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.Scheef@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
If you are compiling with clang openmp might not work.
Peace,
Matt.
On 5/2/14, 2:13 PM, "Bruce Fischl" fischl@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.Scheef@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.
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" fischl@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.Scheef@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@nmr.mgh.harvard.edu
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Bruce Fischl -
Lukas.Scheef＠ukb.uni-bonn.de -
Matt Glasser -
Z K