Re: [Freesurfer] How to run a benchmark on GPU with FreeSufer?
On Wed, Aug 17, 2011 at 5:03 PM, Leo Souza wrote: > Can you provide quick instructions on how to run those tests? I am new to > FreeSurfer. I'll have to defer to others on running those two programs - it's been too long since I worked on Freesurfer. I believe the website has some general information (and should contain instructions for running 'recon-all' on ernie and bert), but only a few programs in the pipeline are accelerated. Although that could be an interesting study in itself - an Amdahl's Law analysis on the entire pipeline :-) Richard ___ 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.
Re: [Freesurfer] How to run a benchmark on GPU with FreeSufer?
Can you provide quick instructions on how to run those tests? I am new to FreeSurfer. Thanks, Leo Souza -Original Message- From: R Edgar [mailto:freesurfer@gmail.com] Sent: Wednesday, August 17, 2011 12:36 PM To: Leo Souza Cc: Freesurfer Mailing List; Douglas N Greve Subject: Re: [Freesurfer] How to run a benchmark on GPU with FreeSufer? On Wed, Aug 17, 2011 at 3:19 PM, Leo Souza wrote: > I want to verify what's the performance of different GPUs using FreeSurfer as > Benchmark App. In that case, the two best programs to run are mri_em_register[_cuda] for linear registration mri_ca_register[_cuda] for nonlinear registration You should know that Freesurfer quite likes the Nehalem memory hardware, whether in CPU or GPU mode. Also, mri_em_register_cuda has an additional pair of 'fast' options which cut the runtime even more (look at the top of the source file), but will sometimes give a different registration to the CPU version. Richard --- This email message is for the sole use of the intended recipient(s) and may contain confidential 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. --- ___ 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.
Re: [Freesurfer] How to run a benchmark on GPU with FreeSufer?
On Wed, Aug 17, 2011 at 3:19 PM, Leo Souza wrote: > I want to verify what's the performance of different GPUs using FreeSurfer as > Benchmark App. In that case, the two best programs to run are mri_em_register[_cuda] for linear registration mri_ca_register[_cuda] for nonlinear registration You should know that Freesurfer quite likes the Nehalem memory hardware, whether in CPU or GPU mode. Also, mri_em_register_cuda has an additional pair of 'fast' options which cut the runtime even more (look at the top of the source file), but will sometimes give a different registration to the CPU version. Richard ___ 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.
Re: [Freesurfer] How to run a benchmark on GPU with FreeSufer?
I want to verify what's the performance of different GPUs using FreeSurfer as Benchmark App. Thanks, Leo Souza -Original Message- From: R Edgar [mailto:freesurfer@gmail.com] Sent: Wednesday, August 17, 2011 6:20 AM To: Leo Souza; Freesurfer Mailing List Cc: Douglas N Greve Subject: Re: [Freesurfer] How to run a benchmark on GPU with FreeSufer? On Tue, Aug 16, 2011 at 1:42 PM, Leo Souza wrote: > Does anyone knows how do I run a benchmark test on GPU with FreeSurfer and > CUDA? Beyond running a comparison between [x] and [x]_cuda? If you want numbers on individual routines, then the cudatest directory holds a lot of test cases which will run one routine and compare timings (these are used by the tests under test_tm). Could you explain what information you're looking for? Richard --- This email message is for the sole use of the intended recipient(s) and may contain confidential 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. --- ___ 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.
Re: [Freesurfer] How to run a benchmark on GPU with FreeSufer?
On Tue, Aug 16, 2011 at 1:42 PM, Leo Souza wrote: > Does anyone knows how do I run a benchmark test on GPU with FreeSurfer and > CUDA? Beyond running a comparison between [x] and [x]_cuda? If you want numbers on individual routines, then the cudatest directory holds a lot of test cases which will run one routine and compare timings (these are used by the tests under test_tm). Could you explain what information you're looking for? Richard ___ 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.
[Freesurfer] How to run a benchmark on GPU with FreeSufer?
Hi Dear All, Does anyone knows how do I run a benchmark test on GPU with FreeSurfer and CUDA? Thanks, Leo Souza --- This email message is for the sole use of the intended recipient(s) and may contain confidential 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. --- ___ 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.
