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<p class="MsoNormal"><span lang="DE-CH" style="font-size:11.0pt;mso-fareast-language:EN-US">Hi Quentin<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">There are some more cp2k 2023.2 docker containers for
<a href="https://github.com/mkrack/cp2k/tree/master/tools/docker/production">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">
READ.me</a> for details). Maybe, you have more luck with one of these.<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>
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<b><span style="font-size:12.0pt;color:black">From: </span></b><span style="font-size:12.0pt;color:black">cp2k@googlegroups.com <cp2k@googlegroups.com> on behalf of Quentin Pessemesse <q.pessemesse@gmail.com><br>
<b>Date: </b>Friday, 6 October 2023 at 10:47<br>
<b>To: </b>cp2k <cp2k@googlegroups.com><br>
<b>Subject: </b>Re: [CP2K:19310] Memory Leak on CP2k 9.1<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt">Dear all, <o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt">The cluster staff has moved to using a docker with a CP2k image, with CP2k 2023.1 (https://hub.docker.com/r/cp2k/cp2k/tags). 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?<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-left:36.0pt"><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.<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-left:36.0pt"><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.<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt">Best,<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt">Quentin<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt">Le mercredi 5 octobre 2022 à 13:19:26 UTC+2, Krack Matthias (PSI) a écrit :<o:p></o:p></span></p>
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<span lang="DE-CH" style="font-size:11.0pt">Hi Quentin</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
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<span lang="DE-CH" style="font-size:11.0pt"> </span><span style="font-size:11.0pt"><o:p></o:p></span></p>
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<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">
this issue</a> and <a href="https://groups.google.com/g/cp2k/c/BJ9c21ey0Ls/m/2UDxnhBRAQAJ" target="_blank">
this discussion</a> here on this forum for further information.</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
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<span lang="EN-US" style="font-size:11.0pt"> </span><span style="font-size:11.0pt"><o:p></o:p></span></p>
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<span lang="EN-US" style="font-size:11.0pt">HTH</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
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<span lang="EN-US" style="font-size:11.0pt"> </span><span style="font-size:11.0pt"><o:p></o:p></span></p>
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<span lang="EN-US" style="font-size:11.0pt">Matthias </span><span style="font-size:11.0pt"><o:p></o:p></span></p>
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<span lang="EN-US" style="font-size:11.0pt"> </span><span style="font-size:11.0pt"><o:p></o:p></span></p>
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<b><span style="font-size:12.0pt;color:black">From: </span></b><span style="font-size:12.0pt;color:black">"<span class="MsoHyperlink">cp...@googlegroups.com</span>" <<span class="MsoHyperlink">cp...@googlegroups.com</span>> on behalf of Quentin Pessemesse <<span class="MsoHyperlink">q.pess...@gmail.com</span>><br>
<b>Reply to: </b>"<span class="MsoHyperlink">cp...@googlegroups.com</span>" <<span class="MsoHyperlink">cp...@googlegroups.com</span>><br>
<b>Date: </b>Wednesday, 5 October 2022 at 12:39<br>
<b>To: </b>"<span class="MsoHyperlink">cp...@googlegroups.com</span>" <<span class="MsoHyperlink">cp...@googlegroups.com</span>><br>
<b>Subject: </b>[CP2K:17807] Memory Leak on CP2k 9.1</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
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<span style="font-size:11.0pt"> <o:p></o:p></span></p>
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<span style="font-size:11.0pt">Dear all, <o:p></o:p></span></p>
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<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.<o:p></o:p></span></p>
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<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 ?<o:p></o:p></span></p>
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<span style="font-size:11.0pt">Best,<o:p></o:p></span></p>
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<span style="font-size:11.0pt">Quentin P.<o:p></o:p></span></p>
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<span style="font-size:11.0pt"> <o:p></o:p></span></p>
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<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)
<o:p></o:p></span></p>
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