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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
---------------------------------------------------------------------------