Alex and Michael,
Thanks for your help and suggestions.
The update of the FLS package seemed to do the trick. I updated today.
Also, i received the same error message talked about in this link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1301&L=fsl&P=R107838&1=fsl&9=A&J=on&d=No+Match%3BMatch%3BMatches&z=4
Unable to run job: Colon (':') not allowed in objectname.
I followed the suggestion of commenting out the following line 373 in fsl_sub:
echo "default queue: \"$queue\""
Now, running tbss_2_reg and bedpostx works.
Thanks,again
D. Michael
________________________________
From: Michael Hanke <[log in to unmask]>
To: [log in to unmask]
Sent: Sunday, January 20, 2013 7:32 AM
Subject: Re: [FSL] Parallel processing SGE and Ubuntu
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
>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
>>>>
>>>
>>
>
>
>
