could not read WPS_GEOG/topobath_30s/index when ./geogrid.exe

[y.su]

when I run ./geogrid.exe ,the log.geogrid occured Segmentation Fault.Then geogrid.log could not read WPS_GEOG/topobath_30s/index

Attachment is log.geogrid.log and geogrid.log
Parsed 50 entries in GEOGRID.TBL
Processing domain 1 of 2
Processing XLAT and XLONG

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

Backtrace for this error:
#0 0x2B61FEFFF6D7
#1 0x2B61FEFFFD1E
#2 0x2B61FFA923FF
#3 0x2B61FFBC6E41
#4 0x2B61FF0DDD08
#5 0x2B61FF00217A
#6 0x49820E in ext_ncd_inquiry_
#7 0x431758 in __output_module_MOD_output_init
#8 0x43B22B in __process_tile_module_MOD_process_tile

2023-11-08 19:51:54.232 --- INFORM: Could not read 'index' file /storage/silver/diamet/lw154933/WPS_GEOG/lake_depth/index for
field LAKE_DEPTH
2023-11-08 19:51:54.233 --- INFORM: This field is optional and will not be processed.
2023-11-08 19:51:54.233 --- INFORM: Using default interpolator sequence for URB_PARAM.
2023-11-08 19:51:54.233 --- INFORM: Using default data source for URB_PARAM.
2023-11-08 19:51:54.233 --- INFORM: Could not read 'index' file /storage/silver/diamet/lw154933/WPS_GEOG/NUDAPT44_1km/index fo

2023-11-08 19:51:54.237 --- INFORM: Could not read 'index' file /storage/silver/diamet/lw154933/WPS_GEOG/topobath_30s/index fo
r field BATHYMETRY
2023-11-08 19:51:54.237 --- INFORM: This field is optional and will not be processed.

 

[kwerner]

Hi,
Can you please attach your full geogrid.log file, as well as your namelist.wps? Thanks!

 

[y.su]

ok,I have attached them.Thanks

 

[y.su]

Hi,
Can you please attach your full geogrid.log file, as well as your namelist.wps? Thanks!

yeah,thanks

 

[kwerner]

Thanks for sending those. The "INFORM" messages you are seeing are just indicating that you don't have some of the "optional" datasets, which you don't need, unless you are intending to use those specific data. Regarding the segmentation fault, I ran a test, using your namelist.wps file and geogrid runs without any issues, so this must be specific to your setup or system.

1) Are you manually stopping geogrid before it finishes, or does it stop on its own with the segmentation fault?
2) Can you check to make sure you have enough disk space to write the geo_em* files to your WPS directory?
3) Did you compile WPS serially, or for dmpar?

 

[y.su]

Thanks for sending those. The "INFORM" messages you are seeing are just indicating that you don't have some of the "optional" datasets, which you don't need, unless you are intending to use those specific data. Regarding the segmentation fault, I ran a test, using your namelist.wps file and geogrid runs without any issues, so this must be specific to your setup or system.

1) Are you manually stopping geogrid before it finishes, or does it stop on its own with the segmentation fault?
2) Can you check to make sure you have enough disk space to write the geo_em* files to your WPS directory?
3) Did you compile WPS serially, or for dmpar?

Thank you for your email.

I first tried to run em_b_wave,the generated data wrfout was not in nc format,it was hdf5.

Later I ran em_real,but when compiling wrf I need to select number,I selected 32(GNU (gfortran/gcc)),when compiling WPS I selected 1. I am not sure how many numbers to select?

1) The geogrid has stopped running on its own when there is a segmentation fault

2) Yes, I have enough disk space to write the geo_em* file to the WPS directory.

3) I selected number 1 when compiling WPS,it is serial compile
Attached are the steps I did before running geogrid, could you please help me to see if there are any errors in my build and compile?
Many Thanks

 

[y.su]

when I configure and compile again my WRF and WPS,a new problem occure,
my compile.log will appear
Fatal Error: Can't open module file ‘netcdf.mod’ for reading at (1): No such file or directory,I can't produce metgrid.exe and geogrid.exe

 

[kwerner]

Fatal Error: Can't open module file ‘netcdf.mod’ for reading at (1): No such file or directory,I can't produce metgrid.exe and geogrid.exe

Regarding this new error, do you have the NETCDF environment variable set? Do you have the netcdf/bin directory set in your PATH? If you set these earlier, but then exited your terminal window, the paths are no longer set, unless you added them to an environment script (e.g., .bashrc).

 

[y.su]

Regarding this new error, do you have the NETCDF environment variable set? Do you have the netcdf/bin directory set in your PATH? If you set these earlier, but then exited your terminal window, the paths are no longer set, unless you added them to an environment script (e.g., .bashrc).

Thanks for your email.
I am compiling WPS with the following setup, no metgrid.exe is generated, log.compile shows that the module file 'netcdf.mod' cannot be opened for reading at (1): no such file or directory

Module unload gcc/10.5.0
Module load netcdf
export NETCDF=/share/apps/Met/netcdf/fortran-4.4.4
Module loading MET

export JASPERLIB=$DIR/grib2/lib
export JASPERINC=$DIR/grib2/include

I followed the setup netcdf environment, the following steps, no geogrid.exe and metgrid.exe generated, the attachment is log.compile


. /clean -a
Module unload gcc/10.5.0
Module loading netcdf
export NETCDF=/share/apps/Met/netcdf/fortran-4.4.4
Module loading MET

export PATH=$DIR/netcdf/bin:$PATH
export NETCDF=$DIR/netcdf
export PATH=$DIR/mpich/bin:$PATH
export JASPERLIB=$DIR/grib2/lib
export JASPERINC=$DIR/grib2/include

 

[kwerner]

Apologies for the long delay in response. I got bogged down in some other time-sensitive obligations and then was out of the office for a bit. Are you still experiencing problems? If so, can you please attach the following files?
1) configure.wrf
2) WRF compile log
3) configure.wps
4) WPS compile log