Closed teresamg closed 4 months ago
Thanks for adding this! IIUC, this is a followup to #1124?
Could you say a little about the errors that you are seeing without the addition of this line?
GroupAFQ's parallel_params defaults to engine: serial, and this should still happen when using ParallelGroupAFQ. If there were errors with this line we can try something else?
Yeah, I think for now users would have to add: "engine" : "serial"
to their code, along the lines of:
import os.path as op
from AFQ.api.group import ParallelGroupAFQ
from AFQ.definitions.image import RoiImage
import AFQ.api.bundle_dict as abd
import AFQ.data.fetch as afd
_, bids_path = afd.fetch_hbn_preproc(
["NDARZT957CWG",
"NDARZU279XR3",
"NDARZU401RCU",
"NDARZU822WN3",
"NDARZV421TCZ",
"NDARZW262ZLV",
"NDARZX163EWC",
],
path="/gscratch/scrubbed/arokem/data/")
my_afq = ParallelGroupAFQ(
bids_path=bids_path,
preproc_pipeline="qsiprep",
parallel_params={
"engine" : "serial",
"submitter_params": {
"plugin": "slurm",
"sbatch_args": "-J test \
-p ckpt \
--nodes=1 \
--cpus-per-task=8 \
--gpus=1 \
-A escience \
--mem=64G \
--time=2:00:00 \
-o /gscratch/scrubbed/arokem/logs/test.out \
-e /gscratch/scrubbed/arokem/logs/test.err \
--mail-user=arokem@uw.edu \
--mail-type=ALL"
},
"cache_dir": "/gscratch/scrubbed/arokem/tmp"
}
)
my_afq.export_all()
Is that correct?
It should run, but users won't always know to specify engine: serial, and don't have to unless specifying other parameters, so I think the default should be in there somehow!
This makes sense to me! Merging
Hello @teresamg! Thanks for opening this PR. We checked the lines you've touched for PEP 8 issues, and found:
AFQ/api/group.py
: