Hey,
Note that I am currently build a FSL package update that addresses an issue
that could be the cause for this behavior. The update should become
available tomorrow.
Michael
On Jan 19, 2013 8:46 PM, "D D" <[log in to unmask]> wrote:
> Alex,
>
> Thanks. Okay, I tried your suggestions with tbss_2_reg and I get this
> error message:
>
> Unable to read script file because of error: error opening dm@localhost:
> No such file or directory
>
> I then tried to run bedpostx on a data set.
>
> I get he following lines:
>
> switching from /data/transfer/preprocess/scrap to /data/transfer/preprocess
> bedpostx /data/transfer/preprocess/scrap --nf=2 --fudge=1 --bi=1000
> /usr/share/fsl/5.0/bin/bedpostx /data/transfer/preprocess/scrap --nf=2
> --fudge=1 --bi=1000
> subjectdir is /data/transfer/preprocess/scrap
> Making bedpostx directory structure
> Queuing preprocessing stages
> Queuing parallel processing stage
> Queuing post processing stage
>
> Type /data/transfer/preprocess/scrap.bedpostX/monitor to show progress.
> Type /data/transfer/preprocess/scrap.bedpostX/cancel to terminate all the
> queued tasks.
>
> You will get an email at the end of the post-processing stage.
>
>
> And then a pop-up window appears stating:
>
> Errors: Unable to run job: At ('@')not allowed in objectname
> Job was rejected because job requests unknown queue "-M".
> Exiting.
> Errors: Unable to run job: At ('@')not allowed in objectname
> Job was rejected because job requests unknown queue "-M".
> Exiting.
> Errors: Unable to run job: At ('@')not allowed in objectname
> Job was rejected because job requests unknown queue "-M".
> Exiting.
>
>
> So, I'm getting there, but still getting these error message when trying
> to run a program that can use parrallel processing.
>
> D.Michael
> ------------------------------
> *From:* "[log in to unmask]" <[log in to unmask]>
> *To:* [log in to unmask]
> *Sent:* Saturday, January 19, 2013 5:51 AM
> *Subject:* Re: [FSL] Parallel processing SGE and Ubuntu
>
> Hi D. Michael,
>
> Thanks for the details on how you did it. I didn't know condor wasn't
> working on 10.04.
>
> Sorry, I might be confusing you.
> Some scripts in FSL already uses fsl_sub to submit different processes to
> a queue then you don't need to execute it with fsl_sub. But that is not the
> case of tbss_1_preproc.
> So, if you want one tbss_1_preproc execution to submit many processes to
> the queue you would have to modify it to do so.
>
> Looking at the TBSS manual, there is an indication that tbss_2_reg does
> use fsl_sub, so if you want to see your SGE working, you might want to
> finish tbss_1_preproc and then use tbss_2_reg.
>
> In some cases, mostly when processing many images (in batch), you can
> execute each process with fsl_sub to use SGE, but you would have to program
> the loop or the batch script.
>
> I hope this helps.
>
> Cheers,
> Alex
>
> Alexandre Manhães Savio <[log in to unmask]>
> Grupo de Inteligencia Computacional <http://www.ehu.es/ccwintco>
> Departamento de CCIA
> UPV/EHU
>
>
> On 18 January 2013 20:59, D. Michael <[log in to unmask]> wrote:
>
> Alex,
>
> Thanks for the feedback.
>
> I tried installing condor,but have been having issues with Ubuntu 10.04.
> Upgrading to 12.04 would be something we'd like to avoid until down the
> line.
>
> I've been trying to use SGE as an alternative.
>
> Thanks for the link below about SGE and FSL. I've seen some other recent
> stuff where I would dowload sgengine and associated applications directly.
> So, that is what I did.
>
> I also came across this link in the fsl forums:
>
>
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1102&L=FSL&D=0&1=FSL&9=A&J=on&d=No+Match%3BMatch%3BMatches&z=4&P=42344
>
>
> I looked into the how to configure from the
> /usr/share/doc/gridengine-common/README.Debian readme file.
>
> I've done the following steps:
>
> + sudo -u sgeadmin qconf -am myuser
>
> * and to a userlist:
> + qconf -au myuser users
>
> * Add a submission host:
> + qconf -as myhost.mydomain
>
> * Add an execution host:
> + qconf -ae
> You will now be prompted for information about the execution host.
>
> * Add a new host group:
> + qconf -ahgrp @allhosts
>
> * Add the exec host to the @allhosts list:
> + qconf -aattr hostgroup hostlist myhost.mydomain @allhosts
>
> * Add a queue:
> + qconf -aq main.q
>
> * Add the host group to the queue:
> + qconf -aattr queue hostlist @allhosts main.q
>
> * Make sure there is a slot allocated to the execd:
> + qconf -aattr queue slots "[myhost.mydomain=1]" main.q
>
> * Running qstat -f should then show you the execd waiting for jobs
>
> I typed export FSLPARALLEL=1 in a given shell, and tried to run an
> "fsl_sub tbss_1_preproc". I'm able to get a jobs list from qstat -f
>
> We want to spread out the job onto a select amount of processors. It seems
> when I type "top", my tbss_1_preproc command is still using one processor
> at 100%. With parallel processing, shouldn't it spread out to multiple
> cpu's? Given the link above, i tried the command
>
> qconf -aattr queue slots "[myhost.mydomain=1]" --> "[myhost.mydomain=6]"
> with my configuration, to use processors 1 through 6. Is this correct? Am
> I on the right track?
>
> Thanks,
>
> D. Michael
>
>
> On Fri, 18 Jan 2013 16:05:24 +0100, [log in to unmask] <
> [log in to unmask]> wrote:
>
> >Hi D. Michael,
> >
> >1.
> >I'm not sure if you have to set the line as: export FSLPARALLEL=1
> >Is your SGE installation working? I guess you would need to configure it
> >first either for it to run on your own machine correctly as to run within
> >FSL "needs".
> >Please, check this:
> >https://www.fmrib.ox.ac.uk/phpwiki/index.php/FslSge
> >
> >2.
> >To submit a job to a SGE queue you would have to run it with fsl_sub as:
> >fsl_sub bedpost <bestpost_args>
> >
> >Please, check fsl_sub help for more arguments.
> >
> >3.
> >If any of this doesn't work:
> >If you are using the Neurodebian repository, I would recommend you to use
> >condor, instead of SGE.
> >In this mailing list there are some details on how to install and use it,
> >or you might want to check this first:
> >
> http://neuro.debian.net/blog/2012/2012-03-09_parallelize_fsl_with_condor.html
> >
> >In summary:
> >sudo apt-get install condor. Choose automatic, personal installation (say
> >yes to everything it asks during installation).
> >
> >Then set the line in fsl.sh to: export FSLPARALLEL=condor.
> >
> >If you have any other problem with this, please ask. I'm not sure if a
> >change to fsl_sub is needed.
> >
> >With the Neurodebian Condor configuration I found the easiest way to have
> >an execution queue engine.
> >
> >Cheers,
> >Alex
> >
> >Alexandre Manh�es Savio <[log in to unmask]>
> >Grupo de Inteligencia Computacional <http://www.ehu.es/ccwintco>
> >Departamento de CCIA
> >UPV/EHU
> >
> >
> >On 18 January 2013 12:29, D. Michael <[log in to unmask]> wrote:
> >
> >> Hello,
> >>
> >> I'm trying to setup parallel processing using FSL on my 10.04 Ubuntu
> >> operating system, and have been searching around to figure out how to
> set
> >> this up.
> >>
> >> I've installed gridengine-master gridengine-exec gridengine-client
> >> gridengine-qmon.
> >>
> >> I also uncommented in my /etc/fsl/5.0/fsl.sh file, the line
> >> "FSLPARALLEL=1".
> >>
> >> Are there more steps involved?
> >>
> >> Say if, I want to run a command line tbss_1_preproc or bedbpost, what
> >> would be the command line to run it in parallel. I have a single machine
> >> with 16 processors available.
> >>
> >> Thanks,
> >>
> >> D. Michael
> >>
> >
>
>
>
>
>
