def test_echo(
tmpdir,
plugin=PLUGIN,
list_lens=LIST_LENS,
job_sbatch_args=JOB_SBATCH_ARGS,
image=IMAGE,
n_procs=N_PROCS,
):
"""no splitting, no result"""
print("Linux container, no bind, splitting on echo")
print("--------------------------------------------------")
print("Singularity Task arguments:")
print(f"image == {image}")
print(f"tmpdir == {str(tmpdir)}")
cmd = "echo"
print(f"cmd == {cmd}")
print()
print("--------------------------------------------------")
print("Submitter args")
print(f"job_sbatch_args == {job_sbatch_args}")
print(f"plugin == {plugin}")
print(f"n_procs == {n_procs}")
image = image
args = dict()
for i in list_lens:
if i == 1:
args = str(1)
else:
args = [str(i) for i in range(1, i + 1)]
sub_tmpdir = str(tmpdir.join(f"fmriprep_echo{i}"))
singu = SingularityTask(name=f"fp{i}",
executable=cmd,
args=args,
image=image,
cache_dir=tmpdir)
# singu = FunctionTask(name='ft', executable=cmd, args=args, cache_dir=tmpdir)
if isinstance(args, list):
singu.split("args")
print()
print(f"Submitting job with {i} split(s)...")
t0 = time.time()
with Submitter(plugin=plugin,
sbatch_args=job_sbatch_args,
n_procs=n_procs) as sub:
# with Submitter(plugin='cf') as sub:
singu(submitter=sub)
t1 = time.time()
print(f"Time to submit: {t1-t0} s")
def submit_task(argv):
parser = argparse.ArgumentParser()
parser.add_argument('-c',
'--command',
metavar='command',
help="fmriprep command")
parser.add_argument('-i',
'--image',
metavar='image_path',
help="fmriprep image path")
parser.add_argument('-pc',
'--pydra_cache',
metavar='pydra-cache',
help="path to store pydra cache")
parser.add_argument('-b', '--base', help="base path of BIDS dataset")
parser.add_argument('-sa', '--sbatch_args', help="SBATCH args")
args = parser.parse_args()
print(args.command)
singu = SingularityTask(
name="fmriprep",
executable=args.command,
image=args.image,
cache_dir=args.pydra_cache,
audit_flags=AuditFlag.ALL,
messengers=FileMessenger(),
messenger_args={"message_dir": os.path.join(args.base, "messages")},
bindings=[(args.base, "/BASE", "rw")],
)
with Submitter(plugin="slurm", sbatch_args=args.sbatch_args) as sb:
singu(submitter=sb)
def test_singularity_fmriprep_1(plugin, tmpdir):
""" split commands
fmriprep container, no binding
"""
cmd = ["pwd", "ls", "echo", "wc", "lh", "ss", "aw", "aa", "lk"]
image = "/om4/group/gablab/data/singularity-images/fmriprep-v1.3.0p2.sif"
singu = SingularityTask(name="singu",
executable=cmd,
image=image,
cache_dir=tmpdir).split("executable")
assert singu.state.splitter == "singu.executable"
res = singu(plugin=plugin)
def test_singularity_linux_1(plugin, tmpdir):
""" split commands
linux container, no binding
"""
cmd = ["pwd", "ls", "echo", "wc", "lh", "ss", "aw", "aa", "lk"]
image = "library://sylabsed/linux/alpine"
singu = SingularityTask(name="singu",
executable=cmd,
image=image,
cache_dir=tmpdir).split("executable")
assert singu.state.splitter == "singu.executable"
res = singu(plugin=plugin)
def test_singularity_fmriprep_2(plugin, tmpdir):
""" command with arguments in docker, checking the distribution
splitter = image
"""
cmd = ["pwd", "ls", "echo", "wc", "lh", "ss", "aw", "aa", "lk"]
image = "/om4/group/gablab/data/singularity-images/fmriprep-v1.3.0p2.sif"
singu = SingularityTask(
name="singu",
executable=cmd,
image=image,
cache_dir=tmpdir,
bindings=[(fmriprep_inputs["base_path"], "/BASE", "rw")],
).split("cmd")
assert singu.state.splitter == "singu.executable"
res = singu(plugin=plugin)
def test_singularity_linux_2(plugin, tmpdir):
""" command with arguments in docker, checking the distribution
splitter = image
"""
cmd = ["pwd", "ls", "echo", "wc", "lh", "ss", "aw", "aa", "lk"]
image = "library://sylabsed/linux/alpine"
singu = SingularityTask(
name="singu",
executable=cmd,
image=image,
cache_dir=tmpdir,
bindings=[(fmriprep_inputs["base_path"], "/BASE", "rw")],
).split("cmd")
assert singu.state.splitter == "singu.executable"
res = singu(plugin=plugin)
]
CMD_LIST = list()
for s in SUBJECT:
CMD = f"fmriprep {DATADIR} {OUTDIR} -w {WORKDIR} \
participant --participant_label {s} --nthreads 1 \
--output-space fsaverage6 --use-aroma --ignore-aroma-denoising-errors \
--skip-bids-validation --mem_mb 9500 --fs-license-file {FS_LICENSE} \
--ignore slicetiming --cifti-output".split(" ")
CMD_LIST.append(CMD)
#####################################################################
singu = SingularityTask(
name="fmriprep",
executable=CMD_LIST,
image=IMAGE,
cache_dir=CACHEDIR,
bindings=[(BASE, "/BASE", "rw")],
).split("executable")
sbatch_args = "-J Yale-50561-5 -t 1-00:00:00 --mem=10GB --cpus-per-task=1"
with Submitter(plugin="slurm", sbatch_args=sbatch_args) as sub:
singu(submitter=sub)
res = singu.result()
print("Done running!")
print(f"res.output.stdout = {res.output.stdout}")
print()
print(f"res.output.return_code = {res.output.return_code}")
site=wf.lzin.site,
))
wf.add(
create_cmd(
name="create_cmd",
subject=wf.get_subject.lzout.out,
base_path=wf.lzin.base_path,
dataset=wf.lzin.dataset,
site=wf.lzin.site,
fs_license=wf.lzin.fs_license,
))
wf.add(
SingularityTask(
name="fmriprep",
executable=wf.create_cmd.lzout.out,
image=wf.lzin.image_path,
bindings=[(wf_inputs['base_path'], "/BASE", "rw")],
))
# set fmriprep commands as workflow output for now
wf.set_output([("out", wf.fmriprep.lzout.stdout),
("err", wf.fmriprep.lzout.stderr)])
sbatch_args = "-J abide-50628 -t 1-00:00:00 --mem=10GB --cpus-per-task=2"
with Submitter(plugin="slurm", sbatch_args=sbatch_args) as sub:
sub(wf)
#res= wf.result()
#print(results.output.out)
--output-space fsaverage6 --use-aroma \
--skip-bids-validation --mem_mb 7500 \
--fs-license-file /BASE/freesurfer_license.txt \
--fs-subjects-dir {OUTDIR}/freesurfer \
--ignore slicetiming --cifti-output -w {SUBWORKDIR}".split()
CMD_LIST.append(CMD)
print("Sample command:")
print(CMD_LIST[0])
#####################################################################
singu = SingularityTask(
name="fmriprep",
executable=CMD_LIST,
image=IMAGE,
cache_dir=CACHEDIR,
bindings=[(BASE, "/BASE", "rw")],
container_xargs=['--cleanenv'],
#audit_flags=AuditFlag.ALL,
#messenger=FileMessenger()
).split("executable")
print()
print("SingularityTask inputs:")
print(singu.inputs)
print()
print("SingularityTask container_args:")
print(singu.container_args)
print()
#SBATCH_ARGS = f"-J {SITE} -t 30:00:00 --mem=8GB --cpus-per-task=2 -p gablab [email protected] --mail-type=ALL,TIME_LIMIT"
#SBATCH_ARGS = f"-J {SITE} -t 36:00:00 --mem=8GB --cpus-per-task=2 -p normal [email protected] --mail-type=ALL,TIME_LIMIT"
site=wf.lzin.site,
fs_license=wf.lzin.fs_license,
workdir=wf.lzin.workdir,
)
)
wf.set_output([("out", wf.create_cmd.lzout.out)])
with Submitter(plugin="cf") as sub:
sub(wf)
res = wf.result()
cmd = res.output.out
# wf2 = Workflow(name="wf2", input_spec=['executable', 'image'])
singu = SingularityTask(
name="fmriprep",
cache_dir=pydra_cache,
executable=cmd,
image="/om4/group/gablab/data/singularity-images/fmriprep-v1.3.0p2.sif",
bindings=[(wf_inputs["base_path"], "/BASE", "rw")],
)
# set fmriprep commands as workflow output for now
# wf.set_output([("out", wf.fmriprep.lzout.stdout),
# ("err", wf.fmriprep.lzout.stderr)])
sbatch_args = "-J {site} -t 1-04:00 --mem=10GB --cpus-per-task=1".format(**wf_inputs)
with Submitter(plugin="slurm", sbatch_args=sbatch_args) as sub:
sub(singu)
