HI,
On 10 Aug 2009, at 09:22, judith wrote:
> Hi,
>
> Thanks for your response.
> Actually, we do use SGE software for our clustering. However we do not
> submit on the default delay of 15 sec, but on a delay of only 1 sec.
> Could the
> problem be caused by the fact that the file is not filled up with
> actual
> commands before SGE starts running it?
It shouldn't be, no - that job is submitted with a 'hold' until the
previous job has completed, so it should be filled with the correct
commands before it gets sent to a cluster node.
To find relevant commands,
grep flameo $FSLDIR/tcl/*
Cheers.
> We would like to try to delay the submission just before the fslsub
> command.
> Could you help us out where this command is actually located? Or is
> it located
> in a binary code?
>
>
> Many thanks
> Judith
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On
> Behalf Of
> Steve Smith
> Sent: zaterdag 8 augustus 2009 8:32
> To: [log in to unmask]
> Subject: Re: [FSL] high level FEAT
>
> Hi - yes, the initial script fills this file with dummy arguments
> (so that it has
> the right length for SGE to see) and a later script fills it up with
> the actual
> commands before SGE gets as far as running it.
>
> I'm guessing that you are not using SGE software for your
> clustering, so this
> doesn't work on your cluster? I guess your clustering software maybe
> reads
> the file immediately it is submitted rather than once the script is
> ready to run?
>
> Cheers.
>
>
> On 7 Aug 2009, at 09:11, judith wrote:
>
>> Hi,
>>
>> Thank you for your repsonse and advise.
>> I spoke with our systems manager about your questions of OS, hardware
>> and FSL version. We also tried again together to locate and fix the
>> error. We ran into the following problems:
>>
>>
>> The program feat starts a lot of featX_YY programs. One of them is
>> feat3b_flame using -t ./.flame as a command file option. However at
>> the time of submitting the .flame file only contains dummy as a
>> program to execute. So the jobs submitted to the cluster all fail.
>> Afterwards the .flame files contains flameo commands. We have no idea
>> where the latter come from. We found line in feat where dummy is
>> added
>> to the .flame file but we don't understand why this is done.
>>
>>
>>
>> We think this is the reason why the error /apps/fsl/current/bin/
>> flameo -- cope=filtered_func_data --
>>> vc=var_filtered_func_data --dvc=tdof_filtered_func_data --mask=mask
>>> --
>>> ld=stats --dm=design.mat --cs=design.grp --tc=design.con --
>>> runmode=fe
>> occurs in the GUI.
>> Indeed when we run one of these flameo commands directly from the
>> command line it works. We tested our hypothesis by changing the
>> fsl_sub script to execute all jobs without submitting to the grid and
>> indeed this too worked fine. For some reason no dummy commands were
>> written to the .flame file at that time...
>>
>>
>> Do you have a solution for this problem?
>>
>>
>>
>> OS: Clustervision OS 5.0 (based on Redhat Enterprise 5 and CentOS 5)
>>
>> Arch: 64bit
>>
>> FSL: 4.1.2
>>
>> kernel: 2.6.18
>>
>> Many thanks
>>
>> Judith & Bart (systems manager)
>>
>>
>>
>> -----Original Message-----
>> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On
>> Behalf Of Steve Smith
>> Sent: woensdag 5 augustus 2009 8:02
>> To: [log in to unmask]
>> Subject: Re: [FSL] high level analysis FEAT
>>
>> Hi,
>>
>> This is a very strange looking error - I suspect either that there is
>> something wrong with your computer or file system mounting, or it
>> is a
>> weird operating system that we've not seen before. Exactly what
>> hardware and OS are you running, and which version of FSL? Have you
>> tried rebooting your computer?
>>
>> Cheers.
>>
>>
>> On 4 Aug 2009, at 08:10, judith wrote:
>>
>>> Hi,
>>>
>>> I am having troubles performing a high level analysis using low
>>> level
>>> feat directories.
>>> For low level processing I was not experiencing any trouble.
>>> However, using
>>> these low level feat directories in a high level analysis, for
>>> example a simple average of one group using mixed effects or fixed
>>> effects, the high level stats crashes at the following command:
>>> /apps/fsl/current/bin/flameo --cope=filtered_func_data --
>>> vc=var_filtered_func_data --dvc=tdof_filtered_func_data --mask=mask
>>> --
>>> ld=stats --dm=design.mat --cs=design.grp --tc=design.con --
>>> runmode=fe
>>> Warning: no access to tty (Bad file descriptor).
>>> Using this command by entering it in the terminal, it runs without
>>> any problems the stats, so the data needed are available.
>>> However since poststats cannot be ran seperatly, I cannot perform
>>> the
>>> analysis needed.
>>> Does anyone have an idea wat I am doing wrong?
>>>
>>> I will add the whole command line below:
>>> Higher-level stats
>>>
>>> cat ../design.lcon | awk '{ print }' > design.lcon
>>> /apps/fsl/current/bin/flameo --cope=filtered_func_data --
>>> vc=var_filtered_func_data --dvc=tdof_filtered_func_data --mask=mask
>>> --
>>> ld=stats --dm=design.mat --cs=design.grp --tc=design.con --
>>> runmode=fe
>>> Warning: no access to tty (Bad file descriptor).
>>> Thus no job control in this shell.
>>> dummy: Command not found.
>>> Warning: no access to tty (Bad file descriptor).
>>> Thus no job control in this shell.
>>>
>>> /bin/rm -f stats/zem* stats/zols* stats/mask* ; /bin/mv dof stats
>>> Warning: no access to tty (Bad file descriptor).
>>> Thus no job control in this shell.
>>>
>>> Post-stats
>>>
>>> couldn't change working directory
>>> to "/mic/jvhoev2/data_taal/data/CO/FE_single_group_average.gfeat/
>>> cope1.feat
>>> /stats": no such file or directory
>>> while executing
>>> "cd ${FD}/stats"
>>> (procedure "feat5:proc_poststats" line 50)
>>>
>>
>>
>> ----------------------------------------------------------------------
>> ----- Stephen M. Smith, Professor of Biomedical Engineering Associate
>> Director, Oxford University FMRIB Centre
>>
>> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
>> +44 (0) 1865 222726 (fax 222717)
>> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
>> ----------------------------------------------------------------------
>> -----
>>
>
>
> ---------------------------------------------------------------------------
> Stephen M. Smith, Professor of Biomedical Engineering Associate
> Director,
> Oxford University FMRIB Centre
>
> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
> +44 (0) 1865 222726 (fax 222717)
> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
> ---------------------------------------------------------------------------
>
---------------------------------------------------------------------------
Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR 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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