Hi Kristian,
In that version of FSL, bedpostx_gpu is not using split_parts_gpu.
The patch is only for FSL 5.0.9.
Did you overwrite the files of FSL 5.0.7 with the ones from the patch ?
Maybe the best solution is to compile the source code.
If you want to try:
cd $FSLDIR/src/fdt
export FSLDEVDIR=$FSLDIR
. $FSLDIR/etc/fslconf/fsl.sh
export FSLCONFDIR=$FSLDIR/config
export FSLMACHTYPE=`$FSLDIR/etc/fslconf/fslmachtype.sh`
export COMPILE_GPU=1
export CUDA= "YOUR CUDA DIRECTORY where there is a bin directory with
nvcc", for example /opt/cuda-7.5
make install
Moises.
On 22 July 2016 at 19:35, Kristian M. Eschenburg <[log in to unmask]> wrote:
> Hi Moises
>
> Thank you for the information -- I forgot to mention that our GPU machine
> is using Ubuntu. Has the 5.0.9 version been released for Debian / Ubuntu
> users? It seems that the most recent FSL version for Debian / Ubuntu users
> is 5.0.7 ( http://neuro.debian.net/pkgs/fsl-complete.html ).
>
> Thanks!
>
>
> Kristian
>
>
>
> On Fri, Jul 22, 2016 at 5:53 AM, Moises Hernandez <[log in to unmask]>
> wrote:
>
>> Hi Kristian,
>>
>> split_parts_gpu was included in FSL 5.0.9.
>> It should be in your ${FSLDIR}/bin directory.
>> Are you using this version of FSL?
>> If for any reason is not there, you can download a binary version
>> compiled with CentOS 6.7 from here:
>>
>> http://users.fmrib.ox.ac.uk/~moisesf/bedpostx/split_parts_gpu_CentOS6/split_parts_gpu.zip
>> And copy it to ${FSLDIR}/bin directory.
>>
>> The patch in
>> http://fsl.fmrib.ox.ac.uk/fsldownloads/patches/bedpostx-patch-fsl-5.0.9.tar.gz is
>> for FSL 5.0.9 as well.
>> Did do applied that patch ?
>> You just need to copy all the files to your ${FSLDIR}/bin directory.
>>
>> Moises.
>>
>> On 21 July 2016 at 22:31, Kristian M. Eschenburg <[log in to unmask]> wrote:
>>
>>> Hi FSL
>>>
>>> I'm trying to run bedpostx_gpu and am producing a series of errors:
>>>
>>> bedpostx_gpu Diffusion/ -n 3 -b 3000 -g --model=3
>>>
>>>
>>> Making bedpostx directory structure
>>> Copying files to bedpostx directory
>>> Pre-processing stage
>>> /usr/share/fsl/bin/fsl_sub: 374: exit: Illegal number: -1
>>> Queueing parallel processing stage
>>>
>>> ----- Bedpostx Monitor -----
>>> /usr/share/fsl/bin/fsl_sub: 374: exit: Illegal number: -1
>>> Queuing post-processing stage
>>> /usr/share/fsl/bin/fsl_sub: 374: exit: Illegal number: -1
>>>
>>>
>>> I found a previous thread (
>>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=fsl;5e9b51c1.1510 ) that
>>> looked to have similar errors, but upon further inspection, I see that
>>> split_parts_gpu does not exist in ${FSLDIR}/bin. Where can I find this
>>> script?
>>>
>>>
>>> Thanks!
>>>
>>>
>>> Kristian
>>>
>>
>>
>
