segmentation fault in error file

SHWETA CHOUDHARY

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Apr 26, 2023, 3:31:14 AM4/26/23

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Hello everyone,

Can anybody please help me with the following error in my error file? I have recently installed cp2k 8.2 version using intel-minimal.psmp arch file with intel 2018 compiler, gcc and fftw. Please guide me with job script and compilation.

forrtl: severe (174): SIGSEGV, segmentation fault occurred

Image PC Routine Line Source

cp2k.psmp 000000000981FE2D Unknown Unknown Unknown

libpthread-2.17.s 00007FE4F42D9630 Unknown Unknown Unknown

cp2k.psmp 0000000002D1A2C1 ps_implicit_metho 240 ps_implicit_methods.F

cp2k.psmp 0000000002C3DDF3 pw_poisson_method 343 pw_poisson_methods.F

cp2k.psmp 0000000001037104 qs_ks_methods_mp_ 438 qs_ks_methods.F

cp2k.psmp 00000000010357E0 qs_ks_methods_mp_ 1223 qs_ks_methods.F

cp2k.psmp 0000000001B23BD9 qs_scf_mp_scf_env 462 qs_scf.F

cp2k.psmp 0000000001B1A269 qs_scf_mp_scf_ 233 qs_scf.F

cp2k.psmp 00000000010A8D6F qs_energy_mp_qs_e 92 qs_energy.F

cp2k.psmp 0000000001919CC1 qs_force_mp_qs_ca 116 qs_force.F

cp2k.psmp 000000000117BA3A force_env_methods 271 force_env_methods.F

cp2k.psmp 0000000000667A1C cp2k_runs_mp_run_ 352 cp2k_runs.F

cp2k.psmp 000000000065E192 MAIN__ 357 cp2k.F

cp2k.psmp 000000000065D50E Unknown Unknown Unknown

libc-2.17.so 00007FE4F3839555 __libc_start_main Unknown Unknown

cp2k.psmp 000000000065D429 Unknown Unknown Unknown

srun: Job 113192 step creation still disabled, retrying (Requested nodes are busy)

srun: Step created for job 113192

srun: Job 113192 step creation still disabled, retrying (Requested nodes are busy)

Many thanks!

Krack Matthias

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Apr 26, 2023, 3:36:00 AM4/26/23

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Hi

Possible causes for such segmentation faults could be insufficient stack sizes. Try to run in advance the following commands (bash):

ulimit -s unlimited
export OMP_STACKSIZE=16M

HTH

Matthias

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Tieyuan Bian

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Apr 28, 2023, 3:25:49 AM4/28/23

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Hi,

I used to meet this problem either. My cp2k version is 2022.2 and complier version is gcc 10.3. At the first time my MPI is OpenMPI with the toolchain option --with-openmpi=install. Then I had the same problem with you. I have fixed this problem by using Intel MPI. I have some advice for you:

1. First check whether you have problem of memory leak.

2. Complie cp2k again and use Intel MPI by setting --with-openmpi=no. You can install Intel MPI by yourself from intel official.

Tieyuan BIAN

Shweta

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May 3, 2023, 2:28:56 AM5/3/23

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Thank you all for reply!

Dear Matthias, I got this error with ulimit -s unlimited settings.

Dear Tieyuan BIAN, can you please help to install cp2k with toolchain. I tried many time it always give me the error of OpenBLAS. I set --with-openblas=no, still it tries to download that. Then I install default Linux-intel-minimal.psmp file in ARCH directory by changing CFLAGS= O3

Can you please help to install via the toolchain or Linix-intel.psmp (not minimal) file?

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