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Merged
forsyth2 merged 1 commit into from
Dec 7, 2022
Merged

Print job ids to file #380

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2 changes: 1 addition & 1 deletion tests/integration/generated/test_bundles_chrysalis.cfg
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@@ -1,7 +1,7 @@
[default]
case = v2.LR.historical_0201
constraint = ""
environment_commands = "source /lcrc/soft/climate/e3sm-unified/test_e3sm_unified_1.8.0rc6_chrysalis.sh"
environment_commands = "source /lcrc/soft/climate/e3sm-unified/load_latest_e3sm_unified_chrysalis.sh"
input = "/lcrc/group/e3sm/ac.forsyth2/E3SMv2/v2.LR.historical_0201"
input_subdir = archive/atm/hist
mapping_file = "/home/ac.zender/data/maps/map_ne30pg2_to_cmip6_180x360_aave.20200201.nc"
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2 changes: 1 addition & 1 deletion tests/integration/generated/test_complete_run_chrysalis.cfg
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@@ -1,7 +1,7 @@
[default]
case = v2.LR.historical_0201
constraint = ""
environment_commands = "source /lcrc/soft/climate/e3sm-unified/test_e3sm_unified_1.8.0rc6_chrysalis.sh"
environment_commands = "source /lcrc/soft/climate/e3sm-unified/load_latest_e3sm_unified_chrysalis.sh"
input = "/lcrc/group/e3sm/ac.forsyth2//E3SMv2/v2.LR.historical_0201"
input_subdir = archive/atm/hist
mapping_file = "/home/ac.zender/data/maps/map_ne30pg2_to_cmip6_180x360_aave.20200201.nc"
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2 changes: 1 addition & 1 deletion tests/integration/utils.py
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Expand Up @@ -281,4 +281,4 @@ def generate_cfgs(unified_testing=False):


if __name__ == "__main__":
generate_cfgs(True)
generate_cfgs()
20 changes: 12 additions & 8 deletions zppy/__main__.py
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Expand Up @@ -66,6 +66,7 @@ def main(): # noqa: C901
username = os.environ.get("USER")
output = output.replace("$USER", username)
scriptDir = os.path.join(output, "post/scripts")
job_ids_file = os.path.join(scriptDir, "jobids.txt")
try:
os.makedirs(scriptDir)
except OSError as exc:
Expand Down Expand Up @@ -134,28 +135,30 @@ def main(): # noqa: C901
existing_bundles = predefined_bundles(config, scriptDir, existing_bundles)

# climo tasks
existing_bundles = climo(config, scriptDir, existing_bundles)
existing_bundles = climo(config, scriptDir, existing_bundles, job_ids_file)

# time series tasks
existing_bundles = ts(config, scriptDir, existing_bundles)
existing_bundles = ts(config, scriptDir, existing_bundles, job_ids_file)

# tc_analysis tasks
existing_bundles = tc_analysis(config, scriptDir, existing_bundles)
existing_bundles = tc_analysis(config, scriptDir, existing_bundles, job_ids_file)

# e3sm_diags tasks
existing_bundles = e3sm_diags(config, scriptDir, existing_bundles)
existing_bundles = e3sm_diags(config, scriptDir, existing_bundles, job_ids_file)

# amwg tasks
existing_bundles = amwg(config, scriptDir, existing_bundles)
existing_bundles = amwg(config, scriptDir, existing_bundles, job_ids_file)

# mpas_analysis tasks
existing_bundles = mpas_analysis(config, scriptDir, existing_bundles)
existing_bundles = mpas_analysis(config, scriptDir, existing_bundles, job_ids_file)

# global time series tasks
existing_bundles = global_time_series(config, scriptDir, existing_bundles)
existing_bundles = global_time_series(
config, scriptDir, existing_bundles, job_ids_file
)

# ilamb tasks
existing_bundles = ilamb(config, scriptDir, existing_bundles)
existing_bundles = ilamb(config, scriptDir, existing_bundles, job_ids_file)

# Submit bundle jobs
for b in existing_bundles:
Expand All @@ -169,6 +172,7 @@ def main(): # noqa: C901
b.bundle_file,
b.bundle_status,
b.export,
job_ids_file,
dependFiles=b.dependencies_external,
)

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8 changes: 6 additions & 2 deletions zppy/amwg.py
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Expand Up @@ -8,7 +8,7 @@


# -----------------------------------------------------------------------------
def amwg(config, scriptDir, existing_bundles):
def amwg(config, scriptDir, existing_bundles, job_ids_file):

# Initialize jinja2 template engine
templateLoader = jinja2.FileSystemLoader(
Expand Down Expand Up @@ -79,7 +79,11 @@ def amwg(config, scriptDir, existing_bundles):
if c["bundle"] == "":
# Submit job
submitScript(
scriptFile, statusFile, export, dependFiles=dependencies
scriptFile,
statusFile,
export,
job_ids_file,
dependFiles=dependencies,
)
else:
print("...adding to bundle '%s'" % (c["bundle"]))
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4 changes: 2 additions & 2 deletions zppy/climo.py
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Expand Up @@ -16,7 +16,7 @@


# -----------------------------------------------------------------------------
def climo(config, scriptDir, existing_bundles):
def climo(config, scriptDir, existing_bundles, job_ids_file):

# --- Initialize jinja2 template engine ---
templateLoader = jinja2.FileSystemLoader(
Expand Down Expand Up @@ -95,7 +95,7 @@ def climo(config, scriptDir, existing_bundles):
if not c["dry_run"]:
if c["bundle"] == "":
# Submit job
submitScript(scriptFile, statusFile, export)
submitScript(scriptFile, statusFile, export, job_ids_file)
else:
print("...adding to bundle '%s'" % (c["bundle"]))

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8 changes: 6 additions & 2 deletions zppy/e3sm_diags.py
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Expand Up @@ -17,7 +17,7 @@

# -----------------------------------------------------------------------------
# FIXME: C901 'e3sm_diags' is too complex (20)
def e3sm_diags(config, scriptDir, existing_bundles): # noqa: C901
def e3sm_diags(config, scriptDir, existing_bundles, job_ids_file): # noqa: C901

# Initialize jinja2 template engine
templateLoader = jinja2.FileSystemLoader(
Expand Down Expand Up @@ -214,7 +214,11 @@ def e3sm_diags(config, scriptDir, existing_bundles): # noqa: C901
if c["bundle"] == "":
# Submit job
submitScript(
scriptFile, statusFile, export, dependFiles=dependencies
scriptFile,
statusFile,
export,
job_ids_file,
dependFiles=dependencies,
)

# Due to a `socket.gaierror: [Errno -2] Name or service not known` error when running e3sm_diags with tc_analysis
Expand Down
8 changes: 6 additions & 2 deletions zppy/global_time_series.py
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Expand Up @@ -15,7 +15,7 @@


# -----------------------------------------------------------------------------
def global_time_series(config, scriptDir, existing_bundles):
def global_time_series(config, scriptDir, existing_bundles, job_ids_file):

# Initialize jinja2 template engine
templateLoader = jinja2.FileSystemLoader(
Expand Down Expand Up @@ -124,7 +124,11 @@ def global_time_series(config, scriptDir, existing_bundles):
if c["bundle"] == "":
# Submit job
submitScript(
scriptFile, statusFile, export, dependFiles=dependencies
scriptFile,
statusFile,
export,
job_ids_file,
dependFiles=dependencies,
)
else:
print("...adding to bundle '%s'" % (c["bundle"]))
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8 changes: 6 additions & 2 deletions zppy/ilamb.py
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Expand Up @@ -16,7 +16,7 @@


# -----------------------------------------------------------------------------
def ilamb(config, scriptDir, existing_bundles):
def ilamb(config, scriptDir, existing_bundles, job_ids_file):

# Initialize jinja2 template engine
templateLoader = jinja2.FileSystemLoader(
Expand Down Expand Up @@ -118,7 +118,11 @@ def ilamb(config, scriptDir, existing_bundles):
if c["bundle"] == "":
# Submit job
submitScript(
scriptFile, statusFile, export, dependFiles=dependencies
scriptFile,
statusFile,
export,
job_ids_file,
dependFiles=dependencies,
)
else:
print("...adding to bundle '%s'" % (c["bundle"]))
Expand Down
8 changes: 6 additions & 2 deletions zppy/mpas_analysis.py
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Expand Up @@ -15,7 +15,7 @@


# -----------------------------------------------------------------------------
def mpas_analysis(config, scriptDir, existing_bundles):
def mpas_analysis(config, scriptDir, existing_bundles, job_ids_file):

# Initialize jinja2 template engine
templateLoader = jinja2.FileSystemLoader(
Expand Down Expand Up @@ -123,7 +123,11 @@ def mpas_analysis(config, scriptDir, existing_bundles):
if c["bundle"] == "":
# Submit job
submitScript(
scriptFile, statusFile, export, dependFiles=dependencies
scriptFile,
statusFile,
export,
job_ids_file,
dependFiles=dependencies,
)

# Note that this line should still be executed even if jobid == -1
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8 changes: 6 additions & 2 deletions zppy/tc_analysis.py
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Expand Up @@ -9,7 +9,7 @@


# -----------------------------------------------------------------------------
def tc_analysis(config, scriptDir, existing_bundles):
def tc_analysis(config, scriptDir, existing_bundles, job_ids_file):

# Initialize jinja2 template engine
templateLoader = jinja2.FileSystemLoader(
Expand Down Expand Up @@ -78,7 +78,11 @@ def tc_analysis(config, scriptDir, existing_bundles):
if c["bundle"] == "":
# Submit job
submitScript(
scriptFile, statusFile, export, dependFiles=dependencies
scriptFile,
statusFile,
export,
job_ids_file,
dependFiles=dependencies,
)

# Note that this line should still be executed even if jobid == -1
Expand Down
4 changes: 2 additions & 2 deletions zppy/ts.py
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Expand Up @@ -17,7 +17,7 @@


# -----------------------------------------------------------------------------
def ts(config, scriptDir, existing_bundles):
def ts(config, scriptDir, existing_bundles, job_ids_file):

# --- Initialize jinja2 template engine ---
templateLoader = jinja2.FileSystemLoader(
Expand Down Expand Up @@ -108,7 +108,7 @@ def ts(config, scriptDir, existing_bundles):
if not c["dry_run"]:
if c["bundle"] == "":
# Submit job
submitScript(scriptFile, statusFile, export)
submitScript(scriptFile, statusFile, export, job_ids_file)
else:
print("...adding to bundle '%s'" % (c["bundle"]))

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7 changes: 6 additions & 1 deletion zppy/utils.py
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Expand Up @@ -153,7 +153,7 @@ def getComponent(input_files):


# -----------------------------------------------------------------------------
def submitScript(scriptFile, statusFile, export, dependFiles=[]):
def submitScript(scriptFile, statusFile, export, job_ids_file, dependFiles=[]):

# id of submitted job, or -1 if not submitted
jobid = None
Expand Down Expand Up @@ -209,6 +209,11 @@ def submitScript(scriptFile, statusFile, export, dependFiles=[]):
print(stderr)
raise RuntimeError(error_str)
jobid = int(out.split()[-1])
with open(job_ids_file, "a") as j:
# To include the scriptFile, use this line:
# j.write(f"{scriptFile}: {jobid}\n")
# To cancel all jobs associated with this zppy run, use `xargs scancel < jobids.txt`.
j.write(f"{jobid}\n")

# Small pause to avoid overloading queueing system
time.sleep(0.2)
Expand Down