glad to hear it
Bruce
On Mon, 12 Jan 2015, Narayanan, Krishnaprasad wrote:
Yeah, it works. I am able to see the load on multi cores.
Regards,
Krishnaprasad
-----Original Message-----
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: Montag, 12. Januar 2015 14:51
To: Freesurfer support list
Subject: Re: [Freesurfer] Openmp option does not work in Ubuntu 12.04
yes, in 5.3 there is only openmp support in a couple of binaries. Those stages
are reached maybe 15 minutes into recon-all depending on your hardware.
cheers
Bruce
On Mon, 12 Jan 2015, Narayanan,
Krishnaprasad wrote:
Hi Bruce,
Thanks for your reply. May be I should not have said it is not working. Sorry
for that.
The command that I used was "recon-all -i
/usr/local/freesurfer/subjects/bert/mri/T1.mgz -subjid exampledata1 -all -openmp 8".
Yeah, I observed the core usage using htop until the end of first minute. Until
the end of first minute, I saw the CPU utilization only on one of the core and
not on all the specified cores.
I guess I have found the mistake. The multi core option is enabled only during
the mri_em_register_stage and mri_ca_register stage.
Can I know approximately at what point in time are these two stages reached?
Regards,
Krishnaprasad
-----Original Message-----
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce
Fischl
Sent: Montag, 12. Januar 2015 14:30
To: Freesurfer support list
Subject: Re: [Freesurfer] Openmp option does not work in Ubuntu 12.04
Hi Krishnaprasad
what is your full recon-all command line? And how do you know it isn't working? Have you
tried running "top" during the mri_ca_register stage?
The upcoming (one of these months!) release will have much more in the
way of openmp optimization
cheers
Bruce
On Mon, 12 Jan 2015, Narayanan, Krishnaprasad
wrote:
Hallo all,
I have installed freesurfer v5.3 on Ubuntu 12.04 LTS. The GCC version
is 4.6. I use the recon-all using –all and -openmp option. I observed
that openmp does not seem to have any effect in the execution of
freesurfer. I verified the installation of openmp using dpkg --status
libgomp1 and found that the package was installed.
Do I have to install or enable any additional library or flags? Can
I kindly get help from the forum to resolve this problem?
Best regards,
Krishnaprasad
_______________________________________________
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.
