Ava Rajh <<a href data-email-masked rel="nofollow">ava....@gmail.com</a>><br> <b>Date: </b>Wednesday, 18 October 2023 at 14:17<br> <b>To: </b>cp2k <<a href data-email-masked rel="nofollow">cp...@googlegroups.com</a>><br> <b>Subject: </b>[CP2K:19379] Help with running cp2k in parallel with Slurm<u></u><u></u></span></p> </div> <p class="MsoNormal" style="margin-left:36.0pt"><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. <u></u><u></u></span></p> <div> <p class="MsoNormal" style="margin-left:36.0pt"><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" rel="nofollow" data-saferedirecturl="https://www.google.com/url?hl=en&q=https://github.com/cp2k/cp2k/tree/master/tools/apptainer&source=gmail&ust=1697783613326000&usg=AOvVaw0uMRBO25Afuqu8314JPnZd">https://github.com/cp2k/cp2k/tree/master/tools/apptainer</a> <u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt"><u></u> <u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><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. <u></u><u></u></span></p> </div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt"><u></u> <u></u></span></p> <div> <p class="MsoNormal" style="margin-left:36.0pt"><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: <u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><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<u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><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. <u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><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. <u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt"><u></u> <u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt">Please let me know if I need to provide any more information to diagnose the issue. <u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt">Thank you very much for the help and kind regards, <u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt">Ava Rajh<u></u><u></u></span></p> </div> </div></div></div></div><div lang="en-CH" link="blue" vlink="purple" style="word-wrap:break-word"><div><div><div><p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt">-- <br> You received this message because you are subscribed to the Google Groups "cp2k" group.<br> To unsubscribe from this group and stop receiving emails from it, send an email to <a href data-email-masked rel="nofollow">cp2k+uns...@googlegroups.com</a>.<br> To view this discussion on the web visit <a href="https://groups.google.com/d/msgid/cp2k/2393b350-7de0-4599-97e0-4f52ffec0c5en%40googlegroups.com?utm_medium=email&utm_source=footer" target="_blank" rel="nofollow" data-saferedirecturl="https://www.google.com/url?hl=en&q=https://groups.google.com/d/msgid/cp2k/2393b350-7de0-4599-97e0-4f52ffec0c5en%2540googlegroups.com?utm_medium%3Demail%26utm_source%3Dfooter&source=gmail&ust=1697783613326000&usg=AOvVaw3nmbGOT1LYUDbmova9tc3U"> https://groups.google.com/d/msgid/cp2k/2393b350-7de0-4599-97e0-4f52ffec0c5en%40googlegroups.com</a>.<u></u><u></u></span></p> </div> </div> </div> </div> </blockquote></div> <p></p> -- <br /> You received this message because you are subscribed to the Google Groups "cp2k" group.<br /> To unsubscribe from this group and stop receiving emails from it, send an email to <a href="mailto:cp2k+unsubscribe@googlegroups.com">cp2k+unsubscribe@googlegroups.com</a>.<br /> To view this discussion on the web visit <a href="https://groups.google.com/d/msgid/cp2k/a34b926f-41df-441d-a250-7e64d939828dn%40googlegroups.com?utm_medium=email&utm_source=footer">https://groups.google.com/d/msgid/cp2k/a34b926f-41df-441d-a250-7e64d939828dn%40googlegroups.com</a>.<br />