Hardware flags for more threads?

[anaphaze]

Dear A-P team,
I am able to run appion-protomo on a dual 10-core CPU system (20 cores total). During the refinement step, I notice protomo launches between 4 to 10 processes, each at up to 100% usage.
I checked the command and couldn't find any obvious flags that control the number of processes. Also, I verified in the docker container with 'lscpu' that docker sees all 20 cores. Is there a way to force protomo to use more -- or all -- of the CPU resources? I'd imagine doing so would make the affordable 32-core AMD machines a very attractive for tomography.
Thanks.
Lu

[alexjnoble]

Hi Lu,

I should check on these issues - sorry about that!

The main Protomo alignment algorithm (as shown in the 'Click to see how Protomo alignment works' animation here) is single-CPU bound; it's a serial algorithm. The video- and image-making processes at the end of each iteration are parallelized. The parallelization can be turned off in the Advanced General Parameters on the coarse alignment and refinement webpages.

I hope to someday find someone to GPU-ize Protomo alignment=) Let me know if you know someone!
Best,
-Alex