I am guessing that the workaround is the TRACE_MASTER as you suggested in case it became messy. I would still like an explanation for why it didn't print anything out - should this be added to the CP2K manual?<br /><br /><div>Thank you kindly for your time,</div><div><br /></div><div>Michela</div><br /><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Thursday, July 24, 2025 at 12:47:59 PM UTC-4 Michela Cavalieri 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;">Hello Dr. Krack,<br><br>I found that the issue was TRACE T that I recently added (see this same thread) under &GLOBAL. <br> <span><p>I did not think of that at all because it was suggested to me here. I took it out and things are running smoothly.</p><p>My guess as to what happened is that the "TRACE" is massive - see attached the file that I got from printing my compute node output. Perhaps it timed out before computing any MD steps (<i>I allocated 42 hours</i>).<br><br>I printed the attached file from the compute node (as I mentioned before, nothing was printed to my working directory even after submitting multiple times) in less than 10 min of runtime. I will keep running this on our HPC compute node and see if outputs any errors that could give us a better idea for why nothing was printed. <br><br>I am not sure why it wouldn't still print the output and why it left me without any restart files at all! That is the complete opposite of why I was trying to use TRACE T!<br><br>I would like to raise this as an issue, unless you can perhaps correct something that I did wrong.<br><br>Thank you,</p><p>Michela</p></span><br><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Tuesday, July 22, 2025 at 4:42:57 AM UTC-4 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 Michela<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">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.<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">Could you run successfully the apptainer self test? E.g. with<u></u><u></u></span></p> <p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt">“</span>apptainer run -B /projects:/projects /shared/container_repository/cp2k/cp2k_2024.1_openmpi_generic_psmp.sif<span lang="EN-US"> run_tests”<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">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.<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></div><div lang="en-CH" link="blue" vlink="purple" style="word-wrap:break-word"><div><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="color:black">From: </span></b><span style="color:black"><a rel="nofollow">cp...@googlegroups.com</a> <<a rel="nofollow">cp...@googlegroups.com</a>> on behalf of Michela Benazzi <<a rel="nofollow">bnzmi...@gmail.com</a>><br> <b>Date: </b>Monday, 21 July 2025 at 19:56<br> <b>To: </b>cp2k <<a rel="nofollow">cp...@googlegroups.com</a>><br> <b>Subject: </b>Re: [CP2K:21677] Implementation Suggestion: job not running due to some SLURM parameters<u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt">Hello Dr. Krack and CP2K community,<u></u><u></u></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><u></u> <u></u></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.<u></u><u></u></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><u></u> <u></u></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.<u></u><u></u></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><u></u> <u></u></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.<u></u><u></u></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><u></u> <u></u></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt">Thank you,<u></u><u></u></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><u></u> <u></u></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt">Michela<u></u><u></u></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><u></u> <u></u></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<u></u><u></u></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:<u></u><u></u></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,<u></u><u></u></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><u></u> <u></u></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt">I will give it a try! <br> <br> Michela<u></u><u></u></p> </div> <p class="MsoNormal" style="margin-left:36.0pt"><u></u> <u></u></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:<u></u><u></u></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="margin-left:36.0pt"> <span lang="EN-US" style="font-size:11.0pt;color:#212121">Hi Michela</span><u></u><u></u></p> <p class="MsoNormal" style="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><u></u><u></u></p> <p class="MsoNormal" style="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" title="https://manual.cp2k.org/trunk/CP2K_INPUT/GLOBAL.html#CP2K_INPUT.GLOBAL.TRACE" rel="nofollow" target="_blank" data-saferedirecturl="https://www.google.com/url?hl=en&q=https://manual.cp2k.org/trunk/CP2K_INPUT/GLOBAL.html%23CP2K_INPUT.GLOBAL.TRACE&source=gmail&ust=1753462090719000&usg=AOvVaw3H6I3KNf4S6mXnrkOrbxoa"><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><u></u><u></u></p> <p class="MsoNormal" style="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><u></u><u></u></p> <p class="MsoNormal" style="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><u></u><u></u></p> <p class="MsoNormal" style="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><u></u><u></u></p> <p class="MsoNormal" style="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><u></u><u></u></p> <p class="MsoNormal" style="margin-left:36.0pt"> <span lang="DE-CH" style="font-size:11.0pt"> </span><u></u><u></u></p> <p class="MsoNormal" style="margin-left:36.0pt"> <span lang="DE-CH" style="font-size:11.0pt"> </span><u></u><u></u></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="margin-bottom:12.0pt;margin-left:72.0pt"> <b><span style="color:black">From: </span></b><span style="color:black"><a rel="nofollow">cp...@googlegroups.com</a> <<a rel="nofollow">cp...@googlegroups.com</a>> on behalf of Michela Benazzi <<a rel="nofollow">bnzmi...@gmail.com</a>><br> <b>Date: </b>Wednesday, 16 July 2025 at 17:31<br> <b>To: </b>cp2k <<a rel="nofollow">cp...@googlegroups.com</a>><br> <b>Subject: </b>[CP2K:21665] Implementation Suggestion: job not running due to some SLURM parameters</span><u></u><u></u></p> </div> <div> <p class="MsoNormal" style="margin-left:72.0pt"> Good morning,<u></u><u></u></p> </div> <div> <p class="MsoNormal" style="margin-left:72.0pt"> <u></u><u></u></p> </div> <div> <p class="MsoNormal" style="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).<u></u><u></u></p> </div> <div> <p class="MsoNormal" style="margin-left:72.0pt"> <u></u><u></u></p> </div> <div> <p class="MsoNormal" style="margin-left:72.0pt"> Those jobs failed without any trace - no output, restart, log, error files at all.<u></u><u></u></p> </div> <div> <p class="MsoNormal" style="margin-left:72.0pt"> <u></u><u></u></p> </div> <div> <p class="MsoNormal" style="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:<u></u><u></u></p> </div> <div> <p class="MsoNormal" style="margin-left:72.0pt"> <u></u><u></u></p> </div> <div> <p class="MsoNormal" style="margin-left:72.0pt"> 1. The job outputs information until memory capacity is failed<u></u><u></u></p> </div> <div> <p class="MsoNormal" style="margin-left:72.0pt"> 2. There is an error message explaining the cause in the .out or .err files<u></u><u></u></p> </div> <div> <p class="MsoNormal" style="margin-left:72.0pt"> <u></u><u></u></p> </div> <div> <p class="MsoNormal" style="margin-left:72.0pt"> Thank you!<br> <br> Michela<u></u><u></u></p> </div> </div> </div> </div> </div> </div> <div> <div> <div> <div> <div> <p class="MsoNormal" style="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 <a rel="nofollow">cp2k+uns...@googlegroups.com</a>.<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" rel="nofollow" target="_blank" data-saferedirecturl="https://www.google.com/url?hl=en&q=https://groups.google.com/d/msgid/cp2k/d4c2d7a3-fb48-4c39-b185-6ebfa692aa35n%2540googlegroups.com?utm_medium%3Demail%26utm_source%3Dfooter&source=gmail&ust=1753462090720000&usg=AOvVaw1ZUFpV1GnYUCgjrVXTNYH9"> https://groups.google.com/d/msgid/cp2k/d4c2d7a3-fb48-4c39-b185-6ebfa692aa35n%40googlegroups.com</a>.<u></u><u></u></p> </div> </div> </div> </div> </div> </blockquote> </div> </blockquote> </div> </div></div></div></div></div><div lang="en-CH" link="blue" vlink="purple" style="word-wrap:break-word"><div><div><div><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 rel="nofollow">cp2k+uns...@googlegroups.com</a>.<br></p></div></div></div></div></div><div lang="en-CH" link="blue" vlink="purple" style="word-wrap:break-word"><div><div><div><div><p class="MsoNormal" style="margin-left:36.0pt"> 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" rel="nofollow" target="_blank" data-saferedirecturl="https://www.google.com/url?hl=en&q=https://groups.google.com/d/msgid/cp2k/90858c2f-b28a-4b39-8c24-6fe4d8997081n%2540googlegroups.com?utm_medium%3Demail%26utm_source%3Dfooter&source=gmail&ust=1753462090720000&usg=AOvVaw0_wff8LRXLPNWC-KL7e_pp"> https://groups.google.com/d/msgid/cp2k/90858c2f-b28a-4b39-8c24-6fe4d8997081n%40googlegroups.com</a>.<u></u><u></u></p> </div> </div> </div> </div> </div> </blockquote></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 visit <a href="https://groups.google.com/d/msgid/cp2k/32fb931f-715b-445b-be74-79d66bfa65d3n%40googlegroups.com?utm_medium=email&utm_source=footer">https://groups.google.com/d/msgid/cp2k/32fb931f-715b-445b-be74-79d66bfa65d3n%40googlegroups.com</a>.<br />