Move file stageing

[jedwards4b]

Move file staging from buildlib to buildnml.
Tested using ERR_Ld5.ne30pg3_t232_wg37.1850_CAM70%LT_CLM60%BGC-CROP_CICE_MOM6_MOSART_DGLC%NOEVOLVE_WW3.derecho_intel

Fixes #9

Mvertens would like to review @alperaltuntas can you add her?

[alperaltuntas]

The ww3_grid executable gets built at the buildlib stage. If file staging gets moved from buildlib to buildnml and if the user attempts to, say, run ./preview_namelists before running ./case.build this change will lead to a failure due to the absence of ww3_grid executable, I think.

[jedwards4b]

See buildnml line 222. Running buildnml before buildlib will print a warning about the missing executable but will no longer fail.

[alperaltuntas]

I am confused about the "resolve git issue" commit that was just pushed. It appears to change the WW3 submodule hash (why?) and when I click on the new submodule, GitHub displays: "This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository."

[jedwards4b]

I tried to undo that but had the same problem. I don't think that it matters because the submodule will need to be updated again when this is merged.

[alperaltuntas]

The issue persists. When I create a test from scratch, buildnml doesn't generate or copy the ww3.mod_def file, causing the run to fail.

[alperaltuntas]

Modifying this line as follows should fix this PR:

run_cmd("./ww3_grid > mod_def.ww3.log", from_dir=output_dir)

[alperaltuntas]

Better yet, I suggest replacing lines 218-223 with the following:

        if os.path.isfile(os.path.join(output_dir,"ww3_grid")): 
            run_cmd("./ww3_grid > mod_def.ww3.log", from_dir=output_dir)
            if not os.path.isfile(os.path.join(output_dir,"mod_def.ww3")):
                raise RuntimeError("mod_def.ww3 was not created, check mod_def.ww3.log for errors.")
            shutil.move(os.path.join(output_dir,"mod_def.ww3"), os.path.join(rundir, "mod_def.ww3"))
        else:
            logger.warning("ww3_grid file not found. The mod_def.ww3 file will be created after the build phase.")

[alperaltuntas]

Actually, even these changes don't fix the issue with TEST runs. It appears like, when you run a TEST case, the buildnml script doesn't get called in between build and run phases. And so the mod_def file never gets created in a TEST run.

[jedwards4b]

I have found the toggle to skip the pnl in tests and am testing a change to unset this when ww3 is in the compset.

[jedwards4b]

I was able to reproduce the issue, I'll work on it this morning.

[jedwards4b]

I've added a fix to my cime branch in ESMCI/cime#4689
That branch will require other components to be updated as well, so here is the specific change that you can try in your current sandbox:

diff --git a/CIME/SystemTests/system_tests_common.py b/CIME/SystemTests/system_tests_common.py
index 70091aa29..a86483ffd 100644
--- a/CIME/SystemTests/system_tests_common.py
+++ b/CIME/SystemTests/system_tests_common.py
@@ -399,7 +399,13 @@ class SystemTestsCommon(object):
         """
         success = True
         start_time = time.time()
-        self._skip_pnl = skip_pnl
+        wav_comp = self._case.get_value("COMP_WAV")
+        # WW3 requires pnl to be run again after the build phase.
+        if wav_comp and wav_comp == "ww3":
+            self._skip_pnl = False
+        else:
+            self._skip_pnl = skip_pnl
+        
         try:
             self._resetup_case(RUN_PHASE)
             do_baseline_ops = True

[alperaltuntas]

Just confirming that this CIME mod, along with the changes I suggest above, fixed the issue.

[jedwards4b]

I've added you to my fork, please feel free to push your additional changes.

[alperaltuntas]

Done.