add om3 test data and tests

ACCESS-NRI · Feb 29, 2024 · bbd8b12 · bbd8b12
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diff --git a/src/access_nri_intake/source/utils.py b/src/access_nri_intake/source/utils.py
@@ -184,7 +184,7 @@ def parse_access_filename(filename):
         r"^ocean.*[^\d]_(\d{2})$",  # A few wierd files in ACCESS-OM2 01deg_jra55v13_ryf9091
         r"^.*\.p.(\d{6})_.*",  # ACCESS-CM2 atmosphere
         r"^.*\.p.-(\d{6})_.*",  # ACCESS-ESM1.5 atmosphere
-        rf"[^\.]*\.{om3_components}\..*({ymds}|{ymd})$",  # ACCESS-OM3
+        rf"[^\.]*\.{om3_components}\..*({ymds}|{ymd}|{ym})$",  # ACCESS-OM3
     ]
     # Frequency translations
     frequencies = {

diff --git a/tests/data/access-om3/README b/tests/data/access-om3/README
@@ -0,0 +1 @@
+These files were copied from a test run using an early version of ACCESS-OM3 and subsequently stripped to a test dataset that includes only single variables/grid points
diff --git a/tests/data/access-om3/error_logs/access-om3.109393186.gadi-pbs.err b/tests/data/access-om3/error_logs/access-om3.109393186.gadi-pbs.err
diff --git a/tests/data/access-om3/error_logs/access-om3.109393186.gadi-pbs.out b/tests/data/access-om3/error_logs/access-om3.109393186.gadi-pbs.out
diff --git a/tests/data/access-om3/error_logs/access-om3.109393326.gadi-pbs.err b/tests/data/access-om3/error_logs/access-om3.109393326.gadi-pbs.err
diff --git a/tests/data/access-om3/error_logs/access-om3.109393326.gadi-pbs.out b/tests/data/access-om3/error_logs/access-om3.109393326.gadi-pbs.out
diff --git a/tests/data/access-om3/error_logs/env.109393186.gadi-pbs.yaml b/tests/data/access-om3/error_logs/env.109393186.gadi-pbs.yaml
diff --git a/tests/data/access-om3/error_logs/env.109393326.gadi-pbs.yaml b/tests/data/access-om3/error_logs/env.109393326.gadi-pbs.yaml
diff --git a/tests/data/access-om3/error_logs/job.109393186.gadi-pbs.yaml b/tests/data/access-om3/error_logs/job.109393186.gadi-pbs.yaml
diff --git a/tests/data/access-om3/error_logs/job.109393326.gadi-pbs.yaml b/tests/data/access-om3/error_logs/job.109393326.gadi-pbs.yaml
diff --git a/tests/data/access-om3/metadata.yaml b/tests/data/access-om3/metadata.yaml
@@ -0,0 +1,7 @@
+experiment_uuid: 4cf0c4ee-09c9-4675-ae1f-ce46f0d848ed
+created: '2024-02-27'
+name: MOM6-CICE6-WW3-1deg_jra55do_ryf-4cf0c4ee
+model: ACCESS-OM3
+url: [email protected]:COSIMA/MOM6-CICE6-WW3.git
+contact: dougiesquire
+email: [email protected]
diff --git a/tests/data/access-om3/output000/GMOM_JRA_WD.cice.h.1900-01-01.nc b/tests/data/access-om3/output000/GMOM_JRA_WD.cice.h.1900-01-01.nc
diff --git a/tests/data/access-om3/output000/GMOM_JRA_WD.mom6.h.native_1900_01.nc b/tests/data/access-om3/output000/GMOM_JRA_WD.mom6.h.native_1900_01.nc
diff --git a/tests/data/access-om3/output000/GMOM_JRA_WD.mom6.h.sfc_1900_01_02.nc b/tests/data/access-om3/output000/GMOM_JRA_WD.mom6.h.sfc_1900_01_02.nc
diff --git a/tests/data/access-om3/output000/GMOM_JRA_WD.mom6.h.static.nc b/tests/data/access-om3/output000/GMOM_JRA_WD.mom6.h.static.nc
diff --git a/tests/data/access-om3/output000/GMOM_JRA_WD.mom6.h.z_1900_01.nc b/tests/data/access-om3/output000/GMOM_JRA_WD.mom6.h.z_1900_01.nc
diff --git a/tests/data/access-om3/output000/GMOM_JRA_WD.ww3.hi.1900-01-02-00000.nc b/tests/data/access-om3/output000/GMOM_JRA_WD.ww3.hi.1900-01-02-00000.nc
diff --git a/tests/data/access-om3/output000/MOM_IC.nc b/tests/data/access-om3/output000/MOM_IC.nc
diff --git a/tests/data/access-om3/output000/MOM_input b/tests/data/access-om3/output000/MOM_input
diff --git a/tests/data/access-om3/output000/MOM_override b/tests/data/access-om3/output000/MOM_override
diff --git a/tests/data/access-om3/output000/MOM_parameter_doc.all b/tests/data/access-om3/output000/MOM_parameter_doc.all
diff --git a/tests/data/access-om3/output000/MOM_parameter_doc.debugging b/tests/data/access-om3/output000/MOM_parameter_doc.debugging
diff --git a/tests/data/access-om3/output000/MOM_parameter_doc.layout b/tests/data/access-om3/output000/MOM_parameter_doc.layout
diff --git a/tests/data/access-om3/output000/MOM_parameter_doc.short b/tests/data/access-om3/output000/MOM_parameter_doc.short
diff --git a/tests/data/access-om3/output000/Vertical_coordinate.nc b/tests/data/access-om3/output000/Vertical_coordinate.nc
diff --git a/tests/data/access-om3/output000/access-om3.err b/tests/data/access-om3/output000/access-om3.err
diff --git a/tests/data/access-om3/output000/access-om3.out b/tests/data/access-om3/output000/access-om3.out
diff --git a/tests/data/access-om3/output000/available_diags.000000 b/tests/data/access-om3/output000/available_diags.000000
diff --git a/tests/data/access-om3/output000/config.yaml b/tests/data/access-om3/output000/config.yaml
diff --git a/tests/data/access-om3/output000/datm.streams.xml b/tests/data/access-om3/output000/datm.streams.xml
diff --git a/tests/data/access-om3/output000/datm_in b/tests/data/access-om3/output000/datm_in
diff --git a/tests/data/access-om3/output000/diag_table b/tests/data/access-om3/output000/diag_table
diff --git a/tests/data/access-om3/output000/drof.streams.xml b/tests/data/access-om3/output000/drof.streams.xml
diff --git a/tests/data/access-om3/output000/drof_in b/tests/data/access-om3/output000/drof_in
diff --git a/tests/data/access-om3/output000/drv_in b/tests/data/access-om3/output000/drv_in
diff --git a/tests/data/access-om3/output000/env.yaml b/tests/data/access-om3/output000/env.yaml
diff --git a/tests/data/access-om3/output000/fd.yaml b/tests/data/access-om3/output000/fd.yaml
diff --git a/tests/data/access-om3/output000/ice_in b/tests/data/access-om3/output000/ice_in
diff --git a/tests/data/access-om3/output000/input.nml b/tests/data/access-om3/output000/input.nml
diff --git a/tests/data/access-om3/output000/job.yaml b/tests/data/access-om3/output000/job.yaml
diff --git a/tests/data/access-om3/output000/logfile.000000.out b/tests/data/access-om3/output000/logfile.000000.out
diff --git a/tests/data/access-om3/output000/manifests/exe.yaml b/tests/data/access-om3/output000/manifests/exe.yaml
diff --git a/tests/data/access-om3/output000/manifests/input.yaml b/tests/data/access-om3/output000/manifests/input.yaml
diff --git a/tests/data/access-om3/output000/manifests/restart.yaml b/tests/data/access-om3/output000/manifests/restart.yaml
diff --git a/tests/data/access-om3/output000/nuopc.runconfig b/tests/data/access-om3/output000/nuopc.runconfig
diff --git a/tests/data/access-om3/output000/nuopc.runseq b/tests/data/access-om3/output000/nuopc.runseq
diff --git a/tests/data/access-om3/output000/ocean.stats b/tests/data/access-om3/output000/ocean.stats
diff --git a/tests/data/access-om3/output000/ocean.stats.nc b/tests/data/access-om3/output000/ocean.stats.nc
diff --git a/tests/data/access-om3/output000/ocean_geometry.nc b/tests/data/access-om3/output000/ocean_geometry.nc
diff --git a/tests/data/access-om3/output000/wav_in b/tests/data/access-om3/output000/wav_in
diff --git a/tests/data/access-om3/output000/ww3_points.list b/tests/data/access-om3/output000/ww3_points.list
diff --git a/tests/data/access-om3/output000/ww3_shel.nml b/tests/data/access-om3/output000/ww3_shel.nml
diff --git a/tests/data/access-om3/output001/GMOM_JRA_WD.cice.h.1900-01-02.nc b/tests/data/access-om3/output001/GMOM_JRA_WD.cice.h.1900-01-02.nc
diff --git a/tests/data/access-om3/output001/GMOM_JRA_WD.mom6.h.native_1900_01.nc b/tests/data/access-om3/output001/GMOM_JRA_WD.mom6.h.native_1900_01.nc
diff --git a/tests/data/access-om3/output001/GMOM_JRA_WD.mom6.h.sfc_1900_01_03.nc b/tests/data/access-om3/output001/GMOM_JRA_WD.mom6.h.sfc_1900_01_03.nc
diff --git a/tests/data/access-om3/output001/GMOM_JRA_WD.mom6.h.static.nc b/tests/data/access-om3/output001/GMOM_JRA_WD.mom6.h.static.nc
diff --git a/tests/data/access-om3/output001/GMOM_JRA_WD.mom6.h.z_1900_01.nc b/tests/data/access-om3/output001/GMOM_JRA_WD.mom6.h.z_1900_01.nc
diff --git a/tests/data/access-om3/output001/GMOM_JRA_WD.ww3.hi.1900-01-03-00000.nc b/tests/data/access-om3/output001/GMOM_JRA_WD.ww3.hi.1900-01-03-00000.nc
diff --git a/tests/data/access-om3/output001/MOM_IC.nc b/tests/data/access-om3/output001/MOM_IC.nc
diff --git a/tests/data/access-om3/output001/MOM_input b/tests/data/access-om3/output001/MOM_input
diff --git a/tests/data/access-om3/output001/MOM_override b/tests/data/access-om3/output001/MOM_override
diff --git a/tests/data/access-om3/output001/MOM_parameter_doc.all b/tests/data/access-om3/output001/MOM_parameter_doc.all
diff --git a/tests/data/access-om3/output001/MOM_parameter_doc.debugging b/tests/data/access-om3/output001/MOM_parameter_doc.debugging
diff --git a/tests/data/access-om3/output001/MOM_parameter_doc.layout b/tests/data/access-om3/output001/MOM_parameter_doc.layout
diff --git a/tests/data/access-om3/output001/MOM_parameter_doc.short b/tests/data/access-om3/output001/MOM_parameter_doc.short
diff --git a/tests/data/access-om3/output001/Vertical_coordinate.nc b/tests/data/access-om3/output001/Vertical_coordinate.nc
diff --git a/tests/data/access-om3/output001/access-om3.err b/tests/data/access-om3/output001/access-om3.err
diff --git a/tests/data/access-om3/output001/access-om3.out b/tests/data/access-om3/output001/access-om3.out
diff --git a/tests/data/access-om3/output001/available_diags.000000 b/tests/data/access-om3/output001/available_diags.000000
diff --git a/tests/data/access-om3/output001/config.yaml b/tests/data/access-om3/output001/config.yaml
diff --git a/tests/data/access-om3/output001/datm.streams.xml b/tests/data/access-om3/output001/datm.streams.xml
diff --git a/tests/data/access-om3/output001/datm_in b/tests/data/access-om3/output001/datm_in
diff --git a/tests/data/access-om3/output001/diag_table b/tests/data/access-om3/output001/diag_table
diff --git a/tests/data/access-om3/output001/drof.streams.xml b/tests/data/access-om3/output001/drof.streams.xml
diff --git a/tests/data/access-om3/output001/drof_in b/tests/data/access-om3/output001/drof_in
diff --git a/tests/data/access-om3/output001/drv_in b/tests/data/access-om3/output001/drv_in
diff --git a/tests/data/access-om3/output001/env.yaml b/tests/data/access-om3/output001/env.yaml
diff --git a/tests/data/access-om3/output001/fd.yaml b/tests/data/access-om3/output001/fd.yaml
diff --git a/tests/data/access-om3/output001/ice_in b/tests/data/access-om3/output001/ice_in
diff --git a/tests/data/access-om3/output001/input.nml b/tests/data/access-om3/output001/input.nml
diff --git a/tests/data/access-om3/output001/job.yaml b/tests/data/access-om3/output001/job.yaml
diff --git a/tests/data/access-om3/output001/logfile.000000.out b/tests/data/access-om3/output001/logfile.000000.out
diff --git a/tests/data/access-om3/output001/manifests/exe.yaml b/tests/data/access-om3/output001/manifests/exe.yaml
diff --git a/tests/data/access-om3/output001/manifests/input.yaml b/tests/data/access-om3/output001/manifests/input.yaml
diff --git a/tests/data/access-om3/output001/manifests/restart.yaml b/tests/data/access-om3/output001/manifests/restart.yaml
diff --git a/tests/data/access-om3/output001/nuopc.runconfig b/tests/data/access-om3/output001/nuopc.runconfig
diff --git a/tests/data/access-om3/output001/nuopc.runseq b/tests/data/access-om3/output001/nuopc.runseq
diff --git a/tests/data/access-om3/output001/ocean.stats b/tests/data/access-om3/output001/ocean.stats
diff --git a/tests/data/access-om3/output001/ocean.stats.nc b/tests/data/access-om3/output001/ocean.stats.nc
diff --git a/tests/data/access-om3/output001/wav_in b/tests/data/access-om3/output001/wav_in
diff --git a/tests/data/access-om3/output001/ww3_points.list b/tests/data/access-om3/output001/ww3_points.list
diff --git a/tests/data/access-om3/output001/ww3_shel.nml b/tests/data/access-om3/output001/ww3_shel.nml
diff --git a/tests/data/access-om3/pbs_logs/1deg_jra55do_ry.e109393186 b/tests/data/access-om3/pbs_logs/1deg_jra55do_ry.e109393186
@@ -0,0 +1,7 @@
+Loading parallelio/2.5.10
+  Loading requirement: hdf5/1.14.1-2 netcdf-c/4.9.2 netcdf-fortran/4.6.0
+Currently Loaded Modulefiles:
+ 1) openmpi/4.1.4(default)    4) hdf5/1.14.1-2          7) parallelio/2.5.10  
+ 2) pbs                       5) netcdf-c/4.9.2        
+ 3) intel-compiler/2021.6.0   6) netcdf-fortran/4.6.0  
+payu: Model exited with error code 233; aborting.
diff --git a/tests/data/access-om3/pbs_logs/1deg_jra55do_ry.e109393326 b/tests/data/access-om3/pbs_logs/1deg_jra55do_ry.e109393326
@@ -0,0 +1,7 @@
+Loading parallelio/2.5.10
+  Loading requirement: hdf5/1.14.1-2 netcdf-c/4.9.2 netcdf-fortran/4.6.0
+Currently Loaded Modulefiles:
+ 1) openmpi/4.1.4(default)    4) hdf5/1.14.1-2          7) parallelio/2.5.10  
+ 2) pbs                       5) netcdf-c/4.9.2        
+ 3) intel-compiler/2021.6.0   6) netcdf-fortran/4.6.0  
+payu: Model exited with error code 14; aborting.
diff --git a/tests/data/access-om3/pbs_logs/1deg_jra55do_ry.e109493795 b/tests/data/access-om3/pbs_logs/1deg_jra55do_ry.e109493795
@@ -0,0 +1,6 @@
+Loading parallelio/2.5.10
+  Loading requirement: hdf5/1.14.1-2 netcdf-c/4.9.2 netcdf-fortran/4.6.0
+Currently Loaded Modulefiles:
+ 1) openmpi/4.1.4(default)    4) hdf5/1.14.1-2          7) parallelio/2.5.10  
+ 2) pbs                       5) netcdf-c/4.9.2        
+ 3) intel-compiler/2021.6.0   6) netcdf-fortran/4.6.0  
diff --git a/tests/data/access-om3/pbs_logs/1deg_jra55do_ry.e109494482 b/tests/data/access-om3/pbs_logs/1deg_jra55do_ry.e109494482
@@ -0,0 +1,6 @@
+Loading parallelio/2.5.10
+  Loading requirement: hdf5/1.14.1-2 netcdf-c/4.9.2 netcdf-fortran/4.6.0
+Currently Loaded Modulefiles:
+ 1) pbs                       4) hdf5/1.14.1-2          7) parallelio/2.5.10  
+ 2) openmpi/4.1.4(default)    5) netcdf-c/4.9.2        
+ 3) intel-compiler/2021.6.0   6) netcdf-fortran/4.6.0  
diff --git a/tests/data/access-om3/pbs_logs/1deg_jra55do_ry.o109393186 b/tests/data/access-om3/pbs_logs/1deg_jra55do_ry.o109393186
@@ -0,0 +1,35 @@
+laboratory path:  /scratch/tm70/ds0092/access-om3
+binary path:  /scratch/tm70/ds0092/access-om3/bin
+input path:  /scratch/tm70/ds0092/access-om3/input
+work path:  /scratch/tm70/ds0092/access-om3/work
+archive path:  /scratch/tm70/ds0092/access-om3/archive
+Pre-existing archive found at: /scratch/tm70/ds0092/access-om3/archive/MOM6-CICE6-WW3. Experiment name will remain: MOM6-CICE6-WW3
+nruns: 1 nruns_per_submit: 1 subrun: 1
+Loading input manifest: manifests/input.yaml
+Loading restart manifest: manifests/restart.yaml
+Loading exe manifest: manifests/exe.yaml
+Setting up access-om3
+Checking exe and input manifests
+Updating full hashes for 1 files in manifests/exe.yaml
+Creating restart manifest
+Writing manifests/restart.yaml
+Writing manifests/exe.yaml
+payu: Found modules in /opt/Modules/v4.3.0
+mpirun  -wdir /scratch/tm70/ds0092/access-om3/work/MOM6-CICE6-WW3 -np 48  /scratch/tm70/ds0092/access-om3/work/MOM6-CICE6-WW3/access-om3-MOM6-CICE6-WW3-3965e25
+/g/data/tm70/ds0092/model/payu/MOM6-CICE6-WW3/access-om3.err /scratch/tm70/ds0092/access-om3/archive/MOM6-CICE6-WW3/error_logs/access-om3.109393186.gadi-pbs.err
+/g/data/tm70/ds0092/model/payu/MOM6-CICE6-WW3/access-om3.out /scratch/tm70/ds0092/access-om3/archive/MOM6-CICE6-WW3/error_logs/access-om3.109393186.gadi-pbs.out
+/g/data/tm70/ds0092/model/payu/MOM6-CICE6-WW3/job.yaml /scratch/tm70/ds0092/access-om3/archive/MOM6-CICE6-WW3/error_logs/job.109393186.gadi-pbs.yaml
+/g/data/tm70/ds0092/model/payu/MOM6-CICE6-WW3/env.yaml /scratch/tm70/ds0092/access-om3/archive/MOM6-CICE6-WW3/error_logs/env.109393186.gadi-pbs.yaml
+
+======================================================================================
+                  Resource Usage on 2024-02-27 13:57:27:
+   Job Id:             109393186.gadi-pbs
+   Project:            tm70
+   Exit Status:        1
+   Service Units:      1.01
+   NCPUs Requested:    48                     NCPUs Used: 48              
+                                           CPU Time Used: 00:04:23        
+   Memory Requested:   192.0GB               Memory Used: 20.95GB         
+   Walltime requested: 01:00:00            Walltime Used: 00:00:38        
+   JobFS requested:    10.0GB                 JobFS used: 0B              
+======================================================================================
diff --git a/tests/data/access-om3/pbs_logs/1deg_jra55do_ry.o109393326 b/tests/data/access-om3/pbs_logs/1deg_jra55do_ry.o109393326
@@ -0,0 +1,34 @@
+laboratory path:  /scratch/tm70/ds0092/access-om3
+binary path:  /scratch/tm70/ds0092/access-om3/bin
+input path:  /scratch/tm70/ds0092/access-om3/input
+work path:  /scratch/tm70/ds0092/access-om3/work
+archive path:  /scratch/tm70/ds0092/access-om3/archive
+nruns: 1 nruns_per_submit: 1 subrun: 1
+Loading input manifest: manifests/input.yaml
+Loading restart manifest: manifests/restart.yaml
+Loading exe manifest: manifests/exe.yaml
+Setting up access-om3
+Checking exe and input manifests
+Updating full hashes for 1 files in manifests/exe.yaml
+Creating restart manifest
+Writing manifests/restart.yaml
+Writing manifests/exe.yaml
+payu: Found modules in /opt/Modules/v4.3.0
+mpirun  -wdir /scratch/tm70/ds0092/access-om3/work/MOM6-CICE6-WW3 -np 48  /scratch/tm70/ds0092/access-om3/work/MOM6-CICE6-WW3/access-om3-MOM6-CICE6-WW3-3965e25
+/g/data/tm70/ds0092/model/payu/MOM6-CICE6-WW3/access-om3.err /scratch/tm70/ds0092/access-om3/archive/MOM6-CICE6-WW3/error_logs/access-om3.109393326.gadi-pbs.err
+/g/data/tm70/ds0092/model/payu/MOM6-CICE6-WW3/access-om3.out /scratch/tm70/ds0092/access-om3/archive/MOM6-CICE6-WW3/error_logs/access-om3.109393326.gadi-pbs.out
+/g/data/tm70/ds0092/model/payu/MOM6-CICE6-WW3/job.yaml /scratch/tm70/ds0092/access-om3/archive/MOM6-CICE6-WW3/error_logs/job.109393326.gadi-pbs.yaml
+/g/data/tm70/ds0092/model/payu/MOM6-CICE6-WW3/env.yaml /scratch/tm70/ds0092/access-om3/archive/MOM6-CICE6-WW3/error_logs/env.109393326.gadi-pbs.yaml
+
+======================================================================================
+                  Resource Usage on 2024-02-27 14:02:41:
+   Job Id:             109393326.gadi-pbs
+   Project:            tm70
+   Exit Status:        1
+   Service Units:      0.88
+   NCPUs Requested:    48                     NCPUs Used: 48              
+                                           CPU Time Used: 00:11:19        
+   Memory Requested:   192.0GB               Memory Used: 34.53GB         
+   Walltime requested: 01:00:00            Walltime Used: 00:00:33        
+   JobFS requested:    10.0GB                 JobFS used: 0B              
+======================================================================================
diff --git a/tests/data/access-om3/pbs_logs/1deg_jra55do_ry.o109493795 b/tests/data/access-om3/pbs_logs/1deg_jra55do_ry.o109493795
@@ -0,0 +1,26 @@
+laboratory path:  /scratch/tm70/ds0092/access-om3
+binary path:  /scratch/tm70/ds0092/access-om3/bin
+input path:  /scratch/tm70/ds0092/access-om3/input
+work path:  /scratch/tm70/ds0092/access-om3/work
+archive path:  /scratch/tm70/ds0092/access-om3/archive
+nruns: 1 nruns_per_submit: 1 subrun: 1
+Loading input manifest: manifests/input.yaml
+Loading restart manifest: manifests/restart.yaml
+Loading exe manifest: manifests/exe.yaml
+Setting up access-om3
+Checking exe and input manifests
+Updating full hashes for 1 files in manifests/exe.yaml
+Creating restart manifest
+
+======================================================================================
+                  Resource Usage on 2024-02-28 12:33:28:
+   Job Id:             109493795.gadi-pbs
+   Project:            tm70
+   Exit Status:        271 (Linux Signal 15 SIGTERM Termination)
+   Service Units:      9.84
+   NCPUs Requested:    48                     NCPUs Used: 48              
+                                           CPU Time Used: 04:38:57        
+   Memory Requested:   192.0GB               Memory Used: 47.51GB         
+   Walltime requested: 01:00:00            Walltime Used: 00:06:09        
+   JobFS requested:    10.0GB                 JobFS used: 8.16MB          
+======================================================================================
diff --git a/tests/data/access-om3/pbs_logs/1deg_jra55do_ry.o109494482 b/tests/data/access-om3/pbs_logs/1deg_jra55do_ry.o109494482
@@ -0,0 +1,30 @@
+laboratory path:  /scratch/tm70/ds0092/access-om3
+binary path:  /scratch/tm70/ds0092/access-om3/bin
+input path:  /scratch/tm70/ds0092/access-om3/input
+work path:  /scratch/tm70/ds0092/access-om3/work
+archive path:  /scratch/tm70/ds0092/access-om3/archive
+nruns: 1 nruns_per_submit: 1 subrun: 1
+Loading input manifest: manifests/input.yaml
+Loading restart manifest: manifests/restart.yaml
+Loading exe manifest: manifests/exe.yaml
+Setting up access-om3
+Checking exe and input manifests
+Updating full hashes for 1 files in manifests/exe.yaml
+Creating restart manifest
+Writing manifests/restart.yaml
+Writing manifests/exe.yaml
+payu: Found modules in /opt/Modules/v4.3.0
+mpirun  -wdir /scratch/tm70/ds0092/access-om3/work/MOM6-CICE6-WW3 -np 48  /scratch/tm70/ds0092/access-om3/work/MOM6-CICE6-WW3/access-om3-MOM6-CICE6-WW3
+
+======================================================================================
+                  Resource Usage on 2024-02-28 12:37:35:
+   Job Id:             109494482.gadi-pbs
+   Project:            tm70
+   Exit Status:        0
+   Service Units:      4.13
+   NCPUs Requested:    48                     NCPUs Used: 48              
+                                           CPU Time Used: 01:51:24        
+   Memory Requested:   192.0GB               Memory Used: 46.95GB         
+   Walltime requested: 01:00:00            Walltime Used: 00:02:35        
+   JobFS requested:    10.0GB                 JobFS used: 8.16MB          
+======================================================================================
diff --git a/tests/data/access-om3/restart000/GMOM_JRA_WD.cice.r.1900-01-02-00000.nc b/tests/data/access-om3/restart000/GMOM_JRA_WD.cice.r.1900-01-02-00000.nc
diff --git a/tests/data/access-om3/restart000/GMOM_JRA_WD.cpl.r.1900-01-02-00000.nc b/tests/data/access-om3/restart000/GMOM_JRA_WD.cpl.r.1900-01-02-00000.nc
diff --git a/tests/data/access-om3/restart000/GMOM_JRA_WD.datm.r.1900-01-02-00000.nc b/tests/data/access-om3/restart000/GMOM_JRA_WD.datm.r.1900-01-02-00000.nc
diff --git a/tests/data/access-om3/restart000/GMOM_JRA_WD.drof.r.1900-01-02-00000.nc b/tests/data/access-om3/restart000/GMOM_JRA_WD.drof.r.1900-01-02-00000.nc
diff --git a/tests/data/access-om3/restart000/GMOM_JRA_WD.mom6.r.1900-01-02-00000.nc b/tests/data/access-om3/restart000/GMOM_JRA_WD.mom6.r.1900-01-02-00000.nc
diff --git a/tests/data/access-om3/restart000/GMOM_JRA_WD.ww3.r.1900-01-02-00000 b/tests/data/access-om3/restart000/GMOM_JRA_WD.ww3.r.1900-01-02-00000
diff --git a/tests/data/access-om3/restart000/rpointer.atm b/tests/data/access-om3/restart000/rpointer.atm
@@ -0,0 +1 @@
+GMOM_JRA_WD.datm.r.1900-01-02-00000.nc                                                                                                                                                                                                                          
diff --git a/tests/data/access-om3/restart000/rpointer.cpl b/tests/data/access-om3/restart000/rpointer.cpl
@@ -0,0 +1 @@
+GMOM_JRA_WD.cpl.r.1900-01-02-00000.nc
diff --git a/tests/data/access-om3/restart000/rpointer.ice b/tests/data/access-om3/restart000/rpointer.ice
@@ -0,0 +1 @@
+./GMOM_JRA_WD.cice.r.1900-01-02-00000.nc                                                                                                                                                                                                                        
diff --git a/tests/data/access-om3/restart000/rpointer.ocn b/tests/data/access-om3/restart000/rpointer.ocn
@@ -0,0 +1 @@
+GMOM_JRA_WD.mom6.r.1900-01-02-00000.nc
diff --git a/tests/data/access-om3/restart000/rpointer.rof b/tests/data/access-om3/restart000/rpointer.rof
@@ -0,0 +1 @@
+GMOM_JRA_WD.drof.r.1900-01-02-00000.nc                                                                                                                                                                                                                          
diff --git a/tests/data/access-om3/restart000/rpointer.wav b/tests/data/access-om3/restart000/rpointer.wav
@@ -0,0 +1 @@
+GMOM_JRA_WD.ww3.r.1900-01-02-00000
diff --git a/tests/data/access-om3/restart001/GMOM_JRA_WD.cice.r.1900-01-03-00000.nc b/tests/data/access-om3/restart001/GMOM_JRA_WD.cice.r.1900-01-03-00000.nc
diff --git a/tests/data/access-om3/restart001/GMOM_JRA_WD.cpl.r.1900-01-03-00000.nc b/tests/data/access-om3/restart001/GMOM_JRA_WD.cpl.r.1900-01-03-00000.nc
diff --git a/tests/data/access-om3/restart001/GMOM_JRA_WD.datm.r.1900-01-03-00000.nc b/tests/data/access-om3/restart001/GMOM_JRA_WD.datm.r.1900-01-03-00000.nc
diff --git a/tests/data/access-om3/restart001/GMOM_JRA_WD.drof.r.1900-01-03-00000.nc b/tests/data/access-om3/restart001/GMOM_JRA_WD.drof.r.1900-01-03-00000.nc
diff --git a/tests/data/access-om3/restart001/GMOM_JRA_WD.mom6.r.1900-01-03-00000.nc b/tests/data/access-om3/restart001/GMOM_JRA_WD.mom6.r.1900-01-03-00000.nc
diff --git a/tests/data/access-om3/restart001/GMOM_JRA_WD.ww3.r.1900-01-03-00000 b/tests/data/access-om3/restart001/GMOM_JRA_WD.ww3.r.1900-01-03-00000
diff --git a/tests/data/access-om3/restart001/rpointer.atm b/tests/data/access-om3/restart001/rpointer.atm
@@ -0,0 +1 @@
+GMOM_JRA_WD.datm.r.1900-01-03-00000.nc                                                                                                                                                                                                                          
diff --git a/tests/data/access-om3/restart001/rpointer.cpl b/tests/data/access-om3/restart001/rpointer.cpl
@@ -0,0 +1 @@
+GMOM_JRA_WD.cpl.r.1900-01-03-00000.nc
diff --git a/tests/data/access-om3/restart001/rpointer.ice b/tests/data/access-om3/restart001/rpointer.ice
@@ -0,0 +1 @@
+./GMOM_JRA_WD.cice.r.1900-01-03-00000.nc                                                                                                                                                                                                                        
diff --git a/tests/data/access-om3/restart001/rpointer.ocn b/tests/data/access-om3/restart001/rpointer.ocn
@@ -0,0 +1 @@
+GMOM_JRA_WD.mom6.r.1900-01-03-00000.nc
diff --git a/tests/data/access-om3/restart001/rpointer.rof b/tests/data/access-om3/restart001/rpointer.rof
@@ -0,0 +1 @@
+GMOM_JRA_WD.drof.r.1900-01-03-00000.nc                                                                                                                                                                                                                          
diff --git a/tests/data/access-om3/restart001/rpointer.wav b/tests/data/access-om3/restart001/rpointer.wav
@@ -0,0 +1 @@
+GMOM_JRA_WD.ww3.r.1900-01-03-00000
diff --git a/tests/test_builders.py b/tests/test_builders.py
@@ -23,6 +23,7 @@
             7,
         ),
         (["access-esm1-5"], "AccessEsm15Builder", {"ensemble": False}, 11, 11, 11),
+        (["access-om3"], "AccessOm3Builder", {}, 12, 12, 6),
     ],
 )
 def test_builder_build(

diff --git a/tests/test_manager.py b/tests/test_manager.py
@@ -13,6 +13,7 @@
     AccessCm2Builder,
     AccessEsm15Builder,
     AccessOm2Builder,
+    AccessOm3Builder,
 )
 
 
@@ -35,6 +36,7 @@ def test_CatalogManager_init(tmp_path):
         (AccessOm2Builder, "access-om2", {}),
         (AccessCm2Builder, "access-cm2/by578", {"ensemble": False}),
         (AccessEsm15Builder, "access-esm1-5", {"ensemble": False}),
+        (AccessOm3Builder, "access-om3", {}),
     ],
 )
 def test_CatalogManager_build_esm(tmp_path, test_data, builder, basedir, kwargs):

diff --git a/tests/test_source_utils.py b/tests/test_source_utils.py
@@ -137,6 +137,14 @@
                 None,
             ),
         ),
+        (
+            "GMOM_JRA.mom6.sfc_1900_01",
+            (
+                "GMOM_JRA_mom6_sfc_XXXX_XX",
+                "1900_01",
+                None,
+            ),
+        ),
         (
             "GMOM_JRA.mom6.static",
             (
@@ -401,6 +409,150 @@ def test_parse_access_filename(filename, expected):
                 ["mmol/m^3", "days"],
             ),
         ),
+        (
+            "access-om3/output000/GMOM_JRA_WD.mom6.h.native_1900_01.nc",
+            (
+                "GMOM_JRA_WD.mom6.h.native_1900_01.nc",
+                "GMOM_JRA_WD_mom6_h_native_XXXX_XX",
+                "1900_01",
+                "1mon",
+                "1900-01-01, 00:00:00",
+                "1900-02-01, 00:00:00",
+                ["average_DT", "average_T1", "average_T2", "thetao", "time_bnds"],
+                [
+                    "Length of average period",
+                    "Start time for average period",
+                    "End time for average period",
+                    "Sea Water Potential Temperature",
+                    "time axis boundaries",
+                ],
+                ["", "", "", "sea_water_potential_temperature", ""],
+                ["", "", "", "area:mean zl:mean yh:mean xh:mean time: mean", ""],
+                [
+                    "days",
+                    "days since 0001-01-01 00:00:00",
+                    "days since 0001-01-01 00:00:00",
+                    "degC",
+                    "days since 0001-01-01 00:00:00",
+                ],
+            ),
+        ),
+        (
+            "access-om3/output000/GMOM_JRA_WD.mom6.h.sfc_1900_01_02.nc",
+            (
+                "GMOM_JRA_WD.mom6.h.sfc_1900_01_02.nc",
+                "GMOM_JRA_WD_mom6_h_sfc_XXXX_XX_XX",
+                "1900_01_02",
+                "1day",
+                "1900-01-01, 00:00:00",
+                "1900-01-02, 00:00:00",
+                ["average_DT", "average_T1", "average_T2", "time_bnds", "tos"],
+                [
+                    "Length of average period",
+                    "Start time for average period",
+                    "End time for average period",
+                    "time axis boundaries",
+                    "Sea Surface Temperature",
+                ],
+                ["", "", "", "", "sea_surface_temperature"],
+                ["", "", "", "", "area:mean yh:mean xh:mean time: mean"],
+                [
+                    "days",
+                    "days since 0001-01-01 00:00:00",
+                    "days since 0001-01-01 00:00:00",
+                    "days since 0001-01-01 00:00:00",
+                    "degC",
+                ],
+            ),
+        ),
+        (
+            "access-om3/output000/GMOM_JRA_WD.mom6.h.static.nc",
+            (
+                "GMOM_JRA_WD.mom6.h.static.nc",
+                "GMOM_JRA_WD_mom6_h_static",
+                None,
+                "fx",
+                "none",
+                "none",
+                ["geolat", "geolon"],
+                ["Latitude of tracer (T) points", "Longitude of tracer (T) points"],
+                ["", ""],
+                ["time: point", "time: point"],
+                ["degrees_north", "degrees_east"],
+            ),
+        ),
+        (
+            "access-om3/output000/GMOM_JRA_WD.mom6.h.z_1900_01.nc",
+            (
+                "GMOM_JRA_WD.mom6.h.z_1900_01.nc",
+                "GMOM_JRA_WD_mom6_h_z_XXXX_XX",
+                "1900_01",
+                "1mon",
+                "1900-01-01, 00:00:00",
+                "1900-02-01, 00:00:00",
+                ["average_DT", "average_T1", "average_T2", "thetao", "time_bnds"],
+                [
+                    "Length of average period",
+                    "Start time for average period",
+                    "End time for average period",
+                    "Sea Water Potential Temperature",
+                    "time axis boundaries",
+                ],
+                ["", "", "", "sea_water_potential_temperature", ""],
+                ["", "", "", "area:mean z_l:mean yh:mean xh:mean time: mean", ""],
+                [
+                    "days",
+                    "days since 0001-01-01 00:00:00",
+                    "days since 0001-01-01 00:00:00",
+                    "degC",
+                    "days since 0001-01-01 00:00:00",
+                ],
+            ),
+        ),
+        (
+            "access-om3/output000/GMOM_JRA_WD.cice.h.1900-01-01.nc",
+            (
+                "GMOM_JRA_WD.cice.h.1900-01-01.nc",
+                "GMOM_JRA_WD_cice_h_XXXX_XX_XX",
+                "1900-01-01",
+                "1day",
+                "1900-01-01, 00:00:00",
+                "1900-01-02, 00:00:00",
+                ["TLAT", "TLON", "aice", "tarea", "time_bounds"],
+                [
+                    "T grid center latitude",
+                    "T grid center longitude",
+                    "ice area  (aggregate)",
+                    "area of T grid cells",
+                    "time interval endpoints",
+                ],
+                ["", "", "", "", ""],
+                ["", "", "time: mean", "", ""],
+                [
+                    "degrees_north",
+                    "degrees_east",
+                    "1",
+                    "m^2",
+                    "days since 0000-01-01 00:00:00",
+                ],
+            ),
+        ),
+        (
+            "access-om3/output000/GMOM_JRA_WD.ww3.hi.1900-01-02-00000.nc",
+            (
+                "GMOM_JRA_WD.ww3.hi.1900-01-02-00000.nc",
+                "GMOM_JRA_WD_ww3_hi_XXXX_XX_XX_XXXXX",
+                "1900-01-02-00000",
+                "fx",  # WW3 provides no time bounds
+                "none",
+                "none",
+                ["EF", "mapsta"],
+                ["1D spectral density", "map status"],
+                ["", ""],
+                ["", ""],
+                ["m2 s", "unitless"],
+            ),
+        ),
     ],
 )
 def test_parse_access_ncfile(test_data, filename, expected):
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		These files were copied from a test run using an early version of ACCESS-OM3 and subsequently stripped to a test dataset that includes only single variables/grid points
-Original file line number
+Diff line change
@@ Expand Up / @@ -23,6 +23,7 @@ @@
 ,
             ),
             (["access-esm1-5"], "AccessEsm15Builder", {"ensemble": False}, 11, 11, 11),
+            (["access-om3"], "AccessOm3Builder", {}, 12, 12, 6),
         ],
     )
     def test_builder_build(
@@ Expand Down @@