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segmentation fault

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Posted by Anonymous at June 10 2025

Hello,

i am trying to run nemo + WRF + OASIS. 
I get the following error:
Segmentation fault: address not mapped to object at address
=== backtrace (tid:  64618) ====
 0  /opt/nvidia/hpc_sdk/Linux_x86_64/24.11/comm_libs/12.6/openmpi4/openmpi-4.1.5/lib/libucs.so.0(ucs_handle_error+0x124) [0x7fba02232084]
 1  /opt/nvidia/hpc_sdk/Linux_x86_64/24.11/comm_libs/12.6/openmpi4/openmpi-4.1.5/lib/libucs.so.0(+0x323ac) [0x7fba022323ac]
 2  /opt/nvidia/hpc_sdk/Linux_x86_64/24.11/comm_libs/12.6/openmpi4/openmpi-4.1.5/lib/libucs.so.0(+0x3261b) [0x7fba0223261b]
 3  /lib64/libc.so.6(+0x57980) [0x7fba03c57980]
 4  ./nemo() [0xddb370]
 5  ./nemo() [0x10a04cf]
 6  ./nemo() [0x9fc9f6]
 7  ./nemo() [0x50b9de]
 8  ./nemo() [0x54bbe9]
 9  ./nemo() [0x4f0736]
10  ./nemo() [0x4f0531]
11  /lib64/libc.so.6(+0x40eec) [0x7fba03c40eec]
12  /lib64/libc.so.6(__libc_start_main+0x87) [0x7fba03c40fb5]
13  ./nemo() [0x4f0421]


my launch command is /opt/nvidia/hpc_sdk/Linux_x86_64/24.11/comm_libs/openmpi4/bin/mpirun -n 1 /usr/local/bin/WRF-4.4-OASIS/wrf.exe : -n 2 ./nemo
Everything is compile with nvdia ogi compiler.

The code stops in the beginning of nemo. in the " ice_dyn_adv: sea-ice advection
" section. The end of ocean.output is:
 ice_dyn_adv: sea-ice advection
 ~~~~~~~~~~~
 -- ice_dyn_adv_pra: Prather advection scheme
 ----  ice-adv-rst  ----
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: sxice defined ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: sxice written ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: syice defined ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: syice written ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: sxxice defined ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: sxxice written ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: syyice defined ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: syyice written ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: sxyice defined ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: sxyice written ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: sxsn defined ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: sxsn written ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: sysn defined ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: sysn written ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: sxxsn defined ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: sxxsn written ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: syysn defined ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: syysn written ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: sxysn defined ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: sxysn written ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: sxa defined ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: sxa written ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: sya defined ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: sya written ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: sxxa defined ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: sxxa written ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: syya defined ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: syya written ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: sxya defined ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: sxya written ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: sxsal defined ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: sxsal written ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: sysal defined ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: sysal written ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: sxxsal defined ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: sxxsal written ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: syysal defined ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: syysal written ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: sxysal defined ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: sxysal written ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: sxage defined ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: sxage written ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: syage defined ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: syage written ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: sxxage defined ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: sxxage written ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: syyage defined ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: syyage written ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: sxyage defined ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: sxyage written ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: sxc0_l01 defined ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: sxc0_l01 written ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: syc0_l01 defined ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: syc0_l01 written ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: sxxc0_l01 defined ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: sxxc0_l01 written ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: syyc0_l01 defined ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: syyc0_l01 written ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: sxyc0_l01 defined ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: sxyc0_l01 written ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: sxc0_l02 defined ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: sxc0_l02 written ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: syc0_l02 defined ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: syc0_l02 written ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: sxxc0_l02 defined ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: sxxc0_l02 written ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: syyc0_l02 defined ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: syyc0_l02 written ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: sxyc0_l02 defined ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: sxyc0_l02 written ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: sxe_l01 defined ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: sxe_l01 written ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: sye_l01 defined ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: sye_l01 written ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: sxxe_l01 defined ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: sxxe_l01 written ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: syye_l01 defined ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: syye_l01 written ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: sxye_l01 defined ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: sxye_l01 written ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: sxe_l02 defined ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: sxe_l02 written ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: sye_l02 defined ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: sye_l02 written ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: sxxe_l02 defined ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: sxxe_l02 written ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: syye_l02 defined ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: syye_l02 written ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: sxye_l02 defined ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: sxye_l02 written ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: sxap defined ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: sxap written ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: syap defined ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: syap written ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: sxxap defined ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: sxxap written ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: syyap defined ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: syyap written ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: sxyap defined ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: sxyap written ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: sxvp defined ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: sxvp written ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: syvp defined ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: syvp written ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: sxxvp defined ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: sxxvp written ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: syyvp defined ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: syyvp written ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: sxyvp defined ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: sxyvp written ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: sxvl defined ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: sxvl written ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: syvl defined ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: syvl written ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: sxxvl defined ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: sxxvl written ok
           iom_nf90_rp0123d, file: ./ORCA2_00000004_restart_ice_0000.nc, var: syyvl 

Thanks for any inights.

best

Posted by Anonymous at June 12 2025

Hi,
This is not clear at all if it is really an OASIS3-MCT problem. I think you should investigate more precisely where nemo has this Segmentation fault ...
  Sorry not to be of much help,
  Sophie

Posted by Anonymous at June 13 2025

Hi,
It is also from ORCA2 due to advection (sharp gradient problem). It's using iom.
Best, 
*.*
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