currently the _cuda binaries are distributed only in the centos4 and centos4_x86_64 distributions. however, those should work in centos5, and i've made a tarball of the _cuda binaries downloadable from here:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc
look for the file 'fscudabins-linux-centos4_x86_64.tgz' and untar in your freesurfer/bin dir.
! note ! this is a beta release of these binaries! they havent been fully tested across a wide subject set, so don't use the -use-gpu flag in any kind of important group analysis yet.
please let of us know though of any problems you encounter. we need to learn what kind of gpu cards people have out there in order to gauge how far we can optimize our routines.
n.
On Tue, 2010-08-17 at 11:35 -0500, joel bruss wrote:
Not to hijack your question, but I have similar questions. I have CUDA toolkit 3.1 installed, "cudadetect" returns: "Detecting CUDA... 32767 CUDA enabled device(s) detected." but, when I run recon-all, e.g.:
recon-all -subjid PC -all -use-gpu
I get the following errors at the mri_em_register_cuda step:
/lcn2/lesion_warp.dir/MAP3_Nifti/freesurfer_subs.dir/PC/mri mri_em_register_cuda -skull nu.mgz /usr/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta mri_em_register_cuda: Command not found. Linux linux-lvmb 2.6.34-12-desktop #1 SMP PREEMPT 2010-06-29 02:39:08 +0200 x86_64 x86_64 x86_64 GNU/LinuxA quick peak in /usr/freesurfer/bin shows that there is no mri_em_register_cuda binary.
Are cuda binaries supposed to be bundled with the new 5.0 release, or are they created on the fly by FreeSurfer, or are they just plain missing? FWIW, I have CentOS 5 x86_64 version of FreeSurfer installed, running on OpenSuse 11.3
recon-all -s PC exited with ERRORS at Tue Aug 17 11:14:35 CDT 2010
On Tue, Aug 17, 2010 at 11:07 AM, Gennan Chen gennan.chen@synarc.com wrote: Hi!
I will like to try the beta CUDA support in 5.0. And I have some questions here 1. Are all needed libraries bundled in the release? Or I need to go to CUDA’s site to get those dependency? And if I need to, what are those dependency I need to grab and install? 2. I have RH 5 64 bit linux box with single NVIDIA FX card and macpro snow leopard box with dual NVIIDA GT 120. Does CUDA support work for both OS? If they do, any idea what the speed up will be?? Gen ______________________________________________________________ This email message is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. If you are the intended recipient, please be advised that the content of this message is subject to access, review and disclosure by the sender's Email System Administrator _______________________________________________ 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.
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