def test_force_dump_tmp_dir():
with tempfile.TemporaryDirectory(prefix="sge") as tmp:
dummy.init_queue_state(path=dummy.QUEUE_STATE_PATH)
results = qmr.map(
function=GOOD_FUNCTION,
jobs=GOOD_JOBS,
work_dir=os.path.join(tmp, "my_work_dir"),
keep_work_dir=True,
polling_interval_qstat=1e-3,
qsub_path=dummy.QSUB_PATH,
qstat_path=dummy.QSTAT_PATH,
qdel_path=dummy.QDEL_PATH,
)
assert os.path.exists(os.path.join(tmp, "my_work_dir"))
def test_minimal_example():
dummy.init_queue_state(path=dummy.QUEUE_STATE_PATH)
results = qmr.map(
function=numpy.sum,
jobs=[numpy.arange(i, 100 + i) for i in range(10)],
polling_interval_qstat=1e-3,
qsub_path=dummy.QSUB_PATH,
qstat_path=dummy.QSTAT_PATH,
qdel_path=dummy.QDEL_PATH,
)
assert len(results) == 10
jobs = [numpy.arange(i, 100 + i) for i in range(10)]
for idx in range(len(results)):
assert results[idx] == numpy.sum(jobs[idx])
def test_bad_function_creating_stderr():
with tempfile.TemporaryDirectory(prefix="sge") as tmp:
dummy.init_queue_state(path=dummy.QUEUE_STATE_PATH)
results = qmr.map(
function=BAD_FUNCTION,
jobs=GOOD_JOBS,
work_dir=os.path.join(tmp, "my_work_dir"),
polling_interval_qstat=1e-3,
qsub_path=dummy.QSUB_PATH,
qstat_path=dummy.QSTAT_PATH,
qdel_path=dummy.QDEL_PATH,
)
assert len(results) == NUM_JOBS
for r in results:
assert r is None
assert os.path.exists(os.path.join(tmp, "my_work_dir"))
def test_full_chain():
function = GOOD_FUNCTION
jobs = GOOD_JOBS
with tempfile.TemporaryDirectory(prefix="sge") as tmp:
dummy.init_queue_state(path=dummy.QUEUE_STATE_PATH)
results = qmr.map(
function=function,
jobs=jobs,
work_dir=os.path.join(tmp, "my_work_dir"),
polling_interval_qstat=1e-3,
qsub_path=dummy.QSUB_PATH,
qstat_path=dummy.QSTAT_PATH,
qdel_path=dummy.QDEL_PATH,
)
assert len(results) == NUM_JOBS
for i in range(NUM_JOBS):
assert results[i] == function(jobs[i])
def test_one_bad_job_creating_stderr():
with tempfile.TemporaryDirectory(prefix="sge") as tmp:
bad_jobs = GOOD_JOBS.copy()
bad_jobs.append("np.sum will not work for me.")
dummy.init_queue_state(path=dummy.QUEUE_STATE_PATH)
results = qmr.map(
function=GOOD_FUNCTION,
jobs=bad_jobs,
work_dir=os.path.join(tmp, "my_work_dir"),
polling_interval_qstat=1e-3,
qsub_path=dummy.QSUB_PATH,
qstat_path=dummy.QSTAT_PATH,
qdel_path=dummy.QDEL_PATH,
)
assert len(results) == NUM_JOBS + 1
for idx in range(NUM_JOBS):
assert results[idx] == GOOD_FUNCTION(GOOD_JOBS[idx])
assert results[idx + 1] is None
assert os.path.exists(os.path.join(tmp, "my_work_dir"))
def test_run_with_failing_job():
"""
The dummy_qsub will run the jobs.
It will intentionally bring idx == 13 into error-state 'E' five times.
This tests if qmr.map can recover this error using 10 trials.
"""
with tempfile.TemporaryDirectory(prefix="sge") as tmp_dir:
qsub_tmp_dir = os.path.join(tmp_dir, "qsub_tmp")
dummy_queue.init_queue_state(
path=dummy_queue.QUEUE_STATE_PATH,
evil_jobs=[{
"idx": 13,
"num_fails": 0,
"max_num_fails": 5
}],
)
NUM_JOBS = 30
jobs = []
for i in range(NUM_JOBS):
job = np.arange(0, 100)
jobs.append(job)
results = qmr.map(
function=np.sum,
jobs=jobs,
polling_interval_qstat=0.1,
work_dir=qsub_tmp_dir,
keep_work_dir=True,
max_num_resubmissions=10,
qsub_path=dummy_queue.QSUB_PATH,
qstat_path=dummy_queue.QSTAT_PATH,
qdel_path=dummy_queue.QDEL_PATH,
error_state_indicator="E",
)
for i in range(NUM_JOBS):
assert results[i] == np.sum(jobs[i])