pisces segmentation runtime error
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
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
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.
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.
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.