<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=us-ascii"> <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="mso-fareast-language:EN-US">Hi<o:p></o:p></span></p> <p class="MsoNormal"><span lang="DE-CH" style="mso-fareast-language:EN-US"><o:p> </o:p></span></p> <p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US">I have just checked in a <a href="https://github.com/mkrack/cp2k/blob/master/tools/apptainer/README.md">README file</a> for CP2K & Apptainer which might give some hints.<o:p></o:p></span></p> <p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US"><o:p> </o:p></span></p> <p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US">Best<o:p></o:p></span></p> <p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US"><o:p> </o:p></span></p> <p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US">Matthias<o:p></o:p></span></p> <p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US"><o:p> </o:p></span></p> <p class="MsoNormal" style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:12.0pt;margin-left:36.0pt"> On 05.04.23, 16:11, "cp2k@googlegroups.com" <cp2k@googlegroups.com> wrote:<o:p></o:p></p> <div> <p class="MsoNormal" style="margin-left:36.0pt">Hello List,<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 have successfully built 2023.1 from the dockerfile that's included<o:p></o:p></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt">with the source code. I have converted the container to singularity<o:p></o:p></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt">and run that on our cluster.<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">Now, I'd like to use cp2k with MPI. I've followed the "hybrid"<o:p></o:p></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt">approach where srun starts multiple containers on multiple nodes, and<o:p></o:p></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt">the MPI inside the container works with the MPI on the hosts (and PMI,<o:p></o:p></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt">and Slurm) to start up the application:<o:p></o:p></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt">srun -vv --ntasks 2 /apps/local/cp2k/2022.2/cp2k.sif cp2k.psmp \<o:p></o:p></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"> -i H2O-64.inp -o cp2k_002.out<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">However, this does not seem to work:<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">GLOBAL| MPI I/O enabled T<o:p></o:p></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt">GLOBAL| Total number of message passing processes 1<o:p></o:p></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt">GLOBAL| Number of threads for this process 32<o:p></o:p></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt">GLOBAL| This output is from process 0<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 have also included a simple test program inside the same container,<o:p></o:p></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt">and this seems to work (although there's an error message):<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">> --------------------------------------------------------------------------<o:p></o:p></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt">> A requested component was not found, or was unable to be opened. This<o:p></o:p></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt">> means that this component is either not installed or is unable to be<o:p></o:p></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt">> used on your system (e.g., sometimes this means that shared libraries<o:p></o:p></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt">> that the component requires are unable to be found/loaded). Note that<o:p></o:p></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt">> PMIx stopped checking at the first component that it did not find.<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">> Host: node77-62<o:p></o:p></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt">> Framework: psec<o:p></o:p></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt">> Component: munge<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">> <o:p></o:p></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt">> [node77-62:2545390] PMIX ERROR: ERROR in file<o:p></o:p></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt">> ../../../../../../src/mca/gds/ds12/gds_ds12_lock_pthread.c at line 169<o:p></o:p></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt">> Hello, I am rank 0/2<o:p></o:p></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt">> Hello, I am rank 1/2<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"><o:p> </o:p></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt">How would I go about debugging the MPI startup of cp2k?<o:p></o:p></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt">Of course, any other ideas are welcome, too.<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">Thanks,<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">A.<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">Ansgar Esztermann<o:p></o:p></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt">Sysadmin Dep. Theoretical and Computational Biophysics<o:p></o:p></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><a href="https://www.mpinat.mpg.de/person/11315/3883774">https://www.mpinat.mpg.de/person/11315/3883774</a><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">-- <o:p></o:p></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt">You received this message because you are subscribed to the Google Groups "cp2k" group.<o:p></o:p></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt">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>.<o:p></o:p></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt">To view this discussion on the web visit <a href="https://groups.google.com/d/msgid/cp2k/ZC2BKBhkpDe0mQOe%40aeszter.mpibpc.intern"> https://groups.google.com/d/msgid/cp2k/ZC2BKBhkpDe0mQOe%40aeszter.mpibpc.intern</a>.<o:p></o:p></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><o:p> </o:p></p> </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 on the web visit <a href="https://groups.google.com/d/msgid/cp2k/ZRAP278MB0827F1CA115078D83BEF6233F4909%40ZRAP278MB0827.CHEP278.PROD.OUTLOOK.COM?utm_medium=email&utm_source=footer">https://groups.google.com/d/msgid/cp2k/ZRAP278MB0827F1CA115078D83BEF6233F4909%40ZRAP278MB0827.CHEP278.PROD.OUTLOOK.COM</a>.<br />