def do_submit(directory, force_restart, yes):
"""Submit the benchmarks."""
# Migrate from MDBenchmark<2 to MDBenchmark=>2
mds_to_dtr.migrate_to_datreant(directory)
bundle = dtr.discover(directory)
# Exit if no bundles were found in the current directory.
if not bundle:
console.error("No benchmarks found.")
grouped_bundles = bundle.categories.groupby("started")
try:
bundles_not_yet_started = grouped_bundles[False]
except KeyError:
bundles_not_yet_started = None
if not bundles_not_yet_started and not force_restart:
console.error(
"All generated benchmarks were already started once. "
"You can force a restart with {}.",
"--force",
)
# Start all benchmark simulations if a restart was requested. Otherwise
# only start the ones that were not run yet.
bundles_to_start = bundle
if not force_restart:
bundles_to_start = bundles_not_yet_started
df = DataFrameFromBundle(bundles_to_start)
# Reformat NaN values nicely into question marks.
df_to_print = df.replace(np.nan, "?")
df_to_print = df.drop(columns=["ns/day", "ncores"])
console.info("{}", "Benchmark Summary:")
df_short = ConsolidateDataFrame(df_to_print)
PrintDataFrame(df_short)
# Ask the user to confirm whether they want to submit the benchmarks
if yes:
console.info("The above benchmarks will be submitted.")
elif not click.confirm("The above benchmarks will be submitted. Continue?"):
console.error("Exiting. No benchmarks submitted.")
batch_cmd = get_batch_command()
console.info("Submitting a total of {} benchmarks.", len(bundles_to_start))
for sim in bundles_to_start:
# Remove files generated by previous mdbenchmark run
if force_restart:
engine = detect_md_engine(sim.categories["module"])
cleanup_before_restart(engine=engine, sim=sim)
sim.categories["started"] = True
os.chdir(sim.abspath)
subprocess.call([batch_cmd, "bench.job"])
console.info(
"Submitted all benchmarks. Run {} once they are finished to get the results.",
"mdbenchmark analyze",
)
def test_cleanup_before_restart(engine, files_to_delete, files_to_keep, tmpdir):
"""Test that the cleanup of each directory works as intended for all MD engines."""
# Create temporary directory
tmp = tmpdir.mkdir("mdbenchmark")
# Create empty files
for f in files_to_delete + files_to_keep:
open("{}/{}".format(tmp, f), "a").close()
# Run the cleanup script
utils.cleanup_before_restart(engine=engine, sim=dtr.Tree(tmp.strpath))
# Look for files that were left
files_found = []
for f in files_to_keep:
files_found.extend(glob(os.path.join(tmp.strpath, f)))
# Get rid of the `tmp` path and only compare the actual filenames
assert files_to_keep == [x[len(str(tmp)) + 1 :] for x in files_found]
def do_submit(directory, force_restart, yes):
"""Submit the benchmarks."""
bundle = dtr.discover(directory)
# Exit if no bundles were found in the current directory.
if not bundle:
console.error("No benchmarks found.")
grouped_bundles = bundle.categories.groupby("started")
try:
bundles_not_yet_started = grouped_bundles[False]
except KeyError:
bundles_not_yet_started = None
if not bundles_not_yet_started and not force_restart:
console.error(
"All generated benchmarks were already started once. "
"You can force a restart with {}.",
"--force",
)
# Start all benchmark simulations if a restart was requested. Otherwise
# only start the ones that were not run yet.
bundles_to_start = bundle
if not force_restart:
bundles_to_start = bundles_not_yet_started
benchmark_version = VersionFactory(
categories=bundles_to_start.categories).version_class
df = parse_bundle(
bundles_to_start,
columns=benchmark_version.submit_categories,
sort_values_by=benchmark_version.analyze_sort,
discard_performance=True,
)
# Reformat NaN values nicely into question marks.
df_to_print = df.replace(np.nan, "?")
columns_to_drop = ["ncores", "version"]
df_to_print = df.drop(columns=columns_to_drop)
# Consolidate the data by grouping on the number of nodes and print to the
# user as an overview.
consolidated_df = consolidate_dataframe(
df_to_print, columns=benchmark_version.consolidate_categories)
print_dataframe(
consolidated_df,
columns=map_columns(
map_dict=benchmark_version.category_mapping,
columns=benchmark_version.generate_printing[1:],
),
)
# Ask the user to confirm whether they want to submit the benchmarks
if yes:
console.info("The above benchmarks will be submitted.")
elif not click.confirm(
"The above benchmarks will be submitted. Continue?"):
console.error("Exiting. No benchmarks submitted.")
batch_cmd = get_batch_command()
console.info("Submitting a total of {} benchmarks.", len(bundles_to_start))
for sim in bundles_to_start:
# Remove files generated by previous mdbenchmark run
if force_restart:
engine = detect_md_engine(sim.categories["module"])
cleanup_before_restart(engine=engine, sim=sim)
sim.categories["started"] = True
os.chdir(sim.abspath)
subprocess.call([batch_cmd, "bench.job"])
console.info(
"Submitted all benchmarks. Run {} once they are finished to get the results.",
"mdbenchmark analyze",
)