On 1/27/2021 2:02 PM, Wei Shao wrote:
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Hi, Douglas
Thanks for your kind reply.
1 I run the same subject on a server with openmp 8 flags cost 7 hours, without openmp 8 flag would be 7h10minutes.
Can you send the two recon-all.log files?
3 Could you be more specific about run them by hand? is this mean I run different tasks like skull strip or parcellation separately within recon rather than recon-all?
Each step in recon-all can be run separately using command line flags. It is not an easy thing to do and not well documented.
Best, Wei
On Mon, Jan 25, 2021 at 10:17 PM Douglas N. Greve <dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu> wrote:
On 1/20/2021 3:39 PM, Wei Shao wrote:External Email - Use Caution Hi, Freesufer experts My name is wei shao, I have a few questions regarding the parallel computing of recon-all 1 According to documents, freesurfer is OpenMP code , I use -openmp 8 flag like: recon-all -alli -i input.file -s output.file -openmp 8 to tun the recon command on a server, but it doesn't work for me (the running time is very similar for the same subject). Cloud you tell me what is wrong?Please specify the difference in times.2 Can Freesufer take advantage of several GPUs?No3 Is it possible to open few threads to run recon-all on different sections parallelly?Only if you run them by handBest, Wei _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1iCbpbp3TlQC67E9mq0PzTzJ5cANh6TRxDqcmmQi1W7zG1jM5MCUQqqsXe3QwM7oVOFj_LjCFo27-8CJfoyO91GKrSBzIxnU_YshInte2aLVCn47Vj32-jMMVrD8rT-_76qE6PP6khCI7B6FR2Yp5MsZI8wpfQDHkafQjCjJcDl8xcasuz_GtojXgPZ9v09wpG8dwOWxahtMB8ldo_6U1rwqRG3OFUZCwWs26DrqqA8xjv-XgB_FKSSrhHHo8xSgDo6iwlh8PgiT7FQY9ZGz_TQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1iCbpbp3TlQC67E9mq0PzTzJ5cANh6TRxDqcmmQi1W7zG1jM5MCUQqqsXe3QwM7oVOFj_LjCFo27-8CJfoyO91GKrSBzIxnU_YshInte2aLVCn47Vj32-jMMVrD8rT-_76qE6PP6khCI7B6FR2Yp5MsZI8wpfQDHkafQjCjJcDl8xcasuz_GtojXgPZ9v09wpG8dwOWxahtMB8ldo_6U1rwqRG3OFUZCwWs26DrqqA8xjv-XgB_FKSSrhHHo8xSgDo6iwlh8PgiT7FQY9ZGz_TQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
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