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SIGSEGV, segmentation fault error using "mksurfdata.pl"


Dear Scientists,

I am trying to create surface data on 0.5 degree with the following command, but keep getting the error message "forrtl: severe (174): SIGSEGV, segmentation fault occurred".

./mksurfdata.pl -res 360x720cru -y 2000

(gridmap_map_read) * file name : /net/fs05/d1/xgao/cesm2.1.3/inputdata/lnd/clm2/mappingdata/maps/360x720/map_0.25x0.25_MODIS_to_360x720cru_nomask_aave_da_c170321.nc
* matrix dimensions rows x cols : 1036800 x 259200
* number of non-zero elements: 545989
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
mksurfdata_map 000000000055E841 Unknown Unknown Unknown
mksurfdata_map 000000000055C97B Unknown Unknown Unknown
mksurfdata_map 00000000005136C4 Unknown Unknown Unknown
mksurfdata_map 00000000005134D6 Unknown Unknown Unknown
mksurfdata_map 00000000004AC059 Unknown Unknown Unknown
mksurfdata_map 00000000004B0786 Unknown Unknown Unknown
libpthread-2.23.s 00007FCC4F1C1C20 Unknown Unknown Unknown
mksurfdata_map 000000000044CE57 mkpftmod_mp_mkpft 563 mkpftMod.F90
mksurfdata_map 000000000046B81D MAIN__ 564 mksurfdat.F90
mksurfdata_map 000000000040A2AE Unknown Unknown Unknown
libc-2.23.so 00007FCC4EE0F731 __libc_start_main Unknown Unknown
mksurfdata_map 000000000040A1A9 Unknown Unknown Unknown
ERROR in mksurfdata_map: 44544

I also tried to add "ulimit -s unlimited" to avoid memory issue based on forrtl: severe (174): SIGSEGV, segmentation fault occurred.
However, it does not help.

I am wondering if it is memory issue or the compiler issue.



Additional information: I am running the job on our own cluster, and I am submit the job to the queue. My submitting script is as follows:

#SBATCH --partition=edr
#SBATCH -n 32
#SBATCH --mem=0
#SBATCH --reservation=xgao_test
#SBATCH --time=1:00:00 # format is DAYS-HOURS:MINUTES:SECONDS
#SBATCH --job-name=testmksurf
#SBATCH --output=testmksurf.out
# End of options

cd /net/fs05/d1/xgao/cesm2.1.3/cesm/components/clm/tools/mksurfdata_map
source /etc/profile.d/modules.csh
module load intel
module load netcdf

ulimit -s unlimited

./mksurfdata.pl -res 360x720cru -y 2000



Erik Kluzek
CSEG and Liaisons
Staff member
Hmmm. I wonder about memory as well. I would try a lower resolution case first. First try a single point and then some low resolution global grids. Look at line 563 in mkpftMod.F90 to see what variable is failing. You might try building with a different compiler as well.