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Overhauled reproducibiity check.

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This commit is contained in:
Eric Winter
2025-08-06 13:22:38 -06:00
parent 19f63b2d47
commit 5b2acc3c94
3 changed files with 124 additions and 73 deletions
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37
testingScripts/mage_reproducibility_check-template.pbs
View File

@@ -20,21 +20,26 @@ echo 'The currently loaded modules are:'
module list
echo 'Loading python environment.'
export CONDARC="{{ condarc }}"
export CONDA_ENVS_PATH="{{ conda_envs_path }}"
mage_miniconda3="{{ mage_test_root }}/miniconda3"
mage_conda="${mage_miniconda3}/bin/conda"
__conda_setup="$($mage_conda 'shell.bash' 'hook' 2> /dev/null)"
if [ $? -eq 0 ]; then
eval "$__conda_setup"
else
if [ -f "$mage_miniconda3/etc/profile.d/conda.sh" ]; then
. "$mage_miniconda3/etc/profile.d/conda.sh"
mage_test_root=$HOME
if [ -d "${mage_test_root}/miniconda3" ]; then
echo 'Loading local miniconda3'
mage_miniconda3="${mage_test_root}/miniconda3"
mage_conda="${mage_miniconda3}/bin/conda"
__conda_setup="$($mage_conda 'shell.bash' 'hook' 2> /dev/null)"
if [ $? -eq 0 ]; then
eval "$__conda_setup"
else
export PATH="$mage_miniconda3/bin:$PATH"
if [ -f "$mage_miniconda3/etc/profile.d/conda.sh" ]; then
. "$mage_miniconda3/etc/profile.d/conda.sh"
else
export PATH="$mage_miniconda3/bin:$PATH"
fi
fi
unset __conda_setup
else
echo 'Loading conda module'
module load conda
fi
unset __conda_setup
conda activate {{ conda_environment }}
echo "The current conda environment is ${CONDA_PREFIX}."
@@ -42,18 +47,14 @@ echo 'Setting up MAGE environment.'
source {{ kaijuhome }}/scripts/setupEnvironment.sh
echo "The kaiju software is located at ${KAIJUHOME}."
echo 'Setting up kaipy environment.'
source {{ kaipy_private_root }}/kaipy/scripts/setupEnvironment.sh
echo "The kaipy software is located at ${KAIPYHOME}."
echo 'Setting environment variables.'
export TMPDIR={{ tmpdir }}
export SLACK_BOT_TOKEN={{ slack_bot_token }}
export OMP_NUM_THREADS=128
export MPI_TYPE_DEPTH=32
export KMP_STACKSIZE=128M
export MAGE_TEST_ROOT="{{ mage_test_root }}"
export MAGE_TEST_SET_ROOT={{ mage_test_set_root }}
export KAIJU_TEST_ROOT="{{ kaiju_test_root }}"
export KAIJU_TEST_SET_ROOT={{ kaiju_test_set_root }}
export BRANCH_OR_COMMIT={{ branch_or_commit }}
echo 'The active environment variables are:'

123
testingScripts/mage_reproducibility_check.py
View File

@@ -9,7 +9,6 @@ Authors
-------
Jeff Garretson
Eric Winter
"""
@@ -40,6 +39,17 @@ DEFAULT_MODULE_SET_FILE = os.path.join(
KAIJUHOME, "testingScripts", "mage_build_test_modules", "intel_mpich.lst"
)
# Default values for command-line arguments when none are supplied (such as
# when this code is called by external code).
args_default = {
"debug": False,
"loud": False,
"slack_on_fail": False,
"test": False,
"verbose": False,
"module_set_file": DEFAULT_MODULE_SET_FILE,
}
# Root of directory tree for this set of tests.
KAIJU_TEST_SET_ROOT = os.environ["KAIJU_TEST_SET_ROOT"]
@@ -53,11 +63,6 @@ REPRODUCIBILITY_CHECK_DIRECTORY_PREFIX = "reproducibility_check_"
# Path to directory containing the test scripts
TEST_SCRIPTS_DIRECTORY = os.path.join(KAIJUHOME, "testingScripts")
# List of weekly dash test files to copy
WEEKLY_DASH_TEST_FILES = [
"weeklyDashGo.xml",
]
# Path to jinja2 template file for PBS script for build job.
BUILD_MAGE_PBS_TEMPLATE_FILE = os.path.join(
TEST_SCRIPTS_DIRECTORY, "build_mage-template.pbs"
@@ -75,6 +80,11 @@ RUN_MAGE_PBS_TEMPLATE_FILE = os.path.join(
RUN1_MAGE_PBS_SCRIPT = "run1_mage.pbs"
RUN2_MAGE_PBS_SCRIPT = "run2_mage.pbs"
# List of weekly dash test files to copy
WEEKLY_DASH_TEST_FILES = [
"weeklyDashGo.xml",
]
# Path to jinja2 template file for PBS script for comparison.
MAGE_REPRODUCIBILITY_CHECK_PBS_TEMPLATE_FILE = os.path.join(
TEST_SCRIPTS_DIRECTORY, "mage_reproducibility_check-template.pbs"
@@ -84,6 +94,35 @@ MAGE_REPRODUCIBILITY_CHECK_PBS_TEMPLATE_FILE = os.path.join(
MAGE_REPRODUCIBILITY_CHECK_PBS_SCRIPT = "mage_reproducibility_check.pbs"
def create_command_line_parser():
"""Create the command-line argument parser.
Create the parser for command-line arguments.
Parameters
----------
None
Returns
-------
parser : argparse.ArgumentParser
Command-line argument parser for this script.
Raises
------
None
"""
parser = common.create_command_line_parser(DESCRIPTION)
parser.add_argument(
"--module_set_file", "-f", default=DEFAULT_MODULE_SET_FILE,
help=(
"Path to text file containing set of modules to build with "
"(default: %(default)s)"
)
)
return parser
def mage_reproducibility_check(args: dict):
"""Perform a MAGE reproducibility check.
@@ -123,13 +162,14 @@ def mage_reproducibility_check(args: dict):
subprocess.CalledProcessError
If an exception occurs in subprocess.run()
"""
# Local convenience variables.
debug = args.get("debug", False)
loud = args.get("loud", False)
slack_on_fail = args.get("slack_on_fail", False)
test = args.get("test", False)
verbose = args.get("verbose", False)
module_set_file = args.get("module_set_file", DEFAULT_MODULE_SET_FILE)
# Set missing arguments to defaults.
args = args_default | args
debug = args["debug"]
loud = args["loud"]
slack_on_fail = args["slack_on_fail"]
test = args["test"]
verbose = args["verbose"]
module_set_file = args["module_set_file"]
# ------------------------------------------------------------------------
@@ -146,7 +186,6 @@ def mage_reproducibility_check(args: dict):
module_names, cmake_environment, cmake_options = (
common.read_build_module_list_file(module_set_file)
)
print(f"module_names = {module_names}")
# Extract the name of the list.
module_set_name = os.path.split(module_set_file)[-1].rstrip(".lst")
@@ -197,8 +236,7 @@ def mage_reproducibility_check(args: dict):
# Submit the job.
cmd = f"qsub {BUILD_MAGE_PBS_SCRIPT}"
cproc = subprocess.run(cmd, shell=True, check=True, text=True,
capture_output=True)
cproc = subprocess.run(cmd, shell=True, text=True, capture_output=True)
jobid_build = cproc.stdout.split(".")[0]
# ------------------------------------------------------------------------
@@ -240,14 +278,12 @@ def mage_reproducibility_check(args: dict):
pbs_options["walltime"] = "08:00:00"
pbs_options["modules"] = module_names
pbs_options["conda_environment"] = os.environ["CONDA_ENVIRONMENT"]
pbs_options["kaiju_test_root"] = os.environ["KAIJU_TEST_ROOT"]
pbs_options["kaiju_test_set_root"] = os.environ["KAIJU_TEST_SET_ROOT"]
pbs_options["kaijuhome"] = KAIJUHOME
pbs_options["tmpdir"] = os.environ["TMPDIR"]
pbs_options["slack_bot_token"] = os.environ["SLACK_BOT_TOKEN"]
pbs_options["kaiju_test_root"] = os.environ["KAIJU_TEST_ROOT"]
pbs_options["kaiju_test_set_root"] = os.environ["KAIJU_TEST_SET_ROOT"]
pbs_options["branch_or_commit"] = os.environ["BRANCH_OR_COMMIT"]
pbs_options["cmake_cmd"] = cmake_cmd
pbs_options["make_cmd"] = make_cmd
pbs_options["genLFM_cmd"] = genLFM_cmd
pbs_options["cda2wind_cmd"] = cda2wind_cmd
pbs_options["mpiexec_cmd"] = mpiexec_cmd
@@ -320,11 +356,11 @@ def mage_reproducibility_check(args: dict):
pbs_options["walltime"] = "02:00:00"
pbs_options["modules"] = module_names
pbs_options["conda_environment"] = os.environ["CONDA_ENVIRONMENT"]
pbs_options["kaiju_test_root"] = os.environ["KAIJU_TEST_ROOT"]
pbs_options["kaiju_test_set_root"] = os.environ["KAIJU_TEST_SET_ROOT"]
pbs_options["kaijuhome"] = KAIJUHOME
pbs_options["tmpdir"] = os.environ["TMPDIR"]
pbs_options["slack_bot_token"] = os.environ["SLACK_BOT_TOKEN"]
pbs_options["kaiju_test_root"] = os.environ["KAIJU_TEST_ROOT"]
pbs_options["kaiju_test_set_root"] = os.environ["KAIJU_TEST_SET_ROOT"]
pbs_options["branch_or_commit"] = os.environ["BRANCH_OR_COMMIT"]
pbs_options["xml1"] = os.path.join(build_directory, "run1",
"weeklyDashGo.xml")
@@ -389,31 +425,44 @@ def mage_reproducibility_check(args: dict):
if debug:
print(f"Ending {sys.argv[0]} at {datetime.datetime.now()}")
# Return nominal status.
return 0
def main():
"""Driver for command-line version of code."""
# Set up the command-line parser.
parser = common.create_command_line_parser(DESCRIPTION)
"""Main program code for the command-line version of this file.
# # Add additional arguments specific to this script.
# parser.add_argument(
# "--module_set_file", "-f", default=DEFAULT_MODULE_SET_FILE,
# help=(
# "Path to text file containing set of modules to build with "
# "(default: %(default)s)"
# )
# )
This is the main program code for the command-line version of this file.
It processes command-line options, then calls the primary code.
Parameters
----------
None
Returns
-------
None
Raises
------
None
"""
# Set up the command-line parser.
parser = create_command_line_parser()
# Parse the command-line arguments.
args = parser.parse_args()
if args.debug:
print(f"args = {args}")
# Convert the arguments from Namespace to dict.
args = vars(args)
# ------------------------------------------------------------------------
# Pass the command-line arguments to the main function as a dict.
mage_reproducibility_check(args)
# Call the main program logic. Note that the Namespace object (args)
# returned from the option parser is converted to a dict using vars().
mage_reproducibility_check(vars(args))
# Exit normally.
sys.exit(0)
if __name__ == "__main__":

37
testingScripts/run_mage-template.pbs
View File

@@ -20,21 +20,26 @@ echo 'The currently loaded modules are:'
module list
echo 'Loading python environment.'
export CONDARC="{{ condarc }}"
export CONDA_ENVS_PATH="{{ conda_envs_path }}"
mage_miniconda3="{{ mage_test_root }}/miniconda3"
mage_conda="${mage_miniconda3}/bin/conda"
__conda_setup="$($mage_conda 'shell.bash' 'hook' 2> /dev/null)"
if [ $? -eq 0 ]; then
eval "$__conda_setup"
else
if [ -f "$mage_miniconda3/etc/profile.d/conda.sh" ]; then
. "$mage_miniconda3/etc/profile.d/conda.sh"
mage_test_root=$HOME
if [ -d "${mage_test_root}/miniconda3" ]; then
echo 'Loading local miniconda3'
mage_miniconda3="${mage_test_root}/miniconda3"
mage_conda="${mage_miniconda3}/bin/conda"
__conda_setup="$($mage_conda 'shell.bash' 'hook' 2> /dev/null)"
if [ $? -eq 0 ]; then
eval "$__conda_setup"
else
export PATH="$mage_miniconda3/bin:$PATH"
if [ -f "$mage_miniconda3/etc/profile.d/conda.sh" ]; then
. "$mage_miniconda3/etc/profile.d/conda.sh"
else
export PATH="$mage_miniconda3/bin:$PATH"
fi
fi
unset __conda_setup
else
echo 'Loading conda module'
module load conda
fi
unset __conda_setup
conda activate {{ conda_environment }}
echo "The current conda environment is ${CONDA_PREFIX}."
@@ -42,18 +47,14 @@ echo 'Setting up MAGE environment.'
source {{ kaijuhome }}/scripts/setupEnvironment.sh
echo "The kaiju software is located at ${KAIJUHOME}."
echo 'Setting up kaipy environment.'
source {{ kaipy_private_root }}/kaipy/scripts/setupEnvironment.sh
echo "The kaipy software is located at ${KAIPYHOME}."
echo 'Setting environment variables.'
export TMPDIR={{ tmpdir }}
export SLACK_BOT_TOKEN={{ slack_bot_token }}
export OMP_NUM_THREADS=128
export MPI_TYPE_DEPTH=32
export KMP_STACKSIZE=128M
export MAGE_TEST_ROOT="{{ mage_test_root }}"
export MAGE_TEST_SET_ROOT={{ mage_test_set_root }}
export KAIJU_TEST_ROOT={{ kaiju_test_root }}
export KAIJU_TEST_SET_ROOT={{ kaiju_test_set_root }}
export BRANCH_OR_COMMIT={{ branch_or_commit }}
echo 'The active environment variables are:'