Hi all,
I am looking for current recommendations for specs for a desktop Linux box for running Freesurfer (and friends), both recon-all, and the interactive graphical tools.
I have read the generic recommendations here:
http://surfer.nmr.mgh.harvard.edu/fswiki/SystemRequirements (also here as surfer is down)... http://webcache.googleusercontent.com/search?q=cache:Q113A-rSkxEJ:surfer.nmr...
Feel free to point me to existing email threads if I've missed the place where this was definitively covered!
I'd like any more detailed input such as:
CPU: Intel vs AMD, and the extent to which more cores increase performance.
Video card: -- AMD/ATI or nVidia? My model is that nVidia has had better support for OpenGL/Mesa -- still true? -- if nVidia, then how many CUDA cores and RAM is beneficial for FS's CUDA code?
Hard drive: Does SSD make much difference while running recon-all?
Linux distro: Which are favored for use with Freesurfer, FSL, etc?
Thanks!
-- Graham
Graham,
Hi, to answer each:
Intel vs AMD: no preference. also, CPU speed is not critical. Its better to have at least 4GB, and budget 4GB per subject you want to process simultaneously. Try to get a 'Sandy bridge' motherboard architecture or whatever is newer. This allows better addressing of scattered memory which is common in freesurfer, and it alone accounts for a 5% or so speedup. AMD might have a similar memory controller.
ATI vs nVidia: we still spec nVidia because we dont have problems with its OpenGL-X driver under linux. perhaps ATI has finally supplied one that works, but I havent tried in a couple years. ATI cards on the Mac work fine with freesurfer though.
GPU: we no longer support CUDA or GPU development because of lack of resources and difficulty, in preference to using OpenMP, which uses CPU cores.
disk: freesurfer is not disk intensive, so SSD is not a benefit. budget 400GB per subject for storage.
Linux: both freesurfer and fsl groups use Centos in our Centers. they seem to work well.
Hope this helps!
Nick
Hi all,
I am looking for current recommendations for specs for a desktop Linux box for running Freesurfer (and friends), both recon-all, and the interactive graphical tools.
I have read the generic recommendations here:
http://surfer.nmr.mgh.harvard.edu/fswiki/SystemRequirements (also here as surfer is down)... http://webcache.googleusercontent.com/search?q=cache:Q113A-rSkxEJ:surfer.nmr...
Feel free to point me to existing email threads if I've missed the place where this was definitively covered!
I'd like any more detailed input such as:
CPU: Intel vs AMD, and the extent to which more cores increase performance.
Video card: -- AMD/ATI or nVidia? My model is that nVidia has had better support for OpenGL/Mesa -- still true? -- if nVidia, then how many CUDA cores and RAM is beneficial for FS's CUDA code?
Hard drive: Does SSD make much difference while running recon-all?
Linux distro: Which are favored for use with Freesurfer, FSL, etc?
Thanks!
-- Graham
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I think Nick meant to say 400MB per subject, not 400GB per subject:)
On 4/24/13 8:42 PM, Nick Schmansky wrote:
Graham,
Hi, to answer each:
Intel vs AMD: no preference. also, CPU speed is not critical. Its better to have at least 4GB, and budget 4GB per subject you want to process simultaneously. Try to get a 'Sandy bridge' motherboard architecture or whatever is newer. This allows better addressing of scattered memory which is common in freesurfer, and it alone accounts for a 5% or so speedup. AMD might have a similar memory controller.
ATI vs nVidia: we still spec nVidia because we dont have problems with its OpenGL-X driver under linux. perhaps ATI has finally supplied one that works, but I havent tried in a couple years. ATI cards on the Mac work fine with freesurfer though.
GPU: we no longer support CUDA or GPU development because of lack of resources and difficulty, in preference to using OpenMP, which uses CPU cores.
disk: freesurfer is not disk intensive, so SSD is not a benefit. budget 400GB per subject for storage.
Linux: both freesurfer and fsl groups use Centos in our Centers. they seem to work well.
Hope this helps!
Nick
Hi all,
I am looking for current recommendations for specs for a desktop Linux box for running Freesurfer (and friends), both recon-all, and the interactive graphical tools.
I have read the generic recommendations here:
http://surfer.nmr.mgh.harvard.edu/fswiki/SystemRequirements (also here as surfer is down)... http://webcache.googleusercontent.com/search?q=cache:Q113A-rSkxEJ:surfer.nmr...
Feel free to point me to existing email threads if I've missed the place where this was definitively covered!
I'd like any more detailed input such as:
CPU: Intel vs AMD, and the extent to which more cores increase performance.
Video card: -- AMD/ATI or nVidia? My model is that nVidia has had better support for OpenGL/Mesa -- still true? -- if nVidia, then how many CUDA cores and RAM is beneficial for FS's CUDA code?
Hard drive: Does SSD make much difference while running recon-all?
Linux distro: Which are favored for use with Freesurfer, FSL, etc?
Thanks!
-- Graham
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
400MB per subject, sorry.
also i should have made clear that we will continue to support the existing GPU CUDA code that runs on recon-all with the -use-gpu switch. by support i mean keeping it running with each new nvidia cuda driver release as best as we can.
Nick
I think Nick meant to say 400MB per subject, not 400GB per subject:)
On 4/24/13 8:42 PM, Nick Schmansky wrote:
Graham,
Hi, to answer each:
Intel vs AMD: no preference. also, CPU speed is not critical. Its better to have at least 4GB, and budget 4GB per subject you want to process simultaneously. Try to get a 'Sandy bridge' motherboard architecture or whatever is newer. This allows better addressing of scattered memory which is common in freesurfer, and it alone accounts for a 5% or so speedup. AMD might have a similar memory controller.
ATI vs nVidia: we still spec nVidia because we dont have problems with its OpenGL-X driver under linux. perhaps ATI has finally supplied one that works, but I havent tried in a couple years. ATI cards on the Mac work fine with freesurfer though.
GPU: we no longer support CUDA or GPU development because of lack of resources and difficulty, in preference to using OpenMP, which uses CPU cores.
disk: freesurfer is not disk intensive, so SSD is not a benefit. budget 400GB per subject for storage.
Linux: both freesurfer and fsl groups use Centos in our Centers. they seem to work well.
Hope this helps!
Nick
Hi all,
I am looking for current recommendations for specs for a desktop Linux box for running Freesurfer (and friends), both recon-all, and the interactive graphical tools.
I have read the generic recommendations here:
http://surfer.nmr.mgh.harvard.edu/fswiki/SystemRequirements (also here as surfer is down)... http://webcache.googleusercontent.com/search?q=cache:Q113A-rSkxEJ:surfer.nmr...
Feel free to point me to existing email threads if I've missed the place where this was definitively covered!
I'd like any more detailed input such as:
CPU: Intel vs AMD, and the extent to which more cores increase performance.
Video card: -- AMD/ATI or nVidia? My model is that nVidia has had better support for OpenGL/Mesa -- still true? -- if nVidia, then how many CUDA cores and RAM is beneficial for FS's CUDA code?
Hard drive: Does SSD make much difference while running recon-all?
Linux distro: Which are favored for use with Freesurfer, FSL, etc?
Thanks!
-- Graham
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Douglas Greve -
Graham Wideman -
Nick Schmansky