[Neurodebian-users] fsl-5.0-gpu

[Michael Hanke]

Hey,

would you mind submitting a patch for all changes you had to make?

Thanks,

Michael


On Tue, Feb 25, 2014 at 9:10 PM, Jonathan Berrebi <Jonathan.Berrebi at ki.se>wrote:

> Thank you Alex and Yury!
>
> I replaced all the #/bin/sh with #/bin/bash in the bedpostx_gpu and
> bedpostx_postproc_gpu.sh and fsl_sub files. I think it worked now. It took
> 6 hours on a 96 cores GPU instead of one day on Intel Xeon. The only
> warning I get is on the monitor "routine" ${subjdir}.bedpostX/monitor about
> zeropadding:
>
> <<FP02.bedpostX/monitor: line 21: /bin/zeropad: No such file or directory>>
>
> I will check that the results are numerically not different than when they
> CPU computed.
>
> Once thing though is that I had to stop gdm3 in order to get it to work. I
> really tried to use the intel HD 3000 integrated GPU for the Graphics by
> changing the settings in the bios. But then the nvidia-detect routine did
> not detect the GPU. So I thought it wouldn't work. Then I even installed
> bumblebee  and changed the settings in the bios into Optimus but that
> become more a bumblebee than a fsl/cuda problem so I gave up. I might retry
> later.
>
> Thank you for your help,
>
> Jonathan
>
> ________________________________________
> De : Neurodebian-users [neurodebian-users-bounces+jonathan.berrebi=
> ki.se at lists.alioth.debian.org] de la part de Alex Waite [
> alexqw85 at gmail.com]
> Envoyé : mardi 25 février 2014 09:52
> À : neurodebian-users at lists.alioth.debian.org
> Objet : Re: [Neurodebian-users] fsl-5.0-gpu
>
> > The result of cat /etc/proc/cpuinfo | grep 'model name' is
> > Intel(R) Core(TM) i7-2630QM CPU @ 2.00GHz which includes an Intel® HD
> Graphics 3000. So I don't need the NVIDIA GPU to have graphics on my laptop.
>
> Excellent.
>
> > However the nvidia-settings program shows that the nvidia gpu is in used.
>  > [snip]
>
> You may need to take a look in your BIOS to change the primary GPU to
> the Intel one. Also, make sure that you're no longer telling X to load
> the nvidia driver (/etc/X11/xorg.conf.d/20-nvidia.conf).
>
> I think this should work. The computer will use the intel GPU from boot,
> X will automatically load the Intel driver, and the nvidia GPU will not
> be used for display.
>
> > Then I got a message "Bad substitution" when bedpostx_gpu entered
> bedpost_postproc_gpu.sh at line 67:
> >
> > subjdir=${@:${#@}}
> >
> > I don't know bash programming so much so I har coded subjdir and it
> still does not work. But at least I can really hear the fan of my GPU for a
> short while and the screen freezes as well which are good signs I guess.
> But the jobs stop
> >
> > /usr/share/fsl/5.0/bin/bedpostx_postproc_gpu.sh: 71:
> /usr/share/fsl/5.0/bin/bedpostx_postproc_gpu.
> > sh: [[: not found
>  >
>  > So again it is the bash programming at the beggining of the
> bedpostx_postproc_gpu.sh that seems to be an issue.
>
> I agree with Yury that these are bashisms in the code. No need to hard
> code the subjdir.
>
> The shebang of the shell script declares /bin/sh as the interpreter. For
> awhile there, many distros (Debian included) made the poor decision to
> point /bin/sh to /bin/bash. The thing is that bash has many more
> features than sh, and this lead a bunch of people to write sh scripts
> that actually rely on bash features. Now debian (and many other distros)
> point /bin/sh to /bin/dash (a small, fast, POSIX compliant shell meant
> to mimic sh's behavior). It lacks many of the features of bash, hence
> the problem here.
>
> Change the first line of that script to:
> #!/bin/bash
>
> > I will look at that tomorrow. Thank you for the help,
>
> Always happy to help out.
>
> ---Alex
>
>
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-- 
Michael Hanke
http://mih.voxindeserto.de
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