I would like to use freesurfer with OpenMP, with 4 processors. I wrote this : recon-all -all -i /mnt/linuxwin/lboumgha/data/CENTER_TBI/tro/suj1/T1.nii.gz -subjid subj1 -openmp <8> and I got this error message :
bash: syntax error near unexpected token `8'
What is the good syntax if I want tu use OpenMP, please? Great regards, Linda Boumghar
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It is -openmp 8 Delete the less than and greater than characters around the 8
On 16 Oct 2015, at 3:25 PM, Linda BOUMGHAR linda.boumghar@upmc.fr wrote:
I would like to use freesurfer with OpenMP, with 4 processors. I wrote this : recon-all -all -i /mnt/linuxwin/lboumgha/data/CENTER_TBI/tro/suj1/T1.nii.gz -subjid subj1 -openmp <8> and I got this error message :
bash: syntax error near unexpected token `8'
What is the good syntax if I want tu use OpenMP, please? Great regards, Linda Boumghar
This message was sent using IMP, the Internet Messaging Program.
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Hi Linda
did you actually include the angle brackets? If so, try without them. And don't you want 4 there instead of 8 (if you have 4 processors)?
On Fri, 16 Oct 2015, Linda BOUMGHAR wrote:
I would like to use freesurfer with OpenMP, with 4 processors. I wrote this : recon-all -all -i /mnt/linuxwin/lboumgha/data/CENTER_TBI/tro/suj1/T1.nii.gz -subjid subj1 -openmp <8> and I got this error message :
bash: syntax error near unexpected token `8'
What is the good syntax if I want tu use OpenMP, please? Great regards, Linda Boumghar
This message was sent using IMP, the Internet Messaging Program.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
One question about "-openmp". If I run multiple "recon-all" in different terminals without using this flag...
Is there any problem with the 'gcareg' stage? For example, is there any interference between subjects reconstruction?
Thanks.
2015-10-16 15:07 GMT+02:00 Bruce Fischl fischl@nmr.mgh.harvard.edu:
Hi Linda
did you actually include the angle brackets? If so, try without them. And don't you want 4 there instead of 8 (if you have 4 processors)?
On Fri, 16 Oct 2015, Linda BOUMGHAR wrote:
I would like to use freesurfer with OpenMP, with 4 processors. I wrote
this :
recon-all -all -i /mnt/linuxwin/lboumgha/data/CENTER_TBI/tro/suj1/T1.nii.gz -subjid subj1 -openmp <8> and I got this error message :
bash: syntax error near unexpected token `8'
What is the good syntax if I want tu use OpenMP, please? Great regards, Linda Boumghar
This message was sent using IMP, the Internet Messaging Program.
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.
there won't be any interferance if you use -openmp 1 (which I think is the default) as long as you have more processors than recon-all jobs (and enough RAM to support them all)
On Tue, 3 Nov 2015, Julio Alberto González Torre wrote:
One question about "-openmp". If I run multiple "recon-all" in different terminals without using this flag...
Is there any problem with the 'gcareg' stage? For example, is there any interference between subjects reconstruction?
Thanks.
2015-10-16 15:07 GMT+02:00 Bruce Fischl fischl@nmr.mgh.harvard.edu: Hi Linda
did you actually include the angle brackets? If so, try without them. And don't you want 4 there instead of 8 (if you have 4 processors)? On Fri, 16 Oct 2015, Linda BOUMGHAR wrote: > I would like to use freesurfer with OpenMP, with 4 processors. I wrote this : > recon-all -all -i > /mnt/linuxwin/lboumgha/data/CENTER_TBI/tro/suj1/T1.nii.gz -subjid > subj1 -openmp <8> > and I got this error message : > > bash: syntax error near unexpected token `8' > > What is the good syntax if I want tu use OpenMP, please? > Great regards, > Linda Boumghar > > ---------------------------------------------------------------- > This message was sent using IMP, the Internet Messaging Program. > > > _______________________________________________ > 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.
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Bruce Fischl -
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Julio Alberto González Torre -
Linda BOUMGHAR