Re: [Freesurfer] using multiple cores
Lukas, The Mac build does not support openmp. This is because the initial version of gcc we were using for the Mac build did not support it. We are now using a version of gcc for the Mac build which does support oppenmp so the current plan is that any subsequent releases of freesurfer will support openmp on both Linux and Mac builds. Sorry for the late response. -Zeke On 05/02/2014 03:16 PM, Matt Glasser wrote: If you are compiling with clang openmp might not work. Peace, Matt. On 5/2/14, 2:13 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Lukas sorry, I'm out of my depth on the mac. Perhaps Zeke knows what's going on? Does OpenMP have to be enabled somehow? Bruce On Fri, 2 May 2014, lukas.sch...@ukb.uni-bonn.de wrote: Hi Bruce! I just run: recon-all -s ernie2 -autorecon2 -openmp 4 mri_ca_register uses 100.9% CPU at most ... Any idea? Should I try to recompile FS for the current MacOS release? If so, do I have to take care on special librariwa in order to enable the openmp option? Best wishes, Lukas Hi Bruce! Thanks for the fast response. I used the current stable version 5.3.0.1 (freesurfer-Darwin-lion-stable-pub-v5.3.0.1). So I will try as you have suggested ... Best wishes, Lukas Bruce Fischl Fri, 02 May 2014 05:47:26 -0700 Hi Luke what version of FS are you running? We see significant speedups. Try running top in a unix terminal and seeing if the cpu usage of mri_ca_register (during autorecon2, the longest single step) is morethan 100% cheers Bruce On Fri, 2 May 2014, lukas.sch...@ukb.uni-bonn.de wrote: Hi folks! I try to use -openmp option on an iMAC with 4 cores. Unfortunately, I do not see any accelartion when processing a single data set with or without the flag -openmp flag set. recon-all -s ernie_1 -all leads to ~6,4h processing time. Unfortunately recon-all -s ernie_2 -all -openmp 4 did not change anything. Do I miss anything? Do I have to prepare my system in a special way? Or run any scripts in advance? (System: iMac, 32GbRam,Intel i5, 4 cores, Mac Os 10.9, latest FS version) Best wishes, Luke ___ 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] using multiple cores
Hi Zeke!Thanks a lot for the response. Better a late response than none :o)! Do you have any vague estimate when a new release will be available? So far I did not try to compile it from the sources, because it is not my daily business and for an inexperienced it most likely ends up with pure frustration. If a new release would be close, I would definitely keep my fingers from compiling ... Or are any "how to's" available for compiling FS from the sources...? Best wishes, Luke ___ 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] using multiple cores
I do not have any information to give in regards to when a new release would be available. Compiling freesurfer from source is not exactly something I would call fun. That said, I have been working on a brief how-to-guide on how to build freesurfer on Mac OSX and I have already packaged the 3rd party libraries into a single bundle. I plan on releasing this guide next week and I will email it to you. Once you have it, compiling should be fairly straight forward. If you dont hear from me by next week feel free to ping me. -Zeke On 05/05/2014 03:59 PM, lukas.sch...@ukb.uni-bonn.de wrote: Hi Zeke! Thanks a lot for the response. Better a late response than none :o)! Do you have any vague estimate when a new release will be available? So far I did not try to compile it from the sources, because it is not my daily business and for an inexperienced it most likely ends up with pure frustration. If a new release would be close, I would definitely keep my fingers from compiling ... Or are any how to's available for compiling FS from the sources...? Best wishes, Luke ___ 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] using multiple cores
And fun, right? On May 5, 2014, at 5:48 PM, Z K zkauf...@nmr.mgh.harvard.edu wrote: I do not have any information to give in regards to when a new release would be available. Compiling freesurfer from source is not exactly something I would call fun. That said, I have been working on a brief how-to-guide on how to build freesurfer on Mac OSX and I have already packaged the 3rd party libraries into a single bundle. I plan on releasing this guide next week and I will email it to you. Once you have it, compiling should be fairly straight forward. If you dont hear from me by next week feel free to ping me. -Zeke On 05/05/2014 03:59 PM, lukas.sch...@ukb.uni-bonn.de wrote: Hi Zeke! Thanks a lot for the response. Better a late response than none :o)! Do you have any vague estimate when a new release will be available? So far I did not try to compile it from the sources, because it is not my daily business and for an inexperienced it most likely ends up with pure frustration. If a new release would be close, I would definitely keep my fingers from compiling ... Or are any how to's available for compiling FS from the sources...? Best wishes, Luke ___ 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 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] using multiple cores
Hi Bruce and others!I am still puzzeling how to speed up the process... I tried 4 prarallel sessions running exactly the same dataset as before. With 4 cores and 32 GB RAM I expected that I won't loose time / session. However, it was about 50% slower. Shell 1:recon-all -s ernie1 -i /Applications/freesurfer/subjects/sample-001.mgz -i /Applications/freesurfer/subjects/sample-002.mgz -all Shell 2:recon-all -s ernie2 -i /Applications/freesurfer/subjects/sample-001.mgz -i /Applications/freesurfer/subjects/sample-002.mgz -all Shell 3:recon-all -s ernie3 -i /Applications/freesurfer/subjects/sample-001.mgz -i /Applications/freesurfer/subjects/sample-002.mgz -all Shell 4: recon-all -s ernie4 -i /Applications/freesurfer/subjects/sample-001.mgz -i /Applications/freesurfer/subjects/sample-002.mgz -all Before it took about 6,48h to process one dataset, but when running 4, the processing time increased to 8.29h. Any ideas?Freesurfer Rel. recon-all,v 1.379.2.73; freesurfer-Darwin-lion-stable-pub-v5.3.0.1 Best wishes, Luke ___ 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] using multiple cores
Hi Bruce! Thanks for the fast response. I used the current stable version 5.3.0.1 (freesurfer-Darwin-lion-stable-pub-v5.3.0.1). So I will try as you have suggested ... Best wishes, Lukas Bruce Fischl Fri, 02 May 2014 05:47:26 -0700 Hi Luke what version of FS are you running? We see significant speedups. Try running top in a unix terminal and seeing if the cpu usage of mri_ca_register (during autorecon2, the longest single step) is morethan 100% cheers Bruce On Fri, 2 May 2014, lukas.sch...@ukb.uni-bonn.de wrote: Hi folks! I try to use -openmp option on an iMAC with 4 cores. Unfortunately, I do not see any accelartion when processing a single data set with or without the flag -openmp flag set. recon-all -s ernie_1 -all leads to ~6,4h processing time. Unfortunately recon-all -s ernie_2 -all -openmp 4 did not change anything. Do I miss anything? Do I have to prepare my system in a special way? Or run any scripts in advance? (System: iMac, 32GbRam,Intel i5, 4 cores, Mac Os 10.9, latest FS version) Best wishes, Luke ___ 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] using multiple cores
Hi Bruce!I just run: recon-all -s ernie2 -autorecon2 -openmp 4 mri_ca_register uses 100.9% CPU at most ... Any idea? Should I try to recompile FS for the current MacOS release? If so, do I have to take care on special librariwa in order to enable the openmp option? Best wishes,LukasHi Bruce! Thanks for the fast response. I used the current stable version 5.3.0.1 (freesurfer-Darwin-lion-stable-pub-v5.3.0.1). So I will try as you have suggested ... Best wishes,Lukas Bruce Fischl Fri, 02 May 2014 05:47:26 -0700 Hi Luke what version of FS are you running? We see significant speedups. Try running top in a unix terminal and seeing if the cpu usage of mri_ca_register (during autorecon2, the longest single step) is morethan 100% cheers Bruce On Fri, 2 May 2014, lukas.sch...@ukb.uni-bonn.de wrote: Hi folks! I try to use -openmp option on an iMAC with 4 cores. Unfortunately, I do not see any accelartion when processing a single data set with or without the flag -openmp flag set. recon-all -s ernie_1 -all leads to ~6,4h processing time. Unfortunately recon-all -s ernie_2 -all -openmp 4 did not change anything. Do I miss anything? Do I have to prepare my system in a special way? Or run any scripts in advance? (System: iMac, 32GbRam,Intel i5, 4 cores, Mac Os 10.9, latest FS version) Best wishes, Luke ___ 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] using multiple cores
Hi Lukas sorry, I'm out of my depth on the mac. Perhaps Zeke knows what's going on? Does OpenMP have to be enabled somehow? Bruce On Fri, 2 May 2014, lukas.sch...@ukb.uni-bonn.de wrote: Hi Bruce! I just run: recon-all -s ernie2 -autorecon2 -openmp 4 mri_ca_register uses 100.9% CPU at most ... Any idea? Should I try to recompile FS for the current MacOS release? If so, do I have to take care on special librariwa in order to enable the openmp option? Best wishes, Lukas Hi Bruce! Thanks for the fast response. I used the current stable version 5.3.0.1 (freesurfer-Darwin-lion-stable-pub-v5.3.0.1). So I will try as you have suggested ... Best wishes, Lukas Bruce Fischl Fri, 02 May 2014 05:47:26 -0700 Hi Luke what version of FS are you running? We see significant speedups. Try running top in a unix terminal and seeing if the cpu usage of mri_ca_register (during autorecon2, the longest single step) is morethan 100% cheers Bruce On Fri, 2 May 2014, lukas.sch...@ukb.uni-bonn.de wrote: Hi folks! I try to use -openmp option on an iMAC with 4 cores. Unfortunately, I do not see any accelartion when processing a single data set with or without the flag -openmp flag set. recon-all -s ernie_1 -all leads to ~6,4h processing time. Unfortunately recon-all -s ernie_2 -all -openmp 4 did not change anything. Do I miss anything? Do I have to prepare my system in a special way? Or run any scripts in advance? (System: iMac, 32GbRam,Intel i5, 4 cores, Mac Os 10.9, latest FS version) Best wishes, Luke ___ 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] using multiple cores
If you are compiling with clang openmp might not work. Peace, Matt. On 5/2/14, 2:13 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Lukas sorry, I'm out of my depth on the mac. Perhaps Zeke knows what's going on? Does OpenMP have to be enabled somehow? Bruce On Fri, 2 May 2014, lukas.sch...@ukb.uni-bonn.de wrote: Hi Bruce! I just run: recon-all -s ernie2 -autorecon2 -openmp 4 mri_ca_register uses 100.9% CPU at most ... Any idea? Should I try to recompile FS for the current MacOS release? If so, do I have to take care on special librariwa in order to enable the openmp option? Best wishes, Lukas Hi Bruce! Thanks for the fast response. I used the current stable version 5.3.0.1 (freesurfer-Darwin-lion-stable-pub-v5.3.0.1). So I will try as you have suggested ... Best wishes, Lukas Bruce Fischl Fri, 02 May 2014 05:47:26 -0700 Hi Luke what version of FS are you running? We see significant speedups. Try running top in a unix terminal and seeing if the cpu usage of mri_ca_register (during autorecon2, the longest single step) is morethan 100% cheers Bruce On Fri, 2 May 2014, lukas.sch...@ukb.uni-bonn.de wrote: Hi folks! I try to use -openmp option on an iMAC with 4 cores. Unfortunately, I do not see any accelartion when processing a single data set with or without the flag -openmp flag set. recon-all -s ernie_1 -all leads to ~6,4h processing time. Unfortunately recon-all -s ernie_2 -all -openmp 4 did not change anything. Do I miss anything? Do I have to prepare my system in a special way? Or run any scripts in advance? (System: iMac, 32GbRam,Intel i5, 4 cores, Mac Os 10.9, latest FS version) Best wishes, Luke ___ 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
