Add e3sm_to_cmip_environment_commands parameter (#556)

tests/integration/generated/test_bundles_chrysalis.cfg

@@ -36,6 +36,7 @@ years = "1850:1854:2", "1850:1854:4",
 [ts]
 active = True
 bundle = "bundle1"
+e3sm_to_cmip_environment_commands = "source /home/ac.forsyth2/miniconda3/etc/profile.d/conda.sh; conda activate e3sm_to_cmip_20240223"
 years = "1850:1854:2",
 
   [[ atm_monthly_180x360_aave ]]

tests/integration/generated/test_complete_run_chrysalis.cfg

@@ -28,6 +28,7 @@ years = "1850:1854:2", "1850:1854:4",
 
 [ts]
 active = True
+e3sm_to_cmip_environment_commands = "source /home/ac.forsyth2/miniconda3/etc/profile.d/conda.sh; conda activate e3sm_to_cmip_20240223"
 walltime = "00:30:00"
 years = "1850:1854:2",
 

tests/integration/generated/test_debug_chrysalis.cfg

@@ -36,12 +36,13 @@ years = "1850:1854:2",
   vars = "PRECT"
 
   [[ land_monthly ]]
+  e3sm_to_cmip_environment_commands = "source /home/ac.forsyth2/miniconda3/etc/profile.d/conda.sh; conda activate e3sm_to_cmip_20240223"
   extra_vars = "landfrac"
   frequency = "monthly"
   input_files = "elm.h0"
   input_subdir = "archive/lnd/hist"
-  #vars = "LAISHA,LAISUN"
-  vars = "FSH,RH2M"
+  vars = "LAISHA,LAISUN"
+  #vars = "FSH,RH2M"
   ts_fmt = "cmip"
 
 [ilamb]

tests/integration/template_bundles.cfg

@@ -36,6 +36,7 @@ years = "1850:1854:2", "1850:1854:4",
 [ts]
 active = True
 bundle = "bundle1"
+e3sm_to_cmip_environment_commands = "#expand e3sm_to_cmip_environment_commands#"
 years = "1850:1854:2",
 
   [[ atm_monthly_180x360_aave ]]

tests/integration/template_complete_run.cfg

@@ -28,6 +28,7 @@ years = "1850:1854:2", "1850:1854:4",
 
 [ts]
 active = True
+e3sm_to_cmip_environment_commands = "#expand e3sm_to_cmip_environment_commands#"
 walltime = "00:30:00"
 years = "1850:1854:2",
 

tests/integration/template_debug.cfg

@@ -36,12 +36,13 @@ years = "1850:1854:2",
   vars = "PRECT"
 
   [[ land_monthly ]]
+  e3sm_to_cmip_environment_commands = "#expand e3sm_to_cmip_environment_commands#"
   extra_vars = "landfrac"
   frequency = "monthly"
   input_files = "elm.h0"
   input_subdir = "archive/lnd/hist"
-  #vars = "LAISHA,LAISUN"
-  vars = "FSH,RH2M"
+  vars = "LAISHA,LAISUN"
+  #vars = "FSH,RH2M"
   ts_fmt = "cmip"
 
 [ilamb]

tests/integration/utils.py

@@ -138,6 +138,7 @@ def get_chyrsalis_expansions(config):
         # To run this test, replace conda environment with your e3sm_diags dev environment
         "diags_environment_commands": "source /home/ac.forsyth2/miniconda3/etc/profile.d/conda.sh; conda activate e3sm_diags_20240214",
         "diags_walltime": "5:00:00",
+        "e3sm_to_cmip_environment_commands": "source /home/ac.forsyth2/miniconda3/etc/profile.d/conda.sh; conda activate e3sm_to_cmip_20240223",
         "environment_commands_test": "source /lcrc/soft/climate/e3sm-unified/test_e3sm_unified_1.9.0rc16_chrysalis.sh",
         "expected_dir": "/lcrc/group/e3sm/public_html/zppy_test_resources/",
         "mpas_analysis_walltime": "00:30:00",
@@ -163,6 +164,7 @@ def get_compy_expansions(config):
         # To run this test, replace conda environment with your e3sm_diags dev environment
         "diags_environment_commands": "source /qfs/people/fors729/mambaforge/etc/profile.d/conda.sh; conda activate e3sm_diags_20230914",
         "diags_walltime": "03:00:00",
+        "e3sm_to_cmip_environment_commands": "",
         "environment_commands_test": "source /share/apps/E3SM/conda_envs/test_e3sm_unified_1.9.0rc16_compy.sh",
         "expected_dir": "/compyfs/www/zppy_test_resources/",
         "mpas_analysis_walltime": "00:30:00",
@@ -188,6 +190,7 @@ def get_perlmutter_expansions(config):
         # To run this test, replace conda environment with your e3sm_diags dev environment
         "diags_environment_commands": "source /global/homes/f/forsyth/miniconda3/etc/profile.d/conda.sh; conda activate e3sm_diags_20230914",
         "diags_walltime": "6:00:00",
+        "e3sm_to_cmip_environment_commands": "",
         "environment_commands_test": "source /global/common/software/e3sm/anaconda_envs/test_e3sm_unified_1.9.0rc16_pm-cpu.sh",
         "expected_dir": "/global/cfs/cdirs/e3sm/www/zppy_test_resources/",
         "mpas_analysis_walltime": "01:00:00",

tests/test_sections.py

@@ -71,6 +71,7 @@ def test_sections(self):
             "constraint": "",
             "debug": False,
             "dry_run": False,
+            "e3sm_to_cmip_environment_commands": "",
             "environment_commands": "",
             "frequency": "monthly",
             "grid": "",
@@ -124,6 +125,7 @@ def test_sections(self):
             "debug": False,
             "dpf": 30,
             "dry_run": False,
+            "e3sm_to_cmip_environment_commands": "",
             "environment_commands": "",
             "extra_vars": "",
             "frequency": "monthly",
@@ -176,6 +178,7 @@ def test_sections(self):
             "constraint": "",
             "debug": False,
             "dry_run": False,
+            "e3sm_to_cmip_environment_commands": "",
             "environment_commands": "",
             "exclude": False,
             "frequency": "monthly",
@@ -228,6 +231,7 @@ def test_subsections(self):
             "constraint": "",
             "debug": False,
             "dry_run": False,
+            "e3sm_to_cmip_environment_commands": "",
             "environment_commands": "",
             "frequency": "monthly",
             "grid": "",
@@ -301,6 +305,7 @@ def test_subsections(self):
             "debug": False,
             "dpf": 30,
             "dry_run": False,
+            "e3sm_to_cmip_environment_commands": "",
             "environment_commands": "",
             "extra_vars": "",
             "frequency": "monthly",
@@ -339,6 +344,7 @@ def test_subsections(self):
             "debug": False,
             "dpf": 30,
             "dry_run": False,
+            "e3sm_to_cmip_environment_commands": "",
             "environment_commands": "",
             "extra_vars": "",
             "frequency": "monthly",
@@ -407,6 +413,7 @@ def test_subsections(self):
             "constraint": "",
             "debug": False,
             "dry_run": False,
+            "e3sm_to_cmip_environment_commands": "",
             "environment_commands": "",
             "exclude": False,
             "frequency": "monthly",
@@ -440,6 +447,7 @@ def test_subsections(self):
             "constraint": "",
             "debug": False,
             "dry_run": False,
+            "e3sm_to_cmip_environment_commands": "",
             "environment_commands": "",
             "exclude": False,
             "frequency": "monthly",

zppy/templates/default.ini

@@ -17,6 +17,11 @@ debug = boolean(default=False)
 # diagnostics_base_path -- NOTE: this parameter is created internally
 # This should be set to True if you don't want the batch jobs to be submitted
 dry_run = boolean(default=False)
+# Set up the environment for e3sm_to_cmip.
+# Because e3sm_to_cmip is used internally in the `ts` task,
+# the `environment_commands` parameter below is insufficient
+# and this parameter must be used instead.
+e3sm_to_cmip_environment_commands = string(default="")
 # Set up the environment -- this is where you can tell zppy to use a custom conda environment.
 # To use a custom conda environment, you can set `environment_commands="source <path to conda.sh>; conda activate <custom environment>"`.
 environment_commands = string(default="")

zppy/templates/ts.bash

@@ -144,6 +144,7 @@ EOF
   input_dir={{ output }}/post/{{ component }}/{{ grid }}/ts/{{ frequency }}/{{ '%dyr' % (ypf) }}
   dest_cmip={{ output }}/post/{{ component }}/{{ grid }}/cmip_ts/{{ frequency }}
   mkdir -p ${dest_cmip}
+  {{ e3sm_to_cmip_environment_commands }}
   srun -N 1 e3sm_to_cmip \
   --output-path \
   ${dest_cmip}/${tmp_dir} \
@@ -173,6 +174,7 @@ EOF
     echo 'ERROR (4)' > {{ prefix }}.status
     exit 4
   fi
+  {{ environment_commands }}
 
   # Move output ts files to final destination
   mv ${dest_cmip}/${tmp_dir}/CMIP6/CMIP/*/*/*/*/*/*/*/*/*.nc ${dest_cmip}