diff --git a/scripts/exgdas_global_marine_analysis_run.sh b/scripts/exgdas_global_marine_analysis_run.sh index 682204f4a..3e938df37 100755 --- a/scripts/exgdas_global_marine_analysis_run.sh +++ b/scripts/exgdas_global_marine_analysis_run.sh @@ -39,6 +39,7 @@ function clean_yaml() ################################################################################ # run 3DVAR FGAT +cp var.yaml var_original.yaml clean_yaml var.yaml $APRUN_OCNANAL $JEDI_BIN/soca_var.x var.yaml export err=$?; err_chk diff --git a/scripts/exgdas_global_marine_analysis_vrfy.py b/scripts/exgdas_global_marine_analysis_vrfy.py index 33699f1d3..04f56afd5 100755 --- a/scripts/exgdas_global_marine_analysis_vrfy.py +++ b/scripts/exgdas_global_marine_analysis_vrfy.py @@ -303,7 +303,7 @@ def plot_zonal_slice(config): evadir = os.path.join(HOMEgfs, 'sorc', f'{RUN}.cd', 'ush', 'eva') marinetemplate = os.path.join(evadir, 'marine_gdas_plots.yaml') -varyaml = os.path.join(comout, 'yaml', 'var.yaml') +varyaml = os.path.join(comout, 'yaml', 'var_original.yaml') # it would be better to refrence the dirs explicitly with the comout path # but eva doesn't allow for specifying output directories diff --git a/test/soca/gw/CMakeLists.txt b/test/soca/gw/CMakeLists.txt index 4b48c7b6a..bf4b77155 100644 --- a/test/soca/gw/CMakeLists.txt +++ b/test/soca/gw/CMakeLists.txt @@ -40,8 +40,8 @@ set(jjob_list "JGDAS_GLOBAL_OCEAN_ANALYSIS_PREP" # "JGDAS_GLOBAL_OCEAN_ANALYSIS_BMAT_VRFY" "JGDAS_GLOBAL_OCEAN_ANALYSIS_RUN" "JGDAS_GLOBAL_OCEAN_ANALYSIS_CHKPT" - "JGDAS_GLOBAL_OCEAN_ANALYSIS_POST") -# "JGDAS_GLOBAL_OCEAN_ANALYSIS_VRFY") + "JGDAS_GLOBAL_OCEAN_ANALYSIS_POST" + "JGDAS_GLOBAL_OCEAN_ANALYSIS_VRFY") set(setup "") foreach(jjob ${jjob_list}) diff --git a/ush/diag_statistics.py b/ush/diag_statistics.py old mode 100644 new mode 100755 index 8068a8c81..5ccb3ab25 --- a/ush/diag_statistics.py +++ b/ush/diag_statistics.py @@ -31,8 +31,13 @@ def get_diag_stats(): zipfilename = diagfilename + '.gz' outfilename = 'cnvstat.' + var + '.gdas.' + pdy + cyc + '.csv' - with tarfile.open(os.path.join(comout, tarfilename), "r") as tf: - tf.extract(member=zipfilename) + try: + with tarfile.open(os.path.join(comout, tarfilename), "r") as tf: + tf.extract(member=zipfilename) + except FileNotFoundError: + print('WARNING: file', os.path.join(comout, tarfilename), + 'not found, this is expected in GDASApp ctests') + return with gzip.open(zipfilename, 'rb') as f_in: with open(diagfilename, 'wb') as f_out: shutil.copyfileobj(f_in, f_out) diff --git a/ush/soca/run_jjobs.py b/ush/soca/run_jjobs.py index 4b4e623be..30700ef99 100755 --- a/ush/soca/run_jjobs.py +++ b/ush/soca/run_jjobs.py @@ -138,8 +138,10 @@ def _conda_envs(self, jjob): """ if self.machine != "container": if jjob in ENVS: - # TODO: This does nothing for now. Make the conda activate work! - self.f.write(f"# conda activate {ENVS[jjob]} \n") + # set +/-u is a workaround for an apparent conda bug + self.f.write(f"set +u \n") + self.f.write(f"conda activate {ENVS[jjob]} \n") + self.f.write(f"set -u \n") def precom(self, com, tmpl): cmd = f"RUN={self.RUN} YMD={self.gPDY} HH={self.gcyc} generate_com -xr {com}:{tmpl}"