Re: [Freesurfer] Speeding Freesurfer
My impression is that CUDA drivers are not available for AMD FirePro graphics boards. Aren't they? Sorry, I dont know the answer to that question. In regard to the next release of freesurfer, my guestimate would be between 1-2 months. -Zeke On 12/03/2014 02:12 AM, Francesco Cardinale wrote: 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 mailto:francesco.cardin...@ospedaleniguarda.it Il giorno 02/dic/2014, alle ore 15:59, Z K zkauf...@nmr.mgh.harvard.edu mailto: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 mailto:francesco.cardin...@ospedaleniguarda.it ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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 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
Re: [Freesurfer] Speeding Freesurfer
CUDA is specific to NVIDIA graphics devices. http://www.nvidia.com/object/cuda_home_new.html On Thu, Dec 4, 2014 at 10:10 AM, Z K zkauf...@nmr.mgh.harvard.edu wrote: My impression is that CUDA drivers are not available for AMD FirePro graphics boards. Aren't they? Sorry, I dont know the answer to that question. In regard to the next release of freesurfer, my guestimate would be between 1-2 months. -Zeke On 12/03/2014 02:12 AM, Francesco Cardinale wrote: 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 mailto:francesco.cardin...@ospedaleniguarda.it Il giorno 02/dic/2014, alle ore 15:59, Z K zkauf...@nmr.mgh.harvard.edu mailto: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 mailto:francesco.cardin...@ospedaleniguarda.it ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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 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
Re: [Freesurfer] Speeding Freesurfer
Hi Francesco we are hoping to have version 6 out in early 2015 cheers Bruce On Wed, 3 Dec 2014, Francesco Cardinale wrote: 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. ___ 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
Re: [Freesurfer] Speeding Freesurfer
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.
Re: [Freesurfer] Speeding Freesurfer
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. ___ 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] Speeding Freesurfer
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 phone 0039 02 64442917 fax 0039 02 64442868 e-mail francesco.cardin...@ospedaleniguarda.it___ 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.
