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Fixes issue #395 regarding use of @ character in experiment path #396

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Merged
danielabdi-noaa merged 5 commits into from
Oct 5, 2022
Merged

Fixes issue #395 regarding use of @ character in experiment path #396

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795adf9
Fix @ issue on LOGDIR.
danielabdi-noaa Oct 4, 2022
7197db9
Get rid of RUN_CMD_* specification in deactivate_tasks.
danielabdi-noaa Oct 4, 2022
fd263c3
Add TEST_ALT_* directories to all machines.
danielabdi-noaa Oct 4, 2022
8272663
Enforce config sourcing order in setup.
danielabdi-noaa Oct 4, 2022
d4ba43a
Also fix DYN/PHY dir @ situation.
danielabdi-noaa Oct 5, 2022
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200 changes: 100 additions & 100 deletions parm/FV3LAM_wflow.xml
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1 change: 1 addition & 0 deletions tests/WE2E/get_expts_status.sh
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Expand Up @@ -67,6 +67,7 @@ USHdir="$HOMEdir/ush"
#-----------------------------------------------------------------------
#
. $USHdir/source_util_funcs.sh
source_config $USHdir/constants.yaml
#
#-----------------------------------------------------------------------
#
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4 changes: 0 additions & 4 deletions tests/WE2E/test_configs/wflow_features/config.deactivate_tasks.yaml
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Expand Up @@ -18,10 +18,6 @@ metadata:
three tasks.
user:
RUN_ENVIR: community
platform:
RUN_CMD_UTILS: cd $yyyymmdd
RUN_CMD_FCST: mpirun -np ${PE_MEMBER01}
RUN_CMD_POST: echo hello $yyyymmdd
workflow:
CCPP_PHYS_SUITE: FV3_GFS_v15p2
DATE_FIRST_CYCL: '20190701'
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2 changes: 2 additions & 0 deletions ush/machine/cheyenne.yaml
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Expand Up @@ -21,6 +21,8 @@ platform:
PRE_TASK_CMDS: '{ ulimit -s unlimited; ulimit -a; }'
TEST_EXTRN_MDL_SOURCE_BASEDIR: /glade/p/ral/jntp/UFS_SRW_App/develop/input_model_data
TEST_PREGEN_BASEDIR: /glade/p/ral/jntp/UFS_SRW_App/develop/FV3LAM_pregen
TEST_ALT_EXTRN_MDL_SYSBASEDIR_ICS: /glade/p/ral/jntp/UFS_SRW_App/develop/dummy_FV3GFS_sys_dir
TEST_ALT_EXTRN_MDL_SYSBASEDIR_LBCS: /glade/p/ral/jntp/UFS_SRW_App/develop/dummy_FV3GFS_sys_dir
task_run_fcst:
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@JeffBeck-NOAA JeffBeck-NOAA Oct 5, 2022

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What's the point of adding these directories and the "TEST_ALT"?

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@danielabdi-noaa danielabdi-noaa Oct 5, 2022

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@JeffBeck-NOAA Test cases such as specify_EXTRN_MDL_SYSBASEDIR_ICS_LBCS fail when I run the comprehensive test without it. Hera and Gaea had them before but the rest of the machines didn't so I added it to all of them in case such test cases are run there. The logic behind TEST_ALT_* seems to not be ideal, for example see this issue #364 that plans to change it.

FIXaer: /glade/p/ral/jntp/UFS_SRW_App/develop/fix/fix_aer
FIXgsm: /glade/p/ral/jntp/UFS_SRW_App/develop/fix/fix_am
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4 changes: 2 additions & 2 deletions ush/machine/gaea.yaml
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Expand Up @@ -21,8 +21,8 @@ platform:
PRE_TASK_CMDS: '{ ulimit -s unlimited; ulimit -a; }'
TEST_EXTRN_MDL_SOURCE_BASEDIR: /lustre/f2/pdata/ncep_shared/UFS_SRW_App/develop/input_model_data
TEST_PREGEN_BASEDIR: /lustre/f2/pdata/ncep_shared/UFS_SRW_App/develop/FV3LAM_pregen
task_make_lbcs:
WTIME_MAKE_LBCS: 00:60:00
TEST_ALT_EXTRN_MDL_SYSBASEDIR_ICS: /lustre/f2/pdata/ncep_shared/UFS_SRW_App/develop/dummy_FV3GFS_sys_dir
TEST_ALT_EXTRN_MDL_SYSBASEDIR_LBCS: /lustre/f2/pdata/ncep_shared/UFS_SRW_App/develop/dummy_FV3GFS_sys_dir
task_run_fcst:
FIXaer: /lustre/f2/pdata/ncep_shared/UFS_SRW_App/develop/fix/fix_aer
FIXgsm: /lustre/f2/pdata/ncep_shared/UFS_SRW_App/develop/fix/fix_am
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2 changes: 2 additions & 0 deletions ush/machine/hera.yaml
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Expand Up @@ -24,6 +24,8 @@ platform:
PRE_TASK_CMDS: '{ ulimit -s unlimited; ulimit -a; }'
TEST_EXTRN_MDL_SOURCE_BASEDIR: /scratch2/BMC/det/UFS_SRW_App/develop/input_model_data
TEST_PREGEN_BASEDIR: /scratch2/BMC/det/UFS_SRW_App/develop/FV3LAM_pregen
TEST_ALT_EXTRN_MDL_SYSBASEDIR_ICS: /scratch2/BMC/det/UFS_SRW_app/develop/dummy_FV3GFS_sys_dir
TEST_ALT_EXTRN_MDL_SYSBASEDIR_LBCS: /scratch2/BMC/det/UFS_SRW_app/develop/dummy_FV3GFS_sys_dir
task_get_extrn_ics:
EXTRN_MDL_DATA_STORES: hpss aws nomads
task_get_extrn_lbcs:
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2 changes: 2 additions & 0 deletions ush/machine/jet.yaml
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Expand Up @@ -24,6 +24,8 @@ platform:
PRE_TASK_CMDS: '{ ulimit -s unlimited; ulimit -a; }'
TEST_EXTRN_MDL_SOURCE_BASEDIR: /mnt/lfs4/BMC/wrfruc/UFS_SRW_App/develop/input_model_data
TEST_PREGEN_BASEDIR: /mnt/lfs4/BMC/wrfruc/UFS_SRW_App/develop/FV3LAM_pregen
TEST_ALT_EXTRN_MDL_SYSBASEDIR_ICS: /mnt/lfs4/BMC/wrfruc/UFS_SRW_App/develop/dummy_FV3GFS_sys_dir
TEST_ALT_EXTRN_MDL_SYSBASEDIR_LBCS: /mnt/lfs4/BMC/wrfruc/UFS_SRW_App/develop/dummy_FV3GFS_sys_dir
task_get_extrn_ics:
EXTRN_MDL_DATA_STORES: hpss aws nomads
task_get_extrn_lbcs:
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3 changes: 3 additions & 0 deletions ush/machine/noaacloud.yaml
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Expand Up @@ -17,6 +17,9 @@ platform:
PRE_TASK_CMDS: '{ ulimit -s unlimited; ulimit -a; }'
BUILD_MOD_FN: wflow_noaacloud
TEST_EXTRN_MDL_SOURCE_BASEDIR: /contrib/EPIC/UFS_SRW_App/develop/input_model_data
TEST_PREGEN_BASEDIR: /contrib/EPIC/UFS_SRW_App/develop/FV3LAM_pregen
TEST_ALT_EXTRN_MDL_SYSBASEDIR_ICS: /contrib/EPIC/UFS_SRW_App/develop/dummy_FV3GFS_sys_dir
TEST_ALT_EXTRN_MDL_SYSBASEDIR_LBCS: /contrib/EPIC/UFS_SRW_App/develop/dummy_FV3GFS_sys_dir
task_get_extrn_ics:
EXTRN_MDL_DATA_STORES: aws nomads
task_get_extrn_lbcs:
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2 changes: 2 additions & 0 deletions ush/machine/odin.yaml
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Expand Up @@ -17,6 +17,8 @@ platform:
PRE_TASK_CMDS: '{ ulimit -s unlimited; ulimit -a; }'
TEST_EXTRN_MDL_SOURCE_BASEDIR: /scratch/ywang/UFS_SRW_App/develop/input_model_data
TEST_PREGEN_BASEDIR: /scratch/ywang/UFS_SRW_App/develop/FV3LAM_pregen
TEST_ALT_EXTRN_MDL_SYSBASEDIR_ICS: /scratch/ywang/UFS_SRW_App/develop/dummy_FV3GFS_sys_dir
TEST_ALT_EXTRN_MDL_SYSBASEDIR_LBCS: /scratch/ywang/UFS_SRW_App/develop/dummy_FV3GFS_sys_dir
task_run_fcst:
FIXaer: /scratch/ywang/UFS_SRW_App/develop/fix/fix_aer
FIXgsm: /scratch/ywang/UFS_SRW_App/develop/fix/fix_am
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2 changes: 2 additions & 0 deletions ush/machine/stampede.yaml
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Expand Up @@ -17,6 +17,8 @@ platform:
PRE_TASK_CMDS: '{ ulimit -s unlimited; ulimit -a; }'
TEST_EXTRN_MDL_SOURCE_BASEDIR: /work2/00315/tg455890/stampede2/UFS_SRW_App/develop/input_model_data
TEST_PREGEN_BASEDIR: /work2/00315/tg455890/stampede2/UFS_SRW_App/develop/FV3LAM_pregen
TEST_ALT_EXTRN_MDL_SYSBASEDIR_ICS: /work2/00315/tg455890/stampede2/UFS_SRW_App/develop/dummy_FV3GFS_sys_dir
TEST_ALT_EXTRN_MDL_SYSBASEDIR_LBCS: /work2/00315/tg455890/stampede2/UFS_SRW_App/develop/dummy_FV3GFS_sys_dir
task_run_fcst:
FIXaer: /work2/00315/tg455890/stampede2/UFS_SRW_App/develop/fix/fix_aer
FIXgsm: /work2/00315/tg455890/stampede2/UFS_SRW_App/develop/fix/fix_am
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61 changes: 37 additions & 24 deletions ush/setup.py
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Expand Up @@ -73,19 +73,21 @@ def setup():
#
# -----------------------------------------------------------------------
#
# Step-1 of config
# ================
# Set the name of the configuration file containing default values for
# the experiment/workflow variables. Then source the file.
# the experiment/workflow variables. Then load its content.
#
# -----------------------------------------------------------------------
#
EXPT_DEFAULT_CONFIG_FN = "config_defaults.yaml"
cfg_d = load_config_file(os.path.join(USHdir, EXPT_DEFAULT_CONFIG_FN))
import_vars(dictionary=flatten_dict(cfg_d))
EXPT_CONFIG_FN = cfg_d["workflow"]["EXPT_CONFIG_FN"]

#
# -----------------------------------------------------------------------
#
# If a user-specified configuration file exists, source it. This file
# Load the user config file but don't source it yet. This file
# contains user-specified values for a subset of the experiment/workflow
# variables that override their default values. Note that the user-
# specified configuration file is not tracked by the repository, whereas
Expand All @@ -94,28 +96,28 @@ def setup():
# -----------------------------------------------------------------------
#
if os.path.exists(EXPT_CONFIG_FN):
#
# We require that the variables being set in the user-specified configu-
# ration file have counterparts in the default configuration file. This
# is so that we do not introduce new variables in the user-specified
# configuration file without also officially introducing them in the de-
# fault configuration file. Thus, before sourcing the user-specified
# configuration file, we check that all variables in the user-specified
# configuration file are also assigned default values in the default
# configuration file.
#
cfg_u = load_config_file(os.path.join(USHdir, EXPT_CONFIG_FN))
cfg_u = flatten_dict(cfg_u)
import_vars(dictionary=cfg_u)
update_dict(cfg_u, cfg_d)
import_vars(dictionary=cfg_u,
env_vars=["MACHINE",
"EXTRN_MDL_NAME_ICS", "EXTRN_MDL_NAME_LBCS",
"FV3GFS_FILE_FMT_ICS", "FV3GFS_FILE_FMT_LBCS"])
else:
print_err_msg_exit(
f'''
User config file not found
EXPT_CONFIG_FN = \"{EXPT_CONFIG_FN}\"'''
)
#
# -----------------------------------------------------------------------
#
# Source machine specific file
# Step-2 of config
# ================
# Source machine specific config file to set default values
#
# -----------------------------------------------------------------------
#
global MACHINE
global MACHINE, EXTRN_MDL_SYSBASEDIR_ICS, EXTRN_MDL_SYSBASEDIR_LBCS
MACHINE_FILE = os.path.join(USHdir, "machine", f"{lowercase(MACHINE)}.yaml")
machine_cfg = load_config_file(MACHINE_FILE)

Expand All @@ -130,11 +132,8 @@ def get_location(xcs,fmt):
else:
return ""

global EXTRN_MDL_SYSBASEDIR_ICS, EXTRN_MDL_SYSBASEDIR_LBCS
EXTRN_MDL_SYSBASEDIR_ICS = EXTRN_MDL_SYSBASEDIR_ICS or \
get_location(EXTRN_MDL_NAME_ICS, FV3GFS_FILE_FMT_ICS)
EXTRN_MDL_SYSBASEDIR_LBCS = EXTRN_MDL_SYSBASEDIR_LBCS or \
get_location(EXTRN_MDL_NAME_LBCS, FV3GFS_FILE_FMT_LBCS)
EXTRN_MDL_SYSBASEDIR_ICS = get_location(EXTRN_MDL_NAME_ICS, FV3GFS_FILE_FMT_ICS)
EXTRN_MDL_SYSBASEDIR_LBCS = get_location(EXTRN_MDL_NAME_LBCS, FV3GFS_FILE_FMT_LBCS)

# remove the data key and provide machine specific default values for cfg_d
if "data" in machine_cfg:
Expand All @@ -144,10 +143,24 @@ def get_location(xcs,fmt):
"EXTRN_MDL_SYSBASEDIR_LBCS": EXTRN_MDL_SYSBASEDIR_LBCS,
})
machine_cfg = flatten_dict(machine_cfg)
update_dict(machine_cfg, cfg_d, True)
update_dict(machine_cfg, cfg_d)

# import cfg_d again
#
# -----------------------------------------------------------------------
#
# Step-3 of config
# ================
# Source user config. This overrides previous two configs
#
# -----------------------------------------------------------------------
#
update_dict(cfg_u, cfg_d)

# Now that all 3 config files have their contribution in cfg_d
# import its content to python globals()
import_vars(dictionary=flatten_dict(cfg_d))

# make machine name uppercase
MACHINE = uppercase(MACHINE)

#
Expand Down