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
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