Hi - it sounds like you have a very specific query relating to your local
network - we have tested the bedpost parallelisation remote calls on just
a few network types - I'm afraid the best thing to do would be for you to
get help from your local sysadmin on how to set this up locally.
Sorry! Cheers, Steve.
On Fri, 4 Feb 2005, Arnaud Guidon wrote:
> Dear FoSsiLers,
>
> First let me thank the contributors of this great software!
>
> I would like to parallelize bedpost according to the explanations given
> in FDT documentation. I am running FSL on 5 G5 (macosx 10.3).
> I set all the FSL environment variables as should be and I obtained from
> my sysadmin remote access to 5 machines (without password).
> When I launch /bedpost/, the process hangs after the connection as if
> the /bedpost_proc/ command weren't running through ssh.
> I've tried providing ssh with options like "*-n*", "*-o* '*BatchMode
> yes'*" or "*-t*" but it didn't change anything.
>
> The only way that I got /diff_pvm/ running on a remote machine was by
> modifying this line of bedpost a tiny bit:
>
> $FSLREMOTECALL -q -o 'BatchMode yes' -t -n $machine ".
> ${HOME}/.fslconf/fsl.sh; ${FSLDIR}/bin/bedpost_proc ${subjdir}
> ${nslices} ${subjdir}.bedpost/logs/pid_${$}"
>
> instead of :
>
> echo "if [ -r /usr/local/etc/fslconf/fsl.sh ];then .
> /usr/local/etc/fslconf/fsl.sh;fi; if [ -r /etc/fslconf/fsl.sh ];then
> . /etc/fslconf/fsl.sh;fi; if [ -r \${HOME}/.fslconf/fsl.sh ]; then .
> \${HOME}/.fslconf/fsl.sh; fi; if [ x\${FSLDIR} != "x" ];then
> \${FSLDIR}/bin/bedpost_proc $subjdir $nslices
> ${subjdir}.bedpost/logs/pid_${$}; else echo FSLDIR not set in any
> default location on machine `hostname`;fi"| $FSLREMOTECALL $machine
> /bin/sh &
>
>
>
> Below are the results of TOP respectively for the first and the second
> machine, notice that both processors of the first machine are working
> whereas the second machine is not doing anything... :
>
> PID COMMAND %CPU TIME #TH #PRTS #MREGS RPRVT RSHRD
> RSIZE VSI
> 5181 top 9.0% 0:00.61 1 17 27 308K 464K
> 688K 27.
> *5176 diff_pvm 90.9% 0:55.22 1 11 26 4.83M+ 1.25M
> 5.65M+ 23.
> 5141 diff_pvm 87.3% 1:38.40 1 11 26 4.77M+ 1.25M
> 5.56M+ 24.*
>
> PID COMMAND %CPU TIME #TH #PRTS #MREGS RPRVT RSHRD
> RSIZE VSI
> 1848 top 10.7% 0:02.62 1 17 27 312K 464K
> 692K 27.
> 1812 bash 0.0% 0:00.04 1 12 19 220K 920K
> 852K 18.
> 1811 sshd 0.0% 0:00.02 1 9 44 104K 1.67M
> 464K 30.
> 1809 sshd 0.0% 0:00.18 1 15 44 116K 1.67M
> 1.48M 30.
>
>
>
> I wonder if anybody faced the same issue before? Any help would be
> greatly appreciated!
>
>
> Thank you.
>
> Arnaud Guidon
>
>
>
> ------------------------------------------------
> A. Guidon Research programmer
> Rochester Center for Brain Imaging
> Rochester, NY
>
>
>
>
>
>
--
Stephen M. Smith DPhil
Associate Director, FMRIB and Analysis Research Coordinator
Oxford University Centre for Functional MRI of the Brain
John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
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