Zeke, Thank you for your prompt response. I've been using for a long time my own bash script that parallelizes the simultaneous computation of the hemisphere-specific steps. Moreover, I re-organized the pipeline for obtaining the pial reconstruction asap. I'm happy to know that next release of Freesurfer will support openmp under MacOS X. Can you roughly estimate when it will be available? I also tried with VMWare Fusion and a VM with CentOS 6.6, and it mapped 12 virtual cores on the real cores. The time needed for CAREG was reduced by about 2/3. My impression is that CUDA drivers are not available for AMD FirePro graphics boards. Aren't they? Thanks again Cico
> Francesco Cardinale > > Neurosurgeon > "Claudio Munari" Centre for Epilepsy and Parkinson Surgery - Ospedale > Niguarda "Ca' Granda" > Piazza dell'Ospedale Maggiore, 3 - 20162 - Milano - Italia > phone 0039 02 64442917 > fax 0039 02 64442868 > e-mail francesco.cardin...@ospedaleniguarda.it > Il giorno 02/dic/2014, alle ore 15:59, Z K <zkauf...@nmr.mgh.harvard.edu> ha > scritto: > > Francesco, > > There are ways to speed up single subject processing time by > parrallelizing the parts of the recon-all stream that deal with the left > and right hemisphere so they get processed simultaneously. This would > require a custom script and thus is a bit more complicated than a single > call to recon-all. But I can provide you the skeleton of such a script > if you like. > > We no longer support CUDA but it is included in the 5.3 release and > people have reported success using it. The gpu can be used along with > the openmp flag to further quicken processing time, but only on CentOS > machines, as openmp is not supported on the Mac build of freesurfer > v5.3. However, the next release of freesurfer WILL support openmp on the > Mac side. > > -Zeke > > > >> On 11/27/2014 04:31 AM, Francesco Cardinale wrote: >> Dear Freesurfer experts, >> I've been using Freesurfer on Mac computers for some years with great >> satisfaction. I just bought a "monster computer", a Mac Pro with 12-core >> Xeon E5, 64 Gb RAM, GPU AMD FirePro D700. This is, out of doubt, a >> marvellous machine to compute many subjects simultaneously, but quite >> often we need to run one single subject as fast as possible. What can I >> do? OpenMP optimization is available only for CentOS, isn't it? What >> about CentOS in a VM, will it be able to exploit multithreading, or is >> it necessary to configure a multiboot machine with BootCamp? Any >> suggestions to do that? Moreover, what about CUDA and GPU acceleration? >> Is it available for FirePro graphic cards? Any other suggestions? >> Anything really new in the field with the next version of Freesurfer? >> Thanks a lot >> Francesco Cardinale, MD >> >> Neurosurgeon >> "Claudio Munari" Centre for Epilepsy and Parkinson Surgery - Ospedale >> Niguarda "Ca' Granda" >> Piazza dell'Ospedale Maggiore, 3 - 20162 - Milano - Italia >> <x-apple-data-detectors://0/0> >> phone 0039 02 64442917 <tel:0039%2002%2064442917> >> fax 0039 02 64442868 <tel:0039%2002%2064442868> >> e-mail francesco.cardin...@ospedaleniguarda.it >> <mailto:francesco.cardin...@ospedaleniguarda.it> >> >> >> _______________________________________________ >> 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 > > > 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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