(RESOLVED) Mismatch between namelist and input file dimensions

[mgeology]

Hi,

I am a newcomer to WRF. I built and run WPS (geogrid.exe, ungrib.exe, and metgrid.exe) completely without any problem based on the tutorial. Then for running WRF, I made some changes in namelist.input, and I linked my met_em* files into the working directory. After that, I wrote the command "mpirun -np 1 ./real.exe" to run real.exe. However, I got the error below.

starting wrf task 0 of 1
-------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code.. Per user-direction, the job has been aborted.
-------------------------------------------------------
--------------------------------------------------------------------------
mpirun detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:

Process name: [[3050,1],0]
Exit code: 1

Actually, I don't know what is the problem. Please help. I attached here namelist.input.

 

[kwerner]

Hi,
Do you have an rsl.error.0000 file? If so, that likely has the error in it. Please attach that file. Thanks!

 

[mgeology]

Hi,

Yes, I have. Please see it below. It seems the error is related to the date; however, I don't know what should I do?

taskid: 0 hostname: gra-login2
module_io_quilt_old.F 2931 T
Ntasks in X 1 , ntasks in Y 1
*************************************
Configuring physics suite 'conus'

mp_physics: 8
cu_physics: 6
ra_lw_physics: 4
ra_sw_physics: 4
bl_pbl_physics: 2
sf_sfclay_physics: 2
sf_surface_physics: 2
*************************************
Domain # 1: dx = 30000.000 m
REAL_EM V4.2.2 PREPROCESSOR
*************************************
Parent domain
ids,ide,jds,jde 1 74 1 61
ims,ime,jms,jme -4 79 -4 66
ips,ipe,jps,jpe 1 74 1 61
*************************************
DYNAMICS OPTION: Eulerian Mass Coordinate
alloc_space_field: domain 1 , 197420780 bytes allocated
-------------- FATAL CALLED ---------------
FATAL CALLED FROM FILE: <stdin> LINE: 403
error opening met_em.d01.2021-01-01_00:00:00.nc for input; bad date in namelist or file not in directory
-------------------------------------------
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0

 

[mgeology]

Hi,

Thanks. I attached it here. Please see and let me know your opinion.

 

[kwerner]

Thanks! Do you have your met_em* files linked to your WRF running directory? The error seems to indicate that you don't have those files in there. If you don't believe that's the case, from the running directory, can you issue

ls -ls >& ls.txt

and attach that ls.txt file? Thanks!

 

[mgeology]

Thanks for your support. Yes, I have linked them into my working directory using the code below:
ln -sf ../../../WPS/met_em*
However, I used the code you sent. So please see the attached file.

 

[mgeology]

Thanks! Do you have your met_em* files linked to your WRF running directory? The error seems to indicate that you don't have those files in there. If you don't believe that's the case, from the running directory, can you issue

ls -ls >& ls.txt

and attach that ls.txt file? Thanks!

Hi,

Did you see my reply? please help.

 

[kwerner]

Hi,
I apologize for the delay. I have been out of the office for the past several business days. Additionally, it can sometimes take us a few days to get to each post, as we have several other work obligations. We appreciate your patience.

I'm not sure what command you used to link your met_em* files to the wrf running directory, but you have it linked as a single "met_em*" file

0 lrwxrwxrwx 1 mbigdeli mbigdeli    33 Feb  1 12:29 met_em* -> /scratch/mbigdeli/WRF/WPS/met_em*

We should be able to see each file linked back to the corresponding file in your WPS directory. From your wrf directory, use this command:

ln -sf /scratch/mbigdeli/WRF/WPS/met_em* .

(Note the "." at the end, that says to link the files "here."
Then issue

ls -ls met_em*

and you should see the individual files. Let me know if that helps.

 

[mgeology]

Hi,
Thanks a lot for your kind reply. I used the below codes:

ln -sf /scratch/mbigdeli/WRF/WPS/met_em* .

ls -ls met_em*

Then I got:
0 lrwxrwxrwx 1 mbigdeli mbigdeli 59 Feb 9 01:38 met_em.d01.2021-01-01_00:00:00.nc -> /scratch/mbigdeli/WRF/WPS/met_em.d01.2021-01-01_00:00:00.nc
0 lrwxrwxrwx 1 mbigdeli mbigdeli 59 Feb 9 01:38 met_em.d01.2021-01-01_03:00:00.nc -> /scratch/mbigdeli/WRF/WPS/met_em.d01.2021-01-01_03:00:00.nc
0 lrwxrwxrwx 1 mbigdeli mbigdeli 59 Feb 9 01:38 met_em.d01.2021-01-01_06:00:00.nc -> /scratch/mbigdeli/WRF/WPS/met_em.d01.2021-01-01_06:00:00.nc
0 lrwxrwxrwx 1 mbigdeli mbigdeli 59 Feb 9 01:38 met_em.d01.2021-01-14_00:00:00.nc -> /scratch/mbigdeli/WRF/WPS/met_em.d01.2021-01-14_00:00:00.nc
0 lrwxrwxrwx 1 mbigdeli mbigdeli 59 Feb 9 01:38 met_em.d01.2021-01-14_03:00:00.nc -> /scratch/mbigdeli/WRF/WPS/met_em.d01.2021-01-14_03:00:00.nc
0 lrwxrwxrwx 1 mbigdeli mbigdeli 59 Feb 9 01:38 met_em.d01.2021-01-14_06:00:00.nc -> /scratch/mbigdeli/WRF/WPS/met_em.d01.2021-01-14_06:00:00.nc

However, my problem in running WRF using the code below has still remained.
mpirun -np 1 ./real.exe

Please help what should I do?

 

[kwerner]

Hi,
I'm not sure if this could be causing the problem, but can you remove these met_em* files from your WRF running directory and try again?
0 lrwxrwxrwx 1 mbigdeli mbigdeli 59 Feb 9 01:38 met_em.d01.2021-01-14_00:00:00.nc -> /scratch/mbigdeli/WRF/WPS/met_em.d01.2021-01-14_00:00:00.nc
0 lrwxrwxrwx 1 mbigdeli mbigdeli 59 Feb 9 01:38 met_em.d01.2021-01-14_03:00:00.nc -> /scratch/mbigdeli/WRF/WPS/met_em.d01.2021-01-14_03:00:00.nc
0 lrwxrwxrwx 1 mbigdeli mbigdeli 59 Feb 9 01:38 met_em.d01.2021-01-14_06:00:00.nc -> /scratch/mbigdeli/WRF/WPS/met_em.d01.2021-01-14_06:00:00.nc

Those dates don't correspond to the dates in your namelist and maybe, for some reason, it's getting confused with those dates there. If you still get the error, please do the 'ls -ls >& ls.txt" command again (for the full wrf running directory) and send me that file, plus the full rsl.error.0000 file. If you've made any changes to your namelist.input file since you first sent it, please attach that, as well.

 

[ChloeNash]

Thank you, there was a same problem. In my case, it helped me.

 

[kwerner]

@ChloeNash,
Thanks for letting us know!

 

[mgeology]

Hi dear kwerner,

Thanks a lot. I am so sorry for my long delay in replying to your comment. I did your points; however, I get the previous error. I've attached two files you mentioned. Please see and let me know your opinion.

 

[mgeology]

Could you check my namelist.input as well? I think some of the dimensions are incorrect.

 

[kwerner]

Hi,
Can you resend that rsl.error file, but make it a *.tar, instead of .rar? Unfortunately we don't have the ability to open .rar files. Thanks!

 

[mgeology]

Hi,

Yes, for sure. I hope it works.

 

[kwerner]

Thanks for sending that. The error in your rsl file is:

d01 2021-01-01_00:00:00  input_wrf.F: SIZE MISMATCH:  namelist num_metgrid_levels           =           32
d01 2021-01-01_00:00:00  input_wrf.F: SIZE MISMATCH:  input file BOTTOM-TOP_GRID_DIMENSION  =           34
d01 2021-01-01_00:00:00 ---- ERROR: Mismatch between namelist and input file dimensions
NOTE:       1 namelist vs input data inconsistencies found.
-------------- FATAL CALLED ---------------
FATAL CALLED FROM FILE:  <stdin>  LINE:    1299
NOTE:  Please check and reset these options

This indicates that your input files have 34 levels in them, but you have the namelist parameter "num_metgrid_levels" set to 32. You just need to change that setting to 34 and try to run again.

 

[mgeology]

Hi,

Thanks for your support. Yes, the problem was solved.

 

[kwerner]

Great! Thanks for letting us know.