NetCDF error: NetCDF: Variable not found QICE_BXS

[Vera]

Hi,

I am currently trying to switch to the lastest wrf version. WPS and real.exe ran succesfully but some variables are not present in the wrfbdy_d01.
Thus, when trying to run wrf.exe, I have the following error :
d01 2010-01-01_00:00:00 Input data is acceptable to use: wrfbdy_d01
d01 2010-01-01_00:00:00 mminlu = 'MODIFIED_IGBP_MODIS_NOAH'
d01 2010-01-01_00:00:00 NetCDF error: NetCDF: Variable not found
d01 2010-01-01_00:00:00 NetCDF error in wrf_io.F90, line 2883 Varname QICE_BXS
d01 2010-01-01_00:00:00 NetCDF error: NetCDF: Variable not found
d01 2010-01-01_00:00:00 NetCDF error in wrf_io.F90, line 2883 Varname QICE_BXE
d01 2010-01-01_00:00:00 NetCDF error: NetCDF: Variable not found
d01 2010-01-01_00:00:00 NetCDF error in wrf_io.F90, line 2883 Varname QICE_BYS
d01 2010-01-01_00:00:00 NetCDF error: NetCDF: Variable not found
d01 2010-01-01_00:00:00 NetCDF error in wrf_io.F90, line 2883 Varname QICE_BYE
d01 2010-01-01_00:00:00 NetCDF error: NetCDF: Variable not found
d01 2010-01-01_00:00:00 NetCDF error in wrf_io.F90, line 2883 Varname QSNOW_BXS
d01 2010-01-01_00:00:00 NetCDF error: NetCDF: Variable not found
d01 2010-01-01_00:00:00 NetCDF error in wrf_io.F90, line 2883 Varname QSNOW_BXE
d01 2010-01-01_00:00:00 NetCDF error: NetCDF: Variable not found
d01 2010-01-01_00:00:00 NetCDF error in wrf_io.F90, line 2883 Varname QSNOW_BYS
d01 2010-01-01_00:00:00 NetCDF error: NetCDF: Variable not found
d01 2010-01-01_00:00:00 NetCDF error in wrf_io.F90, line 2883 Varname QSNOW_BYE
d01 2010-01-01_00:00:00 NetCDF error: NetCDF: Variable not found
d01 2010-01-01_00:00:00 NetCDF error in wrf_io.F90, line 2883 Varname QGRAUP_BXS
d01 2010-01-01_00:00:00 NetCDF error: NetCDF: Variable not found
d01 2010-01-01_00:00:00 NetCDF error in wrf_io.F90, line 2883 Varname QGRAUP_BXE
d01 2010-01-01_00:00:00 NetCDF error: NetCDF: Variable not found
d01 2010-01-01_00:00:00 NetCDF error in wrf_io.F90, line 2883 Varname QGRAUP_BYS
d01 2010-01-01_00:00:00 NetCDF error: NetCDF: Variable not found
d01 2010-01-01_00:00:00 NetCDF error in wrf_io.F90, line 2883 Varname QGRAUP_BYE
d01 2010-01-01_00:00:00 NetCDF error: NetCDF: Variable not found
d01 2010-01-01_00:00:00 NetCDF error in wrf_io.F90, line 2883 Varname QICE_BTXS
d01 2010-01-01_00:00:00 NetCDF error: NetCDF: Variable not found
d01 2010-01-01_00:00:00 NetCDF error in wrf_io.F90, line 2883 Varname QICE_BTXE
d01 2010-01-01_00:00:00 NetCDF error: NetCDF: Variable not found
d01 2010-01-01_00:00:00 NetCDF error in wrf_io.F90, line 2883 Varname QICE_BTYS
d01 2010-01-01_00:00:00 NetCDF error: NetCDF: Variable not found
d01 2010-01-01_00:00:00 NetCDF error in wrf_io.F90, line 2883 Varname QICE_BTYE
d01 2010-01-01_00:00:00 NetCDF error: NetCDF: Variable not found
d01 2010-01-01_00:00:00 NetCDF error in wrf_io.F90, line 2883 Varname QSNOW_BTXS
d01 2010-01-01_00:00:00 NetCDF error: NetCDF: Variable not found
d01 2010-01-01_00:00:00 NetCDF error in wrf_io.F90, line 2883 Varname QSNOW_BTXE
d01 2010-01-01_00:00:00 NetCDF error: NetCDF: Variable not found
d01 2010-01-01_00:00:00 NetCDF error in wrf_io.F90, line 2883 Varname QSNOW_BTYS
d01 2010-01-01_00:00:00 NetCDF error: NetCDF: Variable not found
d01 2010-01-01_00:00:00 NetCDF error in wrf_io.F90, line 2883 Varname QSNOW_BTYE
d01 2010-01-01_00:00:00 NetCDF error: NetCDF: Variable not found
d01 2010-01-01_00:00:00 NetCDF error in wrf_io.F90, line 2883 Varname QGRAUP_BTXS
d01 2010-01-01_00:00:00 NetCDF error: NetCDF: Variable not found
d01 2010-01-01_00:00:00 NetCDF error in wrf_io.F90, line 2883 Varname QGRAUP_BTXE
d01 2010-01-01_00:00:00 NetCDF error: NetCDF: Variable not found
d01 2010-01-01_00:00:00 NetCDF error in wrf_io.F90, line 2883 Varname QGRAUP_BTYS
d01 2010-01-01_00:00:00 NetCDF error: NetCDF: Variable not found
d01 2010-01-01_00:00:00 NetCDF error in wrf_io.F90, line 2883 Varname QGRAUP_BTYE
d01 2010-01-01_00:00:00 NetCDF error: NetCDF: Variable not found
d01 2010-01-01_00:00:00 NetCDF error in wrf_io.F90, line 2883 Varname QNICE_BXS
d01 2010-01-01_00:00:00 NetCDF error: NetCDF: Variable not found
d01 2010-01-01_00:00:00 NetCDF error in wrf_io.F90, line 2883 Varname QNICE_BXE

d01 2010-01-01_00:00:00 NetCDF error: NetCDF: Variable not found
d01 2010-01-01_00:00:00 NetCDF error in wrf_io.F90, line 2883 Varname QNICE_BYS
d01 2010-01-01_00:00:00 NetCDF error: NetCDF: Variable not found
d01 2010-01-01_00:00:00 NetCDF error in wrf_io.F90, line 2883 Varname QNICE_BYE
d01 2010-01-01_00:00:00 NetCDF error: NetCDF: Variable not found
d01 2010-01-01_00:00:00 NetCDF error in wrf_io.F90, line 2883 Varname QNRAIN_BXS
d01 2010-01-01_00:00:00 NetCDF error: NetCDF: Variable not found
d01 2010-01-01_00:00:00 NetCDF error in wrf_io.F90, line 2883 Varname QNRAIN_BXE
d01 2010-01-01_00:00:00 NetCDF error: NetCDF: Variable not found
d01 2010-01-01_00:00:00 NetCDF error in wrf_io.F90, line 2883 Varname QNRAIN_BYS
d01 2010-01-01_00:00:00 NetCDF error: NetCDF: Variable not found
d01 2010-01-01_00:00:00 NetCDF error in wrf_io.F90, line 2883 Varname QNRAIN_BYE
d01 2010-01-01_00:00:00 NetCDF error: NetCDF: Variable not found
d01 2010-01-01_00:00:00 NetCDF error in wrf_io.F90, line 2883 Varname QNICE_BTXS
d01 2010-01-01_00:00:00 NetCDF error: NetCDF: Variable not found
d01 2010-01-01_00:00:00 NetCDF error in wrf_io.F90, line 2883 Varname QNICE_BTXE
d01 2010-01-01_00:00:00 NetCDF error: NetCDF: Variable not found
d01 2010-01-01_00:00:00 NetCDF error in wrf_io.F90, line 2883 Varname QNICE_BTYS
d01 2010-01-01_00:00:00 NetCDF error: NetCDF: Variable not found
d01 2010-01-01_00:00:00 NetCDF error in wrf_io.F90, line 2883 Varname QNICE_BTYE
d01 2010-01-01_00:00:00 NetCDF error: NetCDF: Variable not found
d01 2010-01-01_00:00:00 NetCDF error in wrf_io.F90, line 2883 Varname QNRAIN_BTXS
d01 2010-01-01_00:00:00 NetCDF error: NetCDF: Variable not found
d01 2010-01-01_00:00:00 NetCDF error in wrf_io.F90, line 2883 Varname QNRAIN_BTXE
d01 2010-01-01_00:00:00 NetCDF error: NetCDF: Variable not found
d01 2010-01-01_00:00:00 NetCDF error in wrf_io.F90, line 2883 Varname QNRAIN_BTYS
d01 2010-01-01_00:00:00 NetCDF error: NetCDF: Variable not found
d01 2010-01-01_00:00:00 NetCDF error in wrf_io.F90, line 2883 Varname QNRAIN_BTYE
Timing for processing lateral boundary for domain 1: 0.56173 elapsed seconds
d01 2010-01-01_00:00:00 module_integrate: calling solve interface
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
libpthread-2.17.s 00007F4333A6D5D0 Unknown Unknown Unknown
wrf.exe 00000000016AB65B solve_em 439 solve_em.f90
wrf.exe 00000000014D164F solve_interface 123 solve_interface.f90
wrf.exe 000000000058C9A6 integrate 329 module_integrate.f90
wrf.exe 0000000000414DE2 wrf_run 326 module_wrf_top.f90
wrf.exe 0000000000414499 wrf 29 wrf.f90
wrf.exe 000000000041444D Unknown Unknown Unknown
libc-2.17.so 00007F4332DC83D5 __libc_start_main Unknown Unknown
wrf.exe 0000000000414376 Unknown Unknown Unknown

Please, do you know how I can solve this error?

Thank you

 

[kwerner]

Hi,
Can you make sure to set debug_level=0 in your namelist.input file and then re-run real.exe? Check the end of the out/error log (e.g., rsl.error.0000) to see if the run was successful - it should say "SUCCESS" at the end. If not, please attach that log file (or package all of the rsl* files into a single *.tar file, and attach that).

If real.exe completes successfully, please run wrf.exe again and attach the log file(s) for wrf.exe. Either way, please also attach your namelist.input file. Thanks!

 

[Vera]

Hi kwerner,

Thank you for your help. Yes, the real.exe ran sucessfully. I also tried to make the metgrid and real.exe with version 4.0 with the same result (no QICE_BXS and others in the wrfbdy file). In previous project (with elder version, a few years ago) I never faced this issue : wrfbdy file did had these variables, although values were set to 0.
I attach the namelist.input and the rsl files.

May that come from the Registry?

 

[kwerner]

Thanks for sending those; however, can you please run it again after changing "debug_level" to 0? We do not recommend setting that, as it is rarely helpful and just adds a lot of junk to the rsl files, making them difficult to read. Additionally, will you please package ALL the new rsl* files into a single *.tar or *.zip file and attach that? Thanks!

 

[Vera]

Sorry. Actually real.exe did run with debug_level to 0.
I attach the rsl for wrf.exe

 

[kwerner]

1) Did you also run wrf.exe with debug_level = 0? I ask because the namelist file you sent had debug_level = 100 and the rsl files seem to indicate that it was not set to 0.
2) Can you also check to determine whether you have enough disk space in the directory where you are writing output files?
3) Can you try this without quilting and let me know if you have the problem?

 

[Vera]

Hi,
- Yes, I have now ran with debug_level = 0 and obtain the same result (rsl.tar.gz contain the rsl* files for debug_level = 0).
- I have enough space in the directory (~ 400 Gb free).
- Today I have tried setting namelist.input with
&namelist_quilt
nio_tasks_per_group = 0,
nio_groups = 1,
/
is it enough to do no quilting? If so, I have the same issue.

Thank you very much for your help

 

[kwerner]

Ok thanks. Can you share your met_em* files with me so I can try to run this simulation to repeat the issue? Since it fails right at the beginning, you only need to send the first couple of met_em* files. The files are likely too large to attach, so take a look at the home page of this forum for instructions on sharing large files. Thanks!

 

[Vera]

Hi,

Thank you, I now have uploaded the file on the nextcloud storage (met_Vera.tar.gz)

Best,

 

[Vera]

Ok thanks. Can you share your met_em* files with me so I can try to run this simulation to repeat the issue? Since it fails right at the beginning, you only need to send the first couple of met_em* files. The files are likely too large to attach, so take a look at the home page of this forum for instructions on sharing large files. Thanks!

Hi,

I was wondering whether you have all you need to run the test? Please ask me if you need anything.

Thank you very much,

 

[Ming Chen]

Hi Vera,

I got your data and run your case. I use the standard WRFV4.5. Below is what I did:

(1) I modify yor namelist.input as follows:
time_step = 30
nio_tasks_per_group = 0,
nio_groups = 1,

(2) I delete the options:
nproc_x = 2,
nproc_y = 20,
numtiles = 1
nested = .false., .true., .true.,
periodic_x = .false., .false., .false.,

I run real.exe and wrf.exe, and the case runs to the end. QICE, QSNOW, etc do exist in the wrfbdy file.

Please retry this case with the options I have and run with the standard WRFV4.5 code. Let me know if you still have issues.

 

[Vera]

Hi,

I made the try ... and it works : I realized that, although I tried to run wrf.exe with only domain d01, to prepare my forcing, I used max_dom=3 to prepare the forcing for each domain at once.
When I run the real.exe with max_dom=1 I have all the variables. When I run real.exe with max_dom=3, the previously mentioned variables are missing.

Thank you very much for your help.
Maybe this post could help someone else in the future ...

Best,

 

[Ming Chen]

No matter how many domains in your case, you only need wrfbdy_d01. There shouldn't have wrfbdy_d02, wrfbdy_d03, etc.

 

[Vera]

Hi,

Yes, of course. I did the real.exe to have the wrf_input and wrflowinp for all the domains.

NB : Actually, the segmentation fault still occurred with the new wrfbdy (the warming about the missing variable is no longer there, though). I solved it with :
ulimit -l unlimited
ulimit -s unlimited
export KMP_STACKSIZE=20480000000
Now it is running!

Thank you again for your help.