not sure what is happening. You can run recon-all with -debug and
capture the output (both stdout and stderr) into a file. This will cause
it to print out huge amounts of text specifying what it is doing on each
line. You should also see if there is some stderr output that is not
being caught. You can try running recon-all -fill on the subject that
you created to see if the fill will run at all (this may be easier than
waiting 4 hours).
On 4/8/2024 3:18 PM, Dong, Yilei wrote:
External Email - Use Caution
Hi Freesurfer Support,
The past few weeks, I've emailed about my recon-all processing stream
never completely finishing.
We are still encountering the same problem. For context, our recon-all
job submission script runs recon-all for 1 image. Given a folder of
100 MRI images, we have another script that calls upon the recon-all
script for each image within the folder via a for loop. The result is
100 jobs running in parallel on the cluster.
I have attached a screenshot of the parameters we set whenever we
submit each recon-all job for each image by SLURM to UCSD's cluster.
The maximum time we are allowed for each job is 48 hours. Our jobs are
shared-node jobs, which means we run more than 1 job on a single node.
This time, we increased RAM from 8GB to 16GB in hopes the entire
recon-all processing stream can fully run through for each image, but
it still stops at "mri_pretess done" and does not go on to the -fill
step. Each job submitted to the cluster took around 4 hours and 20
minutes each to run in our most recent attempt.
If increasing the RAM did not change anything for us, how else can we
get more verbose error messages? What other reasons could be why our
recon-all aborts before finishing? I have attached a recon-all.log
from one of our subjects for reference and a screenshot of the
parameters we set for submitting jobs in our cluster for reference.
Freesurfer version: 7.2.0, but already available as module on UCSD's
cluster system
Platform: Rocky Linux release 8.8 (Green Obsidian)
uname -a: Linux login01 4.18.0-477.15.1.el8_8.x86_64 #1 SMP Wed Jun 28
15:04:18 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux
Recon-all log: see attached
Thank you!
Sincerely,
Yilei
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