def test_custom_lsf_per_core_env(tmpdir):
jobstore = tmpdir.join("jobstore").strpath
log = tmpdir.join("log.txt").strpath
options = parsers.ToilBaseArgumentParser().parse_args(
[jobstore, "--logFile", log])
options.batchSystem = "custom_lsf"
options.disableCaching = True
# Set total memory per job
os.environ["TOIL_CONTAINER_LSF_PER_CORE"] = "N"
job_1 = jobs.ContainerJob(options, runtime=1, cores=2, memory="10G")
jobs.ContainerJob.Runner.startToil(job_1, options)
with open(log, "rt", encoding="utf-8") as f:
assert "-M 10000MB -n 2" in f.read()
# Set total memory per core
os.environ["TOIL_CONTAINER_LSF_PER_CORE"] = "Y"
job_2 = jobs.ContainerJob(options, runtime=1, cores=2, memory="10G")
jobs.ContainerJob.Runner.startToil(job_2, options)
with open(log, "rt", encoding="utf-8") as f:
assert "-M 5000MB -n 2" in f.read()
# Use per_core_reservation() from lsf config
del os.environ["TOIL_CONTAINER_LSF_PER_CORE"]
job_3 = jobs.ContainerJob(options, runtime=1, cores=2, memory="10G")
jobs.ContainerJob.Runner.startToil(job_3, options)
with open(log, "rt", encoding="utf-8") as f:
assert ("-M 5000MB -n 2"
if per_core_reservation() else "-M 10000MB -n 2") in f.read()
def test_custom_lsf_resource_retry_runtime(tmpdir):
jobstore = tmpdir.join("jobstore").strpath
log = tmpdir.join("log.txt").strpath
options = parsers.ToilBaseArgumentParser().parse_args([jobstore, "--logFile", log])
options.batchSystem = "CustomLSF"
job = testJobRuntimeRetry(options, memory="10G", runtime=1)
testJobRuntimeRetry.Runner.startToil(job, options)
with open(log) as f:
assert "Detected job killed by LSF" in f.read()
def test_custom_lsf_batch_system(tmpdir):
jobstore = tmpdir.join("jobstore").strpath
log = tmpdir.join("log.txt").strpath
options = parsers.ToilBaseArgumentParser().parse_args([jobstore, "--logFile", log])
options.batchSystem = "CustomLSF"
job = jobs.ContainerJob(options, memory="10G", runtime=1)
jobs.ContainerJob.Runner.startToil(job, options)
with open(log) as f:
assert "-W 1" in f.read()
def test_custom_lsf_resource_retry_runtime(tmpdir):
jobstore = tmpdir.join("jobstore").strpath
log = tmpdir.join("log.txt").strpath
options = parsers.ToilBaseArgumentParser().parse_args(
[jobstore, "--logFile", log])
options.batchSystem = "custom_lsf"
options.disableCaching = True
job = testJobRuntimeRetry(options, runtime=1)
testJobRuntimeRetry.Runner.startToil(job, options)
with open(log, encoding="utf-8") as f:
assert "Detected job killed by LSF" in f.read()
def test_custom_lsf_batch_system(tmpdir):
jobstore = tmpdir.join("jobstore").strpath
log = tmpdir.join("log.txt").strpath
options = parsers.ToilBaseArgumentParser().parse_args(
[jobstore, "--logFile", log])
options.batchSystem = "custom_lsf"
options.disableCaching = True
job = jobs.ContainerJob(options, runtime=1)
jobs.ContainerJob.Runner.startToil(job, options)
with open(log, encoding="utf-8") as f:
assert "-W 1" in f.read()
def test_parser_add_version():
parser = parsers.ToilBaseArgumentParser(version="foo")
assert "version" in parser.format_help()