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geoschem / integrated_methane_inversion

Integrated Methane Inversion workflow repository.
https://imi.readthedocs.org
MIT License
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Program received signal SIGSEGV: Segmentation fault - invalid memory reference. #106

Closed delgadocc closed 1 year ago

delgadocc commented 1 year ago

Institution

University of Otago

IMI Application

I will use IMI to train/validate artificial intelligence models for the estimation of methane emissions from sentinel-5P images

Description of the problem

I am trying to install the IMI framework using Spack on a local server but I am getting the following error at the time of running the Spinup stage:

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:

Could not print backtrace: unrecognized DWARF version in .debug_info at 6

0 0x1513e318cd8f in ???

1 0x1513e36c9cf9 in sflush

at /tmp/delcr974/spack-stage/spack-stage-gcc-8.2.0-ccwpzujgr5ufzpbhjgn74cbv6qdybhl2/spack-src/libgfortran/io/unix.h:89

2 0x4aa38a in __hco_interface_gc_mod_MOD_hcoi_gc_run

at /home/delcr974/integrated_methane_inversion/GCClassic/src/GEOS-Chem/GeosCore/hco_interface_gc_mod.F90:1158

3 0x4509c2 in __emissions_mod_MOD_emissions_run

at /home/delcr974/integrated_methane_inversion/GCClassic/src/GEOS-Chem/GeosCore/emissions_mod.F90:204

4 0x404c21 in geos_chem

at /home/delcr974/integrated_methane_inversion/GCClassic/src/GEOS-Chem/Interfaces/GCClassic/main.F90:703

5 0x4038b6 in main

at /home/delcr974/integrated_methane_inversion/GCClassic/src/GEOS-Chem/Interfaces/GCClassic/main.F90:32

/var/spool/slurmd/job00418/slurm_script: line 29: 1339414 Segmentation fault (core dumped) ./gcclassic >> $log

Attached you find the configuration file (config.txt), the log file (imi_output.txt), the GEOS-CHEM enviroment file (Otago.txt) and the GEOS-CHEM build summary (CMakeCache.txt).

Description of troubleshooting performed

Describe any troubleshooting that you have already performed here. Also include any leads or suspicions here.

IMI version

Already try adding the following options in the GEOS-CHEM environment file but didnt work: ulimit -c unlimited # coredumpsize ulimit -l unlimited # memorylocked ulimit -u 50000 # maxproc ulimit -v unlimited # vmemoryuse ulimit -s unlimited # stacksize

CMakeCache.txt config.txt imi_output.txt Otago.txt

laestrada commented 1 year ago

Hi @delgadocc,

Can you post your GEOS-Chem log file and run file? The paths should be like imi_output_dir/spinup_run/Waikato_winter_Spinup.log and imi_output_dir/spinup_run/Waikato_winter_Spinup.run.

Also what version of GEOS-Chem is being used for the IMI?

delgadocc commented 1 year ago

Dear @laestrada

Thank you for your suggestion, I checked the spinup run log and it was an error reading the file "/home/delcr974/ExtData/HEMCO/CH4/v2022-11/4x5/gmi.ch4loss.geos5_47L.4x5.nc". In AWS this file was in "/home/ubuntu/ExtData/HEMCO/CH4/v2014-09/4x5/gmi.ch4loss.geos5_47L.4x5.nc" but apparently the version of GEOS-CHEM that I downloaded from git-hub requires the updated version. I just downloaded the version v2022-11 and now everything works fine.

Regards