Hi experts,
I would like to find a new high-performance computer to run the reconstruction process in Freesurfer. Currently, I used a single computer (Intel core i7, RAM 8MB) to run the commands (e.g., 'recon-all -all' ) that spent average time 7-9 hours per one subject data.
Please let me know what the best spec of the computer that can reduce the time to 2-3 hours (if possible).
Thank you, Aziz
Hi Aziz
with multiple course you can specify -openmp 8 for exmaple to use 8 cores, which speeds things up a lot. It also depends how many recons you will be running at the same time. A 16 core machine with 64G of ram would be able to run 4 recons in a few hours each.
cheers Bruce
On Fri, 3 Feb 2017, Aziz Nanthaamornphong wrote:
Hi experts, I would like to find a new high-performance computer to run the reconstruction process in Freesurfer. Currently, I used a single computer (Intel core i7, RAM 8MB) to run the commands (e.g., 'recon-all -all' ) that spent average time 7-9 hours per one subject data.
Please let me know what the best spec of the computer that can reduce the time to 2-3 hours (if possible).
Thank you, Aziz
Hi Bruce,
Does FS6 support the 'openmp 8' flag? I tried to use this flag with 'recon-all -all' on FS6, but it took longer time for only one subject.
Thank you, Aziz.
On Fri, Feb 3, 2017 at 10:16 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Aziz
with multiple course you can specify -openmp 8 for exmaple to use 8 cores, which speeds things up a lot. It also depends how many recons you will be running at the same time. A 16 core machine with 64G of ram would be able to run 4 recons in a few hours each.
cheers Bruce
On Fri, 3 Feb 2017, Aziz Nanthaamornphong wrote:
Hi experts,
I would like to find a new high-performance computer to run the reconstruction process in Freesurfer. Currently, I used a single computer (Intel core i7, RAM 8MB) to run the commands (e.g., 'recon-all -all' ) that spent average time 7-9 hours per one subject data.
Please let me know what the best spec of the computer that can reduce the time to 2-3 hours (if possible).
Thank you, Aziz
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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.
yes it does, and it should significantly reduce execution time unless you don't have multiple cores
cheers Bruce On Sat, 4 Feb 2017, Aziz Nanthaamornphong wrote:
Hi Bruce, Does FS6 support the 'openmp 8' flag? I tried to use this flag with 'recon-all -all' on FS6, but it took longer time for only one subject.
Thank you, Aziz.
On Fri, Feb 3, 2017 at 10:16 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Aziz
with multiple course you can specify -openmp 8 for exmaple to use 8 cores, which speeds things up a lot. It also depends how many recons you will be running at the same time. A 16 core machine with 64G of ram would be able to run 4 recons in a few hours each. cheers Bruce On Fri, 3 Feb 2017, Aziz Nanthaamornphong wrote: Hi experts, I would like to find a new high-performance computer to run the reconstruction process in Freesurfer. Currently, I used a single computer (Intel core i7, RAM 8MB) to run the commands (e.g., 'recon-all -all' ) that spent average time 7-9 hours per one subject data. Please let me know what the best spec of the computer that can reduce the time to 2-3 hours (if possible). Thank you, Aziz
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.
--
Aziz Nanthaamornphong, Ph.D., Chair of Master of Science Program in Information Technology Department of ICT Faculty of Technology and Environment Prince of Songkla University, Phuket Campus +66 7627 6716 (v) http://research.te.psu.ac.th/aziz
Hi Bruce,
So, I am not sure if I understand correct. Suppose, I would like to run 4 subjects simultenously, I have to run the recon-all command of each subject on each terminal with -openmp. Otherwise, is there any other options to run 4 subjects in one terminal.
Thank you, Aziz.
On Sat, Feb 4, 2017 at 9:46 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
yes it does, and it should significantly reduce execution time unless you don't have multiple cores
cheers Bruce
On Sat, 4 Feb 2017, Aziz Nanthaamornphong wrote:
Hi Bruce,
Does FS6 support the 'openmp 8' flag? I tried to use this flag with 'recon-all -all' on FS6, but it took longer time for only one subject.
Thank you, Aziz.
On Fri, Feb 3, 2017 at 10:16 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Aziz
with multiple course you can specify -openmp 8 for exmaple to use 8cores, which speeds things up a lot. It also depends how many recons you will be running at the same time. A 16 core machine with 64G of ram would be able to run 4 recons in a few hours each.
cheers Bruce On Fri, 3 Feb 2017, Aziz Nanthaamornphong wrote: Hi experts, I would like to find a new high-performance computer torun the reconstruction process in Freesurfer. Currently, I used a single computer (Intel core i7, RAM 8MB) to run the commands (e.g., 'recon-all -all' ) that spent average time 7-9 hours per one subject data.
Please let me know what the best spec of the computer thatcan reduce the time to 2-3 hours (if possible).
Thank you, Aziz
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.
--
Aziz Nanthaamornphong, Ph.D., Chair of Master of Science Program in Information Technology Department of ICT Faculty of Technology and Environment Prince of Songkla University, Phuket Campus +66 7627 6716 (v) http://research.te.psu.ac.th/aziz
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.
Hi Aziz
-openmp 4 will speed up the recon of a single subject. If you had 16 processors and enough RAM you could run 4 subjects at the same time that way and each of them would be faster. We've had recons complete in 2-3 hours this way, depending on the anatomy.
cheers Bruce On Sat, 4 Feb 2017, Aziz Nanthaamornphong wrote:
Hi Bruce,
So, I am not sure if I understand correct. Suppose, I would like to run 4 subjects simultenously, I have to run the recon-all command of each subject on each terminal with -openmp. Otherwise, is there any other options to run 4 subjects in one terminal. Thank you, Aziz.
On Sat, Feb 4, 2017 at 9:46 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: yes it does, and it should significantly reduce execution time unless you don't have multiple cores
cheers Bruce On Sat, 4 Feb 2017, Aziz Nanthaamornphong wrote: Hi Bruce, Does FS6 support the 'openmp 8' flag? I tried to use this flag with 'recon-all -all' on FS6, but it took longer time for only one subject. Thank you, Aziz. On Fri, Feb 3, 2017 at 10:16 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Aziz with multiple course you can specify -openmp 8 for exmaple to use 8 cores, which speeds things up a lot. It also depends how many recons you will be running at the same time. A 16 core machine with 64G of ram would be able to run 4 recons in a few hours each. cheers Bruce On Fri, 3 Feb 2017, Aziz Nanthaamornphong wrote: Hi experts, I would like to find a new high-performance computer to run the reconstruction process in Freesurfer. Currently, I used a single computer (Intel core i7, RAM 8MB) to run the commands (e.g., 'recon-all -all' ) that spent average time 7-9 hours per one subject data. Please let me know what the best spec of the computer that can reduce the time to 2-3 hours (if possible). Thank you, Aziz _______________________________________________ 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. -- Aziz Nanthaamornphong, Ph.D., Chair of Master of Science Program in Information Technology Department of ICT Faculty of Technology and Environment Prince of Songkla University, Phuket Campus +66 7627 6716 (v) http://research.te.psu.ac.th/aziz
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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