Hi there, I'm currently working on compiling FS source code trying to use CUDA 6, and newer GPUs like Titan series. I haven't got lucky yet, but I will keep on trying... In the meantime I would like to download the CUDA 5 binaries. Are these binaries been published? I can't find anything on the FreeSurfer wiki...
In my previous work you mentioned "Improving Execution Performance of FreeSurfer" we used CUDA 3 binaries that I had compiled with --enable-fermi flag. Just to clarify your concern, we never used openmp on the test setup of that study, we have implemented a scheduler to manage K simultaneous recon-all executions. Thank you, 2014-07-02 19:06 GMT+02:00 Chiu, Bryan (PHTH) <bryan.c...@ubc.ca>: > Hi, > > Turns out if you rename libcudart.so.6.0 to the 5.0 in your respective > lib64, you can pass the cudadetect for Freesurfer. However after it will > crash with a segfault error. This leads me to believe that I installed > correctly. > > I think Freesurfer only supports up to CUDA 5.0 so far (although I know > Freesurfer group stopped supporting the option and left the flags around). > Two options exist: Either in a future patch the program can just be enabled > to call the newer version of CUDA (or if I can find where it tries to find > CUDA from, edit it to accept any version), or to install any version of > CUDA less than or equal to 5.0 > > To others: The OpenMP and -use-gpu flag are quite promising. I took a > recon down from 12 hours to 3.5 hours using the -openmp 8 flag for a 4 core > processor (i7 4770k). I am currently trying to see if I can speed up faster > using the CUDA enabled option. There was a paper titled "Improving the > Execution Performance of Freesurfer" which implements a resource scheduler > on top of the CUDA and openMP option. No comment on the accuracy of the > recon-all using all of these in combination. > > - Bryan > > Date: Mon, 30 Jun 2014 16:34:45 +0000 > From: "Chiu, Bryan (PHTH)" <bryan.c...@ubc.ca> > Subject: Re: [Freesurfer] recon-all CUDA error (Chiu, Bryan (PHTH)) > To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> > Message-ID: > <680d9b8d5feaaf40a1a5878265424ca44a594...@s-itsv-mbx06p.ead.ubc.ca > > > Content-Type: text/plain; charset="iso-8859-1" > > Hi all, > > I am still working on this problem. Does anyone know if Freesurfer is > asking for CUDA 5.0, except that I have CUDA 6.0 installed? > > My next steps will be to find out if Freesurfer is calling an older > version of CUDA that isn't installed, or trying the CUDA samples. I really > want to get this to work. > > -Bryan > > Date: Fri, 27 Jun 2014 17:59:37 +0000 > From: "Chiu, Bryan (PHTH)" <bryan.c...@ubc.ca> > Subject: [Freesurfer] recon-all CUDA error > To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> > Message-ID: > <680d9b8d5feaaf40a1a5878265424ca44a594...@s-itsv-mbx06p.ead.ubc.ca > > > Content-Type: text/plain; charset="iso-8859-1" > > Hi, > > I'm fairly novice at Linux and I've been trying to setup CUDA for > recon-all. I get an error as follows: > > [TLA@COGMOB-linuxPC ~]$ recon-all -s bert -use-gpu -openmp 8 > Testing for CUDA device: > /usr/freesurfer/bin/mri_em_register_cuda: error while loading shared > libraries: libcudart.so.5.0: cannot open shared object file: No such file > or directory > Linux COGMOB-linuxPC 2.6.32-431.el6.x86_64 #1 SMP Fri Nov 22 03:15:09 UTC > 2013 x86_64 x86_64 x86_64 GNU/Linux > > recon-all -s bert exited with ERRORS at Fri Jun 27 10:53:29 PDT 2014 > > For more details, see the log file > To report a problem, see > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > Any idea what is going on? I setup CUDA and my Nvidia drivers according to > this tutorial ( > http://aspratyush.wordpress.com/2012/05/06/install-nvidia-cuda-on-centos-6/). > With, of course some slight changes to install the latest toolkit. > > Thanks in advance, > > - Bryan > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > -- Jordi Delgado Mengual PIC (Port d'Informació CientÃfica)
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
