Condor status writes to me that cores are unclaimed after  
fsl5.0-bedpostx comand.

Name               OpSys      Arch   State     Activity LoadAv Mem    
ActvtyTime

slot1@             LINUX      X86_64 Unclaimed Idle     0.040  3981   
1+22:14:52
slot2@             LINUX      X86_64 Unclaimed Idle     0.000  3981   
1+22:15:21
slot3@             LINUX      X86_64 Unclaimed Idle     0.000  3981   
1+22:15:22
slot4@             LINUX      X86_64 Unclaimed Idle     0.000  3981   
1+22:15:23
                      Total Owner Claimed Unclaimed Matched Preempting Backfill

         X86_64/LINUX     4     0       0         4       0          0        0

                Total     4     0       0         4       0          0        0

Maybe it is important and I forgot to write it. Between last analysis  
when the estimation worked and when it did not work, I have installed  
freesurfer package on my PC with this manual  
http://simnibs.de/installation/installfsandfsl . Since that time, my  
terminal writes next rows on each terminal start.

-------- freesurfer-Linux-centos6_x86pub-v5.3.0 --------
FREESURFER_HOME     /usr/local/freesurfer
FSFAST_HOME         /usr/local/freesurfer/fsfast
FSF_OUTPUT_FORMAT   nii.gz
SUBJECTS_DIR        /usr/local/freesurfer/subjects
MNI_DIR             /usr/local/freesurfer/mni
labounek@PC-E229-455:~$

Best,
Rene

Cituji "[log in to unmask]" <[log in to unmask]>:

> Hi,
>
> Great. I don't know if monitor has been improved, but as long as I know it
> never worked as it was meant. You might need to check condor_status.
>
> Alexandre Manh~aes Savio <[log in to unmask]>
> Grupo de Inteligencia Computacional <http://www.ehu.es/ccwintco>
> Departamento de CCIA
> UPV/EHU
>
>
> On 4 December 2013 20:17, René Labounek <[log in to unmask]> wrote:
>
>>  The errors disappeared but the computer is still not computing. After
>> comand:
>> /media/407285B97285B3E6/Data/humanconnectome/Q3/151526/T1w/Diffusion.bedpostX/monitor,
>> there is written only one output: 0 slices processed.
>>
>> Rene
>>
>> Dne 4.12.2013 17:28, [log in to unmask] napsal(a):
>>
>>   Hi René,
>>
>>  .bash_profile doesn't exist initially.
>>
>>  I see that you are running fsl using "fsl5.0-".
>>
>>  Could you please execute these two commands:
>>
>>  echo ". /etc/fsl/5.0/fsl.sh" >> ~/.bashrc
>> echo "if [ -f ~/.bashrc ]; then . ~/.bashrc; fi" >> ~/.bash_profile
>>
>>  It will add in the first command the settings to your interactive
>> terminals and in the second anything you have .bashrc to your remote login
>> shells (which are used by other softwares as well).
>>
>>  After that, try the experiment again in a new terminal.
>>
>>  Cheers,
>>  Alex
>>
>>
>>
>> Alexandre Manh~aes Savio <[log in to unmask]>
>> Grupo de Inteligencia Computacional <http://www.ehu.es/ccwintco>
>> Departamento de CCIA
>> UPV/EHU
>>
>>
>> On 4 December 2013 16:53, René Labounek <[log in to unmask]>wrote:
>>
>>>  Helo Alex,
>>> I did not set any of these .bash files before. I have added neurodebian
>>> to my repositary and installed fsl. Then I have started to use bedpostx
>>> function but it worked only on one processor. I have found this
>>> instructions about paralelising with condor and installed condor.
>>>
>>>
>>> http://neuro.debian.net/blog/2012/2012-03-09_parallelize_fsl_with_condor.html
>>>
>>> In /etc/fsl/fsl.sh, I have changed: export FSLPARALLEL=condor. The
>>> calculation was working on all my processors. Since that time, I have not
>>> changed anything. Today, I wanted to start new calculation and it is not
>>> working.
>>>
>>> I was looking into all files you have written but nowhere I did not find
>>> any variable called FSL or something like that. Maybe problem is here but I
>>> do not know which variables I should define. If I understand these files
>>> serves for definition of global bash variables. On my PC, I have found
>>> .bashrc and /etc/bash.bashrc, not found ~/.bash_profile.
>>>
>>> In error, there is writen /bin/zeropad: not found and /bin/imtest: not
>>> found. I am not sure what this files should do but truly I have not them on
>>> hard disk.
>>>
>>> Even, I am not sure I should write this problem here or on some
>>> neurodebian forum.
>>>
>>> Rene
>>>
>>>
>>> Dne 4.12.2013 16:03, [log in to unmask] napsal(a):
>>>
>>>    Hello René,
>>>
>>>  Have you set your ~/.bash_profile file?
>>>  It should source either your fsl settings or your .bashrc or
>>> /etc/bash.bashrc file if you have them changed for FSL.
>>>  If that is the case, more info here:
>>> http://mywiki.wooledge.org/DotFiles
>>>
>>>  I hope this helps.
>>>
>>> Cheers,
>>> Alex
>>>
>>> Alexandre Manh~aes Savio <[log in to unmask]>
>>> Grupo de Inteligencia Computacional <http://www.ehu.es/ccwintco>
>>> Departamento de CCIA
>>> UPV/EHU
>>>
>>>
>>> On 4 December 2013 15:50, René Labounek <[log in to unmask]>wrote:
>>>
>>>>  Dear FSL users,
>>>>
>>>> I am using condor for bedpostx paralelising on Ubuntu 12.04. The
>>>> computation worked but suddenly it does not. Does anyone have  
>>>> same problem?
>>>> Some problem with update or something else?
>>>>
>>>> Here is my folder with dMRI data. I think everything should be right.
>>>>
>>>> labounek@PC-E229-455:/media/407285B97285B3E6/Data/humanconnectome/Q3/151526/T1w/Diffusion$
>>>> *ls*
>>>> bedpostx_qsub.RZG87UQEgeo23*      bvals      bvecs      data.nii.gz
>>>>     grad_dev.nii.gz      nodif_brain_mask.nii.gz*
>>>>
>>>> Now, when I will use bedpostx comand with default parameter setting I
>>>> will get the condor output:
>>>>
>>>> *fsl5.0-bedpostx
>>>> /media/407285B97285B3E6/Data/humanconnectome/Q3/151526/T1w/Diffusion*
>>>>
>>>> ______________________________________________________________________________________________________________________________________
>>>> subjectdir is
>>>> /media/407285B97285B3E6/Data/humanconnectome/Q3/151526/T1w/Diffusion
>>>> Making bedpostx directory structure
>>>> Queuing preprocessing stages
>>>> Queuing parallel processing stage
>>>> Queuing post processing stage
>>>>
>>>> Type
>>>> /media/407285B97285B3E6/Data/humanconnectome/Q3/151526/T1w/Diffusion.bedpostX/monitor
>>>> to show progress.
>>>> Type
>>>> /media/407285B97285B3E6/Data/humanconnectome/Q3/151526/T1w/Diffusion.bedpostX/cancel
>>>> to terminate all the queued tasks.
>>>>
>>>> You will get an email at the end of the post-processing stage.
>>>>
>>>> ______________________________________________________________________________________________________________________________________
>>>>
>>>> The Diffusion.bedpostx folder is created including tipical folders and
>>>> files.
>>>>
>>>>
>>>> labounek@PC-E229-455:/media/407285B97285B3E6/Data/humanconnectome/Q2/Q2_diffusion_preprocessed/499566/T1w/Diffusion.bedpostX$
>>>> *ls*
>>>> *cancel  commands.txt  diff_slices  logs  monitor  xfms*
>>>>
>>>>
>>>> After comand:   
>>>> */media/407285B97285B3E6/Data/humanconnectome/Q3/151526/T1w/Diffusion.bedpostX/monitor
>>>> *; I will get lots error messages lokking like these shown below and
>>>> the calculation is not working.
>>>>
>>>> __________________________________________________________________________________________________________________________________________________
>>>> /media/407285B97285B3E6/Data/humanconnectome/Q3/151526/T1w/Diffusion.bedpostX/monitor:
>>>> 1:
>>>> /media/407285B97285B3E6/Data/humanconnectome/Q3/151526/T1w/Diffusion.bedpostX/monitor:
>>>> /bin/zeropad: not found
>>>> /media/407285B97285B3E6/Data/humanconnectome/Q3/151526/T1w/Diffusion.bedpostX/monitor:
>>>> 1:
>>>> /media/407285B97285B3E6/Data/humanconnectome/Q3/151526/T1w/Diffusion.bedpostX/monitor:
>>>> /bin/imtest: not found
>>>> /media/407285B97285B3E6/Data/humanconnectome/Q3/151526/T1w/Diffusion.bedpostX/monitor:
>>>> 10: [: -eq: unexpected operator
>>>>
>>>> __________________________________________________________________________________________________________________________________________________
>>>>
>>>> Preprocessing, processing and postprocessing did not start. I have no
>>>> idea what to do.
>>>>
>>>> Best,
>>>> Rene
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>
>>>
>>
>>
>