AFNI Message Board

Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

History of AFNI updates  

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December 27, 2016 02:28AM
Dear afni experts,

I would like to execute afni commands from python, e.g., using subprocess.check_call() or ipython's ! notation.
However, it seems that commands with OpenMP multithread support, e.g., 3dREMLfit or 3dDeconvolve, only deploy a single thread when executed from python, dramatically slowing down the computation.

For example, when I run
subprocess.check_call(['tcsh', 'stats.REML_cmd'])
or
!tcsh stats.REML_cmd
in ipython, it spawns only one thread and computes very slowly. But when I run the same script directly from the shell
$ tcsh stats.REML_cmd
it spawns 15 thread and runs considerably faster.

Is there a way to execute 3dREMLfit in multithreaded mode from python?

Thanks for help~
Subject Author Posted

Execute 3dREMLfit in multithreaded mode from python

herrlich10 December 27, 2016 02:28AM

Re: Execute 3dREMLfit in multithreaded mode from python

rick reynolds December 27, 2016 08:07AM

Re: Execute 3dREMLfit in multithreaded mode from python

herrlich10 December 27, 2016 10:08AM

Re: Execute 3dREMLfit in multithreaded mode from python

herrlich10 December 27, 2016 10:22AM

Re: Execute 3dREMLfit in multithreaded mode from python

herrlich10 January 08, 2017 08:19PM