Hi again Michael,
Thanks again for your input.
I have made the following changes to the FreeSurferPipeline.sh script.
They are not quite the same as your changes, because for the time being
I want to maintain a level of backward compatibility. That is, if NSLOTS
is set, we'll use it to determine the input value for the -openmp
option. If it is not set, I want to continue to behave just as before
(use 8 as the value for the -openmp option.)
Using the current value of 8 as the default for when NSLOTS is not set
might cause problems if specifying more cores than are actually
available to the recon-all command causes problems with the recon-all
run. I have not been able to find any documentation that indicates what
would happen in that case. So I'm being a bit conservative here and not
changing the default from the current value of 8 to a new value of 1.
My changes look like the following. They have been checked into the
repository, are not yet in a released version, and should end up
(unless someone convinces me to set the default to 1 instead of 8) in
the next release.
cp "$SubjectDIR"/"$SubjectID"/mri/brainmask.auto.mgz
"$SubjectDIR"/"$SubjectID"/mri/brainmask.mgz
# Both the SGE and PBS cluster schedulers use the environment variable
# NSLOTS to indicate the number of cores
# a job will use. If this environment variable is set, we will use it
# to determine the number of cores to
# tell recon-all to use.
if [[ -z ${NSLOTS} ]]
then
num_cores=8
else
num_cores="${NSLOTS}"
fi
recon-all -subjid $SubjectID -sd $SubjectDIR -autorecon2 -nosmooth2 -
noinflate2 -nocurvstats -nosegstats -openmp ${num_cores}
Best Regards,
Tim
On Tue, Jun 16, 2015, at 11:24, m s wrote:
> Version 3.4.0
>
> Hi,
>
> The Pipelines-3.4.0//FreeSurfer/FreeSurferPipeline.sh script has a hard-
> coded value of 8 for the -openmp argument in the call to recon-all.
> This doesn't seem like a good idea. Seems it should be an option and
> default to 1.
>
> We've modified it to work with NSLOTS for SGE on our cluster. Here's
> the diff if you're interested:
>
> < cp "$SubjectDIR"/"$SubjectID"/mri/brainmask.auto.mgz
> "$SubjectDIR"/"$SubjectID"/mri/brainmask.mgz < < # CFN mod - use
> $NSLOTS to define multithreading < if [[ -z "$NSLOTS" ]]; then <
> NSLOTS=1 < fi < < recon-all -subjid $SubjectID -sd $SubjectDIR
> -autorecon2 -nosmooth2 -noinflate2 -nocurvstats -nosegstats -
> openmp $NSLOTS
> ---
> > cp "$SubjectDIR"/"$SubjectID"/mri/brainmask.auto.mgz
> > "$SubjectDIR"/"$SubjectID"/mri/brainmask.mgz recon-all -subjid
> > $SubjectID -sd $SubjectDIR -autorecon2 -nosmooth2 -noinflate2 -
> > nocurvstats -nosegstats -openmp 8
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--
Timothy B. Brown
Business & Technology Application Analyst III
Pipeline Developer (Human Connectome Project)
tbbrown(at)wustl.edu
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