Dear Chintan,
You can ignore the extra job, or better still make the change from -le to -lt.
This is already in our internal code but unfortunately has not yet made it to a patch.
As for the problems you are seeing, have you checked that all the individual
processes are completing correctly and without errors? We see this sort of
behaviour when individual processes fail to generate correct output (or any
output). If this is not the case then please give us some more details about
the set up of your possum job (the saved GUI settings, along with the fslhd
output from any customised input images, would be most useful).
All the best,
Mark
On 14 Sep 2011, at 17:48, Chintan Shah wrote:
> Hi all,
> I am having a few problems with running possum in a cluster environment that I was hoping I could get some help with.
> First, I noticed that possumX was creating an extra job (i.e. 101 jobs for 100 procs) and was wondering whether this was a problem or not. I found the post below (from several years ago) in which I noticed that the line
> for ((procnum=0; procnum < $nproc; procnum++)) ; do
> was replaced with
> procnum=0
> while [ $procnum -le $nproc ]
> It looks like -le was used instead of -lt and so it produces an extra job. I don't think this makes a difference, as looking into possum_sum it seems like it only uses partial signal files from 0 to nproc-1. I just wanted to point it out and also ask if there are any known issues related to it, since I'm not sure exactly how possum splits up jobs.
>
> My main issue is also with regard to how possum splits up jobs. I'm slowly scaling up to run a larger simulation with motion on our cluster, but I first tried a small sim with just a single volume. When I run it with 8 processors it works fine. However when I run the exact same setup with 40 processors, it produces strange, almost rectangular output (in the axial view), which becomes even more distorted with nproc=100. I've attached some images to help describe what I'm talking about. Has anyone else run into a similar issue with changing the number of processors? or does anyone have a suggestion? Any help/comments would be appreciated!!
>
> Thanks,
> Chintan
> <axial_8.png><axial_40.png>
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