Dear Matthias, <br /><div>Thank you very much for your help, we were able to solve the memory leak issue by using the mpi that is compiled with the image, with some modifications to the command you provided to account for specificities of the cluster.</div><div>Best,</div><div>Quentin<br /></div><br /><div class="gmail_quote"><div dir="auto" class="gmail_attr">Le vendredi 6 octobre 2023 à 15:16:09 UTC+2, Krack Matthias a écrit :<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="EN-US" style="font-size:11.0pt">Dear Quentin<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">These containers are built differently following the usual cp2k toolchain installation process. There is no </span><span style="font-size:12.0pt;color:#212121">/opt/cp2k-toolchain/</span><span lang="EN-US" style="font-size:12.0pt;color:#212121"> folder but the folder /opt/cp2k/tools/toolchain/install/. There is no need, however, to source that setup file, because the <a href="https://github.com/mkrack/cp2k/blob/master/tools/docker/production/Dockerfile.2023.2_mpich_generic_psmp#L83" target="_blank" rel="nofollow" data-saferedirecturl="https://www.google.com/url?hl=fr&q=https://github.com/mkrack/cp2k/blob/master/tools/docker/production/Dockerfile.2023.2_mpich_generic_psmp%23L83&source=gmail&ust=1699626615164000&usg=AOvVaw07g1PNA59golenQRBv8v6P"> entrypoint.sh</a> script takes already care of that. You should be able to run the container as described in the</span><span lang="EN-US" style="font-size:11.0pt"> <a href="https://github.com/mkrack/cp2k/blob/master/tools/docker/production/README.md" target="_blank" rel="nofollow" data-saferedirecturl="https://www.google.com/url?hl=fr&q=https://github.com/mkrack/cp2k/blob/master/tools/docker/production/README.md&source=gmail&ust=1699626615164000&usg=AOvVaw0M5LuJGf-KKzYkl1bh9-uk"> READ.me</a>.</span><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"><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 Quentin Pessemesse <<a href data-email-masked rel="nofollow">q.pess...@gmail.com</a>><br> <b>Date: </b>Friday, 6 October 2023 at 14:59<br> <b>To: </b>cp2k <<a href data-email-masked rel="nofollow">cp...@googlegroups.com</a>><br> <b>Subject: </b>Re: [CP2K:19312] Memory Leak on CP2k 9.1<u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt">Dear Matthias, <u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt">Thank you kindly for your advice, I will try these different versions as soon as possible.<u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt">I've built the docker image for an openmpi version of CP2k on the cluster. With version 2023.1, I used to source the environment variables using " source /opt/cp2k-toolchain/install/setup". This does not work anymore. Is it a problem on the image's end or on the cluster end ?<u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt">Best,<u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt">Quentin<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> <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">Le vendredi 6 octobre 2023 à 11:27:26 UTC+2, Krack Matthias a écrit :<u></u><u></u></span></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="DE-CH" style="font-size:11.0pt">Hi Quentin</span><span style="font-size:11.0pt"><u></u><u></u></span></p> <p class="MsoNormal" style="margin-left:36.0pt"> <span lang="DE-CH" style="font-size:11.0pt"> </span><span style="font-size:11.0pt"><u></u><u></u></span></p> <p class="MsoNormal" style="margin-left:36.0pt"> <span lang="EN-US" style="font-size:11.0pt">There are some more cp2k 2023.2 docker containers for <a href="https://github.com/mkrack/cp2k/tree/master/tools/docker/production" target="_blank" rel="nofollow" data-saferedirecturl="https://www.google.com/url?hl=fr&q=https://github.com/mkrack/cp2k/tree/master/tools/docker/production&source=gmail&ust=1699626615164000&usg=AOvVaw0FhAr0gbLBQQerYtMl3LJO"> production</a> available (build with MPICH or OpenMPI) which can also be pulled with apptainer (see <a href="https://github.com/mkrack/cp2k/blob/master/tools/docker/production/README.md" target="_blank" rel="nofollow" data-saferedirecturl="https://www.google.com/url?hl=fr&q=https://github.com/mkrack/cp2k/blob/master/tools/docker/production/README.md&source=gmail&ust=1699626615164000&usg=AOvVaw0M5LuJGf-KKzYkl1bh9-uk"> READ.me</a> for details). Maybe, you have more luck with one of these.</span><span style="font-size:11.0pt"><u></u><u></u></span></p> <p class="MsoNormal" style="margin-left:36.0pt"> <span lang="EN-US" style="font-size:11.0pt"> </span><span style="font-size:11.0pt"><u></u><u></u></span></p> <p class="MsoNormal" style="margin-left:36.0pt"> <span lang="EN-US" style="font-size:11.0pt">Best</span><span style="font-size:11.0pt"><u></u><u></u></span></p> <p class="MsoNormal" style="margin-left:36.0pt"> <span lang="EN-US" style="font-size:11.0pt"> </span><span style="font-size:11.0pt"><u></u><u></u></span></p> <p class="MsoNormal" style="margin-left:36.0pt"> <span lang="EN-US" style="font-size:11.0pt">Matthias</span><span style="font-size:11.0pt"><u></u><u></u></span></p> <p class="MsoNormal" style="margin-left:36.0pt"> <span lang="EN-US" style="font-size:11.0pt"> </span><span style="font-size:11.0pt"><u></u><u></u></span></p> </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="font-size:12.0pt;color:black">From: </span></b><span style="font-size:12.0pt;color:black"><span><a href data-email-masked rel="nofollow">cp...@googlegroups.com</a></span> <<span><a href data-email-masked rel="nofollow">cp...@googlegroups.com</a></span>> on behalf of Quentin Pessemesse <<span><a href data-email-masked rel="nofollow">q.pess...@gmail.com</a></span>><br> <b>Date: </b>Friday, 6 October 2023 at 10:47<br> <b>To: </b>cp2k <<span><a href data-email-masked rel="nofollow">cp...@googlegroups.com</a></span>><br> <b>Subject: </b>Re: [CP2K:19310] Memory Leak on CP2k 9.1</span><span style="font-size:11.0pt"><u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:72.0pt"> <span style="font-size:11.0pt">Dear all, <u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:72.0pt"> <span style="font-size:11.0pt">The cluster staff has moved to using a docker with a CP2k image, with CP2k 2023.1 (<a href="https://hub.docker.com/r/cp2k/cp2k/tags" target="_blank" rel="nofollow" data-saferedirecturl="https://www.google.com/url?hl=fr&q=https://hub.docker.com/r/cp2k/cp2k/tags&source=gmail&ust=1699626615164000&usg=AOvVaw13Bj76jPATMgj9WDLx1R3r">https://hub.docker.com/r/cp2k/cp2k/tags</a>). The program experiences serious memory leaks (out-of-memory crash after less than 24 hours on AIMD with a system less than 100 atoms with 256 GB). The cluster cannot use intelmpi versions older than intelmpi 20. Is there a more recent version of CP2k which is stable and does not experience this type of large memory leaks?<u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:72.0pt"> <span style="font-size:11.0pt">We've tried to compile our own versions of CP2k with multiple versions of openMPI to no avail. The only stable CP2k version we have is CP2k 6.1, which is used with intelMPI 18 but it is on a legacy container where no new software can be installed.<u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:72.0pt"> <span style="font-size:11.0pt">Has anyone managed to use this docker image succesfully, and if so, which MPI package/version have you used ? If necessary, we can downgrade down to CP2k 9.1.<u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:72.0pt"> <span style="font-size:11.0pt">Best,<u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:72.0pt"> <span style="font-size:11.0pt">Quentin<u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:72.0pt"> <span style="font-size:11.0pt"> <u></u><u></u></span></p> </div> <div> <div> <p class="MsoNormal" style="margin-left:72.0pt"> <span style="font-size:11.0pt">Le mercredi 5 octobre 2022 à 13:19:26 UTC+2, Krack Matthias (PSI) a écrit :<u></u><u></u></span></p> </div> <blockquote style="border:none;border-left:solid #cccccc 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-top:5.0pt;margin-right:0cm;margin-bottom:5.0pt"> <div> <div> <p class="MsoNormal" style="margin-left:72.0pt"> <span lang="DE-CH" style="font-size:11.0pt">Hi Quentin</span><span style="font-size:11.0pt"><u></u><u></u></span></p> <p class="MsoNormal" style="margin-left:72.0pt"> <span lang="DE-CH" style="font-size:11.0pt"> </span><span style="font-size:11.0pt"><u></u><u></u></span></p> <p class="MsoNormal" style="margin-left:72.0pt"> <span lang="EN-US" style="font-size:11.0pt">It seems that you are using OpenMPI which is known to have leaks in some versions. Check <a href="https://github.com/cp2k/cp2k/issues/1830#issuecomment-1012561166" target="_blank" rel="nofollow" data-saferedirecturl="https://www.google.com/url?hl=fr&q=https://github.com/cp2k/cp2k/issues/1830%23issuecomment-1012561166&source=gmail&ust=1699626615164000&usg=AOvVaw2vJlr4k9mnbQhrbRpzR_Wb"> this issue</a> and <a href="https://groups.google.com/g/cp2k/c/BJ9c21ey0Ls/m/2UDxnhBRAQAJ" target="_blank" rel="nofollow" data-saferedirecturl="https://www.google.com/url?hl=fr&q=https://groups.google.com/g/cp2k/c/BJ9c21ey0Ls/m/2UDxnhBRAQAJ&source=gmail&ust=1699626615164000&usg=AOvVaw2tGExCGz4bvCSP2LPlwAlh"> this discussion</a> here on this forum for further information.</span><span style="font-size:11.0pt"><u></u><u></u></span></p> <p class="MsoNormal" style="margin-left:72.0pt"> <span lang="EN-US" style="font-size:11.0pt"> </span><span style="font-size:11.0pt"><u></u><u></u></span></p> <p class="MsoNormal" style="margin-left:72.0pt"> <span lang="EN-US" style="font-size:11.0pt">HTH</span><span style="font-size:11.0pt"><u></u><u></u></span></p> <p class="MsoNormal" style="margin-left:72.0pt"> <span lang="EN-US" style="font-size:11.0pt"> </span><span style="font-size:11.0pt"><u></u><u></u></span></p> <p class="MsoNormal" style="margin-left:72.0pt"> <span lang="EN-US" style="font-size:11.0pt">Matthias </span><span style="font-size:11.0pt"><u></u><u></u></span></p> </div> </div> <div> <div> <p class="MsoNormal" style="margin-left:72.0pt"> <span lang="EN-US" style="font-size:11.0pt"> </span><span style="font-size:11.0pt"><u></u><u></u></span></p> <div style="border:none;border-top:solid #b5c4df 1.0pt;padding:3.0pt 0cm 0cm 0cm"> <p class="MsoNormal" style="margin-left:108.0pt"> <b><span style="font-size:12.0pt;color:black">From: </span></b><span style="font-size:12.0pt;color:black">"<span><a href data-email-masked rel="nofollow">cp...@googlegroups.com</a></span>" <<span><a href data-email-masked rel="nofollow">cp...@googlegroups.com</a></span>> on behalf of Quentin Pessemesse <<span><a href data-email-masked rel="nofollow">q.pess...@gmail.com</a></span>><br> <b>Reply to: </b>"<span><a href data-email-masked rel="nofollow">cp...@googlegroups.com</a></span>" <<span><a href data-email-masked rel="nofollow">cp...@googlegroups.com</a></span>><br> <b>Date: </b>Wednesday, 5 October 2022 at 12:39<br> <b>To: </b>"<span><a href data-email-masked rel="nofollow">cp...@googlegroups.com</a></span>" <<span><a href data-email-masked rel="nofollow">cp...@googlegroups.com</a></span>><br> <b>Subject: </b>[CP2K:17807] Memory Leak on CP2k 9.1</span><span style="font-size:11.0pt"><u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:108.0pt"> <span style="font-size:11.0pt"> <u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:108.0pt"> <span style="font-size:11.0pt">Dear all, <u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:108.0pt"> <span style="font-size:11.0pt">Our group is encountering a memory leak issue that makes running DFT-MD impossible with large systems (~100 atoms) on one of the clusters we have access to, even though the same calculations run correctly on other machines.<u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:108.0pt"> <span style="font-size:11.0pt">The cluster support sent me the following valgrind output and asked me to find suggestions on how to proceed. Does anyone have input on how to deal with such memory leaks ?<u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:108.0pt"> <span style="font-size:11.0pt">Best,<u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:108.0pt"> <span style="font-size:11.0pt">Quentin P.<u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:108.0pt"> <span style="font-size:11.0pt"> <u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:108.0pt"> <span style="font-size:11.0pt">==62== Invalid write of size 4 ==62== at 0x1EA9887: grid_ref_create_task_list (in /ccc/products2/cp2k-9.1/Rhel_8__x86_64/gcc--8.3.0__openmpi--4.0.1/plumed/bin/cp2k.psmp) ==62== by 0x1E7A772: grid_create_task_list (in /ccc/products2/cp2k-9.1/Rhel_8__x86_64/gcc--8.3.0__openmpi--4.0.1/plumed/bin/cp2k.psmp) ==62== by 0x1E790B3: __grid_api_MOD_grid_create_task_list (grid_api.F:938) ==62== by 0x104AA67: __task_list_methods_MOD_generate_qs_task_list (task_list_methods.F:623) ==62== by 0xF58353: __qs_update_s_mstruct_MOD_qs_env_update_s_mstruct (qs_update_s_mstruct.F:187) ==62== by 0xCC03AB: __qs_energy_init_MOD_qs_energies_init (qs_energy_init.F:311) ==62== by 0xCBF0A1: __qs_energy_MOD_qs_energies (qs_energy.F:84) ==62== by 0xCE087E: __qs_force_MOD_qs_forces (qs_force.F:212) ==62== by 0xCE4349: __qs_force_MOD_qs_calc_energy_force (qs_force.F:117) ==62== by 0x9AE2C0: __force_env_methods_MOD_force_env_calc_energy_force (force_env_methods.F:271) ==62== by 0x50CD0C: __md_run_MOD_qs_mol_dyn_low (md_run.F:372) ==62== by 0x50DCF2: __md_run_MOD_qs_mol_dyn (md_run.F:153) ==62== Address 0x26d18670 is 16 bytes before a block of size 10 free'd ==62== at 0x4C35FAC: free (vg_replace_malloc.c:538) ==62== by 0x2B73E68: __offload_api_MOD_offload_timeset (offload_api.F:137) ==62== by 0x2B60EDA: __timings_MOD_timeset_handler (timings.F:278) ==62== by 0x2BE2C6D: __message_passing_MOD_mp_waitany (message_passing.F:4597) ==62== by 0x2963EA5: __realspace_grid_types_MOD_rs_pw_transfer_distributed (realspace_grid_types.F:1439) ==62== by 0x2966559: __realspace_grid_types_MOD_rs_pw_transfer (realspace_grid_types.F:711) ==62== by 0xC9310B: __qs_collocate_density_MOD_calculate_rho_core (qs_collocate_density.F:966) ==62== by 0xF57698: __qs_update_s_mstruct_MOD_qs_env_update_s_mstruct (qs_update_s_mstruct.F:109) ==62== by 0xCC03AB: __qs_energy_init_MOD_qs_energies_init (qs_energy_init.F:311) ==62== by 0xCBF0A1: __qs_energy_MOD_qs_energies (qs_energy.F:84) ==62== by 0xCE087E: __qs_force_MOD_qs_forces (qs_force.F:212) ==62== by 0xCE4349: __qs_force_MOD_qs_calc_energy_force (qs_force.F:117) ==62== Block was alloc'd at ==62== at 0x4C34DFF: malloc (vg_replace_malloc.c:307) ==62== by 0x2F21116: _gfortrani_xmallocarray (memory.c:66) ==62== by 0x2F1C271: _gfortran_string_trim (string_intrinsics_inc.c:167) ==62== by 0x2B73E1C: __offload_api_MOD_offload_timeset (offload_api.F:137) ==62== by 0x2B60EDA: __timings_MOD_timeset_handler (timings.F:278) ==62== by 0x2BE2C6D: __message_passing_MOD_mp_waitany (message_passing.F:4597) ==62== by 0x2963EA5: __realspace_grid_types_MOD_rs_pw_transfer_distributed (realspace_grid_types.F:1439) ==62== by 0x2966559: __realspace_grid_types_MOD_rs_pw_transfer (realspace_grid_types.F:711) ==62== by 0xC9310B: __qs_collocate_density_MOD_calculate_rho_core (qs_collocate_density.F:966) ==62== by 0xF57698: __qs_update_s_mstruct_MOD_qs_env_update_s_mstruct (qs_update_s_mstruct.F:109) ==62== by 0xCC03AB: __qs_energy_init_MOD_qs_energies_init (qs_energy_init.F:311) ==62== by 0xCBF0A1: __qs_energy_MOD_qs_energies (qs_energy.F:84) <u></u><u></u></span></p> </div> </div> </div> <div> <div> <p class="MsoNormal" style="margin-bottom:12.0pt;margin-left:108.0pt"> <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, 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