def test_analyze_with_errors(cli_runner, tmpdir, capsys, data):
"""Test that we warn the user of errors in the output files. Also test that we
show a question mark instead of a float in the corresponding cell.
"""
with tmpdir.as_cwd():
result = cli_runner.invoke(cli, [
"analyze", "--directory={}".format(data["analyze-files-w-errors"])
])
version = Version2Categories()
bundle = dtr.discover(data["analyze-files-w-errors"])
df = parse_bundle(
bundle,
columns=version.analyze_categories,
sort_values_by=version.analyze_sort,
)
df = df.iloc[:, :-1]
df = df.replace(np.nan, "?")
print_dataframe(
df,
columns=map_columns(version.category_mapping,
version.analyze_printing),
)
out, _ = capsys.readouterr()
out = "Setting up...\n" + out
assert result.exit_code == 0
assert result.output == "\n".join(out.split("\n"))
def test_consolidate_dataframe(capsys, data):
bundle = dtr.discover(data["analyze-files-gromacs"])
version = VersionFactory(categories=bundle.categories).version_class
df = utils.parse_bundle(
bundle, columns=version.analyze_categories, sort_values_by=version.analyze_sort,
)
test_output = utils.consolidate_dataframe(
df, columns=version.consolidate_categories
)
print_dataframe(
test_output[version.generate_printing[1:]],
columns=map_columns(
map_dict=version.category_mapping, columns=version.generate_printing[1:],
),
)
expected_output = (
"Setting up...\n\n"
"+----------------+---------+--------------+---------+--------+-----------+-------------+-------------------+\n",
"| Module | Nodes | Time (min) | GPUs? | Host | # ranks | # threads | Hyperthreading? |\n",
"|----------------+---------+--------------+---------+--------+-----------+-------------+-------------------|\n",
"| gromacs/2016.3 | 1-5 | 15 | False | draco | nan | nan | nan |\n",
"+----------------+---------+--------------+---------+--------+-----------+-------------+-------------------+\n\n",
)
out, _ = capsys.readouterr()
assert "\n".join(out.split("\n")) == "".join(expected_output)
def test_parse_bundle(data):
bundle = dtr.discover(data["analyze-files-gromacs"])
version = VersionFactory(categories=bundle.categories).version_class
test_output = utils.parse_bundle(
bundle, columns=version.analyze_categories, sort_values_by=version.analyze_sort,
)
expected_output = pd.read_csv(data["analyze-files-gromacs.csv"], index_col=False)
assert_frame_equal(test_output, expected_output)
def do_analyze(directory, save_csv):
"""Analyze benchmarks."""
bundle = dtr.discover(directory)
version = VersionFactory(categories=bundle.categories).version_class
df = parse_bundle(
bundle,
columns=version.analyze_categories,
sort_values_by=version.analyze_sort,
)
# Remove the versions column from the DataFrame
columns_to_drop = ["version"]
df = df.drop(columns=columns_to_drop)
if save_csv is not None:
if not save_csv.endswith(".csv"):
save_csv = "{}.csv".format(save_csv)
df.to_csv(save_csv, index=False)
console.success("Successfully benchmark data to {}.", save_csv)
# Reformat NaN values nicely into question marks.
# move this to the bundle function!
df = df.replace(np.nan, "?")
if df.isnull().values.any():
console.warn(
"We were not able to gather informations for all systems. "
"Systems marked with question marks have either crashed or "
"were not started yet.")
# Warn user that we are going to print more than 50 benchmark results to the console
if df.shape[0] > 50:
if click.confirm(
"We are about to print the results of {} benchmarks to the console. Continue?"
.format(click.style(str(df.shape[0]), bold=True))):
pass
else:
console.error("Exiting.")
# Print the data to the console
print_dataframe(
df,
columns=map_columns(version.category_mapping,
version.analyze_printing),
)
def test_analyze_namd(cli_runner, tmpdir, capsys, data):
with tmpdir.as_cwd():
result = cli_runner.invoke(
cli,
["analyze", "--directory={}".format(data["analyze-files-namd"])])
version = Version2Categories()
bundle = dtr.discover(data["analyze-files-namd"])
df = parse_bundle(
bundle,
columns=version.analyze_categories,
sort_values_by=version.analyze_sort,
)
df = df.iloc[:, :-1]
df = df.replace(np.nan, "?")
print_dataframe(
df,
columns=map_columns(version.category_mapping,
version.analyze_printing),
)
out, _ = capsys.readouterr()
out = "Setting up...\n" + out
assert result.exit_code == 0
assert result.output == "\n".join(out.split("\n"))
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",
)