Re: [Freesurfer] Specification of computer
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 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 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. ___ 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] Specification of computer
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 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 >> 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. > > ___ 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] Specification of computer
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 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.
Re: [Freesurfer] Specification of computer
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 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.
Re: [Freesurfer] Specification of computer
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.
