Hi

The results are exactly same without --xyz flag.

The exit signal from sge is 137 and by some search in web this looks to 
mean that the used program, in this case b0calc, calls abort by itself.

According to sge logs the memory or swap is nor running out.



Mark Jenkinson wrote:
> Hi,
> 
> That's unusual, as this machine seems to have plenty of
> memory and it seems to have passed through the
> difficult stages of creating the FFTs.  Can you try it without
> the --xyz option and see if that works?
> 
> All the best,
>     Mark
> 
> 
> On 13 Apr 2010, at 19:06, Juha Pajula wrote:
> 
>> Hi!
>>
>> Last machine I used was our deparment computing cluster. The used node 
>> had 32 gb of RAM and 10gb of swap. The cluster is running with Redhat 
>> Enterprise Linux operating system and the used FSL is version 4.1.4.
>>
>> The image has 256x256x256 pixels with 1 mm cubic size.
>>
>> The outputs from the program are following:
>> Normal output from the grid engine:
>> ---
>> Calculating Bz field
>> Calculating kernel
>> zero pad
>> Forward FFT
>> Forward FFT
>> Kernel multiplication
>> ---
>>
>> Error output from the grid engine:
>> ---
>> .
>> .
>> .
>> .
>> .
>> .
>> .
>> .
>> Image Exception : #99 :: Out of memory
>> terminate called after throwing an instance of 
>> 'RBD_COMMON::BaseException'
>> #SPOOL PATH#/spool/outolintu16/job_scripts/38441: line 1:  8013 
>> Aborted                 b0calc -i 
>> #PATH#/JH645/JH_anat_kaannetty_atmask -o #PATH#/b0/JH_b0/JH_b0x 
>> --b0x=1 --b0y=0 --b0=0 --xyz --verbose
>> ---
>>
>> I removed the paths from the error report, so don't care about #SPOOL 
>> PATH# and #PATH#.
>>
>>
>>
>> Mark Jenkinson kirjoitti:
>>> Hi,
>>>
>>> Sounds like you are running out of memory for this.
>>> What are the dimensions of your input image?
>>> That is, how many voxels in each direction?
>>>
>>> And do you get any output from the command at all?
>>>
>>> It would also be useful to know how much RAM and swap
>>> your machine has, and what type of machine and OS it is.
>>>
>>> All the best,
>>>    Mark
>>>
>>>
>>> On 13 Apr 2010, at 15:43, Juha Pajula wrote:
>>>
>>>> Hi!
>>>>
>>>> I am trying to create my own B0 inhomogeneities file for POSSUM with 
>>>> b0calc and fslmerge. I have followed the instructions from POSSUM 
>>>> homepage but I can't get the results out while b0calc gives me an 
>>>> error:
>>>>
>>>> Image Exception : #99 :: Out of memory
>>>>
>>>> The used command is like the example at POSSUM homepage:
>>>>
>>>> b0calc -i JH_anat_atmask -o outputut/b0/JH_b0x --b0x=1 --b0y=0 
>>>> --b0=0 --xyz --verbose
>>>>
>>>> I have tried to run this with separeted desktop computer as well as 
>>>> our department computing cluster via N1 Grid Engine. Both give the 
>>>> same result.
>>>>
>>>> The file JH_anat_atmask is in Analyze 7.5 format (with .hdr and .img 
>>>> files)
>>>>
>>>>
>>>> Can you help me to solve the problem?
>>>>
>>>>
>>>> -- 
>>>>
>>>> Juha Pajula,
>>>> Research Assistant,
>>>> Methods and Models for Biological Signals and Images group of Signal
>>>> Processing department in Tampere University of Technology
>>>>
>>>> email: [log in to unmask]
>>>> mobile: +358405426242
>>>>
>>