Dear Colleagues,
Hi. Let me ask a naive question about using AFNI on Biowulf. I know that things are much more complicated than the way I represent them, but let me oversimplify things so that I can get a rough understanding.
I ran a script that combining
/home/picchionid/afni/CD/AFNI_data6/FT_analysis/Qwarp/s00.warper
and
/home/picchionid/afni/CD/AFNI_data6/FT_analysis/Qwarp/s05.ap.Qwarp
with minimum changes on our raid with
(base) picchionid@raid ~> afni_system_check.py -check_all | grep -i cpu
number of CPUs: 8
(base) picchionid@raid ~> 3dQwarp -help | grep -i dante
++ OpenMP thread count = 8
++ 3dQwarp: AFNI version=AFNI_21.0.17 (Mar 13 2021) [64-bit]
++ Authored by: Zhark the (Hermite) Cubically Warped
, and it took about 2 hr. Then I ran it on Biowulf with
number of CPUs: 72
++ OpenMP thread count = 72
, and the processing time only decreased by about 25%. So, is the following basically a correct understanding? On p. 33 of
/home/picchionid/afni/CD/afni_handouts/afni_proc.pdf
, the bullet that reads "Takes a long time, so the script should be submitted to a multi-node cluster" should be interpreted as "Takes a long time, so [when processing multiple subjects, each subject] should be submitted to a multi-node cluster [as different subjobs]." In other words, "typically, AFNI on Biowulf is used to simultaneously process a large number of independent datasets via the swarm utility" (https://hpc.nih.gov/apps/afni.html).
Sincerely,
Dante
