From 7a791460a7e60a4b331f58f66ea5a3ae236887c3 Mon Sep 17 00:00:00 2001 From: Guillaume Vernieres Date: Wed, 7 Aug 2024 14:09:30 -0400 Subject: [PATCH 1/4] Marine DA updates (#2802) Companion PR to GDASApp#1226 Addresses a few issues described in: - GDASApp#1219 - GDASApp#1217 - GDASApp#1232 --- ci/cases/gfsv17/ocnanal.yaml | 2 +- jobs/rocoto/prepoceanobs.sh | 6 ++++-- parm/config/gfs/config.resources | 2 +- sorc/gdas.cd | 2 +- ush/python/pygfs/task/marine_bmat.py | 11 +++++------ ush/python/pygfs/utils/marine_da_utils.py | 23 ----------------------- versions/fix.ver | 2 +- 7 files changed, 13 insertions(+), 35 deletions(-) diff --git a/ci/cases/gfsv17/ocnanal.yaml b/ci/cases/gfsv17/ocnanal.yaml index a2d7363c18..483250db10 100644 --- a/ci/cases/gfsv17/ocnanal.yaml +++ b/ci/cases/gfsv17/ocnanal.yaml @@ -17,7 +17,7 @@ base: ACCOUNT: {{ 'HPC_ACCOUNT' | getenv }} ocnanal: - SOCA_INPUT_FIX_DIR: {{ FIXgfs }}/gdas/soca/1440x1080x75/soca + SOCA_INPUT_FIX_DIR: {{ HOMEgfs }}/fix/gdas/soca/1440x1080x75/soca SOCA_OBS_LIST: {{ HOMEgfs }}/sorc/gdas.cd/parm/soca/obs/obs_list.yaml SOCA_NINNER: 100 diff --git a/jobs/rocoto/prepoceanobs.sh b/jobs/rocoto/prepoceanobs.sh index d8626f5518..20aca4f15a 100755 --- a/jobs/rocoto/prepoceanobs.sh +++ b/jobs/rocoto/prepoceanobs.sh @@ -14,8 +14,10 @@ export jobid="${job}.$$" ############################################################### # setup python path for class defs and utils - -PYTHONPATH="${PYTHONPATH:+${PYTHONPATH}:}${HOMEgfs}/ush" +# shellcheck disable=SC2311 +pyiodaPATH="${HOMEgfs}/sorc/gdas.cd/build/lib/python$(detect_py_ver)/" +PYTHONPATH="${pyiodaPATH}:${PYTHONPATH}" +export PYTHONPATH ############################################################### # Execute the JJOB diff --git a/parm/config/gfs/config.resources b/parm/config/gfs/config.resources index 7b737d05f0..a596629e76 100644 --- a/parm/config/gfs/config.resources +++ b/parm/config/gfs/config.resources @@ -544,7 +544,7 @@ case ${step} in case ${OCNRES} in "025") memory="128GB" - ntasks=40;; + ntasks=16;; "050") memory="32GB" ntasks=16;; diff --git a/sorc/gdas.cd b/sorc/gdas.cd index 52f41a298b..f62b9128a9 160000 --- a/sorc/gdas.cd +++ b/sorc/gdas.cd @@ -1 +1 @@ -Subproject commit 52f41a298b4c6b7bbf6f203b6579516819fbbf36 +Subproject commit f62b9128a98cce3d800dd90ad85753b6e178665f diff --git a/ush/python/pygfs/task/marine_bmat.py b/ush/python/pygfs/task/marine_bmat.py index 9d64e621c9..4770583934 100644 --- a/ush/python/pygfs/task/marine_bmat.py +++ b/ush/python/pygfs/task/marine_bmat.py @@ -43,7 +43,7 @@ def __init__(self, config): 'MARINE_WINDOW_END': _window_end, 'MARINE_WINDOW_MIDDLE': self.task_config.current_cycle, 'BERROR_YAML_DIR': os.path.join(_home_gdas, 'parm', 'soca', 'berror'), - 'GRID_GEN_YAML': os.path.join(_home_gdas, 'parm', 'soca', 'gridgen', 'gridgen.yaml'), + 'UTILITY_YAML_TMPL': os.path.join(_home_gdas, 'parm', 'soca', 'soca_utils_stage.yaml.j2'), 'MARINE_ENSDA_STAGE_BKG_YAML_TMPL': os.path.join(_home_gdas, 'parm', 'soca', 'ensda', 'stage_ens_mem.yaml.j2'), 'MARINE_DET_STAGE_BKG_YAML_TMPL': os.path.join(_home_gdas, 'parm', 'soca', 'soca_det_bkg_stage.yaml.j2'), 'ENSPERT_RELPATH': _enspert_relpath, @@ -82,12 +82,11 @@ def initialize(self: Task) -> None: # TODO(G): Check ocean backgrounds dates for consistency bkg_list = parse_j2yaml(self.task_config.MARINE_DET_STAGE_BKG_YAML_TMPL, self.task_config) FileHandler(bkg_list).sync() - for cice_fname in ['./INPUT/cice.res.nc', './bkg/ice.bkg.f006.nc', './bkg/ice.bkg.f009.nc']: - mdau.cice_hist2fms(cice_fname, cice_fname) - # stage the grid generation yaml - FileHandler({'copy': [[self.task_config.GRID_GEN_YAML, - os.path.join(self.task_config.DATA, 'gridgen.yaml')]]}).sync() + # stage the soca utility yamls (gridgen, fields and ufo mapping yamls) + logger.info(f"Staging SOCA utility yaml files from {self.task_config.HOMEgfs}/parm/gdas/soca") + soca_utility_list = parse_j2yaml(self.task_config.UTILITY_YAML_TMPL, self.task_config) + FileHandler(soca_utility_list).sync() # generate the variance partitioning YAML file logger.debug("Generate variance partitioning YAML file") diff --git a/ush/python/pygfs/utils/marine_da_utils.py b/ush/python/pygfs/utils/marine_da_utils.py index 016551878b..2be76ac028 100644 --- a/ush/python/pygfs/utils/marine_da_utils.py +++ b/ush/python/pygfs/utils/marine_da_utils.py @@ -61,29 +61,6 @@ def prep_input_nml(task_config: AttrDict) -> None: nml.write('mom_input.nml') -@logit(logger) -def cice_hist2fms(input_filename: str, output_filename: str) -> None: - """ Reformat the CICE history file so it can be read by SOCA/FMS - Simple reformatting utility to allow soca/fms to read the CICE history files - """ - - # open the CICE history file - ds = xr.open_dataset(input_filename) - - if 'aicen' in ds.variables and 'hicen' in ds.variables and 'hsnon' in ds.variables: - logger.info(f"*** Already reformatted, skipping.") - return - - # rename the dimensions to xaxis_1 and yaxis_1 - ds = ds.rename({'ni': 'xaxis_1', 'nj': 'yaxis_1'}) - - # rename the variables - ds = ds.rename({'aice_h': 'aicen', 'hi_h': 'hicen', 'hs_h': 'hsnon'}) - - # Save the new netCDF file - ds.to_netcdf(output_filename, mode='w') - - @logit(logger) def stage_ens_mem(task_config: AttrDict) -> None: """ Copy the ensemble members to the DATA directory diff --git a/versions/fix.ver b/versions/fix.ver index c77b0a22c1..3f85a45fee 100644 --- a/versions/fix.ver +++ b/versions/fix.ver @@ -9,7 +9,7 @@ export cpl_ver=20230526 export datm_ver=20220805 export gdas_crtm_ver=20220805 export gdas_fv3jedi_ver=20220805 -export gdas_soca_ver=20240624 +export gdas_soca_ver=20240802 export gdas_gsibec_ver=20240416 export gdas_obs_ver=20240213 export glwu_ver=20220805 From 5c2e9b1a265ea8eb7de16a388e504cad6436da24 Mon Sep 17 00:00:00 2001 From: AntonMFernando-NOAA <167725623+AntonMFernando-NOAA@users.noreply.github.com> Date: Wed, 7 Aug 2024 14:10:49 -0400 Subject: [PATCH 2/4] Feature/get arch adds an empty archive job to GEFS system (#2772) - This feature added an archive task for GEFS system. This task will run in the service queue with a single processor. The task executes with success. - Only xml is generated. Refs #832 Refs #2698 --- jobs/rocoto/arch_test.sh | 3 +++ parm/config/gefs/config.arch | 15 +++++++++++ parm/config/gefs/config.resources | 7 ++++++ workflow/applications/gefs.py | 4 ++- workflow/rocoto/gefs_tasks.py | 41 +++++++++++++++++++++++++++++++ 5 files changed, 69 insertions(+), 1 deletion(-) create mode 100755 jobs/rocoto/arch_test.sh create mode 100644 parm/config/gefs/config.arch diff --git a/jobs/rocoto/arch_test.sh b/jobs/rocoto/arch_test.sh new file mode 100755 index 0000000000..c723c842aa --- /dev/null +++ b/jobs/rocoto/arch_test.sh @@ -0,0 +1,3 @@ +#! /usr/bin/env bash +############################################################### +exit 0 diff --git a/parm/config/gefs/config.arch b/parm/config/gefs/config.arch new file mode 100644 index 0000000000..a23bcce6ae --- /dev/null +++ b/parm/config/gefs/config.arch @@ -0,0 +1,15 @@ +#! /usr/bin/env bash + +########## config.arch ########## +# Archive specific + +echo "BEGIN: config.arch" + +# Get task specific resources +. "${EXPDIR}/config.resources" arch + +export ARCH_GAUSSIAN="YES" +export ARCH_GAUSSIAN_FHMAX=${FHMAX_GFS} +export ARCH_GAUSSIAN_FHINC=${FHOUT_GFS} + +echo "END: config.arch" diff --git a/parm/config/gefs/config.resources b/parm/config/gefs/config.resources index 81d2a20635..8c3ba88940 100644 --- a/parm/config/gefs/config.resources +++ b/parm/config/gefs/config.resources @@ -280,6 +280,13 @@ case ${step} in export is_exclusive=False ;; + "arch") + export walltime="06:00:00" + export ntasks=1 + export tasks_per_node=1 + export threads_per_task=1 + export memory="4096M" + ;; *) echo "FATAL ERROR: Invalid job ${step} passed to ${BASH_SOURCE[0]}" exit 1 diff --git a/workflow/applications/gefs.py b/workflow/applications/gefs.py index 364ee2c48b..c1e001c171 100644 --- a/workflow/applications/gefs.py +++ b/workflow/applications/gefs.py @@ -14,7 +14,7 @@ def _get_app_configs(self): """ Returns the config_files that are involved in gefs """ - configs = ['stage_ic', 'fcst', 'atmos_products'] + configs = ['stage_ic', 'fcst', 'atmos_products', 'arch'] if self.nens > 0: configs += ['efcs', 'atmos_ensstat'] @@ -79,4 +79,6 @@ def get_task_names(self): if self.do_extractvars: tasks += ['extractvars'] + tasks += ['arch'] + return {f"{self._base['RUN']}": tasks} diff --git a/workflow/rocoto/gefs_tasks.py b/workflow/rocoto/gefs_tasks.py index 1b357d8ee3..e78ac96d83 100644 --- a/workflow/rocoto/gefs_tasks.py +++ b/workflow/rocoto/gefs_tasks.py @@ -546,3 +546,44 @@ def extractvars(self): task = rocoto.create_task(member_metatask_dict) return task + + def arch(self): + deps = [] + dep_dict = {'type': 'metatask', 'name': 'atmos_prod'} + deps.append(rocoto.add_dependency(dep_dict)) + dep_dict = {'type': 'metatask', 'name': 'atmos_ensstat'} + deps.append(rocoto.add_dependency(dep_dict)) + if self.app_config.do_ice: + dep_dict = {'type': 'metatask', 'name': 'ice_prod'} + deps.append(rocoto.add_dependency(dep_dict)) + if self.app_config.do_ocean: + dep_dict = {'type': 'metatask', 'name': 'ocean_prod'} + deps.append(rocoto.add_dependency(dep_dict)) + if self.app_config.do_wave: + dep_dict = {'type': 'metatask', 'name': 'wave_post_grid'} + deps.append(rocoto.add_dependency(dep_dict)) + dep_dict = {'type': 'metatask', 'name': 'wave_post_pnt'} + deps.append(rocoto.add_dependency(dep_dict)) + if self.app_config.do_wave_bnd: + dep_dict = {'type': 'metatask', 'name': 'wave_post_bndpnt'} + deps.append(rocoto.add_dependency(dep_dict)) + dep_dict = {'type': 'metatask', 'name': 'wave_post_bndpnt_bull'} + deps.append(rocoto.add_dependency(dep_dict)) + dependencies = rocoto.create_dependency(dep=deps, dep_condition='and') + + resources = self.get_resource('arch') + task_name = 'arch' + task_dict = {'task_name': task_name, + 'resources': resources, + 'envars': self.envars, + 'cycledef': 'gefs', + 'dependency': dependencies, + 'command': f'{self.HOMEgfs}/jobs/rocoto/arch_test.sh', + 'job_name': f'{self.pslot}_{task_name}_@H', + 'log': f'{self.rotdir}/logs/@Y@m@d@H/{task_name}.log', + 'maxtries': '&MAXTRIES;' + } + + task = rocoto.create_task(task_dict) + + return task From ad8d3e9c4b9be972792fc97d8d679e355c8b1ba3 Mon Sep 17 00:00:00 2001 From: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Wed, 7 Aug 2024 14:41:45 -0400 Subject: [PATCH 3/4] Check that a PR driver is still running before trying to kill it (#2799) Adds a check to the SSH command used to kill child PIDs of a defunct driver instance on a different head node to prevent invalid kill commands, preventing CI failures. Resolves #2798 --- ci/scripts/check_ci.sh | 8 ++++---- ci/scripts/driver.sh | 11 +++++++---- 2 files changed, 11 insertions(+), 8 deletions(-) diff --git a/ci/scripts/check_ci.sh b/ci/scripts/check_ci.sh index 04dd92f4a6..24c5e242c3 100755 --- a/ci/scripts/check_ci.sh +++ b/ci/scripts/check_ci.sh @@ -50,14 +50,14 @@ fi export GH rocotostat=$(command -v rocotostat) -if [[ -z ${rocotostat+x} ]]; then +if [[ -z ${rocotostat} ]]; then echo "rocotostat not found on system" exit 1 else echo "rocotostat being used from ${rocotostat}" fi rocotocheck=$(command -v rocotocheck) -if [[ -z ${rocotocheck+x} ]]; then +if [[ -z ${rocotocheck} ]]; then echo "rocotocheck not found on system" exit 1 else @@ -70,7 +70,7 @@ pr_list="" if [[ -f "${pr_list_dbfile}" ]]; then pr_list=$("${HOMEgfs}/ci/scripts/utils/pr_list_database.py" --dbfile "${pr_list_dbfile}" --list Open Running) || true fi -if [[ -z "${pr_list+x}" ]]; then +if [[ -z "${pr_list}" ]]; then echo "no PRs open and ready to run cases on .. exiting" exit 0 fi @@ -124,7 +124,7 @@ for pr in ${pr_list}; do for pslot_dir in "${pr_dir}/RUNTESTS/EXPDIR/"*; do pslot=$(basename "${pslot_dir}") || true - if [[ -z "${pslot+x}" ]]; then + if [[ -z "${pslot}" ]]; then echo "No experiments found in ${pslot_dir} .. exiting" exit 0 fi diff --git a/ci/scripts/driver.sh b/ci/scripts/driver.sh index 0f53ebff6f..8a99817325 100755 --- a/ci/scripts/driver.sh +++ b/ci/scripts/driver.sh @@ -77,8 +77,9 @@ pr_list=$(${GH} pr list --repo "${REPO_URL}" --label "CI-${MACHINE_ID^}-Ready" - for pr in ${pr_list}; do pr_dir="${GFS_CI_ROOT}/PR/${pr}" + [[ ! -d ${pr_dir} ]] && mkdir -p "${pr_dir}" db_list=$("${ROOT_DIR}/ci/scripts/utils/pr_list_database.py" --add_pr "${pr}" --dbfile "${pr_list_dbfile}") - output_ci_single="${GFS_CI_ROOT}/PR/${pr}/output_single.log" + output_ci_single="${pr_dir}/output_single.log" ############################################################# # Check if a Ready labeled PR has changed back from once set # and in that case completely kill the previose driver.sh cron @@ -107,7 +108,9 @@ for pr in ${pr_list}; do echo -e "${pstree_out}" | grep -Pow "(?<=\()[0-9]+(?=\))" | xargs kill fi else - ssh "${driver_HOST}" 'pstree -A -p "${driver_PID}" | grep -Eow "[0-9]+" | xargs kill' + # Check if the driver is still running on the head node; if so, kill it and all child processes + #shellcheck disable=SC2029 + ssh "${driver_HOST}" "pstree -A -p \"${driver_PID}\" | grep -Eow \"[0-9]+\" | xargs kill || echo \"Failed to kill process with PID: ${driver_PID}, it may not be valid.\"" fi { echo "Driver PID: Requested termination of ${driver_PID} and children on ${driver_HOST}" @@ -141,7 +144,7 @@ pr_list="" if [[ -f "${pr_list_dbfile}" ]]; then pr_list=$("${ROOT_DIR}/ci/scripts/utils/pr_list_database.py" --dbfile "${pr_list_dbfile}" --list Open Ready) || true fi -if [[ -z "${pr_list+x}" ]]; then +if [[ -z "${pr_list}" ]]; then echo "no PRs open and ready for checkout/build .. exiting" exit 0 fi @@ -155,7 +158,7 @@ fi for pr in ${pr_list}; do # Skip pr's that are currently Building for when overlapping driver scripts are being called from within cron pr_building=$("${ROOT_DIR}/ci/scripts/utils/pr_list_database.py" --display "${pr}" --dbfile "${pr_list_dbfile}" | grep Building) || true - if [[ -z "${pr_building+x}" ]]; then + if [[ -n "${pr_building}" ]]; then continue fi id=$("${GH}" pr view "${pr}" --repo "${REPO_URL}" --json id --jq '.id') From e2c0f0671a59628f4614637c01900cb265d837d5 Mon Sep 17 00:00:00 2001 From: DavidNew-NOAA <134300700+DavidNew-NOAA@users.noreply.github.com> Date: Wed, 7 Aug 2024 22:55:49 -0400 Subject: [PATCH 4/4] Stage atmospheric backgrounds and UFS cubed-sphere history files (#2792) This PR changes the G-W so that backgrounds for the atmospheric analyses are staged as UFS cubed-sphere history files rather than FMS restarts. The motivation being that FMS restarts include many data we don't need for the analyses and thus take up too much disk space/bandwidth. This is a companion PR to: GDASApp#1236 JCB-GDAS#19 --------- Co-authored-by: danholdaway Co-authored-by: Dan Holdaway <27729500+danholdaway@users.noreply.github.com> Co-authored-by: Walter Kolczynski - NOAA Co-authored-by: RussTreadon-NOAA Co-authored-by: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com> Co-authored-by: Rahul Mahajan Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> --- parm/gdas/staging/atm_lgetkf_bkg.yaml.j2 | 27 ++++++++---------------- parm/gdas/staging/atm_var_bkg.yaml.j2 | 13 ++---------- parm/gdas/staging/atm_var_fv3ens.yaml.j2 | 27 ++++++++---------------- sorc/gdas.cd | 2 +- ush/forecast_postdet.sh | 2 ++ ush/parsing_model_configure_FV3.sh | 4 ++-- 6 files changed, 25 insertions(+), 50 deletions(-) diff --git a/parm/gdas/staging/atm_lgetkf_bkg.yaml.j2 b/parm/gdas/staging/atm_lgetkf_bkg.yaml.j2 index eda3dad5a7..9258d9d875 100644 --- a/parm/gdas/staging/atm_lgetkf_bkg.yaml.j2 +++ b/parm/gdas/staging/atm_lgetkf_bkg.yaml.j2 @@ -1,6 +1,3 @@ -{% set ftype_list = ['fv_core.res', 'fv_srf_wnd.res', 'fv_tracer.res', 'phy_data', 'sfc_data'] %} -{% set time_list = [current_cycle] %} - mkdir: {% for imem in range(1,NMEM_ENS+1) %} {% set memchar = 'mem%03d' | format(imem) %} @@ -14,19 +11,13 @@ mkdir: - '{{ COM_ATMOS_ANALYSIS_TMPL | replace_tmpl(tmpl_dict) }}' {% endfor %} copy: -{% for time in time_list %} - {% for imem in range(1,NMEM_ENS+1) %} - {% set memchar = 'mem%03d' | format(imem) %} - {% set tmpl_dict = ({ '${ROTDIR}': ROTDIR, - '${RUN}': 'enkfgdas', - '${YMD}': previous_cycle | to_YMD, - '${HH}': previous_cycle | strftime('%H'), - '${MEMDIR}': memchar }) %} -- ['{{ COM_ATMOS_RESTART_TMPL | replace_tmpl(tmpl_dict) }}/{{ time | to_fv3time }}.coupler.res', '{{ DATA }}/bkg/{{ memchar }}/'] - {% for ftype in ftype_list %} - {% for itile in range(1,7) %} -- ['{{ COM_ATMOS_RESTART_TMPL | replace_tmpl(tmpl_dict) }}/{{ time | to_fv3time }}.{{ ftype }}.tile{{ itile }}.nc', '{{ DATA }}/bkg/{{ memchar }}/'] - {% endfor %} - {% endfor %} - {% endfor %} +{% for imem in range(1,NMEM_ENS+1) %} + {% set memchar = 'mem%03d' | format(imem) %} + {% set tmpl_dict = ({ '${ROTDIR}': ROTDIR, + '${RUN}': 'enkfgdas', + '${YMD}': previous_cycle | to_YMD, + '${HH}': previous_cycle | strftime('%H'), + '${MEMDIR}': memchar }) %} +- ['{{ COM_ATMOS_HISTORY_TMPL | replace_tmpl(tmpl_dict) }}/enkf{{ GPREFIX }}cubed_sphere_grid_atmf006.nc', '{{ DATA }}/bkg/{{ memchar }}/'] +- ['{{ COM_ATMOS_HISTORY_TMPL | replace_tmpl(tmpl_dict) }}/enkf{{ GPREFIX }}cubed_sphere_grid_sfcf006.nc', '{{ DATA }}/bkg/{{ memchar }}/'] {% endfor %} diff --git a/parm/gdas/staging/atm_var_bkg.yaml.j2 b/parm/gdas/staging/atm_var_bkg.yaml.j2 index 37af833649..92704e1f51 100644 --- a/parm/gdas/staging/atm_var_bkg.yaml.j2 +++ b/parm/gdas/staging/atm_var_bkg.yaml.j2 @@ -1,14 +1,5 @@ -{% set ftype_list = ['fv_core.res', 'fv_srf_wnd.res', 'fv_tracer.res', 'phy_data', 'sfc_data'] %} -{% set time_list = [current_cycle] %} - mkdir: - '{{ DATA }}/bkg' copy: -{% for time in time_list %} -- ['{{ COM_ATMOS_RESTART_PREV }}/{{ time | to_fv3time }}.coupler.res', '{{ DATA }}/bkg/'] - {% for ftype in ftype_list %} - {% for itile in range(1,ntiles+1) %} -- ['{{ COM_ATMOS_RESTART_PREV }}/{{ time | to_fv3time }}.{{ ftype }}.tile{{ itile }}.nc', '{{ DATA }}/bkg/'] - {% endfor %} - {% endfor %} -{% endfor %} +- ['{{ COM_ATMOS_HISTORY_PREV }}/{{ GPREFIX }}cubed_sphere_grid_atmf006.nc', '{{ DATA }}/bkg/'] +- ['{{ COM_ATMOS_HISTORY_PREV }}/{{ GPREFIX }}cubed_sphere_grid_sfcf006.nc', '{{ DATA }}/bkg/'] diff --git a/parm/gdas/staging/atm_var_fv3ens.yaml.j2 b/parm/gdas/staging/atm_var_fv3ens.yaml.j2 index e499c86d57..776a74304d 100644 --- a/parm/gdas/staging/atm_var_fv3ens.yaml.j2 +++ b/parm/gdas/staging/atm_var_fv3ens.yaml.j2 @@ -1,24 +1,15 @@ -{% set ftype_list = ['fv_core.res', 'fv_srf_wnd.res', 'fv_tracer.res', 'phy_data', 'sfc_data'] %} -{% set time_list = [current_cycle] %} - mkdir: {% for imem in range(1,NMEM_ENS+1) %} - '{{ DATA }}/ens/{{ 'mem%03d' | format(imem) }}' {% endfor %} copy: -{% for time in time_list %} - {% for imem in range(1,NMEM_ENS+1) %} - {% set memchar = 'mem%03d' | format(imem) %} - {% set tmpl_dict = ({ '${ROTDIR}': ROTDIR, - '${RUN}': 'enkfgdas', - '${YMD}': previous_cycle | to_YMD, - '${HH}': previous_cycle | strftime('%H'), - '${MEMDIR}': memchar }) %} -- ['{{ COM_ATMOS_RESTART_TMPL | replace_tmpl(tmpl_dict) }}/{{ time | to_fv3time }}.coupler.res', '{{ DATA }}/ens/{{ memchar }}/'] - {% for ftype in ftype_list %} - {% for itile in range(1,ntiles+1) %} -- ['{{ COM_ATMOS_RESTART_TMPL | replace_tmpl(tmpl_dict) }}/{{ time | to_fv3time }}.{{ ftype }}.tile{{ itile }}.nc', '{{ DATA }}/ens/{{ memchar }}/'] - {% endfor %} - {% endfor %} - {% endfor %} +{% for imem in range(1,NMEM_ENS+1) %} + {% set memchar = 'mem%03d' | format(imem) %} + {% set tmpl_dict = ({ '${ROTDIR}': ROTDIR, + '${RUN}': 'enkfgdas', + '${YMD}': previous_cycle | to_YMD, + '${HH}': previous_cycle | strftime('%H'), + '${MEMDIR}': memchar }) %} +- ['{{ COM_ATMOS_HISTORY_TMPL | replace_tmpl(tmpl_dict) }}/enkf{{ GPREFIX }}cubed_sphere_grid_atmf006.nc', '{{ DATA }}/ens/{{ memchar }}/'] +- ['{{ COM_ATMOS_HISTORY_TMPL | replace_tmpl(tmpl_dict) }}/enkf{{ GPREFIX }}cubed_sphere_grid_sfcf006.nc', '{{ DATA }}/ens/{{ memchar }}/'] {% endfor %} diff --git a/sorc/gdas.cd b/sorc/gdas.cd index f62b9128a9..f3fa26d4d6 160000 --- a/sorc/gdas.cd +++ b/sorc/gdas.cd @@ -1 +1 @@ -Subproject commit f62b9128a98cce3d800dd90ad85753b6e178665f +Subproject commit f3fa26d4d6693fcf451184d5ecabb86c1b4190ca diff --git a/ush/forecast_postdet.sh b/ush/forecast_postdet.sh index 7de31d6235..e659d2ce80 100755 --- a/ush/forecast_postdet.sh +++ b/ush/forecast_postdet.sh @@ -209,6 +209,8 @@ EOF ${NLN} "${COMOUT_ATMOS_HISTORY}/${RUN}.t${cyc}z.atmf${FH3}.nc" "atmf${FH3}.nc" ${NLN} "${COMOUT_ATMOS_HISTORY}/${RUN}.t${cyc}z.sfcf${FH3}.nc" "sfcf${FH3}.nc" ${NLN} "${COMOUT_ATMOS_HISTORY}/${RUN}.t${cyc}z.atm.logf${FH3}.txt" "log.atm.f${FH3}" + ${NLN} "${COMOUT_ATMOS_HISTORY}/${RUN}.t${cyc}z.cubed_sphere_grid_atmf${FH3}.nc" "cubed_sphere_grid_atmf${FH3}.nc" + ${NLN} "${COMOUT_ATMOS_HISTORY}/${RUN}.t${cyc}z.cubed_sphere_grid_sfcf${FH3}.nc" "cubed_sphere_grid_sfcf${FH3}.nc" if [[ "${WRITE_DOPOST}" == ".true." ]]; then ${NLN} "${COMOUT_ATMOS_MASTER}/${RUN}.t${cyc}z.master.grb2f${FH3}" "GFSPRS.GrbF${FH2}" ${NLN} "${COMOUT_ATMOS_MASTER}/${RUN}.t${cyc}z.sfluxgrbf${FH3}.grib2" "GFSFLX.GrbF${FH2}" diff --git a/ush/parsing_model_configure_FV3.sh b/ush/parsing_model_configure_FV3.sh index 7d64ab38f9..d2dd434fff 100755 --- a/ush/parsing_model_configure_FV3.sh +++ b/ush/parsing_model_configure_FV3.sh @@ -31,7 +31,7 @@ local WRITE_GROUP=${WRITE_GROUP:-1} local WRTTASK_PER_GROUP=${WRTTASK_PER_GROUP:-24} local ITASKS=1 local OUTPUT_HISTORY=${OUTPUT_HISTORY:-".true."} -local HISTORY_FILE_ON_NATIVE_GRID=".false." +local HISTORY_FILE_ON_NATIVE_GRID=".true." local WRITE_DOPOST=${WRITE_DOPOST:-".false."} local WRITE_NSFLIP=${WRITE_NSFLIP:-".false."} local NUM_FILES=${NUM_FILES:-2} @@ -39,7 +39,7 @@ local FILENAME_BASE="'atm' 'sfc'" # OUTPUT_GRID local OUTPUT_FILE="'${OUTPUT_FILETYPE_ATM}' '${OUTPUT_FILETYPE_SFC}'" local ZSTANDARD_LEVEL=0 -local IDEFLATE=1 # netCDF zlib lossless compression (0-9); 0: no compression +local IDEFLATE=0 # netCDF zlib lossless compression (0-9); 0: no compression local QUANTIZE_NSD=${QUANTIZE_NSD:-0} # netCDF compression local ICHUNK2D=$((4*restile)) local JCHUNK2D=$((2*restile))