Bugfix/nml

[mickaelaccensi]

Pull Request Summary

correct issue with ww3_multi when requesting restart2 and using nml file instead of inp file

Description

the bug was introduced when merging the branch NCEP GFSv16/GEFSv12 #140 in 13 Jan 2020. No regtest was added in matrix to test it.

The PR propose to :
-correct issue for ww3_multi when outputting restart2 and using nml instead of inp. see #1062
-add scotch lib in matrix_cmake_datarmor
-force CFX, CFD, CFK to be outputted as type REAL if NCVARTYPE is set at 2 (=depends) for netCDF output
-add test on ufs switch to enable corresponding regtests
-correct typo in ww3_ufs1.1/namelist*.nml
-correct namelist in ww3_tp2.3 to enable TH1M and STH1M outputs
-replace 'echo' by 'basename' in matrix_cmake_datarmor to restrict the search of keyword in the filename itself

Issue(s) addressed

• fixes UG mesh crashes with ww3_multi.nml when loading input wind field #1062

Commit Message

correct issue with ww3_multi when requesting restart2 and using nml file instead of inp file

Check list

• Branch is up to date with the authoritative repository (NOAA-EMC) develop branch.
• Checked the checklist for a developer submitting to develop.
• If a version number update is required, checked the updating version number checklist.
• If a new feature was added, a regression test for testing the new feature is added.

Testing

• How were these changes tested? matrix
• Are the changes covered by regression tests? (If not, why? Do new tests need to be added?) ww3_tp2.21
• Have the matrix regression tests been run (if yes, please note HPC and compiler)? OK
• Please indicate the expected changes in the regression test output, (Note the list of known non-identical tests.)
• ww3_tp2.21 : now it runs with nml
• ww3_tp2.3 : now it runs TH1MF and STH1MF activated
• ww3_tp2.14 : print differences (duplicated in develop branch)
• ww3_tp2.6 : differences due to truncated variable with scale_factor (corrected in PR QP #1050 )
• Please provide the summary output of matrix.comp (matrix.Diff.txt, matrixCompFull.txt and matrixCompSummary.txt):

matrixCompFull.txt
matrixCompSummary.txt
matrixDiff.txt

[JessicaMeixner-NOAA]

@mickaelaccensi - Thanks for making this fix. Adding the regression test has been on my plate for a while - Hopefully that will come sooner than later, but we'll see. Can we add to the commit message a note about the netcdf update too? It seems a little tangential to the stated update as is.

[mickaelaccensi]

@mickaelaccensi - Thanks for making this fix. Adding the regression test has been on my plate for a while - Hopefully that will come sooner than later, but we'll see. Can we add to the commit message a note about the netcdf update too? It seems a little tangential to the stated update as is.

is it clear enough now ? Let me know if you want me to modify the commit message

[MatthewMasarik-NOAA]

Hi @mickaelaccensi, I ran the matrix and the PR branch run reached the wallclock limit in matrix03.

I believe the issue is in this run test call

Running now options: run_test -b slurm -o all -S -T -s PR3_UNO_MPI_SCRIP -w work_PR3_UNO_MPI_c_c -m grdset_c -g curv -f -p srun -n 24 ../model mww3_test_02

It seems to have had some sort of internal error shown here, but then seems to have got passed it, but then timed out

SI nbPlus=       14884  nbMinus=           0  nbZero=           0
 SI nbPlus=        7396  nbMinus=           0  nbZero=           0
 SI nbPlus=        7396  nbMinus=           0  nbZero=           0
  
 Grid 1 size        3721
 Grid 2 size        1849
 
 grid1 sweep
 grid2 sweep 
 integration stalled: num_subseg exceeded limit
 Cell         1625
 Edge            2
 Grid            1
 Fraction of segment left   0.599999988869029     
 integration stalled: num_subseg exceeded limit
 Cell         1625
 Edge            2
 Grid            1
 Fraction of segment left   0.599999988869029     
 integration stalled: num_subseg exceeded limit
        .
        .

I attached the full matrix03.out file: matrix03.out.txt

[mickaelaccensi]

@MatthewMasarik-NOAA this issue is also present in the develop branch, actually it seems that all the regtests for mww3_test02 with options -m grdset_c and -g curv are crashing. This bug should be solved in another PR since it is not related to my branch. Does it sounds ok for you ?

[MatthewMasarik-NOAA]

Hi @mickaelaccensi, none of my develop runs are crashing. Are they for you?

I just noticed though that this branch is out of date. It's possible updating could resolve the issues. Please sync up and I'll re-run the matrix. Thanks

[mickaelaccensi]

I've updated my branch with the develop. I thought it was done but I may missed the last one.

And yes I have the same issue as you with my up-to-date develop branch. Have checked that you have the postprocessing done for all the mww3_test02 work directories ? Especially those with grdset_c and curv grid. Because in my case it does not crash with an explicit exit code, it just stop and do not create out_grd.* and so the post processing is not done

[MatthewMasarik-NOAA]

Hi @mickaelaccensi, thanks for syncing. I'll try re-running both develop and the PR branch.

Nope, I didn't get an explicit crash either, just what was shown in the matrix03 out posted. We'll see what these re-runs look like.

[MatthewMasarik-NOAA]

@mickaelaccensi Good news, syncing resolved the issue in the new runs.

matrix output

**********************************************************************
********************* non-identical cases ****************************
**********************************************************************
## known non-b4b
mww3_test_03/./work_PR1_MPI_e                     (1 files differ)
mww3_test_03/./work_PR2_UQ_MPI_e                     (1 files differ)
mww3_test_03/./work_PR2_UNO_MPI_e                     (1 files differ)
mww3_test_03/./work_PR2_UNO_MPI_d2                     (16 files differ)
mww3_test_03/./work_PR1_MPI_d2                     (14 files differ)
mww3_test_03/./work_PR3_UNO_MPI_d2_c                     (12 files differ)
mww3_test_03/./work_PR3_UQ_MPI_d2_c                     (15 files differ)
mww3_test_03/./work_PR3_UNO_MPI_d2                     (16 files differ)
mww3_test_03/./work_PR2_UQ_MPI_d2                     (14 files differ)
mww3_test_03/./work_PR3_UQ_MPI_e                     (1 files differ)
mww3_test_03/./work_PR3_UNO_MPI_e_c                     (1 files differ)
mww3_test_03/./work_PR3_UQ_MPI_d2                     (16 files differ)
ww3_tp2.10/./work_MPI_OMPH                     (7 files differ)
ww3_tp2.16/./work_MPI_OMPH                     (4 files differ)
ww3_ufs1.3/./work_a                     (3 files differ)
 
ww3_tp2.3/./work_PR2_UNO                     (6 files differ)
ww3_tp2.3/./work_PR1_MPI                     (6 files differ)
ww3_tp2.3/./work_PR3_UNO_MPI                     (6 files differ)
ww3_tp2.3/./work_PR3_UQ                     (6 files differ)
ww3_tp2.3/./work_PR3_UNO                     (6 files differ)
ww3_tp2.3/./work_PR1                     (6 files differ)
ww3_tp2.3/./work_PR2_UQ                     (6 files differ)
ww3_tp2.3/./work_PR2_UQ_MPI                     (6 files differ)
ww3_tp2.3/./work_PR3_UQ_MPI                     (6 files differ)
ww3_tp2.3/./work_PR2_UNO_MPI                     (6 files differ)

**********************************************************************
************************ identical cases *****************************
**********************************************************************

The new expected diffs are limited to tests within ww3_tp2.3, each due to the following six files:

  log.ww3 
  mod_def.ww3 
  out_grd.ww3 
  ww3_grid.out
  ww3_ounf.out
  ww3_outf.out

• matrixCompSummary.txt
• matrixCompFull.txt
• matrixDiff.txt

Code review

PASS

Testing

PASS

[MatthewMasarik-NOAA]

Thanks @mickaelaccensi for this PR, addressing a number of corrections.