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GEOGRID ERROR: ext_pkg_open_for_write_begin

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lslrsgis

Member
Dear WRF community,

I'm writing for a problem with geogrid.

I have successfully compiled both WRF and WPS (all executables are made). But when I run ./geogrid.exe, errors prompted on the screen as follows:

[slliu@swarm02 WPS_2015_TEST]$ ./geogrid.exe
Parsed 28 entries in GEOGRID.TBL
Processing domain 1 of 2
Processing XLAT and XLONG
ERROR: Error in ext_pkg_open_for_write_begin.

(1) In /WPS/geogrid/src, within output_module.f90, there is a statement: "call mprintf((istatus /= 0), ERROR, 'Error in ext_pkg_write_field')". But I do not know why it comes here.

(2) It might be something relative to writable of WPS_2015_TEST folder. But this error remains when I checked the writable right.

Similar topic has been posted on:
http://mailman.ucar.edu/pipermail/wrf-users/2016/004255.html
http://forum.wrfforum.com/viewtopic.php?f=21&t=10756
http://forum.mmm.ucar.edu/phpBB3/viewtopic.php?f=30&t=5284

The geogrid.log and namelist.wps are attached. Any indications would be appreciated. Thanks in advance,

Liang

P.S. I am using intel/parallelstudio/2019, with option: 19. Linux x86_64, Intel compiler (dmpar). Netcdf
Library version: curl-7.62.0 hdf5-1.10.4 jasper-1.900.1 libpng-1.6.35 zlib-1.2.11 netcdf-4.6.1 netcdf-fortran-4.4.4
 

Attachments

  • namelist.wps
    1.3 KB · Views: 84
  • geogrid.log
    10.5 KB · Views: 100
Hi

I had similar problem. I saw on previous posts it could be due to the fact you compiled WRF parallel and WPS compiled in in serial. is that your case? If so it was suggested you clean -a reconfigure and edit the configure.wps file as below

WRF_LIB = -L$(WRF_DIR)/external/io_grib1 -lio_grib1 \
-L$(WRF_DIR)/external/io_grib_share -lio_grib_share \
-L$(WRF_DIR)/external/io_int -lwrfio_int \
-L$(WRF_DIR)/external/io_netcdf -lwrfio_nf \
-L$(NETCDF)/lib -lnetcdff -lnetcdf
change to

WRF_LIB = -L$(WRF_DIR)/external/io_grib1 -lio_grib1 \
-L$(WRF_DIR)/external/io_grib_share -lio_grib_share \
-L$(WRF_DIR)/external/io_int -lwrfio_int \
-L$(WRF_DIR)/external/io_netcdf -lwrfio_nf \
-L$(NETCDF)/lib -lnetcdff -lnetcdf -liomp5 -lpthread

It worked for me but I am now struggling to create ungrib.exe. Could be a solution to you. Try!

Netsanet
 
Thanks. It is very help for compilation. I tried to ./clean -a and recompiled WRF, and then WPS after adding -liomp5 -lpthread in configure.wps. The executives are generated successfully.

However, it seems the problem still existes:

[slliu@swarm02 WPS_TEST]$ ./geogrid.exe
Parsed 28 entries in GEOGRID.TBL
Processing domain 1 of 2
Processing XLAT and XLONG
ERROR: Error in ext_pkg_open_for_write_begin.
Abort(51201888) on node 0 (rank 0 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 51201888) - process 0
 

Attachments

  • configure.wps
    4 KB · Views: 75
  • namelist.wps
    1.3 KB · Views: 77
Hi,
This error can potentially mean that you don't have permissions to write files to the directory in which you are trying to. You may need to check with the systems administrator of your system to verify that you can write files to the current WPS/ directory.
 
Thanks Kelly. It seems that the errors indicate I can not write NETCDF file. The line "export WRFIO_NCD_LARGE_FILE_SUPPORT=1" has been written in ~/.bashrc.

I changed debug_level=1000 (to get more debug info), and opt_output_from_geogrid_path = '/home/slliu/project/WRF/WPS_TEST/' (to ensure I have permission). The detailed debug error comes:

INFORM: Using default data source for SANDFRAC.
INFORM: Could not read 'index' file /home/slliu/project/WRF/GEOG/WPS_GEOG_HIGH_RES/sandfrac_5m/index for field SANDFRAC
INFORM: This field is optional and will not be processed.
Processing XLAT and XLONG
WRF_DEBUG: NetCDF error: NetCDF: Not a valid ID
WRF_DEBUG: NetCDF error in ext_ncd_open_for_write_begin wrf_io.F90, line
1382
ERROR: Error in ext_pkg_open_for_write_begin.
Abort(48891744) on node 0 (rank 0 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 48891744) - process 0

Then, a geo_em.d01.nc file is generated. However, this file is boken and nearly empty (0B).

namelist.wps, geogrid.log, execution ./geogrid log are attached.

P.S. Should I use pNetCDF for HPC dmpar MPI run?
 

Attachments

  • log.execute.geogrid.txt
    4.6 KB · Views: 60
  • geogrid.log
    10.5 KB · Views: 64
  • namelist.wps
    1.4 KB · Views: 69
Could you try cleaning and recompiling the WRF code with a serial option (and not a dmpar, smpar, or dm+sm option), then doing the same for the WPS? This would rule out any problems with the combination of parallel options in WRF and WPS. I'll see if I can reproduce the issue here using the same library versions and the Intel 19 compilers. Apologies if I missed this, but which version of the WRF and WPS codes are you using?
 
Thanks. I have just tried the serial+Intel compiler+basic nesting option for WRF and WPS. It seems that the same error still exist. I am not sure if it is a problem with my NETCDF libraries.

Parsed 28 entries in GEOGRID.TBL
Processing domain 1 of 2
Processing XLAT and XLONG
ERROR: Error in ext_pkg_open_for_write_begin.

I am working on WRFV4.0 and WPS V4.0.
 

Attachments

  • geogrid.log
    10.5 KB · Views: 67
  • namelist.wps
    1.3 KB · Views: 85
  • log.geogrid.serial.txt
    132 bytes · Views: 68
  • geogrid_screenshot.png
    geogrid_screenshot.png
    63.7 KB · Views: 2,820
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