[CP2K-user] [CP2K:19310] Memory Leak on CP2k 9.1

[Quentin Pessemesse]

Dear all, 
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?
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.
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.
Best,
Quentin

Le mercredi 5 octobre 2022 à 13:19:26 UTC+2, Krack Matthias (PSI) a écrit :

> Hi Quentin
>
>  
>
> It seems that you are using OpenMPI which is known to have leaks in some 
> versions. Check this issue 
> <https://github.com/cp2k/cp2k/issues/1830#issuecomment-1012561166> and this 
> discussion <https://groups.google.com/g/cp2k/c/BJ9c21ey0Ls/m/2UDxnhBRAQAJ> 
> here on this forum for further information.
>
>  
>
> HTH
>
>  
>
> Matthias 
>
>  
>
> *From: *"cp... at googlegroups.com" <cp... at googlegroups.com> on behalf of 
> Quentin Pessemesse <q.pess... at gmail.com>
> *Reply to: *"cp... at googlegroups.com" <cp... at googlegroups.com>
> *Date: *Wednesday, 5 October 2022 at 12:39
> *To: *"cp... at googlegroups.com" <cp... at googlegroups.com>
> *Subject: *[CP2K:17807] Memory Leak on CP2k 9.1
>
>  
>
> Dear all, 
>
> 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.
>
> 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 ?
>
> Best,
>
> Quentin P.
>
>  
>
> ==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) 
>
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