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pisces segmentation runtime error

asked 2022-11-30 11:42:55 +0100

ify gravatar image

Hi Everyone, Big thanks for dev team and the update of the croco code and tools. I try testing a PISCES run with v1.3. After successfully compiling, I ran into this issue during my run:

           *** Total number of passive tracer jptra =           25
[spirit1:304773:0:304773] Caught signal 11 (Segmentation fault: address not mapped to object at address 0x7ffcc449bf58)
==== backtrace (tid: 304773) ====
 0  /net/nfs/tools/u20/22.3/PrgEnv/intel/linux-ubuntu20.04-zen2/ucx/1.11.2-intel-2021.4.0-vqv63n3gh6g4gnchf25ezmkxui4mvyix/lib/libucs.so.0(ucs_handle_error+0x365) [0x7f8a9d9606d5]
 1  /net/nfs/tools/u20/22.3/PrgEnv/intel/linux-ubuntu20.04-zen2/ucx/1.11.2-intel-2021.4.0-vqv63n3gh6g4gnchf25ezmkxui4mvyix/lib/libucs.so.0(+0x2f2eb) [0x7f8a9d9612eb]
 2  /net/nfs/tools/u20/22.3/PrgEnv/intel/linux-ubuntu20.04-zen2/ucx/1.11.2-intel-2021.4.0-vqv63n3gh6g4gnchf25ezmkxui4mvyix/lib/libucs.so.0(+0x2eddb) [0x7f8a9d960ddb]
 3  /lib/x86_64-linux-gnu/libpthread.so.0(+0x14420) [0x7f8a9eee4420]
 4  ./croco() [0x40a9fd]
 5  ./croco() [0x4b7d98]
 6  ./croco() [0x4b9123]
 7  ./croco() [0x52fd27]
 8  ./croco() [0x402692]
 9  /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf3) [0x7f8a9ed02083]
10  ./croco() [0x40259e]
=================================
Segmentation fault (core dumped)

I not sure what the issue is, but i suspect it has to do with the namelist. Is there anyone who had encountered this issue before? Or any ideas to solve this issue.

Thanks

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Hello. I encountered the same "Segmentation fault". In my case, I was running an interannual simulation coupled with PISCES. Could you please give me a hint? MPI (ifort) with ligand cppkey also activated

RMogollon gravatar imageRMogollon ( 2022-12-05 20:43:22 +0100 )edit

Thanks for your comment. I try to avoid using MPI but I did after @Renaud suggestion. My MPI flag uses ifort and the ligand cpp key for the ligand is activated.

ify gravatar imageify ( 2022-12-05 22:00:45 +0100 )edit

Here, the problem comes from the initialization of bgc values to Nan at some points of the domain close to the bottom (deepest points in fact) when creating croco_ini with crocotools. This is due to creation of HR initialisation file with LR data.

Renaud gravatar imageRenaud ( 2022-12-08 11:24:56 +0100 )edit

This can be fixed by setting hmax (crocotools_parama.m) to the nearest lower value of the depth of the NaN filled points or by modifying the initialization file by changing the Nan points to the nearest values.

Renaud gravatar imageRenaud ( 2022-12-08 11:25:57 +0100 )edit

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answered 2022-12-05 22:07:57 +0100

ify gravatar image

Here is my cppdefs.h and jobcomp file.C:\fakepath\cppdefs.h(/upfiles/16702744387487833.h)

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answered 2022-11-30 16:50:35 +0100

Renaud gravatar image

The module loaded: 1) intel/2021.4.0 2) openmpi/4.0.7 3) hdf5/1.10.7-mpi 4) netcdf-fortran/4.5.3-mpi 5) netcdf-c/4.7.4-mpi

Compilation option in the jobcomp: FC=ifort

Check that the key_ligand is activated in the cppdefs.h : define key_ligand

You can also send me the path to your run directory by mail

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answered 2022-11-30 16:18:52 +0100

Renaud gravatar image

updated 2022-11-30 16:21:00 +0100

Hello, I just ran CROCO PISCES v1.3 on the spirit cluster (it seems you are running on this machine) using the Benguela_LR configuration for a one month run (with MPI). Everything went well.

Can you confirm hat you are running on the spirit cluster? In that case, i can send you my environment and check your run directory as well.

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Hi Renaud, Yes, I running on spirit cluster. I just login again to try again but still the issue persist. If you can send me your environment to cross-check mine, that'll perfect. Thanks

ify gravatar imageify ( 2022-11-30 16:25:01 +0100 )edit
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Asked: 2022-11-30 11:42:55 +0100

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Last updated: Dec 05 '22