External Email - Use Caution
Dear Tim,
Sorry, I am a Linux code beginner. I installed the GNU parallel in my Linux. May I know how to adapt the script of “ run_reconall_parallel_wrapper.bash” to my own need? Thank you.
Regards
Frank
On Jan 4, 2020, at 6:12 PM, Tim Schäfer ts+ml@rcmd.org wrote:
External Email - Use CautionHi Frank,
The OS shouldn't make any difference as long as you use the same shell. You will have to install GNU parallel first as it's usually not installed by default under Linux (on Debian-based distros: `sudo apt-get install parallel`).
I have shell scripts for the BASH shell here if you want:
https://github.com/dfsp-spirit/shell-tools/tree/master/gnu_parallel_reconall...
If you need an explanation, you can read this before using them:
https://www.xsmd.org/brain/2019/03/13/using-gnu-parallel-to-speedup-neuroima...
Best,
Tim
-- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
On January 4, 2020 at 7:08 AM Frank Chau cyfrank@hku.hk wrote:
External Email - Use CautionDear Bruce,
No, I want to run recon-all on 4-8 subjects at the same time. I could find detail tutorial on the Mac platform (Run: "ls *.nii | parallel --jobs 4 recon-all -s {.} -i {} -all -qcache", after installing Xcode and Homebrew.) But I couldn't find any similar information on the Linux platform.
Regards
Frank
On Jan 3, 2020 11:15 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Frank
do you mean completing a single recon faster? The easiest way to do that is to use the -openmp <N> flag, and set <N> to the number of threads/cores you want to use. Alternatively if you have enough RAM you can just run multiple recon-alls at the same time (which will give you a bigger effective speed increase)
cheers Bruce On Fri, 3 Jan 2020, Frank Chau wrote:
External Email - Use CautionDear Freesurfer experts,
May I know how to run Recon-all in parallel on Linux? I have read some source said that can use "gnu parallel" to complete it. But they do not describe it in detail how to perform it.
Regards
Frank
FRANK C Y CHAU
Research assistant
Division of Neurology
Department of Medicine
Tel: +852 6340 2553
Fax: 2872 5828
E-mail : cyfrank@hku.hk
Rm 304, 3/F, New Clinical building, Queen Mary Hospital, 102 Pokfulam Road, Hong Kong
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