[Neurodebian-users] Neurodebian with condor for FSL - 'Cannot access initial working directory'

[Jacqueline Scholl]

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Dear all,
I have been trying to narrow down the problem further. When I type condor_q -long <jobID> for one of the failed jobs, I get the information that Owner = brain and User= brain at neurodebian.
When I then go to the filer that produced the 'permission denied' message, and type ls-l it says: drwxrwx--- 1 root vboxsf 2042 Jan 21 12:53 FOLDERNAME.
Could this somehow explain the permission denied error?
Best wishes
Jacquie


Dear all,

I have been trying to use neurodebian with condor on a mac machine to parallelise higher level FSL. Following the instructions form the neurodebian website, I managed without any problems to install virtual machine, neurodebian, fsl and condor. I then also followed the instructions in 'enjoy parallelized fsl' section, namely I typed in the neuordebian terminal:
. /etc/fsl/fsl.sh
export FSLPARALLEL=condor
then I opened feat and started a higher level analysis on first level analyses I had already run on the mac before. This seemed to work fine initially: typing condor_q showed me that many jobs had been created and where on 'running' or 'held'. Also, in the activity monitor, I saw a very high CPU and memory usage, which suggested to me it's running.

But I think now there has been some problem somewhere: since 10pm last night, no new outputs have been created (I started it at 4pm) and now it is 3pm the next day. And when I type condor_q -hold, I see that there are queues on hold because of 'Cannot access initial working directory /media/sf_host/gfeats/design37_Debian/cope33.feat: Permission denied' where 'design37_Debian' is where the FSL output of the higher level analysis is stored. And so '.../design37_Debian/cope33.feat' is a folder that has been created while running the analysis from within debian. When I go within neurodebian to the folders and click on 'properties>permission', it says 'Read & Write' for Owner:root and for Group:vboxsf. In the terminal, when I type ls -l, it tells me 'drwxrwx---'. The timing of this process on hold is about 5 min after I started the initial analysis.

For other processes it says 'submitted on hold at user's request' and the timing of this is the time when I started the initial analysis.

When I type condor_status, it tells me that all 5 processors are in state 'unclaimed' and activity 'idle'.

I would be very grateful for any advice I could get on this
Best wishes
Jacquie
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