External Email - Use Caution Thank you for your reply!
Best regards, Peter On Wed, Nov 8, 2023 at 2:41 PM Huang, Yujing <yhuan...@mgh.harvard.edu> wrote: > Hi Peter, > > > > I would suggest not to use ‘-parallel’. It is handled by recon-all to run > multiple commands in parallel. It can run into collisions if they are not > synchronized. > > > > These recon-all options ‘-threads <>’, ‘-openmp <>’, ‘-nthreads <>’ tell > individual program to split the tasks and run them in parallel. They are > the same flags. > > > > Best, > > > > Yujing > > > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *P Pieperhoff > *Sent:* Wednesday, November 8, 2023 5:28 AM > *To:* freesurfer@nmr.mgh.harvard.edu > *Subject:* [Freesurfer] parallel processing of long-run fails > > > > * External Email - Use Caution * > > Dear FreeSurfer developers, > > > > when I execute a long-run with parallel processing by calling > > > > recon-all -sd <directory> -threads 64 -openmp 64 -parallel -long <imageid> > <template_id> -all > > > > it fails in step "autorecon3" at the surface registration. > > > > But when I start it again without the option "-parallel", it finishs > without errors. > > I'm using FreeSurfer version 7.4.1 with Linux CentOS. > > > > I have attached the log file to this mail. > > > > Best regards, > > Peter > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1exITWwZLg3MpwcTRLBzNrKGHf5hrK6mEEmAmQlV-BNapXsbG2DthWZWuFVh4kp-0jGO1QzSsXB-g2VgVG64H0V5VCQ8rGCt7NJnD7doxideYDV7ESgaDMcd2Zy4apHqiAQEVWqYfSUBwBpjgK5sUGzjFd5L24XPbAd09gdyTlur-N51-kJFV7EnK-KWEpyEx3ReTecc1XWe96mRzSXefc_asnD1VYe5pHvkOSHGxDTyzi-e_GaOiKBzRCLVBOlfXMB13usX8egg6qy2OSWG8KfgwWQ3q03q96h_grsHBirJLMEBREbBIuA-Zw1Eq4pLbLCbRypZAeWjks6Nfl15Y8A/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > 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 Mass General > Brigham Compliance HelpLine at > https://secure-web.cisco.com/19hmlP6cdsy-cgcZj7ziRizzSm6xupU7qjIfNO8UYNA2IvcI5kGIF46R1tRqEKmXPF5quAFTKfbH8qU_GrfAo8h_ZNjYcrfIE_6B2RSRKfBECP2z5hEUNOBR_OhGsi86MrTbDd2FWC49TtwwIe415tlbU_NX_HneTsQWqDUKC8c_JeDtbUFtU6ZjnLlCv106Rkp6yas85WiGGIo-OvGN8Ii7RDdRvd1K8K1uyQx-MYaidzSvhLmPLMYWmC4rZGGd5NikNvShCYySPHVBXk1wgY-S3kw2fHJ-lcNVR06prNtuZCdgDSpLVdQkcW2_U6BDA8tUhLL4KkD3s_jskVxTFwQ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline > < > https://secure-web.cisco.com/19hmlP6cdsy-cgcZj7ziRizzSm6xupU7qjIfNO8UYNA2IvcI5kGIF46R1tRqEKmXPF5quAFTKfbH8qU_GrfAo8h_ZNjYcrfIE_6B2RSRKfBECP2z5hEUNOBR_OhGsi86MrTbDd2FWC49TtwwIe415tlbU_NX_HneTsQWqDUKC8c_JeDtbUFtU6ZjnLlCv106Rkp6yas85WiGGIo-OvGN8Ii7RDdRvd1K8K1uyQx-MYaidzSvhLmPLMYWmC4rZGGd5NikNvShCYySPHVBXk1wgY-S3kw2fHJ-lcNVR06prNtuZCdgDSpLVdQkcW2_U6BDA8tUhLL4KkD3s_jskVxTFwQ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> > . >
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