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PTCLM (CESM2.0 version) fail to run (core dumped)

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geoxiyang@...
PTCLM (CESM2.0 version) fail to run (core dumped)

Hi all,

I followed the instruction under components/clm/tools/PTCLM to create a single-point surface data for US-Ha1 (or the default US-UMB). The run did not work either when it was submitted to the batch or when I ran PTCLMmkdata. Here is the error. Any idea of the reason? Thanks!

./PTCLMmkdata --ctsm_root $CTSM_ROOT --cime_root $CIME_ROOT -s US-UMB -d /glade/p/cesmdata/cseg/inputdata

---------------- PTCLMmkdata version PTCLM2_180611-----------------------------

 

   ./PTCLMmkdata --ctsm_root /glade/u/home/xiyang/cesm2_0_0/components/clm --cime_root /glade/u/home/xiyang/cesm2_0_0/cime -s US-UMB -d /glade/p/cesmdata/cseg/inputdata 

 

   OPTIONS:

 

Site name:US-UMB

 

Root CTSM directory:/glade/u/home/xiyang/cesm2_0_0/components/clm

Root CIME directory:/glade/u/home/xiyang/cesm2_0_0/cime

** Surface data file will be built using site-level data when available unless otherwise specified ** 

 

Extract PFT data from gridded files:False

Extract soil data from gridded files:False

 

Open Site data file: /gpfs/u/home/xiyang/cesm2_0_0/components/clm/tools/PTCLM/PTCLM_sitedata/PTCLMDATA_sitedata.txt

 

CESM input data directory:/glade/p/cesmdata/cseg/inputdata

----------------------------------------------------------------

 

Write /gpfs/u/home/xiyang/cesm2_0_0/components/clm/tools/PTCLM/mydatafiles/1x1pt_US-UMB/README.PTCLM with command line

Run command: /bin/chmod +x /gpfs/u/home/xiyang/cesm2_0_0/components/clm/tools/PTCLM/mydatafiles/1x1pt_US-UMB/shell_commands

Making input files for the point (this may take a while if creating transient datasets)

Creating map file for a point with no ocean

lat=45.5598

/glade/u/apps/ch/opt/ncl/6.4.0/intel/17.0.1/bin/ncl

Run command: /glade/u/home/xiyang/cesm2_0_0/components/clm/tools/mkmapdata/mknoocnmap.pl -p 45.5598,275.2862 -name 1x1pt_US-UMB > /gpfs/u/home/xiyang/cesm2_0_0/components/clm/tools/PTCLM/mydatafiles/1x1pt_US-UMB/mknoocnmap.log

mapfile = /glade/u/home/xiyang/cesm2_0_0/components/clm/tools/mkmapdata/map_1x1pt_US-UMB_noocean_to_1x1pt_US-UMB_nomask_aave_da_181010.nc

scripgridfile = /glade/u/home/xiyang/cesm2_0_0/components/clm/tools/mkmapgrids/SCRIPgrid_1x1pt_US-UMB_nomask_c181010.nc

Creating data domain

Run command: /glade/u/home/xiyang/cesm2_0_0/cime/tools/mapping/gen_domain_files/gen_domain -m /glade/u/home/xiyang/cesm2_0_0/components/clm/tools/mkmapdata/map_1x1pt_US-UMB_noocean_to_1x1pt_US-UMB_nomask_aave_da_181010.nc -o navy -l 1x1pt_US-UMB -c 'Running gen_domain from PTCLMmkdata' > /gpfs/u/home/xiyang/cesm2_0_0/components/clm/tools/PTCLM/mydatafiles/1x1pt_US-UMB/gen_domain.log

domainfile = domain.lnd.1x1pt_US-UMB_navy.181010.nc

 

 

Re-create surface dataset:

 

 

Re-create mapping files for surface dataset:

Run command: /glade/u/home/xiyang/cesm2_0_0/components/clm/tools/mkmapdata/mkmapdata.sh --gridfile /glade/u/home/xiyang/cesm2_0_0/components/clm/tools/mkmapgrids/SCRIPgrid_1x1pt_US-UMB_nomask_c181010.nc --res 1x1pt_US-UMB --gridtype regional -v > /gpfs/u/home/xiyang/cesm2_0_0/components/clm/tools/PTCLM/mydatafiles/1x1pt_US-UMB/mkmapdata.log

rm: cannot remove ‘PET*.Log’: No such file or directory

forrtl: severe (174): SIGSEGV, segmentation fault occurred

Image              PC                Routine            Line        Source             

libirc.so          00007FFFE90857F1  tbk_trace_stack_i     Unknown  Unknown

libirc.so          00007FFFE908392B  tbk_string_stack_     Unknown  Unknown

ESMF_RegridWeight  0000000000471C54  Unknown               Unknown  Unknown

ESMF_RegridWeight  0000000000471A66  Unknown               Unknown  Unknown

ESMF_RegridWeight  0000000000418F89  Unknown               Unknown  Unknown

ESMF_RegridWeight  000000000041D7A6  Unknown               Unknown  Unknown

libpthread-2.19.s  00007FFFE8E61870  Unknown               Unknown  Unknown

libirc.so          00007FFFE90B1279  __intel_avx_rep_m     Unknown  Unknown

libesmf.so         00007FFFEC73BBD7  esmf_regridweight     Unknown  Unknown

libesmf.so         00007FFFEC734689  esmf_regridweight     Unknown  Unknown

ESMF_RegridWeight  0000000000408187  Unknown               Unknown  Unknown

ESMF_RegridWeight  00000000004049CE  Unknown               Unknown  Unknown

libc-2.19.so       00007FFFE86BFB25  __libc_start_main     Unknown  Unknown

ESMF_RegridWeight  00000000004048D9  Unknown               Unknown  Unknown

forrtl: severe (174): SIGSEGV, segmentation fault occurred

Image              PC                Routine            Line        Source             

ESMF_RegridWeight  000000000041DACB  Unknown               Unknown  Unknown

libpthread-2.19.s  00007FFFE8E61870  Unknown               Unknown  Unknown

libiomp5.so        00007FFFE97B1564  Unknown               Unknown  Unknown

ld-2.19.so         00007FFFED8F2F18  Unknown               Unknown  Unknown

libc-2.19.so       00007FFFE86D5B39  Unknown               Unknown  Unknown

libc-2.19.so       00007FFFE86D5B85  Unknown               Unknown  Unknown

ESMF_RegridWeight  0000000000418F29  Unknown               Unknown  Unknown

ESMF_RegridWeight  000000000041D7A6  Unknown               Unknown  Unknown

libpthread-2.19.s  00007FFFE8E61870  Unknown               Unknown  Unknown

libirc.so          00007FFFE90B1279  __intel_avx_rep_m     Unknown  Unknown

libesmf.so         00007FFFEC73BBD7  esmf_regridweight     Unknown  Unknown

libesmf.so         00007FFFEC734689  esmf_regridweight     Unknown  Unknown

ESMF_RegridWeight  0000000000408187  Unknown               Unknown  Unknown

ESMF_RegridWeight  00000000004049CE  Unknown               Unknown  Unknown

libc-2.19.so       00007FFFE86BFB25  __libc_start_main     Unknown  Unknown

ESMF_RegridWeight  00000000004048D9  Unknown               Unknown  Unknown

ERROR(./PTCLMmkdata):: Error running command: /glade/u/home/xiyang/cesm2_0_0/components/clm/tools/mkmapdata/mkmapdata.sh --gridfile /glade/u/home/xiyang/cesm2_0_0/components/clm/tools/mkmapgrids/SCRIPgrid_1x1pt_US-UMB_nomask_c181010.nc --res 1x1pt_US-UMB --gridtype regional -v > /gpfs/u/home/xiyang/cesm2_0_0/components/clm/tools/PTCLM/mydatafiles/1x1pt_US-UMB/mkmapdata.log

Aborted (core dumped)

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