<html xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40"> <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8"> <meta name="Generator" content="Microsoft Word 15 (filtered medium)"> <style></style> </head> <body lang="en-CH" link="blue" vlink="purple" style="word-wrap:break-word"> <div class="WordSection1"> <p class="MsoNormal"><span lang="DE-CH" style="font-size:11.0pt;mso-fareast-language:EN-US">Hi Michela<o:p></o:p></span></p> <p class="MsoNormal"><span lang="DE-CH" 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">Although the downloadable CP2K containers (apptainers) may work on many systems, this is not the case for all cluster systems given the large variety of cluster and slurm configurations.<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> <p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;mso-fareast-language:EN-US">Could you run successfully the apptainer self test? E.g. with<o:p></o:p></span></p> <p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;mso-fareast-language:EN-US">“</span>apptainer run -B /projects:/projects /shared/container_repository/cp2k/cp2k_2024.1_openmpi_generic_psmp.sif<span lang="EN-US"> run_tests”<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> <p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;mso-fareast-language:EN-US">If that test does not work, the container is not suited for your cluster system and you should try to build a CP2K binary from scratch using the appropriate compiler and MPI modules installed on your cluster system. I recommend to ask one of the sysadmins for assistance to perform that task.<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> <p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;mso-fareast-language:EN-US">Best<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> <p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;mso-fareast-language:EN-US">Matthias<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> <div id="mail-editor-reference-message-container"> <div> <div> <div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm"> <p class="MsoNormal" style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:12.0pt;margin-left:36.0pt"> <b><span style="color:black">From: </span></b><span style="color:black">cp2k@googlegroups.com <cp2k@googlegroups.com> on behalf of Michela Benazzi <bnzmichela@gmail.com><br> <b>Date: </b>Monday, 21 July 2025 at 19:56<br> <b>To: </b>cp2k <cp2k@googlegroups.com><br> <b>Subject: </b>Re: [CP2K:21677] Implementation Suggestion: job not running due to some SLURM parameters<o:p></o:p></span></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt">Hello Dr. Krack and CP2K community,<o:p></o:p></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><o:p> </o:p></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt">I hope you are doing well! I have two additional questions after my jobs failed without trace again - SLURM exit code 15, which is supposedly on the side of the software/app being used.<o:p></o:p></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><o:p> </o:p></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt">My improvements: I have added TRACE T under &GLOBAL, and have fixed my bash script settings (I was not requesting enough time and memory). I am seeing a positive improvement there.<o:p></o:p></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><o:p> </o:p></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt">I wish I could troubleshoot, but because my jobs failed immediately upon starting without leaving trace, there's no .err files to refer to. Can I please get some assistance? I am not attaching any more input files because multiple jobs have failed, so I do not think that is the issue. Find my slurm script for reference below my signature.<o:p></o:p></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><o:p> </o:p></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt">Thank you,<o:p></o:p></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><o:p> </o:p></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt">Michela<o:p></o:p></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><o:p> </o:p></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt">#!/bin/bash<br> #SBATCH -p short<br> #SBATCH --mem=36G ##memory per task<br> #SBATCH --job-name=en1<br> #SBATCH --ntasks=8<br> #SBATCH --cpus-per-task=7<br> #SBATCH -N 1 ## containers can only run on one node, and c*n = 56 or 128 (intel nodes top out at 56 cores, zen2 at 128)<br> #SBATCH --constraint=ib<br> #SBATCH --time=42:00:00<br> #SBATCH -o %j.out<br> #SBATCH -e %j.err<br> <br> #set up the number of OpenMP threads:<br> export OMP_NUM_THREADS=7 ## should be the same as cpus-per-task<br> <br> #The setup_new file contains all the instructions for setting up the correct environment before the user can compile and/or run CP2K:<br> <br> export PATH=$PATH:/shared/centos7/cp2k/cp2k-6.1.0/data<br> dir=/home/benazzi.m/BHT/<br> inputFile=$dir/120h_bulk-1.restart<br> <br> apptainer run -B /projects:/projects /shared/container_repository/cp2k/cp2k_2024.1_openmpi_generic_psmp.sif mpirun -n 8 --oversubscribe cp2k.psmp -i $inputFile<o:p></o:p></p> </div> <div> <div> <p class="MsoNormal" style="margin-left:36.0pt">On Wednesday, July 16, 2025 at 4:30:02<span style="font-family:"Arial",sans-serif"> </span>PM UTC-4 Michela Benazzi wrote:<o:p></o:p></p> </div> <blockquote style="border:none;border-left:solid #CCCCCC 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-right:0cm"> <div> <p class="MsoNormal" style="margin-left:36.0pt">Thank you Dr. Krack,<o:p></o:p></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><o:p> </o:p></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt">I will give it a try! <br> <br> Michela<o:p></o:p></p> </div> <p class="MsoNormal" style="margin-left:36.0pt"><o:p> </o:p></p> <div> <div> <p class="MsoNormal" style="margin-left:36.0pt">On Wednesday, July 16, 2025 at 12:01:08<span style="font-family:"Arial",sans-serif"> </span>PM UTC-4 Krack Matthias wrote:<o:p></o:p></p> </div> <blockquote style="border:none;border-left:solid #CCCCCC 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-right:0cm"> <div> <div> <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;color:#212121">Hi Michela</span><o:p></o:p></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt;font-variant-caps:normal;text-align:start;word-spacing:0px"> <span lang="EN-US" style="font-size:11.0pt;color:#212121"> </span><o:p></o:p></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt;font-variant-caps:normal;text-align:start;word-spacing:0px"> <span lang="EN-US" style="font-size:11.0pt;color:#212121">You can try to activate the <a href="https://manual.cp2k.org/trunk/CP2K_INPUT/GLOBAL.html#CP2K_INPUT.GLOBAL.TRACE" target="_blank" title="https://manual.cp2k.org/trunk/CP2K_INPUT/GLOBAL.html#CP2K_INPUT.GLOBAL.TRACE"><span style="color:purple">TRACE input key</span></a> in the &GLOBAL section (or TRACE_MASTER if the output becomes messy because of the large number of MPI ranks).</span><o:p></o:p></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt;font-variant-caps:normal;text-align:start;word-spacing:0px"> <span lang="EN-US" style="font-size:11.0pt;color:#212121"> </span><o:p></o:p></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt;font-variant-caps:normal;text-align:start;word-spacing:0px"> <span lang="EN-US" style="font-size:11.0pt;color:#212121">HTH</span><o:p></o:p></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt;font-variant-caps:normal;text-align:start;word-spacing:0px"> <span lang="EN-US" style="font-size:11.0pt;color:#212121"> </span><o:p></o:p></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt;font-variant-caps:normal;text-align:start;word-spacing:0px"> <span lang="EN-US" style="font-size:11.0pt;color:#212121">Matthias</span><o:p></o:p></p> <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"> </span><o:p></o:p></p> <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"> </span><o:p></o:p></p> </div> </div> <div> <div> <div> <div> <div> <div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm"> <p class="MsoNormal" style="mso-margin-top-alt:auto;margin-bottom:12.0pt;margin-left:72.0pt"> <b><span style="color:black">From: </span></b><span style="color:black">cp...@googlegroups.com <cp...@googlegroups.com> on behalf of Michela Benazzi <bnzmi...@gmail.com><br> <b>Date: </b>Wednesday, 16 July 2025 at 17:31<br> <b>To: </b>cp2k <cp...@googlegroups.com><br> <b>Subject: </b>[CP2K:21665] Implementation Suggestion: job not running due to some SLURM parameters</span><o:p></o:p></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:72.0pt"> Good morning,<o:p></o:p></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:72.0pt"> <o:p></o:p></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:72.0pt"> I have recently noticed that I was not allocating nearly enough memory for my jobs - (25 GB allocated, 32 GB were actually being used).<o:p></o:p></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:72.0pt"> <o:p></o:p></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:72.0pt"> Those jobs failed without any trace - no output, restart, log, error files at all.<o:p></o:p></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:72.0pt"> <o:p></o:p></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:72.0pt"> Is there any way (or any way to implement it if that does not exist yet) to add a feature where:<o:p></o:p></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:72.0pt"> <o:p></o:p></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:72.0pt"> 1. The job outputs information until memory capacity is failed<o:p></o:p></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:72.0pt"> 2. There is an error message explaining the cause in the .out or .err files<o:p></o:p></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:72.0pt"> <o:p></o:p></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:72.0pt"> Thank you!<br> <br> Michela<o:p></o:p></p> </div> </div> </div> </div> </div> </div> <div> <div> <div> <div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:72.0pt"> -- <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 cp2k+uns...@googlegroups.com.<br> To view this discussion visit <a href="https://groups.google.com/d/msgid/cp2k/d4c2d7a3-fb48-4c39-b185-6ebfa692aa35n%40googlegroups.com?utm_medium=email&utm_source=footer" target="_blank"> https://groups.google.com/d/msgid/cp2k/d4c2d7a3-fb48-4c39-b185-6ebfa692aa35n%40googlegroups.com</a>.<o:p></o:p></p> </div> </div> </div> </div> </div> </blockquote> </div> </blockquote> </div> <p class="MsoNormal" style="margin-left:36.0pt">-- <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="mailto:cp2k+unsubscribe@googlegroups.com">cp2k+unsubscribe@googlegroups.com</a>.<br> To view this discussion visit <a href="https://groups.google.com/d/msgid/cp2k/90858c2f-b28a-4b39-8c24-6fe4d8997081n%40googlegroups.com?utm_medium=email&utm_source=footer"> https://groups.google.com/d/msgid/cp2k/90858c2f-b28a-4b39-8c24-6fe4d8997081n%40googlegroups.com</a>.<o:p></o:p></p> </div> </div> </div> </div> </body> </html> <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 visit <a href="https://groups.google.com/d/msgid/cp2k/ZR2P278MB114632ED45DAA951A75D12D1F45CA%40ZR2P278MB1146.CHEP278.PROD.OUTLOOK.COM?utm_medium=email&utm_source=footer">https://groups.google.com/d/msgid/cp2k/ZR2P278MB114632ED45DAA951A75D12D1F45CA%40ZR2P278MB1146.CHEP278.PROD.OUTLOOK.COM</a>.<br />