Update NetCDF comp/link #336

JessicaMeixner-NOAA · 2021-03-19T21:29:10Z

Pull Request Summary

This is a more general way of including the WW3 libraries.

Description

Updated the way NetCDF libraries are including in the comp/link (thanks to @aerorahul help). In addition the matrix_ncep is updated to use the NOAA hpc-stack libraries.

Issue(s) addressed

fixes Update to NetCDF libraries linked for use with NOAA hpc-stack #332

Check list

Is your feature branch up to date with the authoritative repository (NOAA/develop)? yes
Reviewers: @aliabdolali

Testing

How were these changes tested? Tested with hera.intel and orion.intel
Are the changes covered by regression tests? yes
If a new feature was added, was a new regression test added? no
Have regression tests been run? Re-running after merge with develop (will attach summary output when finished). No differences (other than the normal diffs) are expected.

@aerorahul

fixes from @aerorahul

aliabdolali · 2021-03-19T22:03:29Z

@JessicaMeixner-NOAA i reviewed it, all look ok to me. Why did you revert 8 to 24 again? are we going to do it in a separate PR?

aliabdolali

I approve it, but please merge it once the matrix is done. Thanks.

JessicaMeixner-NOAA · 2021-03-24T13:20:53Z

@mickaelaccensi I had to update the makefile in regtests/ww3_tp2.14/input/oasis3-mct/util/make_dir/cmplr.tmpl to get this to work. This should work for you too, but thought maybe I should double check?

JessicaMeixner-NOAA · 2021-03-24T13:21:45Z

@aliabdolali the regtests now all run, I'll compare with the develop branch when I started and then will re-do this with the top of develop as well. Are there other PRs coming in soon that I should wait before I run these again?

aliabdolali · 2021-03-24T13:25:14Z

@aliabdolali the regtests now all run, I'll compare with the develop branch when I started and then will re-do this with the top of develop as well. Are there other PRs coming in soon that I should wait before I run these again?

The divider is going in before this one. I will add the regression test comparison in a few minutes.

JessicaMeixner-NOAA · 2021-03-24T13:27:39Z

Awesome! I will gladly wait for that as it will make this 10000000x easier! Thanks @aliabdolali

JessicaMeixner-NOAA · 2021-03-24T17:35:03Z

regtests are running now

JessicaMeixner-NOAA · 2021-03-25T10:06:56Z

Regtests have finished, running matrix.comp now.

ufs-weather-model WW3 tests on hera.intel also passed.

JessicaMeixner-NOAA · 2021-03-25T15:26:29Z

The wind.ww3 binary file is different for test case: ww3_tp2.15 both work_5km and work_MPI_5km

Otherwise the differences are as usual on NCEP machines:

********************* non-identical cases ****************************

mww3_test_03/./work_PR2_UQ_MPI_d2 (7 files differ)
mww3_test_03/./work_PR3_UNO_MPI_d2_c (10 files differ)
mww3_test_03/./work_PR3_UNO_MPI_d2 (8 files differ)
mww3_test_03/./work_PR2_UNO_MPI_d2 (6 files differ)
mww3_test_03/./work_PR1_MPI_d2 (8 files differ)
mww3_test_03/./work_PR3_UQ_MPI_d2_c (8 files differ)
mww3_test_03/./work_PR3_UQ_MPI_d2 (8 files differ)
mww3_test_07/./work_PR3_UQ (3 files differ)
ww3_tp2.10/./work_MPI_OMPH (7 files differ)
ww3_tp2.15/./work_5km (1 files differ)
ww3_tp2.15/./work_MPI_5km (1 files differ)
ww3_tp2.18/./work_TIDE_MPI (1 files differ)

regtests.tar.gz

JessicaMeixner-NOAA · 2021-03-25T15:28:15Z

@aliabdolali I'm going to run the ww3_tp2.15 test again from the develop and this branch to see if this difference was introduced in this PR or before.

aliabdolali · 2021-03-25T15:36:06Z

@JessicaMeixner-NOAA This is introduced in a PR from UKMET and in these cases, we expected changes, but do not expect them to remain. So I'll go ahead and merge your work if you agree and will coordinate with them in that regard.
AA

JessicaMeixner-NOAA · 2021-03-25T15:54:12Z

So the differences are from comparing my branch commit hash: 8b1d62e and the top of develop 78b0148

If those diffs are expected in 2.15, please go ahead and merge. If they are not then ?

mickaelaccensi

I'm not able to compile WW3 anymore and it is related to this PR. I've detailed the problems below

mickaelaccensi · 2021-06-01T09:43:29Z

regtests/ww3_tp2.14/input/oasis3-mct/util/make_dir/cmplr.tmpl

-NETCDF_INCLUDE  = $(shell $(NETCDF_CONFIG) --includedir) 
-NETCDF_LIBRARY  = $(shell $(NETCDF_CONFIG) --flibs) 
+NETCDF_INCLUDE  = $(shell $(NETCDF_CONFIG) --cflags) 
+NETCDF_LIBRARY  = $(shell $(NETCDF_CONFIG) --flibs) $(shell $(NETCDF_CONFIG) --libs) 


If the netcdf-fortran library is correctly compiled, all the needed dependencies are defined in --flibs.
the option --libs does not exist for all netcdf libraries (like version 4.5.2) so it crashes.

@mickaelaccensi we have an issue now to make the manual specifically say nc-config consistently: #392 and any other checks to make sure things are working for everyone are welcome. Sorry this got pushed through while you were out and is now causing issues.

mickaelaccensi · 2021-06-01T09:44:34Z

regtests/ww3_tp2.14/input/oasis3-mct/util/make_dir/cmplr.tmpl

@@ -30,8 +30,8 @@ COUPLE          = $(WWATCH3_DIR)/../regtests/ww3_tp2.14/input/oasis3-mct
 ARCHDIR         = $(WWATCH3_DIR)/../regtests/ww3_tp2.14/work_oasis3-mct
 #
 # NetCDF library
-NETCDF_INCLUDE  = $(shell $(NETCDF_CONFIG) --includedir) 
-NETCDF_LIBRARY  = $(shell $(NETCDF_CONFIG) --flibs) 
+NETCDF_INCLUDE  = $(shell $(NETCDF_CONFIG) --cflags) 


--cflags is for c-compiler
for fortran-compiler, it must be --fflags to be used

mickaelaccensi · 2021-06-01T09:45:04Z

model/bin/link.tmpl

@@ -116,7 +116,7 @@
    case $WWATCH3_NETCDF in
      NC3) libs="$libs -L$NETCDF_LIBDIR -lnetcdf" ;;
      NC4) if [ "$mpi_mod" = 'no' ]; then comp="`$NETCDF_CONFIG --fc`"; fi
-           libs="$libs `$NETCDF_CONFIG --flibs`" ;;
+           libs="$libs `$NETCDF_CONFIG --flibs` `$NETCDF_CONFIG --libs`" ;;


If the netcdf-fortran library is correctly compiled, all the needed dependencies are defined in --flibs.
the option --libs does not exist for all netcdf libraries (like version 4.5.2) so it crashes.

mickaelaccensi · 2021-06-01T09:45:18Z

model/bin/comp.tmpl

@@ -82,7 +82,8 @@
    case $WWATCH3_NETCDF in
      NC3) opt="$opt -I$NETCDF_INCDIR" ;;
      NC4) if [ "$mpi_mod" = 'no' ]; then comp="`$NETCDF_CONFIG --fc`"; fi
-           opt="$opt -I`$NETCDF_CONFIG --includedir`" ;;
+           #opt="$opt -I`$NETCDF_CONFIG --includedir`" ;;
+           opt="$opt `$NETCDF_CONFIG --cflags`" ;;


--cflags is for c-compiler
for fortran-compiler, it must be --fflags to be used

store nodes status for tidal analysis to output the list by NAPOUT

JessicaMeixner-NOAA added 5 commits March 16, 2021 15:12

updates for NetCDF comp/linking Issue NOAA-EMC#332

e3d24a5

fixes from @aerorahul

Updating matrix_ncep to use hpc-stack modules

4cf48e7

update path for orion hpc-stack and change np, nr, nth

17e3295

add module purge and revert 8->24

868ca8c

Merge remote-tracking branch 'EMC/develop' into NetCDFcomplink

bfc1f03

JessicaMeixner-NOAA requested a review from aliabdolali March 19, 2021 21:29

aliabdolali approved these changes Mar 19, 2021

View reviewed changes

update NetCDF in ww3_tp2.14 oasis test makefile

3e4f764

Merge remote-tracking branch 'EMC/develop' into NetCDFcomplink

8b1d62e

aliabdolali merged commit 64a27d6 into NOAA-EMC:develop Mar 25, 2021

mickaelaccensi reviewed Jun 1, 2021

View reviewed changes

mickaelaccensi added a commit to umr-lops/WW3 that referenced this pull request Jun 1, 2021

revert link.tmpl to be able to compile ww3 as before PR NOAA-EMC#336

918c7a0

store nodes status for tidal analysis to output the list by NAPOUT

JessicaMeixner-NOAA deleted the NetCDFcomplink branch November 13, 2021 12:39

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Update NetCDF comp/link #336

Update NetCDF comp/link #336

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Update NetCDF comp/link #336

Update NetCDF comp/link #336

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JessicaMeixner-NOAA commented Mar 19, 2021

Pull Request Summary

Description

Issue(s) addressed

Check list

Testing

aliabdolali commented Mar 19, 2021

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