From d7785243d81a3bb6226a942c86291c9fdc8717b9 Mon Sep 17 00:00:00 2001 From: "zachary.burnett" Date: Thu, 6 May 2021 12:38:20 -0400 Subject: [PATCH 1/8] use conda pyproj --- tests/test_utilities.py | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/tests/test_utilities.py b/tests/test_utilities.py index fa81c063..a087a9bb 100644 --- a/tests/test_utilities.py +++ b/tests/test_utilities.py @@ -5,7 +5,8 @@ from pyproj import CRS import pytest -from coupledmodeldriver.utilities import convert_to_json, convert_value, create_symlink +from coupledmodeldriver.utilities import convert_to_json, convert_value, \ + create_symlink DATA_DIRECTORY = Path(__file__).parent / 'data' INPUT_DIRECTORY = DATA_DIRECTORY / 'input' @@ -126,11 +127,11 @@ def test_convert_value(): assert ( crs_1 - == 'GEOGCRS["WGS 84",DATUM["World Geodetic System 1984",ELLIPSOID["WGS 84",6378137,298.257223563,LENGTHUNIT["metre",1]]],PRIMEM["Greenwich",0,ANGLEUNIT["degree",0.0174532925199433]],CS[ellipsoidal,2],AXIS["geodetic latitude (Lat)",north,ORDER[1],ANGLEUNIT["degree",0.0174532925199433]],AXIS["geodetic longitude (Lon)",east,ORDER[2],ANGLEUNIT["degree",0.0174532925199433]],USAGE[SCOPE["Horizontal component of 3D system."],AREA["World."],BBOX[-90,-180,90,180]],ID["EPSG",4326]]' + == 'GEOGCRS["WGS 84",DATUM["World Geodetic System 1984",ELLIPSOID["WGS 84",6378137,298.257223563,LENGTHUNIT["metre",1]]],PRIMEM["Greenwich",0,ANGLEUNIT["degree",0.0174532925199433]],CS[ellipsoidal,2],AXIS["geodetic latitude (Lat)",north,ORDER[1],ANGLEUNIT["degree",0.0174532925199433]],AXIS["geodetic longitude (Lon)",east,ORDER[2],ANGLEUNIT["degree",0.0174532925199433]],USAGE[SCOPE["unknown"],AREA["World"],BBOX[-90,-180,90,180]],ID["EPSG",4326]]' ) assert crs_2 == 4326 assert crs_3 == { - '$schema': 'https://proj.org/schemas/v0.2/projjson.schema.json', + '$schema': 'https://proj.org/schemas/v0.1/projjson.schema.json', 'type': 'GeographicCRS', 'name': 'WGS 84', 'datum': { @@ -159,8 +160,7 @@ def test_convert_value(): }, ], }, - 'scope': 'Horizontal component of 3D system.', - 'area': 'World.', + 'area': 'World', 'bbox': { 'south_latitude': -90, 'west_longitude': -180, From 60a26484c623fba30526accf76bf2343fe6811fa Mon Sep 17 00:00:00 2001 From: "zachary.burnett" Date: Thu, 6 May 2021 12:44:27 -0400 Subject: [PATCH 2/8] update reference files --- tests/data/reference/adcirc/hera_shinnecock_ike/cleanup.sh | 2 +- .../reference/adcirc/hera_shinnecock_ike/configure_slurm.json | 1 - .../adcirc/hera_shinnecock_ike/runs/unperturbed/fort.15 | 2 +- tests/data/reference/adcirc/hera_shinnecock_ike/spinup/fort.15 | 2 +- .../reference/adcirc/hera_shinnecock_ike_nospinup/cleanup.sh | 2 +- .../adcirc/hera_shinnecock_ike_nospinup/configure_slurm.json | 1 - .../hera_shinnecock_ike_nospinup/runs/unperturbed/fort.15 | 2 +- tests/data/reference/adcirc/local_shinnecock_ike/cleanup.sh | 2 +- .../reference/adcirc/local_shinnecock_ike/configure_slurm.json | 1 - .../adcirc/local_shinnecock_ike/runs/unperturbed/fort.15 | 2 +- tests/data/reference/adcirc/local_shinnecock_ike/spinup/fort.15 | 2 +- tests/data/reference/adcirc/stampede2_shinnecock_ike/cleanup.sh | 2 +- .../adcirc/stampede2_shinnecock_ike/configure_slurm.json | 1 - .../adcirc/stampede2_shinnecock_ike/runs/unperturbed/fort.15 | 2 +- .../reference/adcirc/stampede2_shinnecock_ike/spinup/fort.15 | 2 +- tests/data/reference/nems_adcirc/hera_shinnecock_ike/cleanup.sh | 2 +- .../nems_adcirc/hera_shinnecock_ike/config.rc.coldstart | 2 +- .../nems_adcirc/hera_shinnecock_ike/config.rc.hotstart | 2 +- .../nems_adcirc/hera_shinnecock_ike/configure_slurm.json | 1 - .../nems_adcirc/hera_shinnecock_ike/model_configure.coldstart | 2 +- .../nems_adcirc/hera_shinnecock_ike/model_configure.hotstart | 2 +- .../nems_adcirc/hera_shinnecock_ike/nems.configure.coldstart | 2 +- .../nems_adcirc/hera_shinnecock_ike/nems.configure.hotstart | 2 +- .../nems_adcirc/hera_shinnecock_ike/runs/unperturbed/config.rc | 2 +- .../nems_adcirc/hera_shinnecock_ike/runs/unperturbed/fort.15 | 2 +- .../hera_shinnecock_ike/runs/unperturbed/model_configure | 2 +- .../hera_shinnecock_ike/runs/unperturbed/nems.configure | 2 +- .../reference/nems_adcirc/hera_shinnecock_ike/spinup/config.rc | 2 +- .../reference/nems_adcirc/hera_shinnecock_ike/spinup/fort.15 | 2 +- .../nems_adcirc/hera_shinnecock_ike/spinup/model_configure | 2 +- .../nems_adcirc/hera_shinnecock_ike/spinup/nems.configure | 2 +- .../nems_adcirc/hera_shinnecock_ike_nospinup/cleanup.sh | 2 +- .../hera_shinnecock_ike_nospinup/config.rc.coldstart | 2 +- .../hera_shinnecock_ike_nospinup/configure_slurm.json | 1 - .../hera_shinnecock_ike_nospinup/model_configure.coldstart | 2 +- .../hera_shinnecock_ike_nospinup/nems.configure.coldstart | 2 +- .../hera_shinnecock_ike_nospinup/runs/unperturbed/config.rc | 2 +- .../hera_shinnecock_ike_nospinup/runs/unperturbed/fort.15 | 2 +- .../runs/unperturbed/model_configure | 2 +- .../runs/unperturbed/nems.configure | 2 +- .../data/reference/nems_adcirc/local_shinnecock_ike/cleanup.sh | 2 +- .../nems_adcirc/local_shinnecock_ike/config.rc.coldstart | 2 +- .../nems_adcirc/local_shinnecock_ike/config.rc.hotstart | 2 +- .../nems_adcirc/local_shinnecock_ike/configure_slurm.json | 1 - .../nems_adcirc/local_shinnecock_ike/model_configure.coldstart | 2 +- .../nems_adcirc/local_shinnecock_ike/model_configure.hotstart | 2 +- .../nems_adcirc/local_shinnecock_ike/nems.configure.coldstart | 2 +- .../nems_adcirc/local_shinnecock_ike/nems.configure.hotstart | 2 +- .../nems_adcirc/local_shinnecock_ike/runs/unperturbed/config.rc | 2 +- .../nems_adcirc/local_shinnecock_ike/runs/unperturbed/fort.15 | 2 +- .../local_shinnecock_ike/runs/unperturbed/model_configure | 2 +- .../local_shinnecock_ike/runs/unperturbed/nems.configure | 2 +- .../reference/nems_adcirc/local_shinnecock_ike/spinup/config.rc | 2 +- .../reference/nems_adcirc/local_shinnecock_ike/spinup/fort.15 | 2 +- .../nems_adcirc/local_shinnecock_ike/spinup/model_configure | 2 +- .../nems_adcirc/local_shinnecock_ike/spinup/nems.configure | 2 +- .../reference/nems_adcirc/stampede2_shinnecock_ike/cleanup.sh | 2 +- .../nems_adcirc/stampede2_shinnecock_ike/config.rc.coldstart | 2 +- .../nems_adcirc/stampede2_shinnecock_ike/config.rc.hotstart | 2 +- .../nems_adcirc/stampede2_shinnecock_ike/configure_slurm.json | 1 - .../stampede2_shinnecock_ike/model_configure.coldstart | 2 +- .../stampede2_shinnecock_ike/model_configure.hotstart | 2 +- .../stampede2_shinnecock_ike/nems.configure.coldstart | 2 +- .../stampede2_shinnecock_ike/nems.configure.hotstart | 2 +- .../stampede2_shinnecock_ike/runs/unperturbed/config.rc | 2 +- .../stampede2_shinnecock_ike/runs/unperturbed/fort.15 | 2 +- .../stampede2_shinnecock_ike/runs/unperturbed/model_configure | 2 +- .../stampede2_shinnecock_ike/runs/unperturbed/nems.configure | 2 +- .../nems_adcirc/stampede2_shinnecock_ike/spinup/config.rc | 2 +- .../nems_adcirc/stampede2_shinnecock_ike/spinup/fort.15 | 2 +- .../nems_adcirc/stampede2_shinnecock_ike/spinup/model_configure | 2 +- .../nems_adcirc/stampede2_shinnecock_ike/spinup/nems.configure | 2 +- 72 files changed, 64 insertions(+), 72 deletions(-) diff --git a/tests/data/reference/adcirc/hera_shinnecock_ike/cleanup.sh b/tests/data/reference/adcirc/hera_shinnecock_ike/cleanup.sh index d34fb8f4..e3ec736e 100644 --- a/tests/data/reference/adcirc/hera_shinnecock_ike/cleanup.sh +++ b/tests/data/reference/adcirc/hera_shinnecock_ike/cleanup.sh @@ -8,6 +8,6 @@ popd >/dev/null 2>&1 # clean run configurations for hotstart in ${DIRECTORY}/runs/*/; do pushd ${hotstart} >/dev/null 2>&1 - rm -rf PE* ADC_* max* partmesh.txt metis_graph.txt fort.16 fort.6* fort.80 + rm -rf PE* ADC_* max* partmesh.txt metis_graph.txt fort.16 fort.63 fort.64 fort.80 popd >/dev/null 2>&1 done diff --git a/tests/data/reference/adcirc/hera_shinnecock_ike/configure_slurm.json b/tests/data/reference/adcirc/hera_shinnecock_ike/configure_slurm.json index 4a95dad2..feebd5be 100644 --- a/tests/data/reference/adcirc/hera_shinnecock_ike/configure_slurm.json +++ b/tests/data/reference/adcirc/hera_shinnecock_ike/configure_slurm.json @@ -1,6 +1,5 @@ { "account": "coastal", - "tasks": 600, "partition": null, "job_duration": 21600.0, "run_directory": null, diff --git a/tests/data/reference/adcirc/hera_shinnecock_ike/runs/unperturbed/fort.15 b/tests/data/reference/adcirc/hera_shinnecock_ike/runs/unperturbed/fort.15 index 75fa5bfe..7a40d8e6 100644 --- a/tests/data/reference/adcirc/hera_shinnecock_ike/runs/unperturbed/fort.15 +++ b/tests/data/reference/adcirc/hera_shinnecock_ike/runs/unperturbed/fort.15 @@ -1,4 +1,4 @@ -created on 2021-04-29 08:12 ! RUNDES - 32 CHARACTER ALPHANUMERIC RUN DESCRIPTION +created on 2021-05-06 12:42 ! RUNDES - 32 CHARACTER ALPHANUMERIC RUN DESCRIPTION Shinacock Inlet Coarse Grid ! RUNID - 24 CHARACTER ALPANUMERIC RUN IDENTIFICATION 1 ! NFOVER - NONFATAL ERROR OVERRIDE OPTION 1 ! NABOUT - ABREVIATED OUTPUT OPTION PARAMETER diff --git a/tests/data/reference/adcirc/hera_shinnecock_ike/spinup/fort.15 b/tests/data/reference/adcirc/hera_shinnecock_ike/spinup/fort.15 index cf0c25e7..3a353182 100644 --- a/tests/data/reference/adcirc/hera_shinnecock_ike/spinup/fort.15 +++ b/tests/data/reference/adcirc/hera_shinnecock_ike/spinup/fort.15 @@ -1,4 +1,4 @@ -created on 2021-04-29 08:12 ! RUNDES - 32 CHARACTER ALPHANUMERIC RUN DESCRIPTION +created on 2021-05-06 12:42 ! RUNDES - 32 CHARACTER ALPHANUMERIC RUN DESCRIPTION Shinacock Inlet Coarse Grid ! RUNID - 24 CHARACTER ALPANUMERIC RUN IDENTIFICATION 1 ! NFOVER - NONFATAL ERROR OVERRIDE OPTION 1 ! NABOUT - ABREVIATED OUTPUT OPTION PARAMETER diff --git a/tests/data/reference/adcirc/hera_shinnecock_ike_nospinup/cleanup.sh b/tests/data/reference/adcirc/hera_shinnecock_ike_nospinup/cleanup.sh index d34fb8f4..e3ec736e 100644 --- a/tests/data/reference/adcirc/hera_shinnecock_ike_nospinup/cleanup.sh +++ b/tests/data/reference/adcirc/hera_shinnecock_ike_nospinup/cleanup.sh @@ -8,6 +8,6 @@ popd >/dev/null 2>&1 # clean run configurations for hotstart in ${DIRECTORY}/runs/*/; do pushd ${hotstart} >/dev/null 2>&1 - rm -rf PE* ADC_* max* partmesh.txt metis_graph.txt fort.16 fort.6* fort.80 + rm -rf PE* ADC_* max* partmesh.txt metis_graph.txt fort.16 fort.63 fort.64 fort.80 popd >/dev/null 2>&1 done diff --git a/tests/data/reference/adcirc/hera_shinnecock_ike_nospinup/configure_slurm.json b/tests/data/reference/adcirc/hera_shinnecock_ike_nospinup/configure_slurm.json index 4a95dad2..feebd5be 100644 --- a/tests/data/reference/adcirc/hera_shinnecock_ike_nospinup/configure_slurm.json +++ b/tests/data/reference/adcirc/hera_shinnecock_ike_nospinup/configure_slurm.json @@ -1,6 +1,5 @@ { "account": "coastal", - "tasks": 600, "partition": null, "job_duration": 21600.0, "run_directory": null, diff --git a/tests/data/reference/adcirc/hera_shinnecock_ike_nospinup/runs/unperturbed/fort.15 b/tests/data/reference/adcirc/hera_shinnecock_ike_nospinup/runs/unperturbed/fort.15 index 097a4045..1a0830f4 100644 --- a/tests/data/reference/adcirc/hera_shinnecock_ike_nospinup/runs/unperturbed/fort.15 +++ b/tests/data/reference/adcirc/hera_shinnecock_ike_nospinup/runs/unperturbed/fort.15 @@ -1,4 +1,4 @@ -created on 2021-04-29 08:12 ! RUNDES - 32 CHARACTER ALPHANUMERIC RUN DESCRIPTION +created on 2021-05-06 12:42 ! RUNDES - 32 CHARACTER ALPHANUMERIC RUN DESCRIPTION Shinacock Inlet Coarse Grid ! RUNID - 24 CHARACTER ALPANUMERIC RUN IDENTIFICATION 1 ! NFOVER - NONFATAL ERROR OVERRIDE OPTION 1 ! NABOUT - ABREVIATED OUTPUT OPTION PARAMETER diff --git a/tests/data/reference/adcirc/local_shinnecock_ike/cleanup.sh b/tests/data/reference/adcirc/local_shinnecock_ike/cleanup.sh index d34fb8f4..e3ec736e 100644 --- a/tests/data/reference/adcirc/local_shinnecock_ike/cleanup.sh +++ b/tests/data/reference/adcirc/local_shinnecock_ike/cleanup.sh @@ -8,6 +8,6 @@ popd >/dev/null 2>&1 # clean run configurations for hotstart in ${DIRECTORY}/runs/*/; do pushd ${hotstart} >/dev/null 2>&1 - rm -rf PE* ADC_* max* partmesh.txt metis_graph.txt fort.16 fort.6* fort.80 + rm -rf PE* ADC_* max* partmesh.txt metis_graph.txt fort.16 fort.63 fort.64 fort.80 popd >/dev/null 2>&1 done diff --git a/tests/data/reference/adcirc/local_shinnecock_ike/configure_slurm.json b/tests/data/reference/adcirc/local_shinnecock_ike/configure_slurm.json index cc1b9848..c8b34644 100644 --- a/tests/data/reference/adcirc/local_shinnecock_ike/configure_slurm.json +++ b/tests/data/reference/adcirc/local_shinnecock_ike/configure_slurm.json @@ -1,6 +1,5 @@ { "account": null, - "tasks": 11, "partition": null, "job_duration": 21600.0, "run_directory": null, diff --git a/tests/data/reference/adcirc/local_shinnecock_ike/runs/unperturbed/fort.15 b/tests/data/reference/adcirc/local_shinnecock_ike/runs/unperturbed/fort.15 index 75fa5bfe..7a40d8e6 100644 --- a/tests/data/reference/adcirc/local_shinnecock_ike/runs/unperturbed/fort.15 +++ b/tests/data/reference/adcirc/local_shinnecock_ike/runs/unperturbed/fort.15 @@ -1,4 +1,4 @@ -created on 2021-04-29 08:12 ! RUNDES - 32 CHARACTER ALPHANUMERIC RUN DESCRIPTION +created on 2021-05-06 12:42 ! RUNDES - 32 CHARACTER ALPHANUMERIC RUN DESCRIPTION Shinacock Inlet Coarse Grid ! RUNID - 24 CHARACTER ALPANUMERIC RUN IDENTIFICATION 1 ! NFOVER - NONFATAL ERROR OVERRIDE OPTION 1 ! NABOUT - ABREVIATED OUTPUT OPTION PARAMETER diff --git a/tests/data/reference/adcirc/local_shinnecock_ike/spinup/fort.15 b/tests/data/reference/adcirc/local_shinnecock_ike/spinup/fort.15 index cf0c25e7..3a353182 100644 --- a/tests/data/reference/adcirc/local_shinnecock_ike/spinup/fort.15 +++ b/tests/data/reference/adcirc/local_shinnecock_ike/spinup/fort.15 @@ -1,4 +1,4 @@ -created on 2021-04-29 08:12 ! RUNDES - 32 CHARACTER ALPHANUMERIC RUN DESCRIPTION +created on 2021-05-06 12:42 ! RUNDES - 32 CHARACTER ALPHANUMERIC RUN DESCRIPTION Shinacock Inlet Coarse Grid ! RUNID - 24 CHARACTER ALPANUMERIC RUN IDENTIFICATION 1 ! NFOVER - NONFATAL ERROR OVERRIDE OPTION 1 ! NABOUT - ABREVIATED OUTPUT OPTION PARAMETER diff --git a/tests/data/reference/adcirc/stampede2_shinnecock_ike/cleanup.sh b/tests/data/reference/adcirc/stampede2_shinnecock_ike/cleanup.sh index d34fb8f4..e3ec736e 100644 --- a/tests/data/reference/adcirc/stampede2_shinnecock_ike/cleanup.sh +++ b/tests/data/reference/adcirc/stampede2_shinnecock_ike/cleanup.sh @@ -8,6 +8,6 @@ popd >/dev/null 2>&1 # clean run configurations for hotstart in ${DIRECTORY}/runs/*/; do pushd ${hotstart} >/dev/null 2>&1 - rm -rf PE* ADC_* max* partmesh.txt metis_graph.txt fort.16 fort.6* fort.80 + rm -rf PE* ADC_* max* partmesh.txt metis_graph.txt fort.16 fort.63 fort.64 fort.80 popd >/dev/null 2>&1 done diff --git a/tests/data/reference/adcirc/stampede2_shinnecock_ike/configure_slurm.json b/tests/data/reference/adcirc/stampede2_shinnecock_ike/configure_slurm.json index 1488d941..feebd5be 100644 --- a/tests/data/reference/adcirc/stampede2_shinnecock_ike/configure_slurm.json +++ b/tests/data/reference/adcirc/stampede2_shinnecock_ike/configure_slurm.json @@ -1,6 +1,5 @@ { "account": "coastal", - "tasks": 1020, "partition": null, "job_duration": 21600.0, "run_directory": null, diff --git a/tests/data/reference/adcirc/stampede2_shinnecock_ike/runs/unperturbed/fort.15 b/tests/data/reference/adcirc/stampede2_shinnecock_ike/runs/unperturbed/fort.15 index 75fa5bfe..7a40d8e6 100644 --- a/tests/data/reference/adcirc/stampede2_shinnecock_ike/runs/unperturbed/fort.15 +++ b/tests/data/reference/adcirc/stampede2_shinnecock_ike/runs/unperturbed/fort.15 @@ -1,4 +1,4 @@ -created on 2021-04-29 08:12 ! RUNDES - 32 CHARACTER ALPHANUMERIC RUN DESCRIPTION +created on 2021-05-06 12:42 ! RUNDES - 32 CHARACTER ALPHANUMERIC RUN DESCRIPTION Shinacock Inlet Coarse Grid ! RUNID - 24 CHARACTER ALPANUMERIC RUN IDENTIFICATION 1 ! NFOVER - NONFATAL ERROR OVERRIDE OPTION 1 ! NABOUT - ABREVIATED OUTPUT OPTION PARAMETER diff --git a/tests/data/reference/adcirc/stampede2_shinnecock_ike/spinup/fort.15 b/tests/data/reference/adcirc/stampede2_shinnecock_ike/spinup/fort.15 index cf0c25e7..3a353182 100644 --- a/tests/data/reference/adcirc/stampede2_shinnecock_ike/spinup/fort.15 +++ b/tests/data/reference/adcirc/stampede2_shinnecock_ike/spinup/fort.15 @@ -1,4 +1,4 @@ -created on 2021-04-29 08:12 ! RUNDES - 32 CHARACTER ALPHANUMERIC RUN DESCRIPTION +created on 2021-05-06 12:42 ! RUNDES - 32 CHARACTER ALPHANUMERIC RUN DESCRIPTION Shinacock Inlet Coarse Grid ! RUNID - 24 CHARACTER ALPANUMERIC RUN IDENTIFICATION 1 ! NFOVER - NONFATAL ERROR OVERRIDE OPTION 1 ! NABOUT - ABREVIATED OUTPUT OPTION PARAMETER diff --git a/tests/data/reference/nems_adcirc/hera_shinnecock_ike/cleanup.sh b/tests/data/reference/nems_adcirc/hera_shinnecock_ike/cleanup.sh index d34fb8f4..e3ec736e 100644 --- a/tests/data/reference/nems_adcirc/hera_shinnecock_ike/cleanup.sh +++ b/tests/data/reference/nems_adcirc/hera_shinnecock_ike/cleanup.sh @@ -8,6 +8,6 @@ popd >/dev/null 2>&1 # clean run configurations for hotstart in ${DIRECTORY}/runs/*/; do pushd ${hotstart} >/dev/null 2>&1 - rm -rf PE* ADC_* max* partmesh.txt metis_graph.txt fort.16 fort.6* fort.80 + rm -rf PE* ADC_* max* partmesh.txt metis_graph.txt fort.16 fort.63 fort.64 fort.80 popd >/dev/null 2>&1 done diff --git a/tests/data/reference/nems_adcirc/hera_shinnecock_ike/config.rc.coldstart b/tests/data/reference/nems_adcirc/hera_shinnecock_ike/config.rc.coldstart index dcf55421..068bebb6 100644 --- a/tests/data/reference/nems_adcirc/hera_shinnecock_ike/config.rc.coldstart +++ b/tests/data/reference/nems_adcirc/hera_shinnecock_ike/config.rc.coldstart @@ -1,2 +1,2 @@ -# `config.rc` generated with NEMSpy 1.2.21.post8.dev0+fc8a6ef +# `config.rc` generated with NEMSpy 1.2.21.post17.dev0+3f84e56 diff --git a/tests/data/reference/nems_adcirc/hera_shinnecock_ike/config.rc.hotstart b/tests/data/reference/nems_adcirc/hera_shinnecock_ike/config.rc.hotstart index 726d1b9e..2bbf41b6 100644 --- a/tests/data/reference/nems_adcirc/hera_shinnecock_ike/config.rc.hotstart +++ b/tests/data/reference/nems_adcirc/hera_shinnecock_ike/config.rc.hotstart @@ -1,4 +1,4 @@ -# `config.rc` generated with NEMSpy 1.2.21.post8.dev0+fc8a6ef +# `config.rc` generated with NEMSpy 1.2.21.post17.dev0+3f84e56 atm_dir: ../../../input/shinnecock_ike/forcings atm_nam: wind_atm_fin_ch_time_vec.nc wav_dir: ../../../input/shinnecock_ike/forcings diff --git a/tests/data/reference/nems_adcirc/hera_shinnecock_ike/configure_slurm.json b/tests/data/reference/nems_adcirc/hera_shinnecock_ike/configure_slurm.json index 8ea87617..feebd5be 100644 --- a/tests/data/reference/nems_adcirc/hera_shinnecock_ike/configure_slurm.json +++ b/tests/data/reference/nems_adcirc/hera_shinnecock_ike/configure_slurm.json @@ -1,6 +1,5 @@ { "account": "coastal", - "tasks": 602, "partition": null, "job_duration": 21600.0, "run_directory": null, diff --git a/tests/data/reference/nems_adcirc/hera_shinnecock_ike/model_configure.coldstart b/tests/data/reference/nems_adcirc/hera_shinnecock_ike/model_configure.coldstart index 0789a9d1..d80d7c35 100644 --- a/tests/data/reference/nems_adcirc/hera_shinnecock_ike/model_configure.coldstart +++ b/tests/data/reference/nems_adcirc/hera_shinnecock_ike/model_configure.coldstart @@ -1,4 +1,4 @@ -# `model_configure` generated with NEMSpy 1.2.21.post8.dev0+fc8a6ef +# `model_configure` generated with NEMSpy 1.2.21.post17.dev0+3f84e56 total_member: 1 print_esmf: .true. namelist: atm_namelist diff --git a/tests/data/reference/nems_adcirc/hera_shinnecock_ike/model_configure.hotstart b/tests/data/reference/nems_adcirc/hera_shinnecock_ike/model_configure.hotstart index 7f14d67c..ba4dd9fc 100644 --- a/tests/data/reference/nems_adcirc/hera_shinnecock_ike/model_configure.hotstart +++ b/tests/data/reference/nems_adcirc/hera_shinnecock_ike/model_configure.hotstart @@ -1,4 +1,4 @@ -# `model_configure` generated with NEMSpy 1.2.21.post8.dev0+fc8a6ef +# `model_configure` generated with NEMSpy 1.2.21.post17.dev0+3f84e56 total_member: 1 print_esmf: .true. namelist: atm_namelist diff --git a/tests/data/reference/nems_adcirc/hera_shinnecock_ike/nems.configure.coldstart b/tests/data/reference/nems_adcirc/hera_shinnecock_ike/nems.configure.coldstart index 47bd11f8..8f9a67d3 100644 --- a/tests/data/reference/nems_adcirc/hera_shinnecock_ike/nems.configure.coldstart +++ b/tests/data/reference/nems_adcirc/hera_shinnecock_ike/nems.configure.coldstart @@ -1,4 +1,4 @@ -# `nems.configure` generated with NEMSpy 1.2.21.post8.dev0+fc8a6ef +# `nems.configure` generated with NEMSpy 1.2.21.post17.dev0+3f84e56 # EARTH # EARTH_component_list: OCN EARTH_attributes:: diff --git a/tests/data/reference/nems_adcirc/hera_shinnecock_ike/nems.configure.hotstart b/tests/data/reference/nems_adcirc/hera_shinnecock_ike/nems.configure.hotstart index 16cb064b..2a15f7e1 100644 --- a/tests/data/reference/nems_adcirc/hera_shinnecock_ike/nems.configure.hotstart +++ b/tests/data/reference/nems_adcirc/hera_shinnecock_ike/nems.configure.hotstart @@ -1,4 +1,4 @@ -# `nems.configure` generated with NEMSpy 1.2.21.post8.dev0+fc8a6ef +# `nems.configure` generated with NEMSpy 1.2.21.post17.dev0+3f84e56 # EARTH # EARTH_component_list: ATM WAV OCN EARTH_attributes:: diff --git a/tests/data/reference/nems_adcirc/hera_shinnecock_ike/runs/unperturbed/config.rc b/tests/data/reference/nems_adcirc/hera_shinnecock_ike/runs/unperturbed/config.rc index 726d1b9e..2bbf41b6 100644 --- a/tests/data/reference/nems_adcirc/hera_shinnecock_ike/runs/unperturbed/config.rc +++ b/tests/data/reference/nems_adcirc/hera_shinnecock_ike/runs/unperturbed/config.rc @@ -1,4 +1,4 @@ -# `config.rc` generated with NEMSpy 1.2.21.post8.dev0+fc8a6ef +# `config.rc` generated with NEMSpy 1.2.21.post17.dev0+3f84e56 atm_dir: ../../../input/shinnecock_ike/forcings atm_nam: wind_atm_fin_ch_time_vec.nc wav_dir: ../../../input/shinnecock_ike/forcings diff --git a/tests/data/reference/nems_adcirc/hera_shinnecock_ike/runs/unperturbed/fort.15 b/tests/data/reference/nems_adcirc/hera_shinnecock_ike/runs/unperturbed/fort.15 index 0b43effe..c4807439 100644 --- a/tests/data/reference/nems_adcirc/hera_shinnecock_ike/runs/unperturbed/fort.15 +++ b/tests/data/reference/nems_adcirc/hera_shinnecock_ike/runs/unperturbed/fort.15 @@ -1,4 +1,4 @@ -created on 2021-04-29 08:11 ! RUNDES - 32 CHARACTER ALPHANUMERIC RUN DESCRIPTION +created on 2021-05-06 12:36 ! RUNDES - 32 CHARACTER ALPHANUMERIC RUN DESCRIPTION Shinacock Inlet Coarse Grid ! RUNID - 24 CHARACTER ALPANUMERIC RUN IDENTIFICATION 1 ! NFOVER - NONFATAL ERROR OVERRIDE OPTION 1 ! NABOUT - ABREVIATED OUTPUT OPTION PARAMETER diff --git a/tests/data/reference/nems_adcirc/hera_shinnecock_ike/runs/unperturbed/model_configure b/tests/data/reference/nems_adcirc/hera_shinnecock_ike/runs/unperturbed/model_configure index 7f14d67c..ba4dd9fc 100644 --- a/tests/data/reference/nems_adcirc/hera_shinnecock_ike/runs/unperturbed/model_configure +++ b/tests/data/reference/nems_adcirc/hera_shinnecock_ike/runs/unperturbed/model_configure @@ -1,4 +1,4 @@ -# `model_configure` generated with NEMSpy 1.2.21.post8.dev0+fc8a6ef +# `model_configure` generated with NEMSpy 1.2.21.post17.dev0+3f84e56 total_member: 1 print_esmf: .true. namelist: atm_namelist diff --git a/tests/data/reference/nems_adcirc/hera_shinnecock_ike/runs/unperturbed/nems.configure b/tests/data/reference/nems_adcirc/hera_shinnecock_ike/runs/unperturbed/nems.configure index 16cb064b..2a15f7e1 100644 --- a/tests/data/reference/nems_adcirc/hera_shinnecock_ike/runs/unperturbed/nems.configure +++ b/tests/data/reference/nems_adcirc/hera_shinnecock_ike/runs/unperturbed/nems.configure @@ -1,4 +1,4 @@ -# `nems.configure` generated with NEMSpy 1.2.21.post8.dev0+fc8a6ef +# `nems.configure` generated with NEMSpy 1.2.21.post17.dev0+3f84e56 # EARTH # EARTH_component_list: ATM WAV OCN EARTH_attributes:: diff --git a/tests/data/reference/nems_adcirc/hera_shinnecock_ike/spinup/config.rc b/tests/data/reference/nems_adcirc/hera_shinnecock_ike/spinup/config.rc index dcf55421..068bebb6 100644 --- a/tests/data/reference/nems_adcirc/hera_shinnecock_ike/spinup/config.rc +++ b/tests/data/reference/nems_adcirc/hera_shinnecock_ike/spinup/config.rc @@ -1,2 +1,2 @@ -# `config.rc` generated with NEMSpy 1.2.21.post8.dev0+fc8a6ef +# `config.rc` generated with NEMSpy 1.2.21.post17.dev0+3f84e56 diff --git a/tests/data/reference/nems_adcirc/hera_shinnecock_ike/spinup/fort.15 b/tests/data/reference/nems_adcirc/hera_shinnecock_ike/spinup/fort.15 index bf5b0e3a..3889769b 100644 --- a/tests/data/reference/nems_adcirc/hera_shinnecock_ike/spinup/fort.15 +++ b/tests/data/reference/nems_adcirc/hera_shinnecock_ike/spinup/fort.15 @@ -1,4 +1,4 @@ -created on 2021-04-29 08:10 ! RUNDES - 32 CHARACTER ALPHANUMERIC RUN DESCRIPTION +created on 2021-05-06 12:36 ! RUNDES - 32 CHARACTER ALPHANUMERIC RUN DESCRIPTION Shinacock Inlet Coarse Grid ! RUNID - 24 CHARACTER ALPANUMERIC RUN IDENTIFICATION 1 ! NFOVER - NONFATAL ERROR OVERRIDE OPTION 1 ! NABOUT - ABREVIATED OUTPUT OPTION PARAMETER diff --git a/tests/data/reference/nems_adcirc/hera_shinnecock_ike/spinup/model_configure b/tests/data/reference/nems_adcirc/hera_shinnecock_ike/spinup/model_configure index 0789a9d1..d80d7c35 100644 --- a/tests/data/reference/nems_adcirc/hera_shinnecock_ike/spinup/model_configure +++ b/tests/data/reference/nems_adcirc/hera_shinnecock_ike/spinup/model_configure @@ -1,4 +1,4 @@ -# `model_configure` generated with NEMSpy 1.2.21.post8.dev0+fc8a6ef +# `model_configure` generated with NEMSpy 1.2.21.post17.dev0+3f84e56 total_member: 1 print_esmf: .true. namelist: atm_namelist diff --git a/tests/data/reference/nems_adcirc/hera_shinnecock_ike/spinup/nems.configure b/tests/data/reference/nems_adcirc/hera_shinnecock_ike/spinup/nems.configure index 47bd11f8..8f9a67d3 100644 --- a/tests/data/reference/nems_adcirc/hera_shinnecock_ike/spinup/nems.configure +++ b/tests/data/reference/nems_adcirc/hera_shinnecock_ike/spinup/nems.configure @@ -1,4 +1,4 @@ -# `nems.configure` generated with NEMSpy 1.2.21.post8.dev0+fc8a6ef +# `nems.configure` generated with NEMSpy 1.2.21.post17.dev0+3f84e56 # EARTH # EARTH_component_list: OCN EARTH_attributes:: diff --git a/tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/cleanup.sh b/tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/cleanup.sh index d34fb8f4..e3ec736e 100644 --- a/tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/cleanup.sh +++ b/tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/cleanup.sh @@ -8,6 +8,6 @@ popd >/dev/null 2>&1 # clean run configurations for hotstart in ${DIRECTORY}/runs/*/; do pushd ${hotstart} >/dev/null 2>&1 - rm -rf PE* ADC_* max* partmesh.txt metis_graph.txt fort.16 fort.6* fort.80 + rm -rf PE* ADC_* max* partmesh.txt metis_graph.txt fort.16 fort.63 fort.64 fort.80 popd >/dev/null 2>&1 done diff --git a/tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/config.rc.coldstart b/tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/config.rc.coldstart index 726d1b9e..2bbf41b6 100644 --- a/tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/config.rc.coldstart +++ b/tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/config.rc.coldstart @@ -1,4 +1,4 @@ -# `config.rc` generated with NEMSpy 1.2.21.post8.dev0+fc8a6ef +# `config.rc` generated with NEMSpy 1.2.21.post17.dev0+3f84e56 atm_dir: ../../../input/shinnecock_ike/forcings atm_nam: wind_atm_fin_ch_time_vec.nc wav_dir: ../../../input/shinnecock_ike/forcings diff --git a/tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/configure_slurm.json b/tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/configure_slurm.json index 8ea87617..feebd5be 100644 --- a/tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/configure_slurm.json +++ b/tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/configure_slurm.json @@ -1,6 +1,5 @@ { "account": "coastal", - "tasks": 602, "partition": null, "job_duration": 21600.0, "run_directory": null, diff --git a/tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/model_configure.coldstart b/tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/model_configure.coldstart index 7f14d67c..ba4dd9fc 100644 --- a/tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/model_configure.coldstart +++ b/tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/model_configure.coldstart @@ -1,4 +1,4 @@ -# `model_configure` generated with NEMSpy 1.2.21.post8.dev0+fc8a6ef +# `model_configure` generated with NEMSpy 1.2.21.post17.dev0+3f84e56 total_member: 1 print_esmf: .true. namelist: atm_namelist diff --git a/tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/nems.configure.coldstart b/tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/nems.configure.coldstart index 16cb064b..2a15f7e1 100644 --- a/tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/nems.configure.coldstart +++ b/tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/nems.configure.coldstart @@ -1,4 +1,4 @@ -# `nems.configure` generated with NEMSpy 1.2.21.post8.dev0+fc8a6ef +# `nems.configure` generated with NEMSpy 1.2.21.post17.dev0+3f84e56 # EARTH # EARTH_component_list: ATM WAV OCN EARTH_attributes:: diff --git a/tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/runs/unperturbed/config.rc b/tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/runs/unperturbed/config.rc index 726d1b9e..2bbf41b6 100644 --- a/tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/runs/unperturbed/config.rc +++ b/tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/runs/unperturbed/config.rc @@ -1,4 +1,4 @@ -# `config.rc` generated with NEMSpy 1.2.21.post8.dev0+fc8a6ef +# `config.rc` generated with NEMSpy 1.2.21.post17.dev0+3f84e56 atm_dir: ../../../input/shinnecock_ike/forcings atm_nam: wind_atm_fin_ch_time_vec.nc wav_dir: ../../../input/shinnecock_ike/forcings diff --git a/tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/runs/unperturbed/fort.15 b/tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/runs/unperturbed/fort.15 index 68bfb1a8..92bd01fb 100644 --- a/tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/runs/unperturbed/fort.15 +++ b/tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/runs/unperturbed/fort.15 @@ -1,4 +1,4 @@ -created on 2021-04-29 08:11 ! RUNDES - 32 CHARACTER ALPHANUMERIC RUN DESCRIPTION +created on 2021-05-06 12:36 ! RUNDES - 32 CHARACTER ALPHANUMERIC RUN DESCRIPTION Shinacock Inlet Coarse Grid ! RUNID - 24 CHARACTER ALPANUMERIC RUN IDENTIFICATION 1 ! NFOVER - NONFATAL ERROR OVERRIDE OPTION 1 ! NABOUT - ABREVIATED OUTPUT OPTION PARAMETER diff --git a/tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/runs/unperturbed/model_configure b/tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/runs/unperturbed/model_configure index 7f14d67c..ba4dd9fc 100644 --- a/tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/runs/unperturbed/model_configure +++ b/tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/runs/unperturbed/model_configure @@ -1,4 +1,4 @@ -# `model_configure` generated with NEMSpy 1.2.21.post8.dev0+fc8a6ef +# `model_configure` generated with NEMSpy 1.2.21.post17.dev0+3f84e56 total_member: 1 print_esmf: .true. namelist: atm_namelist diff --git a/tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/runs/unperturbed/nems.configure b/tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/runs/unperturbed/nems.configure index 16cb064b..2a15f7e1 100644 --- a/tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/runs/unperturbed/nems.configure +++ b/tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/runs/unperturbed/nems.configure @@ -1,4 +1,4 @@ -# `nems.configure` generated with NEMSpy 1.2.21.post8.dev0+fc8a6ef +# `nems.configure` generated with NEMSpy 1.2.21.post17.dev0+3f84e56 # EARTH # EARTH_component_list: ATM WAV OCN EARTH_attributes:: diff --git a/tests/data/reference/nems_adcirc/local_shinnecock_ike/cleanup.sh b/tests/data/reference/nems_adcirc/local_shinnecock_ike/cleanup.sh index d34fb8f4..e3ec736e 100644 --- a/tests/data/reference/nems_adcirc/local_shinnecock_ike/cleanup.sh +++ b/tests/data/reference/nems_adcirc/local_shinnecock_ike/cleanup.sh @@ -8,6 +8,6 @@ popd >/dev/null 2>&1 # clean run configurations for hotstart in ${DIRECTORY}/runs/*/; do pushd ${hotstart} >/dev/null 2>&1 - rm -rf PE* ADC_* max* partmesh.txt metis_graph.txt fort.16 fort.6* fort.80 + rm -rf PE* ADC_* max* partmesh.txt metis_graph.txt fort.16 fort.63 fort.64 fort.80 popd >/dev/null 2>&1 done diff --git a/tests/data/reference/nems_adcirc/local_shinnecock_ike/config.rc.coldstart b/tests/data/reference/nems_adcirc/local_shinnecock_ike/config.rc.coldstart index dcf55421..068bebb6 100644 --- a/tests/data/reference/nems_adcirc/local_shinnecock_ike/config.rc.coldstart +++ b/tests/data/reference/nems_adcirc/local_shinnecock_ike/config.rc.coldstart @@ -1,2 +1,2 @@ -# `config.rc` generated with NEMSpy 1.2.21.post8.dev0+fc8a6ef +# `config.rc` generated with NEMSpy 1.2.21.post17.dev0+3f84e56 diff --git a/tests/data/reference/nems_adcirc/local_shinnecock_ike/config.rc.hotstart b/tests/data/reference/nems_adcirc/local_shinnecock_ike/config.rc.hotstart index 726d1b9e..2bbf41b6 100644 --- a/tests/data/reference/nems_adcirc/local_shinnecock_ike/config.rc.hotstart +++ b/tests/data/reference/nems_adcirc/local_shinnecock_ike/config.rc.hotstart @@ -1,4 +1,4 @@ -# `config.rc` generated with NEMSpy 1.2.21.post8.dev0+fc8a6ef +# `config.rc` generated with NEMSpy 1.2.21.post17.dev0+3f84e56 atm_dir: ../../../input/shinnecock_ike/forcings atm_nam: wind_atm_fin_ch_time_vec.nc wav_dir: ../../../input/shinnecock_ike/forcings diff --git a/tests/data/reference/nems_adcirc/local_shinnecock_ike/configure_slurm.json b/tests/data/reference/nems_adcirc/local_shinnecock_ike/configure_slurm.json index 32df1e8c..c8b34644 100644 --- a/tests/data/reference/nems_adcirc/local_shinnecock_ike/configure_slurm.json +++ b/tests/data/reference/nems_adcirc/local_shinnecock_ike/configure_slurm.json @@ -1,6 +1,5 @@ { "account": null, - "tasks": 13, "partition": null, "job_duration": 21600.0, "run_directory": null, diff --git a/tests/data/reference/nems_adcirc/local_shinnecock_ike/model_configure.coldstart b/tests/data/reference/nems_adcirc/local_shinnecock_ike/model_configure.coldstart index a21842eb..d702236f 100644 --- a/tests/data/reference/nems_adcirc/local_shinnecock_ike/model_configure.coldstart +++ b/tests/data/reference/nems_adcirc/local_shinnecock_ike/model_configure.coldstart @@ -1,4 +1,4 @@ -# `model_configure` generated with NEMSpy 1.2.21.post8.dev0+fc8a6ef +# `model_configure` generated with NEMSpy 1.2.21.post17.dev0+3f84e56 total_member: 1 print_esmf: .true. namelist: atm_namelist diff --git a/tests/data/reference/nems_adcirc/local_shinnecock_ike/model_configure.hotstart b/tests/data/reference/nems_adcirc/local_shinnecock_ike/model_configure.hotstart index 7e0d6ed3..f72018e6 100644 --- a/tests/data/reference/nems_adcirc/local_shinnecock_ike/model_configure.hotstart +++ b/tests/data/reference/nems_adcirc/local_shinnecock_ike/model_configure.hotstart @@ -1,4 +1,4 @@ -# `model_configure` generated with NEMSpy 1.2.21.post8.dev0+fc8a6ef +# `model_configure` generated with NEMSpy 1.2.21.post17.dev0+3f84e56 total_member: 1 print_esmf: .true. namelist: atm_namelist diff --git a/tests/data/reference/nems_adcirc/local_shinnecock_ike/nems.configure.coldstart b/tests/data/reference/nems_adcirc/local_shinnecock_ike/nems.configure.coldstart index 24090b19..e5506d4b 100644 --- a/tests/data/reference/nems_adcirc/local_shinnecock_ike/nems.configure.coldstart +++ b/tests/data/reference/nems_adcirc/local_shinnecock_ike/nems.configure.coldstart @@ -1,4 +1,4 @@ -# `nems.configure` generated with NEMSpy 1.2.21.post8.dev0+fc8a6ef +# `nems.configure` generated with NEMSpy 1.2.21.post17.dev0+3f84e56 # EARTH # EARTH_component_list: OCN EARTH_attributes:: diff --git a/tests/data/reference/nems_adcirc/local_shinnecock_ike/nems.configure.hotstart b/tests/data/reference/nems_adcirc/local_shinnecock_ike/nems.configure.hotstart index d75857c2..e5462cd1 100644 --- a/tests/data/reference/nems_adcirc/local_shinnecock_ike/nems.configure.hotstart +++ b/tests/data/reference/nems_adcirc/local_shinnecock_ike/nems.configure.hotstart @@ -1,4 +1,4 @@ -# `nems.configure` generated with NEMSpy 1.2.21.post8.dev0+fc8a6ef +# `nems.configure` generated with NEMSpy 1.2.21.post17.dev0+3f84e56 # EARTH # EARTH_component_list: ATM WAV OCN EARTH_attributes:: diff --git a/tests/data/reference/nems_adcirc/local_shinnecock_ike/runs/unperturbed/config.rc b/tests/data/reference/nems_adcirc/local_shinnecock_ike/runs/unperturbed/config.rc index 726d1b9e..2bbf41b6 100644 --- a/tests/data/reference/nems_adcirc/local_shinnecock_ike/runs/unperturbed/config.rc +++ b/tests/data/reference/nems_adcirc/local_shinnecock_ike/runs/unperturbed/config.rc @@ -1,4 +1,4 @@ -# `config.rc` generated with NEMSpy 1.2.21.post8.dev0+fc8a6ef +# `config.rc` generated with NEMSpy 1.2.21.post17.dev0+3f84e56 atm_dir: ../../../input/shinnecock_ike/forcings atm_nam: wind_atm_fin_ch_time_vec.nc wav_dir: ../../../input/shinnecock_ike/forcings diff --git a/tests/data/reference/nems_adcirc/local_shinnecock_ike/runs/unperturbed/fort.15 b/tests/data/reference/nems_adcirc/local_shinnecock_ike/runs/unperturbed/fort.15 index 0b43effe..c4807439 100644 --- a/tests/data/reference/nems_adcirc/local_shinnecock_ike/runs/unperturbed/fort.15 +++ b/tests/data/reference/nems_adcirc/local_shinnecock_ike/runs/unperturbed/fort.15 @@ -1,4 +1,4 @@ -created on 2021-04-29 08:11 ! RUNDES - 32 CHARACTER ALPHANUMERIC RUN DESCRIPTION +created on 2021-05-06 12:36 ! RUNDES - 32 CHARACTER ALPHANUMERIC RUN DESCRIPTION Shinacock Inlet Coarse Grid ! RUNID - 24 CHARACTER ALPANUMERIC RUN IDENTIFICATION 1 ! NFOVER - NONFATAL ERROR OVERRIDE OPTION 1 ! NABOUT - ABREVIATED OUTPUT OPTION PARAMETER diff --git a/tests/data/reference/nems_adcirc/local_shinnecock_ike/runs/unperturbed/model_configure b/tests/data/reference/nems_adcirc/local_shinnecock_ike/runs/unperturbed/model_configure index 7e0d6ed3..f72018e6 100644 --- a/tests/data/reference/nems_adcirc/local_shinnecock_ike/runs/unperturbed/model_configure +++ b/tests/data/reference/nems_adcirc/local_shinnecock_ike/runs/unperturbed/model_configure @@ -1,4 +1,4 @@ -# `model_configure` generated with NEMSpy 1.2.21.post8.dev0+fc8a6ef +# `model_configure` generated with NEMSpy 1.2.21.post17.dev0+3f84e56 total_member: 1 print_esmf: .true. namelist: atm_namelist diff --git a/tests/data/reference/nems_adcirc/local_shinnecock_ike/runs/unperturbed/nems.configure b/tests/data/reference/nems_adcirc/local_shinnecock_ike/runs/unperturbed/nems.configure index d75857c2..e5462cd1 100644 --- a/tests/data/reference/nems_adcirc/local_shinnecock_ike/runs/unperturbed/nems.configure +++ b/tests/data/reference/nems_adcirc/local_shinnecock_ike/runs/unperturbed/nems.configure @@ -1,4 +1,4 @@ -# `nems.configure` generated with NEMSpy 1.2.21.post8.dev0+fc8a6ef +# `nems.configure` generated with NEMSpy 1.2.21.post17.dev0+3f84e56 # EARTH # EARTH_component_list: ATM WAV OCN EARTH_attributes:: diff --git a/tests/data/reference/nems_adcirc/local_shinnecock_ike/spinup/config.rc b/tests/data/reference/nems_adcirc/local_shinnecock_ike/spinup/config.rc index dcf55421..068bebb6 100644 --- a/tests/data/reference/nems_adcirc/local_shinnecock_ike/spinup/config.rc +++ b/tests/data/reference/nems_adcirc/local_shinnecock_ike/spinup/config.rc @@ -1,2 +1,2 @@ -# `config.rc` generated with NEMSpy 1.2.21.post8.dev0+fc8a6ef +# `config.rc` generated with NEMSpy 1.2.21.post17.dev0+3f84e56 diff --git a/tests/data/reference/nems_adcirc/local_shinnecock_ike/spinup/fort.15 b/tests/data/reference/nems_adcirc/local_shinnecock_ike/spinup/fort.15 index bf5b0e3a..3889769b 100644 --- a/tests/data/reference/nems_adcirc/local_shinnecock_ike/spinup/fort.15 +++ b/tests/data/reference/nems_adcirc/local_shinnecock_ike/spinup/fort.15 @@ -1,4 +1,4 @@ -created on 2021-04-29 08:10 ! RUNDES - 32 CHARACTER ALPHANUMERIC RUN DESCRIPTION +created on 2021-05-06 12:36 ! RUNDES - 32 CHARACTER ALPHANUMERIC RUN DESCRIPTION Shinacock Inlet Coarse Grid ! RUNID - 24 CHARACTER ALPANUMERIC RUN IDENTIFICATION 1 ! NFOVER - NONFATAL ERROR OVERRIDE OPTION 1 ! NABOUT - ABREVIATED OUTPUT OPTION PARAMETER diff --git a/tests/data/reference/nems_adcirc/local_shinnecock_ike/spinup/model_configure b/tests/data/reference/nems_adcirc/local_shinnecock_ike/spinup/model_configure index a21842eb..d702236f 100644 --- a/tests/data/reference/nems_adcirc/local_shinnecock_ike/spinup/model_configure +++ b/tests/data/reference/nems_adcirc/local_shinnecock_ike/spinup/model_configure @@ -1,4 +1,4 @@ -# `model_configure` generated with NEMSpy 1.2.21.post8.dev0+fc8a6ef +# `model_configure` generated with NEMSpy 1.2.21.post17.dev0+3f84e56 total_member: 1 print_esmf: .true. namelist: atm_namelist diff --git a/tests/data/reference/nems_adcirc/local_shinnecock_ike/spinup/nems.configure b/tests/data/reference/nems_adcirc/local_shinnecock_ike/spinup/nems.configure index 24090b19..e5506d4b 100644 --- a/tests/data/reference/nems_adcirc/local_shinnecock_ike/spinup/nems.configure +++ b/tests/data/reference/nems_adcirc/local_shinnecock_ike/spinup/nems.configure @@ -1,4 +1,4 @@ -# `nems.configure` generated with NEMSpy 1.2.21.post8.dev0+fc8a6ef +# `nems.configure` generated with NEMSpy 1.2.21.post17.dev0+3f84e56 # EARTH # EARTH_component_list: OCN EARTH_attributes:: diff --git a/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/cleanup.sh b/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/cleanup.sh index d34fb8f4..e3ec736e 100644 --- a/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/cleanup.sh +++ b/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/cleanup.sh @@ -8,6 +8,6 @@ popd >/dev/null 2>&1 # clean run configurations for hotstart in ${DIRECTORY}/runs/*/; do pushd ${hotstart} >/dev/null 2>&1 - rm -rf PE* ADC_* max* partmesh.txt metis_graph.txt fort.16 fort.6* fort.80 + rm -rf PE* ADC_* max* partmesh.txt metis_graph.txt fort.16 fort.63 fort.64 fort.80 popd >/dev/null 2>&1 done diff --git a/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/config.rc.coldstart b/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/config.rc.coldstart index dcf55421..068bebb6 100644 --- a/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/config.rc.coldstart +++ b/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/config.rc.coldstart @@ -1,2 +1,2 @@ -# `config.rc` generated with NEMSpy 1.2.21.post8.dev0+fc8a6ef +# `config.rc` generated with NEMSpy 1.2.21.post17.dev0+3f84e56 diff --git a/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/config.rc.hotstart b/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/config.rc.hotstart index 726d1b9e..2bbf41b6 100644 --- a/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/config.rc.hotstart +++ b/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/config.rc.hotstart @@ -1,4 +1,4 @@ -# `config.rc` generated with NEMSpy 1.2.21.post8.dev0+fc8a6ef +# `config.rc` generated with NEMSpy 1.2.21.post17.dev0+3f84e56 atm_dir: ../../../input/shinnecock_ike/forcings atm_nam: wind_atm_fin_ch_time_vec.nc wav_dir: ../../../input/shinnecock_ike/forcings diff --git a/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/configure_slurm.json b/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/configure_slurm.json index a840dd65..feebd5be 100644 --- a/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/configure_slurm.json +++ b/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/configure_slurm.json @@ -1,6 +1,5 @@ { "account": "coastal", - "tasks": 1022, "partition": null, "job_duration": 21600.0, "run_directory": null, diff --git a/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/model_configure.coldstart b/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/model_configure.coldstart index 9f0ecd71..7909f8af 100644 --- a/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/model_configure.coldstart +++ b/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/model_configure.coldstart @@ -1,4 +1,4 @@ -# `model_configure` generated with NEMSpy 1.2.21.post8.dev0+fc8a6ef +# `model_configure` generated with NEMSpy 1.2.21.post17.dev0+3f84e56 total_member: 1 print_esmf: .true. namelist: atm_namelist diff --git a/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/model_configure.hotstart b/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/model_configure.hotstart index 1397f01f..f64d6171 100644 --- a/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/model_configure.hotstart +++ b/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/model_configure.hotstart @@ -1,4 +1,4 @@ -# `model_configure` generated with NEMSpy 1.2.21.post8.dev0+fc8a6ef +# `model_configure` generated with NEMSpy 1.2.21.post17.dev0+3f84e56 total_member: 1 print_esmf: .true. namelist: atm_namelist diff --git a/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/nems.configure.coldstart b/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/nems.configure.coldstart index ae69bdec..c57898a8 100644 --- a/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/nems.configure.coldstart +++ b/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/nems.configure.coldstart @@ -1,4 +1,4 @@ -# `nems.configure` generated with NEMSpy 1.2.21.post8.dev0+fc8a6ef +# `nems.configure` generated with NEMSpy 1.2.21.post17.dev0+3f84e56 # EARTH # EARTH_component_list: OCN EARTH_attributes:: diff --git a/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/nems.configure.hotstart b/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/nems.configure.hotstart index 775bd430..af94bf93 100644 --- a/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/nems.configure.hotstart +++ b/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/nems.configure.hotstart @@ -1,4 +1,4 @@ -# `nems.configure` generated with NEMSpy 1.2.21.post8.dev0+fc8a6ef +# `nems.configure` generated with NEMSpy 1.2.21.post17.dev0+3f84e56 # EARTH # EARTH_component_list: ATM WAV OCN EARTH_attributes:: diff --git a/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/runs/unperturbed/config.rc b/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/runs/unperturbed/config.rc index 726d1b9e..2bbf41b6 100644 --- a/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/runs/unperturbed/config.rc +++ b/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/runs/unperturbed/config.rc @@ -1,4 +1,4 @@ -# `config.rc` generated with NEMSpy 1.2.21.post8.dev0+fc8a6ef +# `config.rc` generated with NEMSpy 1.2.21.post17.dev0+3f84e56 atm_dir: ../../../input/shinnecock_ike/forcings atm_nam: wind_atm_fin_ch_time_vec.nc wav_dir: ../../../input/shinnecock_ike/forcings diff --git a/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/runs/unperturbed/fort.15 b/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/runs/unperturbed/fort.15 index 0b43effe..c4807439 100644 --- a/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/runs/unperturbed/fort.15 +++ b/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/runs/unperturbed/fort.15 @@ -1,4 +1,4 @@ -created on 2021-04-29 08:11 ! RUNDES - 32 CHARACTER ALPHANUMERIC RUN DESCRIPTION +created on 2021-05-06 12:36 ! RUNDES - 32 CHARACTER ALPHANUMERIC RUN DESCRIPTION Shinacock Inlet Coarse Grid ! RUNID - 24 CHARACTER ALPANUMERIC RUN IDENTIFICATION 1 ! NFOVER - NONFATAL ERROR OVERRIDE OPTION 1 ! NABOUT - ABREVIATED OUTPUT OPTION PARAMETER diff --git a/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/runs/unperturbed/model_configure b/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/runs/unperturbed/model_configure index 1397f01f..f64d6171 100644 --- a/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/runs/unperturbed/model_configure +++ b/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/runs/unperturbed/model_configure @@ -1,4 +1,4 @@ -# `model_configure` generated with NEMSpy 1.2.21.post8.dev0+fc8a6ef +# `model_configure` generated with NEMSpy 1.2.21.post17.dev0+3f84e56 total_member: 1 print_esmf: .true. namelist: atm_namelist diff --git a/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/runs/unperturbed/nems.configure b/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/runs/unperturbed/nems.configure index 775bd430..af94bf93 100644 --- a/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/runs/unperturbed/nems.configure +++ b/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/runs/unperturbed/nems.configure @@ -1,4 +1,4 @@ -# `nems.configure` generated with NEMSpy 1.2.21.post8.dev0+fc8a6ef +# `nems.configure` generated with NEMSpy 1.2.21.post17.dev0+3f84e56 # EARTH # EARTH_component_list: ATM WAV OCN EARTH_attributes:: diff --git a/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/spinup/config.rc b/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/spinup/config.rc index dcf55421..068bebb6 100644 --- a/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/spinup/config.rc +++ b/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/spinup/config.rc @@ -1,2 +1,2 @@ -# `config.rc` generated with NEMSpy 1.2.21.post8.dev0+fc8a6ef +# `config.rc` generated with NEMSpy 1.2.21.post17.dev0+3f84e56 diff --git a/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/spinup/fort.15 b/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/spinup/fort.15 index bf5b0e3a..3889769b 100644 --- a/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/spinup/fort.15 +++ b/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/spinup/fort.15 @@ -1,4 +1,4 @@ -created on 2021-04-29 08:10 ! RUNDES - 32 CHARACTER ALPHANUMERIC RUN DESCRIPTION +created on 2021-05-06 12:36 ! RUNDES - 32 CHARACTER ALPHANUMERIC RUN DESCRIPTION Shinacock Inlet Coarse Grid ! RUNID - 24 CHARACTER ALPANUMERIC RUN IDENTIFICATION 1 ! NFOVER - NONFATAL ERROR OVERRIDE OPTION 1 ! NABOUT - ABREVIATED OUTPUT OPTION PARAMETER diff --git a/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/spinup/model_configure b/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/spinup/model_configure index 9f0ecd71..7909f8af 100644 --- a/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/spinup/model_configure +++ b/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/spinup/model_configure @@ -1,4 +1,4 @@ -# `model_configure` generated with NEMSpy 1.2.21.post8.dev0+fc8a6ef +# `model_configure` generated with NEMSpy 1.2.21.post17.dev0+3f84e56 total_member: 1 print_esmf: .true. namelist: atm_namelist diff --git a/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/spinup/nems.configure b/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/spinup/nems.configure index ae69bdec..c57898a8 100644 --- a/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/spinup/nems.configure +++ b/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/spinup/nems.configure @@ -1,4 +1,4 @@ -# `nems.configure` generated with NEMSpy 1.2.21.post8.dev0+fc8a6ef +# `nems.configure` generated with NEMSpy 1.2.21.post17.dev0+3f84e56 # EARTH # EARTH_component_list: OCN EARTH_attributes:: From 1a553a0524d1c633df5d0147f778f8b7b765fdf6 Mon Sep 17 00:00:00 2001 From: Zachary Burnett Date: Fri, 7 May 2021 11:30:37 -0400 Subject: [PATCH 3/8] add `aswip` to setup script (#97) * add aswipt to setup script * Revert "use conda pyproj" This reverts commit d7785243 --- coupledmodeldriver/generate/adcirc/base.py | 4 + .../generate/adcirc/generate.py | 73 ++++++++++--------- coupledmodeldriver/generate/adcirc/script.py | 39 +++++++--- coupledmodeldriver/script.py | 52 +++++++------ .../hera_shinnecock_ike/configure_adcirc.json | 1 + ...ob_adcprep_hera.job => job_setup_hera.job} | 6 +- .../adcirc/hera_shinnecock_ike/run_hera.sh | 8 +- .../runs/unperturbed/fort.15 | 2 +- .../unperturbed/{adcprep.job => setup.job} | 6 +- .../adcirc/hera_shinnecock_ike/spinup/fort.15 | 2 +- .../spinup/{adcprep.job => setup.job} | 6 +- .../configure_adcirc.json | 1 + ...ob_adcprep_hera.job => job_setup_hera.job} | 6 +- .../hera_shinnecock_ike_nospinup/run_hera.sh | 4 +- .../runs/unperturbed/adcprep.job | 15 ---- .../runs/unperturbed/fort.15 | 2 +- .../runs/unperturbed/setup.job | 15 ++++ .../configure_adcirc.json | 1 + ..._adcprep_local.job => job_setup_local.job} | 0 .../adcirc/local_shinnecock_ike/run_local.sh | 4 +- .../runs/unperturbed/fort.15 | 2 +- .../unperturbed/{adcprep.job => setup.job} | 0 .../local_shinnecock_ike/spinup/fort.15 | 2 +- .../spinup/{adcprep.job => setup.job} | 0 .../configure_adcirc.json | 1 + ..._stampede2.job => job_setup_stampede2.job} | 6 +- .../stampede2_shinnecock_ike/run_stampede2.sh | 8 +- .../runs/unperturbed/fort.15 | 2 +- .../unperturbed/{adcprep.job => setup.job} | 6 +- .../stampede2_shinnecock_ike/spinup/fort.15 | 2 +- .../spinup/{adcprep.job => setup.job} | 6 +- .../hera_shinnecock_ike/config.rc.coldstart | 2 +- .../hera_shinnecock_ike/config.rc.hotstart | 2 +- .../hera_shinnecock_ike/configure_adcirc.json | 1 + .../hera_shinnecock_ike/job_adcprep_hera.job | 15 ---- .../hera_shinnecock_ike/job_setup_hera.job | 15 ++++ .../model_configure.coldstart | 2 +- .../model_configure.hotstart | 2 +- .../nems.configure.coldstart | 2 +- .../nems.configure.hotstart | 2 +- .../hera_shinnecock_ike/run_hera.sh | 8 +- .../runs/unperturbed/adcprep.job | 15 ---- .../runs/unperturbed/config.rc | 2 +- .../runs/unperturbed/fort.15 | 2 +- .../runs/unperturbed/model_configure | 2 +- .../runs/unperturbed/nems.configure | 2 +- .../runs/unperturbed/setup.job | 15 ++++ .../hera_shinnecock_ike/spinup/adcprep.job | 15 ---- .../hera_shinnecock_ike/spinup/config.rc | 2 +- .../hera_shinnecock_ike/spinup/fort.15 | 2 +- .../spinup/model_configure | 2 +- .../hera_shinnecock_ike/spinup/nems.configure | 2 +- .../hera_shinnecock_ike/spinup/setup.job | 15 ++++ .../config.rc.coldstart | 2 +- .../configure_adcirc.json | 1 + .../job_adcprep_hera.job | 15 ---- .../job_setup_hera.job | 15 ++++ .../model_configure.coldstart | 2 +- .../nems.configure.coldstart | 2 +- .../hera_shinnecock_ike_nospinup/run_hera.sh | 4 +- .../runs/unperturbed/adcprep.job | 15 ---- .../runs/unperturbed/config.rc | 2 +- .../runs/unperturbed/fort.15 | 2 +- .../runs/unperturbed/model_configure | 2 +- .../runs/unperturbed/nems.configure | 2 +- .../runs/unperturbed/setup.job | 15 ++++ .../local_shinnecock_ike/config.rc.coldstart | 2 +- .../local_shinnecock_ike/config.rc.hotstart | 2 +- .../configure_adcirc.json | 1 + ..._adcprep_local.job => job_setup_local.job} | 0 .../model_configure.coldstart | 2 +- .../model_configure.hotstart | 2 +- .../nems.configure.coldstart | 2 +- .../nems.configure.hotstart | 2 +- .../local_shinnecock_ike/run_local.sh | 4 +- .../runs/unperturbed/config.rc | 2 +- .../runs/unperturbed/fort.15 | 2 +- .../runs/unperturbed/model_configure | 2 +- .../runs/unperturbed/nems.configure | 2 +- .../unperturbed/{adcprep.job => setup.job} | 0 .../local_shinnecock_ike/spinup/config.rc | 2 +- .../local_shinnecock_ike/spinup/fort.15 | 2 +- .../spinup/model_configure | 2 +- .../spinup/nems.configure | 2 +- .../spinup/{adcprep.job => setup.job} | 0 .../config.rc.coldstart | 2 +- .../config.rc.hotstart | 2 +- .../configure_adcirc.json | 1 + ..._stampede2.job => job_setup_stampede2.job} | 6 +- .../model_configure.coldstart | 2 +- .../model_configure.hotstart | 2 +- .../nems.configure.coldstart | 2 +- .../nems.configure.hotstart | 2 +- .../stampede2_shinnecock_ike/run_stampede2.sh | 8 +- .../runs/unperturbed/adcprep.job | 16 ---- .../runs/unperturbed/config.rc | 2 +- .../runs/unperturbed/fort.15 | 2 +- .../runs/unperturbed/model_configure | 2 +- .../runs/unperturbed/nems.configure | 2 +- .../runs/unperturbed/setup.job | 16 ++++ .../spinup/adcprep.job | 16 ---- .../stampede2_shinnecock_ike/spinup/config.rc | 2 +- .../stampede2_shinnecock_ike/spinup/fort.15 | 2 +- .../spinup/model_configure | 2 +- .../spinup/nems.configure | 2 +- .../stampede2_shinnecock_ike/spinup/setup.job | 16 ++++ tests/test_utilities.py | 7 +- 107 files changed, 334 insertions(+), 301 deletions(-) rename tests/data/reference/adcirc/hera_shinnecock_ike/{job_adcprep_hera.job => job_setup_hera.job} (68%) rename tests/data/reference/adcirc/hera_shinnecock_ike/runs/unperturbed/{adcprep.job => setup.job} (68%) rename tests/data/reference/adcirc/hera_shinnecock_ike/spinup/{adcprep.job => setup.job} (68%) rename tests/data/reference/adcirc/hera_shinnecock_ike_nospinup/{job_adcprep_hera.job => job_setup_hera.job} (68%) delete mode 100644 tests/data/reference/adcirc/hera_shinnecock_ike_nospinup/runs/unperturbed/adcprep.job create mode 100644 tests/data/reference/adcirc/hera_shinnecock_ike_nospinup/runs/unperturbed/setup.job rename tests/data/reference/adcirc/local_shinnecock_ike/{job_adcprep_local.job => job_setup_local.job} (100%) rename tests/data/reference/adcirc/local_shinnecock_ike/runs/unperturbed/{adcprep.job => setup.job} (100%) rename tests/data/reference/adcirc/local_shinnecock_ike/spinup/{adcprep.job => setup.job} (100%) rename tests/data/reference/adcirc/stampede2_shinnecock_ike/{job_adcprep_stampede2.job => job_setup_stampede2.job} (71%) rename tests/data/reference/adcirc/stampede2_shinnecock_ike/runs/unperturbed/{adcprep.job => setup.job} (71%) rename tests/data/reference/adcirc/stampede2_shinnecock_ike/spinup/{adcprep.job => setup.job} (71%) delete mode 100644 tests/data/reference/nems_adcirc/hera_shinnecock_ike/job_adcprep_hera.job create mode 100644 tests/data/reference/nems_adcirc/hera_shinnecock_ike/job_setup_hera.job delete mode 100644 tests/data/reference/nems_adcirc/hera_shinnecock_ike/runs/unperturbed/adcprep.job create mode 100644 tests/data/reference/nems_adcirc/hera_shinnecock_ike/runs/unperturbed/setup.job delete mode 100644 tests/data/reference/nems_adcirc/hera_shinnecock_ike/spinup/adcprep.job create mode 100644 tests/data/reference/nems_adcirc/hera_shinnecock_ike/spinup/setup.job delete mode 100644 tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/job_adcprep_hera.job create mode 100644 tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/job_setup_hera.job delete mode 100644 tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/runs/unperturbed/adcprep.job create mode 100644 tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/runs/unperturbed/setup.job rename tests/data/reference/nems_adcirc/local_shinnecock_ike/{job_adcprep_local.job => job_setup_local.job} (100%) rename tests/data/reference/nems_adcirc/local_shinnecock_ike/runs/unperturbed/{adcprep.job => setup.job} (100%) rename tests/data/reference/nems_adcirc/local_shinnecock_ike/spinup/{adcprep.job => setup.job} (100%) rename tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/{job_adcprep_stampede2.job => job_setup_stampede2.job} (71%) delete mode 100644 tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/runs/unperturbed/adcprep.job create mode 100644 tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/runs/unperturbed/setup.job delete mode 100644 tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/spinup/adcprep.job create mode 100644 tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/spinup/setup.job diff --git a/coupledmodeldriver/generate/adcirc/base.py b/coupledmodeldriver/generate/adcirc/base.py index 6c3c69c2..ba264c8f 100644 --- a/coupledmodeldriver/generate/adcirc/base.py +++ b/coupledmodeldriver/generate/adcirc/base.py @@ -129,6 +129,7 @@ class ADCIRCJSON(ModelJSON, NEMSCapJSON, AttributeJSON): field_types = { 'adcirc_executable_path': Path, 'adcprep_executable_path': Path, + 'aswip_executable_path': Path, 'modeled_start_time': datetime, 'modeled_end_time': datetime, 'modeled_timestep': timedelta, @@ -162,6 +163,7 @@ def __init__( tidal_spinup_duration: timedelta = None, tidal_spinup_timestep: timedelta = None, forcings: [Forcing] = None, + aswip_executable_path: PathLike = None, source_filename: PathLike = None, slurm_configuration: SlurmJSON = None, use_original_mesh: bool = False, @@ -185,6 +187,7 @@ def __init__( :param adcirc_executable_path: file path to `adcirc` or `NEMS.x` :param adcprep_executable_path: file path to `adcprep` + :param aswip_executable_path: file path to `aswip` :param modeled_start_time: start time in model run :param modeled_end_time: edn time in model run :param modeled_timestep: time interval between model steps @@ -226,6 +229,7 @@ def __init__( self['adcirc_executable_path'] = adcirc_executable_path self['adcprep_executable_path'] = adcprep_executable_path + self['aswip_executable_path'] = aswip_executable_path self['modeled_start_time'] = modeled_start_time self['modeled_end_time'] = modeled_end_time self['modeled_timestep'] = modeled_timestep diff --git a/coupledmodeldriver/generate/adcirc/generate.py b/coupledmodeldriver/generate/adcirc/generate.py index 305b339c..ebf75a06 100644 --- a/coupledmodeldriver/generate/adcirc/generate.py +++ b/coupledmodeldriver/generate/adcirc/generate.py @@ -11,9 +11,12 @@ ADCIRCRunConfiguration, NEMSADCIRCRunConfiguration, ) -from coupledmodeldriver.generate.adcirc.script import AdcircMeshPartitionJob, AdcircRunJob -from coupledmodeldriver.script import EnsembleCleanupScript, EnsembleRunScript -from coupledmodeldriver.utilities import LOGGER, create_symlink, get_logger +from coupledmodeldriver.generate.adcirc.script import AdcircRunJob, \ + AdcircSetupJob +from coupledmodeldriver.script import EnsembleCleanupScript, \ + EnsembleRunScript +from coupledmodeldriver.utilities import LOGGER, create_symlink, \ + get_logger class RunPhase(Enum): @@ -105,38 +108,38 @@ def generate_adcirc_configuration( if original_fort14_filename is None or not original_fort14_filename.exists(): raise FileNotFoundError(f'mesh XY not found at "{original_fort14_filename}"') - adcprep_run_name = 'ADCIRC_MESH_PREP' - adcprep_job_script_filename = output_directory / f'job_adcprep_{platform.name.lower()}.job' + setup_job_name = 'ADCIRC_SETUP' + setup_script_filename = output_directory / f'job_setup_{platform.name.lower()}.job' local_fort13_filename = output_directory / 'fort.13' local_fort14_filename = output_directory / 'fort.14' local_fort15_filename = output_directory / 'fort.15' - spinup_tides = tidal_spinup_duration is not None + run_tidal_spinup = tidal_spinup_duration is not None - if spinup_tides: + if run_tidal_spinup: run_phase = RunPhase.HOTSTART coldstart_run_name = 'ADCIRC_SPINUP' hotstart_run_name = 'ADCIRC_HOTSTART' - coldstart_run_script_filename = ( + coldstart_script_filename = ( output_directory / f'job_adcirc_{platform.name.lower()}.job.spinup' ) - hotstart_run_script_filename = ( + hotstart_script_filename = ( output_directory / f'job_adcirc_{platform.name.lower()}.job.hotstart' ) - run_script_filename = hotstart_run_script_filename + run_script_filename = hotstart_script_filename else: run_phase = RunPhase.COLDSTART coldstart_run_name = 'ADCIRC_COLDSTART' hotstart_run_name = None - coldstart_run_script_filename = ( + coldstart_script_filename = ( output_directory / f'job_adcirc_{platform.name.lower()}.job.coldstart' ) - hotstart_run_script_filename = None - run_script_filename = coldstart_run_script_filename + hotstart_script_filename = None + run_script_filename = coldstart_script_filename if use_nems: - if spinup_tides: + if run_tidal_spinup: LOGGER.debug(f'setting spinup to {tidal_spinup_duration}') tidal_spinup_nems_configuration = ModelingSystem( nems_configuration.start_time - tidal_spinup_duration, @@ -174,7 +177,7 @@ def generate_adcirc_configuration( else: filename.rename(coldstart_filename) - if spinup_tides: + if run_tidal_spinup: hotstart_filenames = nems_configuration.write( output_directory, overwrite=overwrite, @@ -203,26 +206,26 @@ def generate_adcirc_configuration( ensemble_cleanup_script_filename = output_directory / f'cleanup.sh' LOGGER.debug(f'setting mesh partitioner "{adcprep_executable_path}"') - adcprep_script = AdcircMeshPartitionJob( + setup_script = AdcircSetupJob( platform=platform, adcirc_mesh_partitions=adcirc_processors, slurm_account=slurm_account, slurm_duration=job_duration, slurm_partition=partition, - slurm_run_name=adcprep_run_name, + slurm_run_name=setup_job_name, adcprep_path=adcprep_executable_path, slurm_email_type=email_type, slurm_email_address=email_address, - slurm_error_filename=f'{adcprep_run_name}.err.log', - slurm_log_filename=f'{adcprep_run_name}.out.log', + slurm_error_filename=f'{setup_job_name}.err.log', + slurm_log_filename=f'{setup_job_name}.out.log', source_filename=source_filename, ) - LOGGER.debug(f'writing mesh partitioning job script "{adcprep_job_script_filename.name}"') - adcprep_script.write(adcprep_job_script_filename, overwrite=overwrite) + LOGGER.debug(f'writing setup job script "{setup_script_filename.name}"') + setup_script.write(setup_script_filename, overwrite=overwrite) LOGGER.debug(f'setting run executable "{run_executable}"') - coldstart_run_script = AdcircRunJob( + coldstart_script = AdcircRunJob( platform=platform, slurm_tasks=run_processors, slurm_account=slurm_account, @@ -237,11 +240,11 @@ def generate_adcirc_configuration( source_filename=source_filename, ) - LOGGER.debug(f'writing coldstart run script "{coldstart_run_script_filename.name}"') - coldstart_run_script.write(coldstart_run_script_filename, overwrite=overwrite) + LOGGER.debug(f'writing coldstart run script "{coldstart_script_filename.name}"') + coldstart_script.write(coldstart_script_filename, overwrite=overwrite) - if spinup_tides: - hotstart_run_script = AdcircRunJob( + if run_tidal_spinup: + hotstart_script = AdcircRunJob( platform=platform, slurm_tasks=run_processors, slurm_account=slurm_account, @@ -256,8 +259,8 @@ def generate_adcirc_configuration( source_filename=source_filename, ) - LOGGER.debug(f'writing hotstart run script "{hotstart_run_script_filename.name}"') - hotstart_run_script.write(hotstart_run_script_filename, overwrite=overwrite) + LOGGER.debug(f'writing hotstart run script "{hotstart_script_filename.name}"') + hotstart_script.write(hotstart_script_filename, overwrite=overwrite) try: # instantiate AdcircRun object. @@ -289,7 +292,7 @@ def generate_adcirc_configuration( if local_fort15_filename.exists(): os.remove(local_fort15_filename) - if spinup_tides: + if run_tidal_spinup: tidal_spinup_directory = output_directory / 'spinup' if not tidal_spinup_directory.exists(): tidal_spinup_directory.mkdir(parents=True, exist_ok=True) @@ -313,12 +316,10 @@ def generate_adcirc_configuration( local_fort14_filename, tidal_spinup_directory / 'fort.14', relative=True ) create_symlink( - adcprep_job_script_filename, tidal_spinup_directory / 'adcprep.job', relative=True, + setup_script_filename, tidal_spinup_directory / 'setup.job', relative=True, ) create_symlink( - coldstart_run_script_filename, - tidal_spinup_directory / 'adcirc.job', - relative=True, + coldstart_script_filename, tidal_spinup_directory / 'adcirc.job', relative=True, ) if use_nems: create_symlink( @@ -366,7 +367,7 @@ def generate_adcirc_configuration( create_symlink(local_fort13_filename, run_directory / 'fort.13', relative=True) create_symlink(local_fort14_filename, run_directory / 'fort.14', relative=True) create_symlink( - adcprep_job_script_filename, run_directory / 'adcprep.job', relative=True, + setup_script_filename, run_directory / 'setup.job', relative=True, ) create_symlink( run_script_filename, run_directory / 'adcirc.job', relative=True, @@ -387,7 +388,7 @@ def generate_adcirc_configuration( run_directory / 'config.rc', relative=True, ) - if spinup_tides: + if run_tidal_spinup: for hotstart_filename in ['fort.67.nc', 'fort.68.nc']: try: create_symlink( @@ -412,7 +413,7 @@ def generate_adcirc_configuration( 'echo deleting previous ADCIRC output', f'sh {ensemble_cleanup_script_filename.name}', ], - spinup=spinup_tides, + run_spinup=run_tidal_spinup, ) run_script.write(ensemble_run_script_filename, overwrite=overwrite) diff --git a/coupledmodeldriver/generate/adcirc/script.py b/coupledmodeldriver/generate/adcirc/script.py index 0d515317..8ec49962 100644 --- a/coupledmodeldriver/generate/adcirc/script.py +++ b/coupledmodeldriver/generate/adcirc/script.py @@ -73,7 +73,7 @@ def __init__( ) -class AdcircMeshPartitionJob(AdcircJob): +class AdcircSetupJob(AdcircJob): """ script for performing domain decomposition with `adcprep` """ def __init__( @@ -84,6 +84,8 @@ def __init__( slurm_duration: timedelta, slurm_run_name: str, adcprep_path: PathLike = None, + aswip_path: PathLike = None, + use_aswip: bool = False, slurm_tasks: int = 1, commands: [str] = None, **kwargs, @@ -106,22 +108,35 @@ def __init__( if isinstance(adcprep_path, Path): adcprep_path = adcprep_path.as_posix() - self.adcprep_path = adcprep_path - if self.launcher is not None: - self.commands.extend( - [ - f'{self.launcher} {self.adcprep_path} --np {self.adcirc_partitions} --partmesh', - f'{self.launcher} {self.adcprep_path} --np {self.adcirc_partitions} --prepall', - ] - ) + if aswip_path is None: + aswip_path = 'aswip' else: - self.commands.extend( + if isinstance(aswip_path, Path): + aswip_path = aswip_path.as_posix() + + self.adcprep_path = adcprep_path + self.aswip_path = aswip_path + self.use_aswip = use_aswip + + setup_commands = [ + f'{self.adcprep_path} --np {self.adcirc_partitions} --partmesh', + f'{self.adcprep_path} --np {self.adcirc_partitions} --prepall', + ] + + if self.use_aswip: + setup_commands.extend( [ - f'{self.adcprep_path} --np {self.adcirc_partitions} --partmesh', - f'{self.adcprep_path} --np {self.adcirc_partitions} --prepall', + f'{self.aswip_path}', + 'mv fort.22 fort.22.original', + 'mv NWS_20_fort.22 fort.22', ] ) + if self.launcher is not None: + setup_commands = [f'{self.launcher} {line}' for line in setup_commands] + + self.commands.extend(setup_commands) + class ADCIRCGenerationScript(Script): """ Bash script for generating an ADCIRC run configuration from JSON files """ diff --git a/coupledmodeldriver/script.py b/coupledmodeldriver/script.py index 3a2f5b5f..762a092b 100644 --- a/coupledmodeldriver/script.py +++ b/coupledmodeldriver/script.py @@ -240,9 +240,9 @@ def write(self, filename: PathLike, overwrite: bool = False): class EnsembleRunScript(Script): - def __init__(self, platform: Platform, spinup: bool = True, commands: [str] = None): + def __init__(self, platform: Platform, run_spinup: bool = True, commands: [str] = None): self.platform = platform - self.spinup = spinup + self.run_spinup = run_spinup super().__init__(commands) def __str__(self) -> str: @@ -251,42 +251,46 @@ def __str__(self) -> str: 'DIRECTORY="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd -P)"', '', ] - if self.spinup: - lines.extend(['# run spinup', 'pushd ${DIRECTORY}/spinup >/dev/null 2>&1']) + + spinup_lines = [] + if self.run_spinup: + spinup_lines.extend(['# run spinup', 'pushd ${DIRECTORY}/spinup >/dev/null 2>&1']) if self.platform.value['uses_slurm']: - lines.extend( + dependencies = ['afterok:$setup_jobid'] + if len(dependencies) > 0: + dependencies = f'--dependency={",".join(dependencies)}' + spinup_lines.extend( [ - "spinup_adcprep_jobid=$(sbatch adcprep.job | awk '{print $NF}')", - "spinup_jobid=$(sbatch --dependency=afterany:$spinup_adcprep_jobid adcirc.job | awk '{print $NF}')", + "setup_jobid=$(sbatch setup.job | awk '{print $NF}')", + f"spinup_jobid=$(sbatch adcirc.job {dependencies} | awk '{{print $NF}}')", ] ) else: - lines.extend(['sh adcprep.job', 'sh adcirc.job']) - lines.extend(['popd >/dev/null 2>&1', '']) + spinup_lines.extend(['sh setup.job', 'sh adcirc.job']) + spinup_lines.extend(['popd >/dev/null 2>&1', '']) + lines.extend(spinup_lines) hotstart_lines = ['pushd ${hotstart} >/dev/null 2>&1'] if self.platform.value['uses_slurm']: - if self.spinup: - run_command = 'sbatch --dependency=afterany:$spinup_jobid' - else: - run_command = 'sbatch' - + dependencies = ['afterok:$setup_jobid'] + if self.run_spinup: + dependencies.append('afterok:$spinup_jobid') + if len(dependencies) > 0: + dependencies = f'--dependency={",".join(dependencies)}' hotstart_lines.extend( [ - f"hotstart_adcprep_jobid=$({run_command} adcprep.job | awk '{{print $NF}}')", - 'sbatch --dependency=afterany:$hotstart_adcprep_jobid adcirc.job', + f"setup_jobid=$(sbatch setup.job | awk '{{print $NF}}')", + f'sbatch adcirc.job {dependencies}', ] ) else: - hotstart_lines.extend(['sh adcprep.job', 'sh adcirc.job']) + hotstart_lines.extend(['sh setup.job', 'sh adcirc.job']) hotstart_lines.append('popd >/dev/null 2>&1') - - lines.extend( - [ - '# run configurations', - bash_for_loop('for hotstart in ${DIRECTORY}/runs/*/', hotstart_lines), - ] - ) + hotstart_lines = [ + '# run configurations', + bash_for_loop('for hotstart in ${DIRECTORY}/runs/*/', hotstart_lines), + ] + lines.extend(hotstart_lines) if self.platform.value['uses_slurm']: # slurm queue output https://slurm.schedmd.com/squeue.html diff --git a/tests/data/reference/adcirc/hera_shinnecock_ike/configure_adcirc.json b/tests/data/reference/adcirc/hera_shinnecock_ike/configure_adcirc.json index 2a0987f0..74050b36 100644 --- a/tests/data/reference/adcirc/hera_shinnecock_ike/configure_adcirc.json +++ b/tests/data/reference/adcirc/hera_shinnecock_ike/configure_adcirc.json @@ -1,6 +1,7 @@ { "adcirc_executable_path": "../../../adcirc", "adcprep_executable_path": "../../../adcprep", + "aswip_executable_path": null, "modeled_start_time": "2008-08-23 00:00:00", "modeled_end_time": "2008-09-06 12:00:00", "modeled_timestep": 2.0, diff --git a/tests/data/reference/adcirc/hera_shinnecock_ike/job_adcprep_hera.job b/tests/data/reference/adcirc/hera_shinnecock_ike/job_setup_hera.job similarity index 68% rename from tests/data/reference/adcirc/hera_shinnecock_ike/job_adcprep_hera.job rename to tests/data/reference/adcirc/hera_shinnecock_ike/job_setup_hera.job index b789e746..86552773 100644 --- a/tests/data/reference/adcirc/hera_shinnecock_ike/job_adcprep_hera.job +++ b/tests/data/reference/adcirc/hera_shinnecock_ike/job_setup_hera.job @@ -1,10 +1,10 @@ #!/bin/bash --login -#SBATCH -J ADCIRC_MESH_PREP +#SBATCH -J ADCIRC_SETUP #SBATCH -A coastal #SBATCH --mail-type=ALL #SBATCH --mail-user=example@email.gov -#SBATCH --error=ADCIRC_MESH_PREP.err.log -#SBATCH --output=ADCIRC_MESH_PREP.out.log +#SBATCH --error=ADCIRC_SETUP.err.log +#SBATCH --output=ADCIRC_SETUP.out.log #SBATCH -n 1 #SBATCH -N 1 #SBATCH --time=06:00:00 diff --git a/tests/data/reference/adcirc/hera_shinnecock_ike/run_hera.sh b/tests/data/reference/adcirc/hera_shinnecock_ike/run_hera.sh index f1e712a0..e48535b2 100644 --- a/tests/data/reference/adcirc/hera_shinnecock_ike/run_hera.sh +++ b/tests/data/reference/adcirc/hera_shinnecock_ike/run_hera.sh @@ -4,15 +4,15 @@ DIRECTORY="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd -P)" # run spinup pushd ${DIRECTORY}/spinup >/dev/null 2>&1 -spinup_adcprep_jobid=$(sbatch adcprep.job | awk '{print $NF}') -spinup_jobid=$(sbatch --dependency=afterany:$spinup_adcprep_jobid adcirc.job | awk '{print $NF}') +setup_jobid=$(sbatch setup.job | awk '{print $NF}') +spinup_jobid=$(sbatch adcirc.job --dependency=afterok:$setup_jobid | awk '{print $NF}') popd >/dev/null 2>&1 # run configurations for hotstart in ${DIRECTORY}/runs/*/; do pushd ${hotstart} >/dev/null 2>&1 - hotstart_adcprep_jobid=$(sbatch --dependency=afterany:$spinup_jobid adcprep.job | awk '{print $NF}') - sbatch --dependency=afterany:$hotstart_adcprep_jobid adcirc.job + setup_jobid=$(sbatch setup.job | awk '{print $NF}') + sbatch adcirc.job --dependency=afterok:$setup_jobid,afterok:$spinup_jobid popd >/dev/null 2>&1 done diff --git a/tests/data/reference/adcirc/hera_shinnecock_ike/runs/unperturbed/fort.15 b/tests/data/reference/adcirc/hera_shinnecock_ike/runs/unperturbed/fort.15 index 7a40d8e6..09f3fc88 100644 --- a/tests/data/reference/adcirc/hera_shinnecock_ike/runs/unperturbed/fort.15 +++ b/tests/data/reference/adcirc/hera_shinnecock_ike/runs/unperturbed/fort.15 @@ -1,4 +1,4 @@ -created on 2021-05-06 12:42 ! RUNDES - 32 CHARACTER ALPHANUMERIC RUN DESCRIPTION +created on 2021-05-07 11:22 ! RUNDES - 32 CHARACTER ALPHANUMERIC RUN DESCRIPTION Shinacock Inlet Coarse Grid ! RUNID - 24 CHARACTER ALPANUMERIC RUN IDENTIFICATION 1 ! NFOVER - NONFATAL ERROR OVERRIDE OPTION 1 ! NABOUT - ABREVIATED OUTPUT OPTION PARAMETER diff --git a/tests/data/reference/adcirc/hera_shinnecock_ike/runs/unperturbed/adcprep.job b/tests/data/reference/adcirc/hera_shinnecock_ike/runs/unperturbed/setup.job similarity index 68% rename from tests/data/reference/adcirc/hera_shinnecock_ike/runs/unperturbed/adcprep.job rename to tests/data/reference/adcirc/hera_shinnecock_ike/runs/unperturbed/setup.job index b789e746..86552773 100644 --- a/tests/data/reference/adcirc/hera_shinnecock_ike/runs/unperturbed/adcprep.job +++ b/tests/data/reference/adcirc/hera_shinnecock_ike/runs/unperturbed/setup.job @@ -1,10 +1,10 @@ #!/bin/bash --login -#SBATCH -J ADCIRC_MESH_PREP +#SBATCH -J ADCIRC_SETUP #SBATCH -A coastal #SBATCH --mail-type=ALL #SBATCH --mail-user=example@email.gov -#SBATCH --error=ADCIRC_MESH_PREP.err.log -#SBATCH --output=ADCIRC_MESH_PREP.out.log +#SBATCH --error=ADCIRC_SETUP.err.log +#SBATCH --output=ADCIRC_SETUP.out.log #SBATCH -n 1 #SBATCH -N 1 #SBATCH --time=06:00:00 diff --git a/tests/data/reference/adcirc/hera_shinnecock_ike/spinup/fort.15 b/tests/data/reference/adcirc/hera_shinnecock_ike/spinup/fort.15 index 3a353182..aa800b5e 100644 --- a/tests/data/reference/adcirc/hera_shinnecock_ike/spinup/fort.15 +++ b/tests/data/reference/adcirc/hera_shinnecock_ike/spinup/fort.15 @@ -1,4 +1,4 @@ -created on 2021-05-06 12:42 ! RUNDES - 32 CHARACTER ALPHANUMERIC RUN DESCRIPTION +created on 2021-05-07 11:21 ! RUNDES - 32 CHARACTER ALPHANUMERIC RUN DESCRIPTION Shinacock Inlet Coarse Grid ! RUNID - 24 CHARACTER ALPANUMERIC RUN IDENTIFICATION 1 ! NFOVER - NONFATAL ERROR OVERRIDE OPTION 1 ! NABOUT - ABREVIATED OUTPUT OPTION PARAMETER diff --git a/tests/data/reference/adcirc/hera_shinnecock_ike/spinup/adcprep.job b/tests/data/reference/adcirc/hera_shinnecock_ike/spinup/setup.job similarity index 68% rename from tests/data/reference/adcirc/hera_shinnecock_ike/spinup/adcprep.job rename to tests/data/reference/adcirc/hera_shinnecock_ike/spinup/setup.job index b789e746..86552773 100644 --- a/tests/data/reference/adcirc/hera_shinnecock_ike/spinup/adcprep.job +++ b/tests/data/reference/adcirc/hera_shinnecock_ike/spinup/setup.job @@ -1,10 +1,10 @@ #!/bin/bash --login -#SBATCH -J ADCIRC_MESH_PREP +#SBATCH -J ADCIRC_SETUP #SBATCH -A coastal #SBATCH --mail-type=ALL #SBATCH --mail-user=example@email.gov -#SBATCH --error=ADCIRC_MESH_PREP.err.log -#SBATCH --output=ADCIRC_MESH_PREP.out.log +#SBATCH --error=ADCIRC_SETUP.err.log +#SBATCH --output=ADCIRC_SETUP.out.log #SBATCH -n 1 #SBATCH -N 1 #SBATCH --time=06:00:00 diff --git a/tests/data/reference/adcirc/hera_shinnecock_ike_nospinup/configure_adcirc.json b/tests/data/reference/adcirc/hera_shinnecock_ike_nospinup/configure_adcirc.json index ffdd050f..f4beecd3 100644 --- a/tests/data/reference/adcirc/hera_shinnecock_ike_nospinup/configure_adcirc.json +++ b/tests/data/reference/adcirc/hera_shinnecock_ike_nospinup/configure_adcirc.json @@ -1,6 +1,7 @@ { "adcirc_executable_path": "../../../adcirc", "adcprep_executable_path": "../../../adcprep", + "aswip_executable_path": null, "modeled_start_time": "2008-08-23 00:00:00", "modeled_end_time": "2008-09-06 12:00:00", "modeled_timestep": 2.0, diff --git a/tests/data/reference/adcirc/hera_shinnecock_ike_nospinup/job_adcprep_hera.job b/tests/data/reference/adcirc/hera_shinnecock_ike_nospinup/job_setup_hera.job similarity index 68% rename from tests/data/reference/adcirc/hera_shinnecock_ike_nospinup/job_adcprep_hera.job rename to tests/data/reference/adcirc/hera_shinnecock_ike_nospinup/job_setup_hera.job index b789e746..86552773 100644 --- a/tests/data/reference/adcirc/hera_shinnecock_ike_nospinup/job_adcprep_hera.job +++ b/tests/data/reference/adcirc/hera_shinnecock_ike_nospinup/job_setup_hera.job @@ -1,10 +1,10 @@ #!/bin/bash --login -#SBATCH -J ADCIRC_MESH_PREP +#SBATCH -J ADCIRC_SETUP #SBATCH -A coastal #SBATCH --mail-type=ALL #SBATCH --mail-user=example@email.gov -#SBATCH --error=ADCIRC_MESH_PREP.err.log -#SBATCH --output=ADCIRC_MESH_PREP.out.log +#SBATCH --error=ADCIRC_SETUP.err.log +#SBATCH --output=ADCIRC_SETUP.out.log #SBATCH -n 1 #SBATCH -N 1 #SBATCH --time=06:00:00 diff --git a/tests/data/reference/adcirc/hera_shinnecock_ike_nospinup/run_hera.sh b/tests/data/reference/adcirc/hera_shinnecock_ike_nospinup/run_hera.sh index 6e4ccdff..cc4162ea 100644 --- a/tests/data/reference/adcirc/hera_shinnecock_ike_nospinup/run_hera.sh +++ b/tests/data/reference/adcirc/hera_shinnecock_ike_nospinup/run_hera.sh @@ -5,8 +5,8 @@ DIRECTORY="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd -P)" # run configurations for hotstart in ${DIRECTORY}/runs/*/; do pushd ${hotstart} >/dev/null 2>&1 - hotstart_adcprep_jobid=$(sbatch adcprep.job | awk '{print $NF}') - sbatch --dependency=afterany:$hotstart_adcprep_jobid adcirc.job + setup_jobid=$(sbatch setup.job | awk '{print $NF}') + sbatch adcirc.job --dependency=afterok:$setup_jobid popd >/dev/null 2>&1 done diff --git a/tests/data/reference/adcirc/hera_shinnecock_ike_nospinup/runs/unperturbed/adcprep.job b/tests/data/reference/adcirc/hera_shinnecock_ike_nospinup/runs/unperturbed/adcprep.job deleted file mode 100644 index b789e746..00000000 --- a/tests/data/reference/adcirc/hera_shinnecock_ike_nospinup/runs/unperturbed/adcprep.job +++ /dev/null @@ -1,15 +0,0 @@ -#!/bin/bash --login -#SBATCH -J ADCIRC_MESH_PREP -#SBATCH -A coastal -#SBATCH --mail-type=ALL -#SBATCH --mail-user=example@email.gov -#SBATCH --error=ADCIRC_MESH_PREP.err.log -#SBATCH --output=ADCIRC_MESH_PREP.out.log -#SBATCH -n 1 -#SBATCH -N 1 -#SBATCH --time=06:00:00 - -set -e - -srun ../../../adcprep --np 600 --partmesh -srun ../../../adcprep --np 600 --prepall diff --git a/tests/data/reference/adcirc/hera_shinnecock_ike_nospinup/runs/unperturbed/fort.15 b/tests/data/reference/adcirc/hera_shinnecock_ike_nospinup/runs/unperturbed/fort.15 index 1a0830f4..7d3dea5b 100644 --- a/tests/data/reference/adcirc/hera_shinnecock_ike_nospinup/runs/unperturbed/fort.15 +++ b/tests/data/reference/adcirc/hera_shinnecock_ike_nospinup/runs/unperturbed/fort.15 @@ -1,4 +1,4 @@ -created on 2021-05-06 12:42 ! RUNDES - 32 CHARACTER ALPHANUMERIC RUN DESCRIPTION +created on 2021-05-07 11:21 ! RUNDES - 32 CHARACTER ALPHANUMERIC RUN DESCRIPTION Shinacock Inlet Coarse Grid ! RUNID - 24 CHARACTER ALPANUMERIC RUN IDENTIFICATION 1 ! NFOVER - NONFATAL ERROR OVERRIDE OPTION 1 ! NABOUT - ABREVIATED OUTPUT OPTION PARAMETER diff --git a/tests/data/reference/adcirc/hera_shinnecock_ike_nospinup/runs/unperturbed/setup.job b/tests/data/reference/adcirc/hera_shinnecock_ike_nospinup/runs/unperturbed/setup.job new file mode 100644 index 00000000..86552773 --- /dev/null +++ b/tests/data/reference/adcirc/hera_shinnecock_ike_nospinup/runs/unperturbed/setup.job @@ -0,0 +1,15 @@ +#!/bin/bash --login +#SBATCH -J ADCIRC_SETUP +#SBATCH -A coastal +#SBATCH --mail-type=ALL +#SBATCH --mail-user=example@email.gov +#SBATCH --error=ADCIRC_SETUP.err.log +#SBATCH --output=ADCIRC_SETUP.out.log +#SBATCH -n 1 +#SBATCH -N 1 +#SBATCH --time=06:00:00 + +set -e + +srun ../../../adcprep --np 600 --partmesh +srun ../../../adcprep --np 600 --prepall diff --git a/tests/data/reference/adcirc/local_shinnecock_ike/configure_adcirc.json b/tests/data/reference/adcirc/local_shinnecock_ike/configure_adcirc.json index ab865d4e..9e20bf1d 100644 --- a/tests/data/reference/adcirc/local_shinnecock_ike/configure_adcirc.json +++ b/tests/data/reference/adcirc/local_shinnecock_ike/configure_adcirc.json @@ -1,6 +1,7 @@ { "adcirc_executable_path": "../../../adcirc", "adcprep_executable_path": "../../../adcprep", + "aswip_executable_path": null, "modeled_start_time": "2008-08-23 00:00:00", "modeled_end_time": "2008-09-06 12:00:00", "modeled_timestep": 2.0, diff --git a/tests/data/reference/adcirc/local_shinnecock_ike/job_adcprep_local.job b/tests/data/reference/adcirc/local_shinnecock_ike/job_setup_local.job similarity index 100% rename from tests/data/reference/adcirc/local_shinnecock_ike/job_adcprep_local.job rename to tests/data/reference/adcirc/local_shinnecock_ike/job_setup_local.job diff --git a/tests/data/reference/adcirc/local_shinnecock_ike/run_local.sh b/tests/data/reference/adcirc/local_shinnecock_ike/run_local.sh index 8c0f9d1a..b1826ed1 100644 --- a/tests/data/reference/adcirc/local_shinnecock_ike/run_local.sh +++ b/tests/data/reference/adcirc/local_shinnecock_ike/run_local.sh @@ -4,14 +4,14 @@ DIRECTORY="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd -P)" # run spinup pushd ${DIRECTORY}/spinup >/dev/null 2>&1 -sh adcprep.job +sh setup.job sh adcirc.job popd >/dev/null 2>&1 # run configurations for hotstart in ${DIRECTORY}/runs/*/; do pushd ${hotstart} >/dev/null 2>&1 - sh adcprep.job + sh setup.job sh adcirc.job popd >/dev/null 2>&1 done diff --git a/tests/data/reference/adcirc/local_shinnecock_ike/runs/unperturbed/fort.15 b/tests/data/reference/adcirc/local_shinnecock_ike/runs/unperturbed/fort.15 index 7a40d8e6..09f3fc88 100644 --- a/tests/data/reference/adcirc/local_shinnecock_ike/runs/unperturbed/fort.15 +++ b/tests/data/reference/adcirc/local_shinnecock_ike/runs/unperturbed/fort.15 @@ -1,4 +1,4 @@ -created on 2021-05-06 12:42 ! RUNDES - 32 CHARACTER ALPHANUMERIC RUN DESCRIPTION +created on 2021-05-07 11:22 ! RUNDES - 32 CHARACTER ALPHANUMERIC RUN DESCRIPTION Shinacock Inlet Coarse Grid ! RUNID - 24 CHARACTER ALPANUMERIC RUN IDENTIFICATION 1 ! NFOVER - NONFATAL ERROR OVERRIDE OPTION 1 ! NABOUT - ABREVIATED OUTPUT OPTION PARAMETER diff --git a/tests/data/reference/adcirc/local_shinnecock_ike/runs/unperturbed/adcprep.job b/tests/data/reference/adcirc/local_shinnecock_ike/runs/unperturbed/setup.job similarity index 100% rename from tests/data/reference/adcirc/local_shinnecock_ike/runs/unperturbed/adcprep.job rename to tests/data/reference/adcirc/local_shinnecock_ike/runs/unperturbed/setup.job diff --git a/tests/data/reference/adcirc/local_shinnecock_ike/spinup/fort.15 b/tests/data/reference/adcirc/local_shinnecock_ike/spinup/fort.15 index 3a353182..aa800b5e 100644 --- a/tests/data/reference/adcirc/local_shinnecock_ike/spinup/fort.15 +++ b/tests/data/reference/adcirc/local_shinnecock_ike/spinup/fort.15 @@ -1,4 +1,4 @@ -created on 2021-05-06 12:42 ! RUNDES - 32 CHARACTER ALPHANUMERIC RUN DESCRIPTION +created on 2021-05-07 11:21 ! RUNDES - 32 CHARACTER ALPHANUMERIC RUN DESCRIPTION Shinacock Inlet Coarse Grid ! RUNID - 24 CHARACTER ALPANUMERIC RUN IDENTIFICATION 1 ! NFOVER - NONFATAL ERROR OVERRIDE OPTION 1 ! NABOUT - ABREVIATED OUTPUT OPTION PARAMETER diff --git a/tests/data/reference/adcirc/local_shinnecock_ike/spinup/adcprep.job b/tests/data/reference/adcirc/local_shinnecock_ike/spinup/setup.job similarity index 100% rename from tests/data/reference/adcirc/local_shinnecock_ike/spinup/adcprep.job rename to tests/data/reference/adcirc/local_shinnecock_ike/spinup/setup.job diff --git a/tests/data/reference/adcirc/stampede2_shinnecock_ike/configure_adcirc.json b/tests/data/reference/adcirc/stampede2_shinnecock_ike/configure_adcirc.json index ee3fe4da..81f16be2 100644 --- a/tests/data/reference/adcirc/stampede2_shinnecock_ike/configure_adcirc.json +++ b/tests/data/reference/adcirc/stampede2_shinnecock_ike/configure_adcirc.json @@ -1,6 +1,7 @@ { "adcirc_executable_path": "../../../adcirc", "adcprep_executable_path": "../../../adcprep", + "aswip_executable_path": null, "modeled_start_time": "2008-08-23 00:00:00", "modeled_end_time": "2008-09-06 12:00:00", "modeled_timestep": 2.0, diff --git a/tests/data/reference/adcirc/stampede2_shinnecock_ike/job_adcprep_stampede2.job b/tests/data/reference/adcirc/stampede2_shinnecock_ike/job_setup_stampede2.job similarity index 71% rename from tests/data/reference/adcirc/stampede2_shinnecock_ike/job_adcprep_stampede2.job rename to tests/data/reference/adcirc/stampede2_shinnecock_ike/job_setup_stampede2.job index 92117a59..664057a6 100644 --- a/tests/data/reference/adcirc/stampede2_shinnecock_ike/job_adcprep_stampede2.job +++ b/tests/data/reference/adcirc/stampede2_shinnecock_ike/job_setup_stampede2.job @@ -1,10 +1,10 @@ #!/bin/bash --login -#SBATCH -J ADCIRC_MESH_PREP +#SBATCH -J ADCIRC_SETUP #SBATCH -A coastal #SBATCH --mail-type=ALL #SBATCH --mail-user=example@email.gov -#SBATCH --error=ADCIRC_MESH_PREP.err.log -#SBATCH --output=ADCIRC_MESH_PREP.out.log +#SBATCH --error=ADCIRC_SETUP.err.log +#SBATCH --output=ADCIRC_SETUP.out.log #SBATCH -n 1 #SBATCH -N 1 #SBATCH --time=06:00:00 diff --git a/tests/data/reference/adcirc/stampede2_shinnecock_ike/run_stampede2.sh b/tests/data/reference/adcirc/stampede2_shinnecock_ike/run_stampede2.sh index f1e712a0..e48535b2 100644 --- a/tests/data/reference/adcirc/stampede2_shinnecock_ike/run_stampede2.sh +++ b/tests/data/reference/adcirc/stampede2_shinnecock_ike/run_stampede2.sh @@ -4,15 +4,15 @@ DIRECTORY="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd -P)" # run spinup pushd ${DIRECTORY}/spinup >/dev/null 2>&1 -spinup_adcprep_jobid=$(sbatch adcprep.job | awk '{print $NF}') -spinup_jobid=$(sbatch --dependency=afterany:$spinup_adcprep_jobid adcirc.job | awk '{print $NF}') +setup_jobid=$(sbatch setup.job | awk '{print $NF}') +spinup_jobid=$(sbatch adcirc.job --dependency=afterok:$setup_jobid | awk '{print $NF}') popd >/dev/null 2>&1 # run configurations for hotstart in ${DIRECTORY}/runs/*/; do pushd ${hotstart} >/dev/null 2>&1 - hotstart_adcprep_jobid=$(sbatch --dependency=afterany:$spinup_jobid adcprep.job | awk '{print $NF}') - sbatch --dependency=afterany:$hotstart_adcprep_jobid adcirc.job + setup_jobid=$(sbatch setup.job | awk '{print $NF}') + sbatch adcirc.job --dependency=afterok:$setup_jobid,afterok:$spinup_jobid popd >/dev/null 2>&1 done diff --git a/tests/data/reference/adcirc/stampede2_shinnecock_ike/runs/unperturbed/fort.15 b/tests/data/reference/adcirc/stampede2_shinnecock_ike/runs/unperturbed/fort.15 index 7a40d8e6..09f3fc88 100644 --- a/tests/data/reference/adcirc/stampede2_shinnecock_ike/runs/unperturbed/fort.15 +++ b/tests/data/reference/adcirc/stampede2_shinnecock_ike/runs/unperturbed/fort.15 @@ -1,4 +1,4 @@ -created on 2021-05-06 12:42 ! RUNDES - 32 CHARACTER ALPHANUMERIC RUN DESCRIPTION +created on 2021-05-07 11:22 ! RUNDES - 32 CHARACTER ALPHANUMERIC RUN DESCRIPTION Shinacock Inlet Coarse Grid ! RUNID - 24 CHARACTER ALPANUMERIC RUN IDENTIFICATION 1 ! NFOVER - NONFATAL ERROR OVERRIDE OPTION 1 ! NABOUT - ABREVIATED OUTPUT OPTION PARAMETER diff --git a/tests/data/reference/adcirc/stampede2_shinnecock_ike/runs/unperturbed/adcprep.job b/tests/data/reference/adcirc/stampede2_shinnecock_ike/runs/unperturbed/setup.job similarity index 71% rename from tests/data/reference/adcirc/stampede2_shinnecock_ike/runs/unperturbed/adcprep.job rename to tests/data/reference/adcirc/stampede2_shinnecock_ike/runs/unperturbed/setup.job index 92117a59..664057a6 100644 --- a/tests/data/reference/adcirc/stampede2_shinnecock_ike/runs/unperturbed/adcprep.job +++ b/tests/data/reference/adcirc/stampede2_shinnecock_ike/runs/unperturbed/setup.job @@ -1,10 +1,10 @@ #!/bin/bash --login -#SBATCH -J ADCIRC_MESH_PREP +#SBATCH -J ADCIRC_SETUP #SBATCH -A coastal #SBATCH --mail-type=ALL #SBATCH --mail-user=example@email.gov -#SBATCH --error=ADCIRC_MESH_PREP.err.log -#SBATCH --output=ADCIRC_MESH_PREP.out.log +#SBATCH --error=ADCIRC_SETUP.err.log +#SBATCH --output=ADCIRC_SETUP.out.log #SBATCH -n 1 #SBATCH -N 1 #SBATCH --time=06:00:00 diff --git a/tests/data/reference/adcirc/stampede2_shinnecock_ike/spinup/fort.15 b/tests/data/reference/adcirc/stampede2_shinnecock_ike/spinup/fort.15 index 3a353182..aa800b5e 100644 --- a/tests/data/reference/adcirc/stampede2_shinnecock_ike/spinup/fort.15 +++ b/tests/data/reference/adcirc/stampede2_shinnecock_ike/spinup/fort.15 @@ -1,4 +1,4 @@ -created on 2021-05-06 12:42 ! RUNDES - 32 CHARACTER ALPHANUMERIC RUN DESCRIPTION +created on 2021-05-07 11:21 ! RUNDES - 32 CHARACTER ALPHANUMERIC RUN DESCRIPTION Shinacock Inlet Coarse Grid ! RUNID - 24 CHARACTER ALPANUMERIC RUN IDENTIFICATION 1 ! NFOVER - NONFATAL ERROR OVERRIDE OPTION 1 ! NABOUT - ABREVIATED OUTPUT OPTION PARAMETER diff --git a/tests/data/reference/adcirc/stampede2_shinnecock_ike/spinup/adcprep.job b/tests/data/reference/adcirc/stampede2_shinnecock_ike/spinup/setup.job similarity index 71% rename from tests/data/reference/adcirc/stampede2_shinnecock_ike/spinup/adcprep.job rename to tests/data/reference/adcirc/stampede2_shinnecock_ike/spinup/setup.job index 92117a59..664057a6 100644 --- a/tests/data/reference/adcirc/stampede2_shinnecock_ike/spinup/adcprep.job +++ b/tests/data/reference/adcirc/stampede2_shinnecock_ike/spinup/setup.job @@ -1,10 +1,10 @@ #!/bin/bash --login -#SBATCH -J ADCIRC_MESH_PREP +#SBATCH -J ADCIRC_SETUP #SBATCH -A coastal #SBATCH --mail-type=ALL #SBATCH --mail-user=example@email.gov -#SBATCH --error=ADCIRC_MESH_PREP.err.log -#SBATCH --output=ADCIRC_MESH_PREP.out.log +#SBATCH --error=ADCIRC_SETUP.err.log +#SBATCH --output=ADCIRC_SETUP.out.log #SBATCH -n 1 #SBATCH -N 1 #SBATCH --time=06:00:00 diff --git a/tests/data/reference/nems_adcirc/hera_shinnecock_ike/config.rc.coldstart b/tests/data/reference/nems_adcirc/hera_shinnecock_ike/config.rc.coldstart index 068bebb6..bfa6b19a 100644 --- a/tests/data/reference/nems_adcirc/hera_shinnecock_ike/config.rc.coldstart +++ b/tests/data/reference/nems_adcirc/hera_shinnecock_ike/config.rc.coldstart @@ -1,2 +1,2 @@ -# `config.rc` generated with NEMSpy 1.2.21.post17.dev0+3f84e56 +# `config.rc` generated with NEMSpy 1.2.21.post19.dev0+60a2648 diff --git a/tests/data/reference/nems_adcirc/hera_shinnecock_ike/config.rc.hotstart b/tests/data/reference/nems_adcirc/hera_shinnecock_ike/config.rc.hotstart index 2bbf41b6..d7e9c3d8 100644 --- a/tests/data/reference/nems_adcirc/hera_shinnecock_ike/config.rc.hotstart +++ b/tests/data/reference/nems_adcirc/hera_shinnecock_ike/config.rc.hotstart @@ -1,4 +1,4 @@ -# `config.rc` generated with NEMSpy 1.2.21.post17.dev0+3f84e56 +# `config.rc` generated with NEMSpy 1.2.21.post19.dev0+60a2648 atm_dir: ../../../input/shinnecock_ike/forcings atm_nam: wind_atm_fin_ch_time_vec.nc wav_dir: ../../../input/shinnecock_ike/forcings diff --git a/tests/data/reference/nems_adcirc/hera_shinnecock_ike/configure_adcirc.json b/tests/data/reference/nems_adcirc/hera_shinnecock_ike/configure_adcirc.json index 2a0987f0..74050b36 100644 --- a/tests/data/reference/nems_adcirc/hera_shinnecock_ike/configure_adcirc.json +++ b/tests/data/reference/nems_adcirc/hera_shinnecock_ike/configure_adcirc.json @@ -1,6 +1,7 @@ { "adcirc_executable_path": "../../../adcirc", "adcprep_executable_path": "../../../adcprep", + "aswip_executable_path": null, "modeled_start_time": "2008-08-23 00:00:00", "modeled_end_time": "2008-09-06 12:00:00", "modeled_timestep": 2.0, diff --git a/tests/data/reference/nems_adcirc/hera_shinnecock_ike/job_adcprep_hera.job b/tests/data/reference/nems_adcirc/hera_shinnecock_ike/job_adcprep_hera.job deleted file mode 100644 index b789e746..00000000 --- a/tests/data/reference/nems_adcirc/hera_shinnecock_ike/job_adcprep_hera.job +++ /dev/null @@ -1,15 +0,0 @@ -#!/bin/bash --login -#SBATCH -J ADCIRC_MESH_PREP -#SBATCH -A coastal -#SBATCH --mail-type=ALL -#SBATCH --mail-user=example@email.gov -#SBATCH --error=ADCIRC_MESH_PREP.err.log -#SBATCH --output=ADCIRC_MESH_PREP.out.log -#SBATCH -n 1 -#SBATCH -N 1 -#SBATCH --time=06:00:00 - -set -e - -srun ../../../adcprep --np 600 --partmesh -srun ../../../adcprep --np 600 --prepall diff --git a/tests/data/reference/nems_adcirc/hera_shinnecock_ike/job_setup_hera.job b/tests/data/reference/nems_adcirc/hera_shinnecock_ike/job_setup_hera.job new file mode 100644 index 00000000..86552773 --- /dev/null +++ b/tests/data/reference/nems_adcirc/hera_shinnecock_ike/job_setup_hera.job @@ -0,0 +1,15 @@ +#!/bin/bash --login +#SBATCH -J ADCIRC_SETUP +#SBATCH -A coastal +#SBATCH --mail-type=ALL +#SBATCH --mail-user=example@email.gov +#SBATCH --error=ADCIRC_SETUP.err.log +#SBATCH --output=ADCIRC_SETUP.out.log +#SBATCH -n 1 +#SBATCH -N 1 +#SBATCH --time=06:00:00 + +set -e + +srun ../../../adcprep --np 600 --partmesh +srun ../../../adcprep --np 600 --prepall diff --git a/tests/data/reference/nems_adcirc/hera_shinnecock_ike/model_configure.coldstart b/tests/data/reference/nems_adcirc/hera_shinnecock_ike/model_configure.coldstart index d80d7c35..8426ca1a 100644 --- a/tests/data/reference/nems_adcirc/hera_shinnecock_ike/model_configure.coldstart +++ b/tests/data/reference/nems_adcirc/hera_shinnecock_ike/model_configure.coldstart @@ -1,4 +1,4 @@ -# `model_configure` generated with NEMSpy 1.2.21.post17.dev0+3f84e56 +# `model_configure` generated with NEMSpy 1.2.21.post19.dev0+60a2648 total_member: 1 print_esmf: .true. namelist: atm_namelist diff --git a/tests/data/reference/nems_adcirc/hera_shinnecock_ike/model_configure.hotstart b/tests/data/reference/nems_adcirc/hera_shinnecock_ike/model_configure.hotstart index ba4dd9fc..61fbdf36 100644 --- a/tests/data/reference/nems_adcirc/hera_shinnecock_ike/model_configure.hotstart +++ b/tests/data/reference/nems_adcirc/hera_shinnecock_ike/model_configure.hotstart @@ -1,4 +1,4 @@ -# `model_configure` generated with NEMSpy 1.2.21.post17.dev0+3f84e56 +# `model_configure` generated with NEMSpy 1.2.21.post19.dev0+60a2648 total_member: 1 print_esmf: .true. namelist: atm_namelist diff --git a/tests/data/reference/nems_adcirc/hera_shinnecock_ike/nems.configure.coldstart b/tests/data/reference/nems_adcirc/hera_shinnecock_ike/nems.configure.coldstart index 8f9a67d3..f9ed6329 100644 --- a/tests/data/reference/nems_adcirc/hera_shinnecock_ike/nems.configure.coldstart +++ b/tests/data/reference/nems_adcirc/hera_shinnecock_ike/nems.configure.coldstart @@ -1,4 +1,4 @@ -# `nems.configure` generated with NEMSpy 1.2.21.post17.dev0+3f84e56 +# `nems.configure` generated with NEMSpy 1.2.21.post19.dev0+60a2648 # EARTH # EARTH_component_list: OCN EARTH_attributes:: diff --git a/tests/data/reference/nems_adcirc/hera_shinnecock_ike/nems.configure.hotstart b/tests/data/reference/nems_adcirc/hera_shinnecock_ike/nems.configure.hotstart index 2a15f7e1..ce7b6ce7 100644 --- a/tests/data/reference/nems_adcirc/hera_shinnecock_ike/nems.configure.hotstart +++ b/tests/data/reference/nems_adcirc/hera_shinnecock_ike/nems.configure.hotstart @@ -1,4 +1,4 @@ -# `nems.configure` generated with NEMSpy 1.2.21.post17.dev0+3f84e56 +# `nems.configure` generated with NEMSpy 1.2.21.post19.dev0+60a2648 # EARTH # EARTH_component_list: ATM WAV OCN EARTH_attributes:: diff --git a/tests/data/reference/nems_adcirc/hera_shinnecock_ike/run_hera.sh b/tests/data/reference/nems_adcirc/hera_shinnecock_ike/run_hera.sh index f1e712a0..e48535b2 100644 --- a/tests/data/reference/nems_adcirc/hera_shinnecock_ike/run_hera.sh +++ b/tests/data/reference/nems_adcirc/hera_shinnecock_ike/run_hera.sh @@ -4,15 +4,15 @@ DIRECTORY="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd -P)" # run spinup pushd ${DIRECTORY}/spinup >/dev/null 2>&1 -spinup_adcprep_jobid=$(sbatch adcprep.job | awk '{print $NF}') -spinup_jobid=$(sbatch --dependency=afterany:$spinup_adcprep_jobid adcirc.job | awk '{print $NF}') +setup_jobid=$(sbatch setup.job | awk '{print $NF}') +spinup_jobid=$(sbatch adcirc.job --dependency=afterok:$setup_jobid | awk '{print $NF}') popd >/dev/null 2>&1 # run configurations for hotstart in ${DIRECTORY}/runs/*/; do pushd ${hotstart} >/dev/null 2>&1 - hotstart_adcprep_jobid=$(sbatch --dependency=afterany:$spinup_jobid adcprep.job | awk '{print $NF}') - sbatch --dependency=afterany:$hotstart_adcprep_jobid adcirc.job + setup_jobid=$(sbatch setup.job | awk '{print $NF}') + sbatch adcirc.job --dependency=afterok:$setup_jobid,afterok:$spinup_jobid popd >/dev/null 2>&1 done diff --git a/tests/data/reference/nems_adcirc/hera_shinnecock_ike/runs/unperturbed/adcprep.job b/tests/data/reference/nems_adcirc/hera_shinnecock_ike/runs/unperturbed/adcprep.job deleted file mode 100644 index b789e746..00000000 --- a/tests/data/reference/nems_adcirc/hera_shinnecock_ike/runs/unperturbed/adcprep.job +++ /dev/null @@ -1,15 +0,0 @@ -#!/bin/bash --login -#SBATCH -J ADCIRC_MESH_PREP -#SBATCH -A coastal -#SBATCH --mail-type=ALL -#SBATCH --mail-user=example@email.gov -#SBATCH --error=ADCIRC_MESH_PREP.err.log -#SBATCH --output=ADCIRC_MESH_PREP.out.log -#SBATCH -n 1 -#SBATCH -N 1 -#SBATCH --time=06:00:00 - -set -e - -srun ../../../adcprep --np 600 --partmesh -srun ../../../adcprep --np 600 --prepall diff --git a/tests/data/reference/nems_adcirc/hera_shinnecock_ike/runs/unperturbed/config.rc b/tests/data/reference/nems_adcirc/hera_shinnecock_ike/runs/unperturbed/config.rc index 2bbf41b6..d7e9c3d8 100644 --- a/tests/data/reference/nems_adcirc/hera_shinnecock_ike/runs/unperturbed/config.rc +++ b/tests/data/reference/nems_adcirc/hera_shinnecock_ike/runs/unperturbed/config.rc @@ -1,4 +1,4 @@ -# `config.rc` generated with NEMSpy 1.2.21.post17.dev0+3f84e56 +# `config.rc` generated with NEMSpy 1.2.21.post19.dev0+60a2648 atm_dir: ../../../input/shinnecock_ike/forcings atm_nam: wind_atm_fin_ch_time_vec.nc wav_dir: ../../../input/shinnecock_ike/forcings diff --git a/tests/data/reference/nems_adcirc/hera_shinnecock_ike/runs/unperturbed/fort.15 b/tests/data/reference/nems_adcirc/hera_shinnecock_ike/runs/unperturbed/fort.15 index c4807439..d7a726b0 100644 --- a/tests/data/reference/nems_adcirc/hera_shinnecock_ike/runs/unperturbed/fort.15 +++ b/tests/data/reference/nems_adcirc/hera_shinnecock_ike/runs/unperturbed/fort.15 @@ -1,4 +1,4 @@ -created on 2021-05-06 12:36 ! RUNDES - 32 CHARACTER ALPHANUMERIC RUN DESCRIPTION +created on 2021-05-07 11:17 ! RUNDES - 32 CHARACTER ALPHANUMERIC RUN DESCRIPTION Shinacock Inlet Coarse Grid ! RUNID - 24 CHARACTER ALPANUMERIC RUN IDENTIFICATION 1 ! NFOVER - NONFATAL ERROR OVERRIDE OPTION 1 ! NABOUT - ABREVIATED OUTPUT OPTION PARAMETER diff --git a/tests/data/reference/nems_adcirc/hera_shinnecock_ike/runs/unperturbed/model_configure b/tests/data/reference/nems_adcirc/hera_shinnecock_ike/runs/unperturbed/model_configure index ba4dd9fc..61fbdf36 100644 --- a/tests/data/reference/nems_adcirc/hera_shinnecock_ike/runs/unperturbed/model_configure +++ b/tests/data/reference/nems_adcirc/hera_shinnecock_ike/runs/unperturbed/model_configure @@ -1,4 +1,4 @@ -# `model_configure` generated with NEMSpy 1.2.21.post17.dev0+3f84e56 +# `model_configure` generated with NEMSpy 1.2.21.post19.dev0+60a2648 total_member: 1 print_esmf: .true. namelist: atm_namelist diff --git a/tests/data/reference/nems_adcirc/hera_shinnecock_ike/runs/unperturbed/nems.configure b/tests/data/reference/nems_adcirc/hera_shinnecock_ike/runs/unperturbed/nems.configure index 2a15f7e1..ce7b6ce7 100644 --- a/tests/data/reference/nems_adcirc/hera_shinnecock_ike/runs/unperturbed/nems.configure +++ b/tests/data/reference/nems_adcirc/hera_shinnecock_ike/runs/unperturbed/nems.configure @@ -1,4 +1,4 @@ -# `nems.configure` generated with NEMSpy 1.2.21.post17.dev0+3f84e56 +# `nems.configure` generated with NEMSpy 1.2.21.post19.dev0+60a2648 # EARTH # EARTH_component_list: ATM WAV OCN EARTH_attributes:: diff --git a/tests/data/reference/nems_adcirc/hera_shinnecock_ike/runs/unperturbed/setup.job b/tests/data/reference/nems_adcirc/hera_shinnecock_ike/runs/unperturbed/setup.job new file mode 100644 index 00000000..86552773 --- /dev/null +++ b/tests/data/reference/nems_adcirc/hera_shinnecock_ike/runs/unperturbed/setup.job @@ -0,0 +1,15 @@ +#!/bin/bash --login +#SBATCH -J ADCIRC_SETUP +#SBATCH -A coastal +#SBATCH --mail-type=ALL +#SBATCH --mail-user=example@email.gov +#SBATCH --error=ADCIRC_SETUP.err.log +#SBATCH --output=ADCIRC_SETUP.out.log +#SBATCH -n 1 +#SBATCH -N 1 +#SBATCH --time=06:00:00 + +set -e + +srun ../../../adcprep --np 600 --partmesh +srun ../../../adcprep --np 600 --prepall diff --git a/tests/data/reference/nems_adcirc/hera_shinnecock_ike/spinup/adcprep.job b/tests/data/reference/nems_adcirc/hera_shinnecock_ike/spinup/adcprep.job deleted file mode 100644 index b789e746..00000000 --- a/tests/data/reference/nems_adcirc/hera_shinnecock_ike/spinup/adcprep.job +++ /dev/null @@ -1,15 +0,0 @@ -#!/bin/bash --login -#SBATCH -J ADCIRC_MESH_PREP -#SBATCH -A coastal -#SBATCH --mail-type=ALL -#SBATCH --mail-user=example@email.gov -#SBATCH --error=ADCIRC_MESH_PREP.err.log -#SBATCH --output=ADCIRC_MESH_PREP.out.log -#SBATCH -n 1 -#SBATCH -N 1 -#SBATCH --time=06:00:00 - -set -e - -srun ../../../adcprep --np 600 --partmesh -srun ../../../adcprep --np 600 --prepall diff --git a/tests/data/reference/nems_adcirc/hera_shinnecock_ike/spinup/config.rc b/tests/data/reference/nems_adcirc/hera_shinnecock_ike/spinup/config.rc index 068bebb6..bfa6b19a 100644 --- a/tests/data/reference/nems_adcirc/hera_shinnecock_ike/spinup/config.rc +++ b/tests/data/reference/nems_adcirc/hera_shinnecock_ike/spinup/config.rc @@ -1,2 +1,2 @@ -# `config.rc` generated with NEMSpy 1.2.21.post17.dev0+3f84e56 +# `config.rc` generated with NEMSpy 1.2.21.post19.dev0+60a2648 diff --git a/tests/data/reference/nems_adcirc/hera_shinnecock_ike/spinup/fort.15 b/tests/data/reference/nems_adcirc/hera_shinnecock_ike/spinup/fort.15 index 3889769b..91f0a738 100644 --- a/tests/data/reference/nems_adcirc/hera_shinnecock_ike/spinup/fort.15 +++ b/tests/data/reference/nems_adcirc/hera_shinnecock_ike/spinup/fort.15 @@ -1,4 +1,4 @@ -created on 2021-05-06 12:36 ! RUNDES - 32 CHARACTER ALPHANUMERIC RUN DESCRIPTION +created on 2021-05-07 11:17 ! RUNDES - 32 CHARACTER ALPHANUMERIC RUN DESCRIPTION Shinacock Inlet Coarse Grid ! RUNID - 24 CHARACTER ALPANUMERIC RUN IDENTIFICATION 1 ! NFOVER - NONFATAL ERROR OVERRIDE OPTION 1 ! NABOUT - ABREVIATED OUTPUT OPTION PARAMETER diff --git a/tests/data/reference/nems_adcirc/hera_shinnecock_ike/spinup/model_configure b/tests/data/reference/nems_adcirc/hera_shinnecock_ike/spinup/model_configure index d80d7c35..8426ca1a 100644 --- a/tests/data/reference/nems_adcirc/hera_shinnecock_ike/spinup/model_configure +++ b/tests/data/reference/nems_adcirc/hera_shinnecock_ike/spinup/model_configure @@ -1,4 +1,4 @@ -# `model_configure` generated with NEMSpy 1.2.21.post17.dev0+3f84e56 +# `model_configure` generated with NEMSpy 1.2.21.post19.dev0+60a2648 total_member: 1 print_esmf: .true. namelist: atm_namelist diff --git a/tests/data/reference/nems_adcirc/hera_shinnecock_ike/spinup/nems.configure b/tests/data/reference/nems_adcirc/hera_shinnecock_ike/spinup/nems.configure index 8f9a67d3..f9ed6329 100644 --- a/tests/data/reference/nems_adcirc/hera_shinnecock_ike/spinup/nems.configure +++ b/tests/data/reference/nems_adcirc/hera_shinnecock_ike/spinup/nems.configure @@ -1,4 +1,4 @@ -# `nems.configure` generated with NEMSpy 1.2.21.post17.dev0+3f84e56 +# `nems.configure` generated with NEMSpy 1.2.21.post19.dev0+60a2648 # EARTH # EARTH_component_list: OCN EARTH_attributes:: diff --git a/tests/data/reference/nems_adcirc/hera_shinnecock_ike/spinup/setup.job b/tests/data/reference/nems_adcirc/hera_shinnecock_ike/spinup/setup.job new file mode 100644 index 00000000..86552773 --- /dev/null +++ b/tests/data/reference/nems_adcirc/hera_shinnecock_ike/spinup/setup.job @@ -0,0 +1,15 @@ +#!/bin/bash --login +#SBATCH -J ADCIRC_SETUP +#SBATCH -A coastal +#SBATCH --mail-type=ALL +#SBATCH --mail-user=example@email.gov +#SBATCH --error=ADCIRC_SETUP.err.log +#SBATCH --output=ADCIRC_SETUP.out.log +#SBATCH -n 1 +#SBATCH -N 1 +#SBATCH --time=06:00:00 + +set -e + +srun ../../../adcprep --np 600 --partmesh +srun ../../../adcprep --np 600 --prepall diff --git a/tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/config.rc.coldstart b/tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/config.rc.coldstart index 2bbf41b6..d7e9c3d8 100644 --- a/tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/config.rc.coldstart +++ b/tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/config.rc.coldstart @@ -1,4 +1,4 @@ -# `config.rc` generated with NEMSpy 1.2.21.post17.dev0+3f84e56 +# `config.rc` generated with NEMSpy 1.2.21.post19.dev0+60a2648 atm_dir: ../../../input/shinnecock_ike/forcings atm_nam: wind_atm_fin_ch_time_vec.nc wav_dir: ../../../input/shinnecock_ike/forcings diff --git a/tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/configure_adcirc.json b/tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/configure_adcirc.json index ffdd050f..f4beecd3 100644 --- a/tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/configure_adcirc.json +++ b/tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/configure_adcirc.json @@ -1,6 +1,7 @@ { "adcirc_executable_path": "../../../adcirc", "adcprep_executable_path": "../../../adcprep", + "aswip_executable_path": null, "modeled_start_time": "2008-08-23 00:00:00", "modeled_end_time": "2008-09-06 12:00:00", "modeled_timestep": 2.0, diff --git a/tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/job_adcprep_hera.job b/tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/job_adcprep_hera.job deleted file mode 100644 index b789e746..00000000 --- a/tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/job_adcprep_hera.job +++ /dev/null @@ -1,15 +0,0 @@ -#!/bin/bash --login -#SBATCH -J ADCIRC_MESH_PREP -#SBATCH -A coastal -#SBATCH --mail-type=ALL -#SBATCH --mail-user=example@email.gov -#SBATCH --error=ADCIRC_MESH_PREP.err.log -#SBATCH --output=ADCIRC_MESH_PREP.out.log -#SBATCH -n 1 -#SBATCH -N 1 -#SBATCH --time=06:00:00 - -set -e - -srun ../../../adcprep --np 600 --partmesh -srun ../../../adcprep --np 600 --prepall diff --git a/tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/job_setup_hera.job b/tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/job_setup_hera.job new file mode 100644 index 00000000..86552773 --- /dev/null +++ b/tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/job_setup_hera.job @@ -0,0 +1,15 @@ +#!/bin/bash --login +#SBATCH -J ADCIRC_SETUP +#SBATCH -A coastal +#SBATCH --mail-type=ALL +#SBATCH --mail-user=example@email.gov +#SBATCH --error=ADCIRC_SETUP.err.log +#SBATCH --output=ADCIRC_SETUP.out.log +#SBATCH -n 1 +#SBATCH -N 1 +#SBATCH --time=06:00:00 + +set -e + +srun ../../../adcprep --np 600 --partmesh +srun ../../../adcprep --np 600 --prepall diff --git a/tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/model_configure.coldstart b/tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/model_configure.coldstart index ba4dd9fc..61fbdf36 100644 --- a/tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/model_configure.coldstart +++ b/tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/model_configure.coldstart @@ -1,4 +1,4 @@ -# `model_configure` generated with NEMSpy 1.2.21.post17.dev0+3f84e56 +# `model_configure` generated with NEMSpy 1.2.21.post19.dev0+60a2648 total_member: 1 print_esmf: .true. namelist: atm_namelist diff --git a/tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/nems.configure.coldstart b/tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/nems.configure.coldstart index 2a15f7e1..ce7b6ce7 100644 --- a/tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/nems.configure.coldstart +++ b/tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/nems.configure.coldstart @@ -1,4 +1,4 @@ -# `nems.configure` generated with NEMSpy 1.2.21.post17.dev0+3f84e56 +# `nems.configure` generated with NEMSpy 1.2.21.post19.dev0+60a2648 # EARTH # EARTH_component_list: ATM WAV OCN EARTH_attributes:: diff --git a/tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/run_hera.sh b/tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/run_hera.sh index 6e4ccdff..cc4162ea 100644 --- a/tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/run_hera.sh +++ b/tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/run_hera.sh @@ -5,8 +5,8 @@ DIRECTORY="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd -P)" # run configurations for hotstart in ${DIRECTORY}/runs/*/; do pushd ${hotstart} >/dev/null 2>&1 - hotstart_adcprep_jobid=$(sbatch adcprep.job | awk '{print $NF}') - sbatch --dependency=afterany:$hotstart_adcprep_jobid adcirc.job + setup_jobid=$(sbatch setup.job | awk '{print $NF}') + sbatch adcirc.job --dependency=afterok:$setup_jobid popd >/dev/null 2>&1 done diff --git a/tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/runs/unperturbed/adcprep.job b/tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/runs/unperturbed/adcprep.job deleted file mode 100644 index b789e746..00000000 --- a/tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/runs/unperturbed/adcprep.job +++ /dev/null @@ -1,15 +0,0 @@ -#!/bin/bash --login -#SBATCH -J ADCIRC_MESH_PREP -#SBATCH -A coastal -#SBATCH --mail-type=ALL -#SBATCH --mail-user=example@email.gov -#SBATCH --error=ADCIRC_MESH_PREP.err.log -#SBATCH --output=ADCIRC_MESH_PREP.out.log -#SBATCH -n 1 -#SBATCH -N 1 -#SBATCH --time=06:00:00 - -set -e - -srun ../../../adcprep --np 600 --partmesh -srun ../../../adcprep --np 600 --prepall diff --git a/tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/runs/unperturbed/config.rc b/tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/runs/unperturbed/config.rc index 2bbf41b6..d7e9c3d8 100644 --- a/tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/runs/unperturbed/config.rc +++ b/tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/runs/unperturbed/config.rc @@ -1,4 +1,4 @@ -# `config.rc` generated with NEMSpy 1.2.21.post17.dev0+3f84e56 +# `config.rc` generated with NEMSpy 1.2.21.post19.dev0+60a2648 atm_dir: ../../../input/shinnecock_ike/forcings atm_nam: wind_atm_fin_ch_time_vec.nc wav_dir: ../../../input/shinnecock_ike/forcings diff --git a/tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/runs/unperturbed/fort.15 b/tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/runs/unperturbed/fort.15 index 92bd01fb..320b314b 100644 --- a/tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/runs/unperturbed/fort.15 +++ b/tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/runs/unperturbed/fort.15 @@ -1,4 +1,4 @@ -created on 2021-05-06 12:36 ! RUNDES - 32 CHARACTER ALPHANUMERIC RUN DESCRIPTION +created on 2021-05-07 11:17 ! RUNDES - 32 CHARACTER ALPHANUMERIC RUN DESCRIPTION Shinacock Inlet Coarse Grid ! RUNID - 24 CHARACTER ALPANUMERIC RUN IDENTIFICATION 1 ! NFOVER - NONFATAL ERROR OVERRIDE OPTION 1 ! NABOUT - ABREVIATED OUTPUT OPTION PARAMETER diff --git a/tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/runs/unperturbed/model_configure b/tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/runs/unperturbed/model_configure index ba4dd9fc..61fbdf36 100644 --- a/tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/runs/unperturbed/model_configure +++ b/tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/runs/unperturbed/model_configure @@ -1,4 +1,4 @@ -# `model_configure` generated with NEMSpy 1.2.21.post17.dev0+3f84e56 +# `model_configure` generated with NEMSpy 1.2.21.post19.dev0+60a2648 total_member: 1 print_esmf: .true. namelist: atm_namelist diff --git a/tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/runs/unperturbed/nems.configure b/tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/runs/unperturbed/nems.configure index 2a15f7e1..ce7b6ce7 100644 --- a/tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/runs/unperturbed/nems.configure +++ b/tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/runs/unperturbed/nems.configure @@ -1,4 +1,4 @@ -# `nems.configure` generated with NEMSpy 1.2.21.post17.dev0+3f84e56 +# `nems.configure` generated with NEMSpy 1.2.21.post19.dev0+60a2648 # EARTH # EARTH_component_list: ATM WAV OCN EARTH_attributes:: diff --git a/tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/runs/unperturbed/setup.job b/tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/runs/unperturbed/setup.job new file mode 100644 index 00000000..86552773 --- /dev/null +++ b/tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/runs/unperturbed/setup.job @@ -0,0 +1,15 @@ +#!/bin/bash --login +#SBATCH -J ADCIRC_SETUP +#SBATCH -A coastal +#SBATCH --mail-type=ALL +#SBATCH --mail-user=example@email.gov +#SBATCH --error=ADCIRC_SETUP.err.log +#SBATCH --output=ADCIRC_SETUP.out.log +#SBATCH -n 1 +#SBATCH -N 1 +#SBATCH --time=06:00:00 + +set -e + +srun ../../../adcprep --np 600 --partmesh +srun ../../../adcprep --np 600 --prepall diff --git a/tests/data/reference/nems_adcirc/local_shinnecock_ike/config.rc.coldstart b/tests/data/reference/nems_adcirc/local_shinnecock_ike/config.rc.coldstart index 068bebb6..bfa6b19a 100644 --- a/tests/data/reference/nems_adcirc/local_shinnecock_ike/config.rc.coldstart +++ b/tests/data/reference/nems_adcirc/local_shinnecock_ike/config.rc.coldstart @@ -1,2 +1,2 @@ -# `config.rc` generated with NEMSpy 1.2.21.post17.dev0+3f84e56 +# `config.rc` generated with NEMSpy 1.2.21.post19.dev0+60a2648 diff --git a/tests/data/reference/nems_adcirc/local_shinnecock_ike/config.rc.hotstart b/tests/data/reference/nems_adcirc/local_shinnecock_ike/config.rc.hotstart index 2bbf41b6..d7e9c3d8 100644 --- a/tests/data/reference/nems_adcirc/local_shinnecock_ike/config.rc.hotstart +++ b/tests/data/reference/nems_adcirc/local_shinnecock_ike/config.rc.hotstart @@ -1,4 +1,4 @@ -# `config.rc` generated with NEMSpy 1.2.21.post17.dev0+3f84e56 +# `config.rc` generated with NEMSpy 1.2.21.post19.dev0+60a2648 atm_dir: ../../../input/shinnecock_ike/forcings atm_nam: wind_atm_fin_ch_time_vec.nc wav_dir: ../../../input/shinnecock_ike/forcings diff --git a/tests/data/reference/nems_adcirc/local_shinnecock_ike/configure_adcirc.json b/tests/data/reference/nems_adcirc/local_shinnecock_ike/configure_adcirc.json index ab865d4e..9e20bf1d 100644 --- a/tests/data/reference/nems_adcirc/local_shinnecock_ike/configure_adcirc.json +++ b/tests/data/reference/nems_adcirc/local_shinnecock_ike/configure_adcirc.json @@ -1,6 +1,7 @@ { "adcirc_executable_path": "../../../adcirc", "adcprep_executable_path": "../../../adcprep", + "aswip_executable_path": null, "modeled_start_time": "2008-08-23 00:00:00", "modeled_end_time": "2008-09-06 12:00:00", "modeled_timestep": 2.0, diff --git a/tests/data/reference/nems_adcirc/local_shinnecock_ike/job_adcprep_local.job b/tests/data/reference/nems_adcirc/local_shinnecock_ike/job_setup_local.job similarity index 100% rename from tests/data/reference/nems_adcirc/local_shinnecock_ike/job_adcprep_local.job rename to tests/data/reference/nems_adcirc/local_shinnecock_ike/job_setup_local.job diff --git a/tests/data/reference/nems_adcirc/local_shinnecock_ike/model_configure.coldstart b/tests/data/reference/nems_adcirc/local_shinnecock_ike/model_configure.coldstart index d702236f..bdd7bd1b 100644 --- a/tests/data/reference/nems_adcirc/local_shinnecock_ike/model_configure.coldstart +++ b/tests/data/reference/nems_adcirc/local_shinnecock_ike/model_configure.coldstart @@ -1,4 +1,4 @@ -# `model_configure` generated with NEMSpy 1.2.21.post17.dev0+3f84e56 +# `model_configure` generated with NEMSpy 1.2.21.post19.dev0+60a2648 total_member: 1 print_esmf: .true. namelist: atm_namelist diff --git a/tests/data/reference/nems_adcirc/local_shinnecock_ike/model_configure.hotstart b/tests/data/reference/nems_adcirc/local_shinnecock_ike/model_configure.hotstart index f72018e6..a6b8ded6 100644 --- a/tests/data/reference/nems_adcirc/local_shinnecock_ike/model_configure.hotstart +++ b/tests/data/reference/nems_adcirc/local_shinnecock_ike/model_configure.hotstart @@ -1,4 +1,4 @@ -# `model_configure` generated with NEMSpy 1.2.21.post17.dev0+3f84e56 +# `model_configure` generated with NEMSpy 1.2.21.post19.dev0+60a2648 total_member: 1 print_esmf: .true. namelist: atm_namelist diff --git a/tests/data/reference/nems_adcirc/local_shinnecock_ike/nems.configure.coldstart b/tests/data/reference/nems_adcirc/local_shinnecock_ike/nems.configure.coldstart index e5506d4b..bafe6de9 100644 --- a/tests/data/reference/nems_adcirc/local_shinnecock_ike/nems.configure.coldstart +++ b/tests/data/reference/nems_adcirc/local_shinnecock_ike/nems.configure.coldstart @@ -1,4 +1,4 @@ -# `nems.configure` generated with NEMSpy 1.2.21.post17.dev0+3f84e56 +# `nems.configure` generated with NEMSpy 1.2.21.post19.dev0+60a2648 # EARTH # EARTH_component_list: OCN EARTH_attributes:: diff --git a/tests/data/reference/nems_adcirc/local_shinnecock_ike/nems.configure.hotstart b/tests/data/reference/nems_adcirc/local_shinnecock_ike/nems.configure.hotstart index e5462cd1..7362a7f3 100644 --- a/tests/data/reference/nems_adcirc/local_shinnecock_ike/nems.configure.hotstart +++ b/tests/data/reference/nems_adcirc/local_shinnecock_ike/nems.configure.hotstart @@ -1,4 +1,4 @@ -# `nems.configure` generated with NEMSpy 1.2.21.post17.dev0+3f84e56 +# `nems.configure` generated with NEMSpy 1.2.21.post19.dev0+60a2648 # EARTH # EARTH_component_list: ATM WAV OCN EARTH_attributes:: diff --git a/tests/data/reference/nems_adcirc/local_shinnecock_ike/run_local.sh b/tests/data/reference/nems_adcirc/local_shinnecock_ike/run_local.sh index 8c0f9d1a..b1826ed1 100644 --- a/tests/data/reference/nems_adcirc/local_shinnecock_ike/run_local.sh +++ b/tests/data/reference/nems_adcirc/local_shinnecock_ike/run_local.sh @@ -4,14 +4,14 @@ DIRECTORY="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd -P)" # run spinup pushd ${DIRECTORY}/spinup >/dev/null 2>&1 -sh adcprep.job +sh setup.job sh adcirc.job popd >/dev/null 2>&1 # run configurations for hotstart in ${DIRECTORY}/runs/*/; do pushd ${hotstart} >/dev/null 2>&1 - sh adcprep.job + sh setup.job sh adcirc.job popd >/dev/null 2>&1 done diff --git a/tests/data/reference/nems_adcirc/local_shinnecock_ike/runs/unperturbed/config.rc b/tests/data/reference/nems_adcirc/local_shinnecock_ike/runs/unperturbed/config.rc index 2bbf41b6..d7e9c3d8 100644 --- a/tests/data/reference/nems_adcirc/local_shinnecock_ike/runs/unperturbed/config.rc +++ b/tests/data/reference/nems_adcirc/local_shinnecock_ike/runs/unperturbed/config.rc @@ -1,4 +1,4 @@ -# `config.rc` generated with NEMSpy 1.2.21.post17.dev0+3f84e56 +# `config.rc` generated with NEMSpy 1.2.21.post19.dev0+60a2648 atm_dir: ../../../input/shinnecock_ike/forcings atm_nam: wind_atm_fin_ch_time_vec.nc wav_dir: ../../../input/shinnecock_ike/forcings diff --git a/tests/data/reference/nems_adcirc/local_shinnecock_ike/runs/unperturbed/fort.15 b/tests/data/reference/nems_adcirc/local_shinnecock_ike/runs/unperturbed/fort.15 index c4807439..d7a726b0 100644 --- a/tests/data/reference/nems_adcirc/local_shinnecock_ike/runs/unperturbed/fort.15 +++ b/tests/data/reference/nems_adcirc/local_shinnecock_ike/runs/unperturbed/fort.15 @@ -1,4 +1,4 @@ -created on 2021-05-06 12:36 ! RUNDES - 32 CHARACTER ALPHANUMERIC RUN DESCRIPTION +created on 2021-05-07 11:17 ! RUNDES - 32 CHARACTER ALPHANUMERIC RUN DESCRIPTION Shinacock Inlet Coarse Grid ! RUNID - 24 CHARACTER ALPANUMERIC RUN IDENTIFICATION 1 ! NFOVER - NONFATAL ERROR OVERRIDE OPTION 1 ! NABOUT - ABREVIATED OUTPUT OPTION PARAMETER diff --git a/tests/data/reference/nems_adcirc/local_shinnecock_ike/runs/unperturbed/model_configure b/tests/data/reference/nems_adcirc/local_shinnecock_ike/runs/unperturbed/model_configure index f72018e6..a6b8ded6 100644 --- a/tests/data/reference/nems_adcirc/local_shinnecock_ike/runs/unperturbed/model_configure +++ b/tests/data/reference/nems_adcirc/local_shinnecock_ike/runs/unperturbed/model_configure @@ -1,4 +1,4 @@ -# `model_configure` generated with NEMSpy 1.2.21.post17.dev0+3f84e56 +# `model_configure` generated with NEMSpy 1.2.21.post19.dev0+60a2648 total_member: 1 print_esmf: .true. namelist: atm_namelist diff --git a/tests/data/reference/nems_adcirc/local_shinnecock_ike/runs/unperturbed/nems.configure b/tests/data/reference/nems_adcirc/local_shinnecock_ike/runs/unperturbed/nems.configure index e5462cd1..7362a7f3 100644 --- a/tests/data/reference/nems_adcirc/local_shinnecock_ike/runs/unperturbed/nems.configure +++ b/tests/data/reference/nems_adcirc/local_shinnecock_ike/runs/unperturbed/nems.configure @@ -1,4 +1,4 @@ -# `nems.configure` generated with NEMSpy 1.2.21.post17.dev0+3f84e56 +# `nems.configure` generated with NEMSpy 1.2.21.post19.dev0+60a2648 # EARTH # EARTH_component_list: ATM WAV OCN EARTH_attributes:: diff --git a/tests/data/reference/nems_adcirc/local_shinnecock_ike/runs/unperturbed/adcprep.job b/tests/data/reference/nems_adcirc/local_shinnecock_ike/runs/unperturbed/setup.job similarity index 100% rename from tests/data/reference/nems_adcirc/local_shinnecock_ike/runs/unperturbed/adcprep.job rename to tests/data/reference/nems_adcirc/local_shinnecock_ike/runs/unperturbed/setup.job diff --git a/tests/data/reference/nems_adcirc/local_shinnecock_ike/spinup/config.rc b/tests/data/reference/nems_adcirc/local_shinnecock_ike/spinup/config.rc index 068bebb6..bfa6b19a 100644 --- a/tests/data/reference/nems_adcirc/local_shinnecock_ike/spinup/config.rc +++ b/tests/data/reference/nems_adcirc/local_shinnecock_ike/spinup/config.rc @@ -1,2 +1,2 @@ -# `config.rc` generated with NEMSpy 1.2.21.post17.dev0+3f84e56 +# `config.rc` generated with NEMSpy 1.2.21.post19.dev0+60a2648 diff --git a/tests/data/reference/nems_adcirc/local_shinnecock_ike/spinup/fort.15 b/tests/data/reference/nems_adcirc/local_shinnecock_ike/spinup/fort.15 index 3889769b..91f0a738 100644 --- a/tests/data/reference/nems_adcirc/local_shinnecock_ike/spinup/fort.15 +++ b/tests/data/reference/nems_adcirc/local_shinnecock_ike/spinup/fort.15 @@ -1,4 +1,4 @@ -created on 2021-05-06 12:36 ! RUNDES - 32 CHARACTER ALPHANUMERIC RUN DESCRIPTION +created on 2021-05-07 11:17 ! RUNDES - 32 CHARACTER ALPHANUMERIC RUN DESCRIPTION Shinacock Inlet Coarse Grid ! RUNID - 24 CHARACTER ALPANUMERIC RUN IDENTIFICATION 1 ! NFOVER - NONFATAL ERROR OVERRIDE OPTION 1 ! NABOUT - ABREVIATED OUTPUT OPTION PARAMETER diff --git a/tests/data/reference/nems_adcirc/local_shinnecock_ike/spinup/model_configure b/tests/data/reference/nems_adcirc/local_shinnecock_ike/spinup/model_configure index d702236f..bdd7bd1b 100644 --- a/tests/data/reference/nems_adcirc/local_shinnecock_ike/spinup/model_configure +++ b/tests/data/reference/nems_adcirc/local_shinnecock_ike/spinup/model_configure @@ -1,4 +1,4 @@ -# `model_configure` generated with NEMSpy 1.2.21.post17.dev0+3f84e56 +# `model_configure` generated with NEMSpy 1.2.21.post19.dev0+60a2648 total_member: 1 print_esmf: .true. namelist: atm_namelist diff --git a/tests/data/reference/nems_adcirc/local_shinnecock_ike/spinup/nems.configure b/tests/data/reference/nems_adcirc/local_shinnecock_ike/spinup/nems.configure index e5506d4b..bafe6de9 100644 --- a/tests/data/reference/nems_adcirc/local_shinnecock_ike/spinup/nems.configure +++ b/tests/data/reference/nems_adcirc/local_shinnecock_ike/spinup/nems.configure @@ -1,4 +1,4 @@ -# `nems.configure` generated with NEMSpy 1.2.21.post17.dev0+3f84e56 +# `nems.configure` generated with NEMSpy 1.2.21.post19.dev0+60a2648 # EARTH # EARTH_component_list: OCN EARTH_attributes:: diff --git a/tests/data/reference/nems_adcirc/local_shinnecock_ike/spinup/adcprep.job b/tests/data/reference/nems_adcirc/local_shinnecock_ike/spinup/setup.job similarity index 100% rename from tests/data/reference/nems_adcirc/local_shinnecock_ike/spinup/adcprep.job rename to tests/data/reference/nems_adcirc/local_shinnecock_ike/spinup/setup.job diff --git a/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/config.rc.coldstart b/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/config.rc.coldstart index 068bebb6..bfa6b19a 100644 --- a/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/config.rc.coldstart +++ b/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/config.rc.coldstart @@ -1,2 +1,2 @@ -# `config.rc` generated with NEMSpy 1.2.21.post17.dev0+3f84e56 +# `config.rc` generated with NEMSpy 1.2.21.post19.dev0+60a2648 diff --git a/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/config.rc.hotstart b/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/config.rc.hotstart index 2bbf41b6..d7e9c3d8 100644 --- a/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/config.rc.hotstart +++ b/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/config.rc.hotstart @@ -1,4 +1,4 @@ -# `config.rc` generated with NEMSpy 1.2.21.post17.dev0+3f84e56 +# `config.rc` generated with NEMSpy 1.2.21.post19.dev0+60a2648 atm_dir: ../../../input/shinnecock_ike/forcings atm_nam: wind_atm_fin_ch_time_vec.nc wav_dir: ../../../input/shinnecock_ike/forcings diff --git a/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/configure_adcirc.json b/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/configure_adcirc.json index ee3fe4da..81f16be2 100644 --- a/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/configure_adcirc.json +++ b/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/configure_adcirc.json @@ -1,6 +1,7 @@ { "adcirc_executable_path": "../../../adcirc", "adcprep_executable_path": "../../../adcprep", + "aswip_executable_path": null, "modeled_start_time": "2008-08-23 00:00:00", "modeled_end_time": "2008-09-06 12:00:00", "modeled_timestep": 2.0, diff --git a/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/job_adcprep_stampede2.job b/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/job_setup_stampede2.job similarity index 71% rename from tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/job_adcprep_stampede2.job rename to tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/job_setup_stampede2.job index 92117a59..664057a6 100644 --- a/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/job_adcprep_stampede2.job +++ b/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/job_setup_stampede2.job @@ -1,10 +1,10 @@ #!/bin/bash --login -#SBATCH -J ADCIRC_MESH_PREP +#SBATCH -J ADCIRC_SETUP #SBATCH -A coastal #SBATCH --mail-type=ALL #SBATCH --mail-user=example@email.gov -#SBATCH --error=ADCIRC_MESH_PREP.err.log -#SBATCH --output=ADCIRC_MESH_PREP.out.log +#SBATCH --error=ADCIRC_SETUP.err.log +#SBATCH --output=ADCIRC_SETUP.out.log #SBATCH -n 1 #SBATCH -N 1 #SBATCH --time=06:00:00 diff --git a/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/model_configure.coldstart b/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/model_configure.coldstart index 7909f8af..bd0cf7f9 100644 --- a/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/model_configure.coldstart +++ b/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/model_configure.coldstart @@ -1,4 +1,4 @@ -# `model_configure` generated with NEMSpy 1.2.21.post17.dev0+3f84e56 +# `model_configure` generated with NEMSpy 1.2.21.post19.dev0+60a2648 total_member: 1 print_esmf: .true. namelist: atm_namelist diff --git a/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/model_configure.hotstart b/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/model_configure.hotstart index f64d6171..40f7f3ed 100644 --- a/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/model_configure.hotstart +++ b/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/model_configure.hotstart @@ -1,4 +1,4 @@ -# `model_configure` generated with NEMSpy 1.2.21.post17.dev0+3f84e56 +# `model_configure` generated with NEMSpy 1.2.21.post19.dev0+60a2648 total_member: 1 print_esmf: .true. namelist: atm_namelist diff --git a/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/nems.configure.coldstart b/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/nems.configure.coldstart index c57898a8..f02f830f 100644 --- a/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/nems.configure.coldstart +++ b/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/nems.configure.coldstart @@ -1,4 +1,4 @@ -# `nems.configure` generated with NEMSpy 1.2.21.post17.dev0+3f84e56 +# `nems.configure` generated with NEMSpy 1.2.21.post19.dev0+60a2648 # EARTH # EARTH_component_list: OCN EARTH_attributes:: diff --git a/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/nems.configure.hotstart b/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/nems.configure.hotstart index af94bf93..008534c9 100644 --- a/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/nems.configure.hotstart +++ b/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/nems.configure.hotstart @@ -1,4 +1,4 @@ -# `nems.configure` generated with NEMSpy 1.2.21.post17.dev0+3f84e56 +# `nems.configure` generated with NEMSpy 1.2.21.post19.dev0+60a2648 # EARTH # EARTH_component_list: ATM WAV OCN EARTH_attributes:: diff --git a/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/run_stampede2.sh b/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/run_stampede2.sh index f1e712a0..e48535b2 100644 --- a/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/run_stampede2.sh +++ b/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/run_stampede2.sh @@ -4,15 +4,15 @@ DIRECTORY="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd -P)" # run spinup pushd ${DIRECTORY}/spinup >/dev/null 2>&1 -spinup_adcprep_jobid=$(sbatch adcprep.job | awk '{print $NF}') -spinup_jobid=$(sbatch --dependency=afterany:$spinup_adcprep_jobid adcirc.job | awk '{print $NF}') +setup_jobid=$(sbatch setup.job | awk '{print $NF}') +spinup_jobid=$(sbatch adcirc.job --dependency=afterok:$setup_jobid | awk '{print $NF}') popd >/dev/null 2>&1 # run configurations for hotstart in ${DIRECTORY}/runs/*/; do pushd ${hotstart} >/dev/null 2>&1 - hotstart_adcprep_jobid=$(sbatch --dependency=afterany:$spinup_jobid adcprep.job | awk '{print $NF}') - sbatch --dependency=afterany:$hotstart_adcprep_jobid adcirc.job + setup_jobid=$(sbatch setup.job | awk '{print $NF}') + sbatch adcirc.job --dependency=afterok:$setup_jobid,afterok:$spinup_jobid popd >/dev/null 2>&1 done diff --git a/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/runs/unperturbed/adcprep.job b/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/runs/unperturbed/adcprep.job deleted file mode 100644 index 92117a59..00000000 --- a/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/runs/unperturbed/adcprep.job +++ /dev/null @@ -1,16 +0,0 @@ -#!/bin/bash --login -#SBATCH -J ADCIRC_MESH_PREP -#SBATCH -A coastal -#SBATCH --mail-type=ALL -#SBATCH --mail-user=example@email.gov -#SBATCH --error=ADCIRC_MESH_PREP.err.log -#SBATCH --output=ADCIRC_MESH_PREP.out.log -#SBATCH -n 1 -#SBATCH -N 1 -#SBATCH --time=06:00:00 -#SBATCH --partition=development - -set -e - -ibrun ../../../adcprep --np 1020 --partmesh -ibrun ../../../adcprep --np 1020 --prepall diff --git a/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/runs/unperturbed/config.rc b/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/runs/unperturbed/config.rc index 2bbf41b6..d7e9c3d8 100644 --- a/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/runs/unperturbed/config.rc +++ b/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/runs/unperturbed/config.rc @@ -1,4 +1,4 @@ -# `config.rc` generated with NEMSpy 1.2.21.post17.dev0+3f84e56 +# `config.rc` generated with NEMSpy 1.2.21.post19.dev0+60a2648 atm_dir: ../../../input/shinnecock_ike/forcings atm_nam: wind_atm_fin_ch_time_vec.nc wav_dir: ../../../input/shinnecock_ike/forcings diff --git a/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/runs/unperturbed/fort.15 b/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/runs/unperturbed/fort.15 index c4807439..d7a726b0 100644 --- a/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/runs/unperturbed/fort.15 +++ b/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/runs/unperturbed/fort.15 @@ -1,4 +1,4 @@ -created on 2021-05-06 12:36 ! RUNDES - 32 CHARACTER ALPHANUMERIC RUN DESCRIPTION +created on 2021-05-07 11:17 ! RUNDES - 32 CHARACTER ALPHANUMERIC RUN DESCRIPTION Shinacock Inlet Coarse Grid ! RUNID - 24 CHARACTER ALPANUMERIC RUN IDENTIFICATION 1 ! NFOVER - NONFATAL ERROR OVERRIDE OPTION 1 ! NABOUT - ABREVIATED OUTPUT OPTION PARAMETER diff --git a/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/runs/unperturbed/model_configure b/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/runs/unperturbed/model_configure index f64d6171..40f7f3ed 100644 --- a/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/runs/unperturbed/model_configure +++ b/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/runs/unperturbed/model_configure @@ -1,4 +1,4 @@ -# `model_configure` generated with NEMSpy 1.2.21.post17.dev0+3f84e56 +# `model_configure` generated with NEMSpy 1.2.21.post19.dev0+60a2648 total_member: 1 print_esmf: .true. namelist: atm_namelist diff --git a/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/runs/unperturbed/nems.configure b/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/runs/unperturbed/nems.configure index af94bf93..008534c9 100644 --- a/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/runs/unperturbed/nems.configure +++ b/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/runs/unperturbed/nems.configure @@ -1,4 +1,4 @@ -# `nems.configure` generated with NEMSpy 1.2.21.post17.dev0+3f84e56 +# `nems.configure` generated with NEMSpy 1.2.21.post19.dev0+60a2648 # EARTH # EARTH_component_list: ATM WAV OCN EARTH_attributes:: diff --git a/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/runs/unperturbed/setup.job b/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/runs/unperturbed/setup.job new file mode 100644 index 00000000..664057a6 --- /dev/null +++ b/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/runs/unperturbed/setup.job @@ -0,0 +1,16 @@ +#!/bin/bash --login +#SBATCH -J ADCIRC_SETUP +#SBATCH -A coastal +#SBATCH --mail-type=ALL +#SBATCH --mail-user=example@email.gov +#SBATCH --error=ADCIRC_SETUP.err.log +#SBATCH --output=ADCIRC_SETUP.out.log +#SBATCH -n 1 +#SBATCH -N 1 +#SBATCH --time=06:00:00 +#SBATCH --partition=development + +set -e + +ibrun ../../../adcprep --np 1020 --partmesh +ibrun ../../../adcprep --np 1020 --prepall diff --git a/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/spinup/adcprep.job b/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/spinup/adcprep.job deleted file mode 100644 index 92117a59..00000000 --- a/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/spinup/adcprep.job +++ /dev/null @@ -1,16 +0,0 @@ -#!/bin/bash --login -#SBATCH -J ADCIRC_MESH_PREP -#SBATCH -A coastal -#SBATCH --mail-type=ALL -#SBATCH --mail-user=example@email.gov -#SBATCH --error=ADCIRC_MESH_PREP.err.log -#SBATCH --output=ADCIRC_MESH_PREP.out.log -#SBATCH -n 1 -#SBATCH -N 1 -#SBATCH --time=06:00:00 -#SBATCH --partition=development - -set -e - -ibrun ../../../adcprep --np 1020 --partmesh -ibrun ../../../adcprep --np 1020 --prepall diff --git a/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/spinup/config.rc b/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/spinup/config.rc index 068bebb6..bfa6b19a 100644 --- a/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/spinup/config.rc +++ b/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/spinup/config.rc @@ -1,2 +1,2 @@ -# `config.rc` generated with NEMSpy 1.2.21.post17.dev0+3f84e56 +# `config.rc` generated with NEMSpy 1.2.21.post19.dev0+60a2648 diff --git a/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/spinup/fort.15 b/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/spinup/fort.15 index 3889769b..91f0a738 100644 --- a/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/spinup/fort.15 +++ b/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/spinup/fort.15 @@ -1,4 +1,4 @@ -created on 2021-05-06 12:36 ! RUNDES - 32 CHARACTER ALPHANUMERIC RUN DESCRIPTION +created on 2021-05-07 11:17 ! RUNDES - 32 CHARACTER ALPHANUMERIC RUN DESCRIPTION Shinacock Inlet Coarse Grid ! RUNID - 24 CHARACTER ALPANUMERIC RUN IDENTIFICATION 1 ! NFOVER - NONFATAL ERROR OVERRIDE OPTION 1 ! NABOUT - ABREVIATED OUTPUT OPTION PARAMETER diff --git a/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/spinup/model_configure b/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/spinup/model_configure index 7909f8af..bd0cf7f9 100644 --- a/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/spinup/model_configure +++ b/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/spinup/model_configure @@ -1,4 +1,4 @@ -# `model_configure` generated with NEMSpy 1.2.21.post17.dev0+3f84e56 +# `model_configure` generated with NEMSpy 1.2.21.post19.dev0+60a2648 total_member: 1 print_esmf: .true. namelist: atm_namelist diff --git a/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/spinup/nems.configure b/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/spinup/nems.configure index c57898a8..f02f830f 100644 --- a/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/spinup/nems.configure +++ b/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/spinup/nems.configure @@ -1,4 +1,4 @@ -# `nems.configure` generated with NEMSpy 1.2.21.post17.dev0+3f84e56 +# `nems.configure` generated with NEMSpy 1.2.21.post19.dev0+60a2648 # EARTH # EARTH_component_list: OCN EARTH_attributes:: diff --git a/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/spinup/setup.job b/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/spinup/setup.job new file mode 100644 index 00000000..664057a6 --- /dev/null +++ b/tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/spinup/setup.job @@ -0,0 +1,16 @@ +#!/bin/bash --login +#SBATCH -J ADCIRC_SETUP +#SBATCH -A coastal +#SBATCH --mail-type=ALL +#SBATCH --mail-user=example@email.gov +#SBATCH --error=ADCIRC_SETUP.err.log +#SBATCH --output=ADCIRC_SETUP.out.log +#SBATCH -n 1 +#SBATCH -N 1 +#SBATCH --time=06:00:00 +#SBATCH --partition=development + +set -e + +ibrun ../../../adcprep --np 1020 --partmesh +ibrun ../../../adcprep --np 1020 --prepall diff --git a/tests/test_utilities.py b/tests/test_utilities.py index a087a9bb..649afa71 100644 --- a/tests/test_utilities.py +++ b/tests/test_utilities.py @@ -127,11 +127,11 @@ def test_convert_value(): assert ( crs_1 - == 'GEOGCRS["WGS 84",DATUM["World Geodetic System 1984",ELLIPSOID["WGS 84",6378137,298.257223563,LENGTHUNIT["metre",1]]],PRIMEM["Greenwich",0,ANGLEUNIT["degree",0.0174532925199433]],CS[ellipsoidal,2],AXIS["geodetic latitude (Lat)",north,ORDER[1],ANGLEUNIT["degree",0.0174532925199433]],AXIS["geodetic longitude (Lon)",east,ORDER[2],ANGLEUNIT["degree",0.0174532925199433]],USAGE[SCOPE["unknown"],AREA["World"],BBOX[-90,-180,90,180]],ID["EPSG",4326]]' + == 'GEOGCRS["WGS 84",DATUM["World Geodetic System 1984",ELLIPSOID["WGS 84",6378137,298.257223563,LENGTHUNIT["metre",1]]],PRIMEM["Greenwich",0,ANGLEUNIT["degree",0.0174532925199433]],CS[ellipsoidal,2],AXIS["geodetic latitude (Lat)",north,ORDER[1],ANGLEUNIT["degree",0.0174532925199433]],AXIS["geodetic longitude (Lon)",east,ORDER[2],ANGLEUNIT["degree",0.0174532925199433]],USAGE[SCOPE["Horizontal component of 3D system."],AREA["World."],BBOX[-90,-180,90,180]],ID["EPSG",4326]]' ) assert crs_2 == 4326 assert crs_3 == { - '$schema': 'https://proj.org/schemas/v0.1/projjson.schema.json', + '$schema': 'https://proj.org/schemas/v0.2/projjson.schema.json', 'type': 'GeographicCRS', 'name': 'WGS 84', 'datum': { @@ -160,7 +160,8 @@ def test_convert_value(): }, ], }, - 'area': 'World', + 'scope': 'Horizontal component of 3D system.', + 'area': 'World.', 'bbox': { 'south_latitude': -90, 'west_longitude': -180, From 093cca92568bdb90f86e9d1e85d40896e704ca7a Mon Sep 17 00:00:00 2001 From: "zachary.burnett" Date: Fri, 7 May 2021 11:50:04 -0400 Subject: [PATCH 4/8] only use `aswip` if NWS is 20 --- coupledmodeldriver/generate/adcirc/generate.py | 18 +++++++++++++----- 1 file changed, 13 insertions(+), 5 deletions(-) diff --git a/coupledmodeldriver/generate/adcirc/generate.py b/coupledmodeldriver/generate/adcirc/generate.py index ebf75a06..6bc7e129 100644 --- a/coupledmodeldriver/generate/adcirc/generate.py +++ b/coupledmodeldriver/generate/adcirc/generate.py @@ -86,8 +86,9 @@ def generate_adcirc_configuration( original_fort13_filename = ensemble_configuration['adcirc']['fort_13_path'] original_fort14_filename = ensemble_configuration['adcirc']['fort_14_path'] - adcirc_executable_path = ensemble_configuration['adcirc']['adcirc_executable_path'] - adcprep_executable_path = ensemble_configuration['adcirc']['adcprep_executable_path'] + adcirc_path = ensemble_configuration['adcirc']['adcirc_executable_path'] + adcprep_path = ensemble_configuration['adcirc']['adcprep_executable_path'] + aswip_path = ensemble_configuration['adcirc']['aswip_executable_path'] adcirc_processors = ensemble_configuration['adcirc']['processors'] tidal_spinup_duration = ensemble_configuration['adcirc']['tidal_spinup_duration'] source_filename = ensemble_configuration['adcirc']['source_filename'] @@ -100,7 +101,7 @@ def generate_adcirc_configuration( else: nems_configuration = None run_processors = adcirc_processors - run_executable = adcirc_executable_path + run_executable = adcirc_path if source_filename is not None: LOGGER.debug(f'sourcing modules from "{source_filename}"') @@ -205,7 +206,12 @@ def generate_adcirc_configuration( ensemble_run_script_filename = output_directory / f'run_{platform.name.lower()}.sh' ensemble_cleanup_script_filename = output_directory / f'cleanup.sh' - LOGGER.debug(f'setting mesh partitioner "{adcprep_executable_path}"') + if 'besttrack' in ensemble_configuration: + use_aswip = ensemble_configuration['besttrack']['nws'] == 20 + else: + use_aswip = False + + LOGGER.debug(f'setting mesh partitioner "{adcprep_path}"') setup_script = AdcircSetupJob( platform=platform, adcirc_mesh_partitions=adcirc_processors, @@ -213,7 +219,9 @@ def generate_adcirc_configuration( slurm_duration=job_duration, slurm_partition=partition, slurm_run_name=setup_job_name, - adcprep_path=adcprep_executable_path, + adcprep_path=adcprep_path, + aswip_path=aswip_path, + use_aswip=use_aswip, slurm_email_type=email_type, slurm_email_address=email_address, slurm_error_filename=f'{setup_job_name}.err.log', From 68d30c9f19e7f1f259010c873ca70c5bc79ebbb6 Mon Sep 17 00:00:00 2001 From: "zachary.burnett" Date: Fri, 7 May 2021 14:21:24 -0400 Subject: [PATCH 5/8] only use launcher for executables --- coupledmodeldriver/generate/adcirc/script.py | 18 +++++++++++++----- 1 file changed, 13 insertions(+), 5 deletions(-) diff --git a/coupledmodeldriver/generate/adcirc/script.py b/coupledmodeldriver/generate/adcirc/script.py index 8ec49962..068a2c49 100644 --- a/coupledmodeldriver/generate/adcirc/script.py +++ b/coupledmodeldriver/generate/adcirc/script.py @@ -118,23 +118,31 @@ def __init__( self.aswip_path = aswip_path self.use_aswip = use_aswip - setup_commands = [ + setup_commands = [] + + adcprep_commands = [ f'{self.adcprep_path} --np {self.adcirc_partitions} --partmesh', f'{self.adcprep_path} --np {self.adcirc_partitions} --prepall', ] + if self.launcher is not None: + adcprep_commands = [f'{self.launcher} {line}' for line in adcprep_commands] + setup_commands.extend(adcprep_commands) if self.use_aswip: + setup_commands.append('') + + aswip_command = f'{self.aswip_path}' + if self.launcher is not None: + setup_commands.append(f'{self.launcher} {aswip_command}') + setup_commands.append(aswip_command) + setup_commands.extend( [ - f'{self.aswip_path}', 'mv fort.22 fort.22.original', 'mv NWS_20_fort.22 fort.22', ] ) - if self.launcher is not None: - setup_commands = [f'{self.launcher} {line}' for line in setup_commands] - self.commands.extend(setup_commands) From c3bff4a2769c055094f64616cd661c8b1cdd808d Mon Sep 17 00:00:00 2001 From: "zachary.burnett" Date: Fri, 7 May 2021 14:33:27 -0400 Subject: [PATCH 6/8] fix dependency parameter --- coupledmodeldriver/script.py | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/coupledmodeldriver/script.py b/coupledmodeldriver/script.py index 762a092b..7f23a8ee 100644 --- a/coupledmodeldriver/script.py +++ b/coupledmodeldriver/script.py @@ -256,9 +256,9 @@ def __str__(self) -> str: if self.run_spinup: spinup_lines.extend(['# run spinup', 'pushd ${DIRECTORY}/spinup >/dev/null 2>&1']) if self.platform.value['uses_slurm']: - dependencies = ['afterok:$setup_jobid'] + dependencies = ['$setup_jobid'] if len(dependencies) > 0: - dependencies = f'--dependency={",".join(dependencies)}' + dependencies = f'--dependency=afterok{":".join(dependencies)}' spinup_lines.extend( [ "setup_jobid=$(sbatch setup.job | awk '{print $NF}')", @@ -272,11 +272,11 @@ def __str__(self) -> str: hotstart_lines = ['pushd ${hotstart} >/dev/null 2>&1'] if self.platform.value['uses_slurm']: - dependencies = ['afterok:$setup_jobid'] + dependencies = ['$setup_jobid'] if self.run_spinup: - dependencies.append('afterok:$spinup_jobid') + dependencies.append('$spinup_jobid') if len(dependencies) > 0: - dependencies = f'--dependency={",".join(dependencies)}' + dependencies = f'--dependency=afterok:{":".join(dependencies)}' hotstart_lines.extend( [ f"setup_jobid=$(sbatch setup.job | awk '{{print $NF}}')", From beca55e8434a590d5e98930a2047f183c7e1a6ee Mon Sep 17 00:00:00 2001 From: "zachary.burnett" Date: Fri, 7 May 2021 14:34:09 -0400 Subject: [PATCH 7/8] fix dependency parameter --- coupledmodeldriver/script.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/coupledmodeldriver/script.py b/coupledmodeldriver/script.py index 7f23a8ee..bdaae7e7 100644 --- a/coupledmodeldriver/script.py +++ b/coupledmodeldriver/script.py @@ -259,6 +259,8 @@ def __str__(self) -> str: dependencies = ['$setup_jobid'] if len(dependencies) > 0: dependencies = f'--dependency=afterok{":".join(dependencies)}' + else: + dependencies = '' spinup_lines.extend( [ "setup_jobid=$(sbatch setup.job | awk '{print $NF}')", @@ -277,6 +279,8 @@ def __str__(self) -> str: dependencies.append('$spinup_jobid') if len(dependencies) > 0: dependencies = f'--dependency=afterok:{":".join(dependencies)}' + else: + dependencies = '' hotstart_lines.extend( [ f"setup_jobid=$(sbatch setup.job | awk '{{print $NF}}')", From cdf69d8fbed353f3ce1d5f53a313dd72ca71339a Mon Sep 17 00:00:00 2001 From: "zachary.burnett" Date: Fri, 7 May 2021 15:13:32 -0400 Subject: [PATCH 8/8] don't use launcher for aswip --- coupledmodeldriver/generate/adcirc/script.py | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/coupledmodeldriver/generate/adcirc/script.py b/coupledmodeldriver/generate/adcirc/script.py index 068a2c49..a9da65c7 100644 --- a/coupledmodeldriver/generate/adcirc/script.py +++ b/coupledmodeldriver/generate/adcirc/script.py @@ -131,13 +131,9 @@ def __init__( if self.use_aswip: setup_commands.append('') - aswip_command = f'{self.aswip_path}' - if self.launcher is not None: - setup_commands.append(f'{self.launcher} {aswip_command}') - setup_commands.append(aswip_command) - setup_commands.extend( [ + f'{self.aswip_path}', 'mv fort.22 fort.22.original', 'mv NWS_20_fort.22 fort.22', ]