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 <[email protected]>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" ${subjdir}.bedpostX/monitor about > zeropadding: > > <<FP02.bedpostX/monitor: line 21: /bin/zeropad: No such file or directory>> > > I will check that the results are numerically not different than when they > CPU computed. > > Once thing though is that I had to stop gdm3 in order to get it to work. I > really tried to use the intel HD 3000 integrated GPU for the Graphics by > changing the settings in the bios. But then the nvidia-detect routine did > not detect the GPU. So I thought it wouldn't work. Then I even installed > bumblebee and changed the settings in the bios into Optimus but that > become more a bumblebee than a fsl/cuda problem so I gave up. I might retry > later. > > Thank you for your help, > > Jonathan > > ________________________________________ > De : Neurodebian-users [neurodebian-users-bounces+jonathan.berrebi= > [email protected]] de la part de Alex Waite [ > [email protected]] > Envoyé : mardi 25 février 2014 09:52 > À : [email protected] > Objet : Re: [Neurodebian-users] fsl-5.0-gpu > > > The result of cat /etc/proc/cpuinfo | grep 'model name' is > > Intel(R) Core(TM) i7-2630QM CPU @ 2.00GHz which includes an Intel® HD > Graphics 3000. So I don't need the NVIDIA GPU to have graphics on my laptop. > > Excellent. > > > However the nvidia-settings program shows that the nvidia gpu is in used. > > [snip] > > You may need to take a look in your BIOS to change the primary GPU to > the Intel one. Also, make sure that you're no longer telling X to load > the nvidia driver (/etc/X11/xorg.conf.d/20-nvidia.conf). > > I think this should work. The computer will use the intel GPU from boot, > X will automatically load the Intel driver, and the nvidia GPU will not > be used for display. > > > Then I got a message "Bad substitution" when bedpostx_gpu entered > bedpost_postproc_gpu.sh at line 67: > > > > subjdir=${@:${#@}} > > > > 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 > > > _______________________________________________ > Neurodebian-users mailing list > [email protected] > http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/neurodebian-users > _______________________________________________ > Neurodebian-users mailing list > [email protected] > http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/neurodebian-users > -- Michael Hanke http://mih.voxindeserto.de
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