Hi Nicolas,
the GPUs are only used during the expectation steps of the single
iterations and not during the maximization steps.
You can continuously monitor the GPU usage by using "watch -n 0,5
nvidia-smi" it basically refreshes the nvidia-smi command every 0.5
sec what gives you a quasi continuously view. By doing so you should
see the GPU usage during the expectation steps and no GPU usage during
initialization and maximization and so.
Best,
Julian
Quoting "Coudray, Nicolas" <[log in to unmask]>:
> Hi,
>
> We're currently checking how relion performs on our GPU nodes and
> were looking at the GPU usage using nvidia-smi for different jobs.
> We see the usage at some point for the 2D classification and 3D
> refinement jobs, but haven't seen anything yet for the 3D
> classification.
>
> Whenever we checked (start of iteration, during maximization step,
> etc), we see "No running processes" for the GPUs.
>
> +-----------------------------------------------------------------------------+
> | Processes:
> GPU Memory |
> | GPU PID Type Process name
> Usage |
> |=============================================================================|
> | No running processes found
> |
> +-----------------------------------------------------------------------------+
>
>
> Are we just not looking at the right moment or is there something
> wrong with the use of GPUs in 3D classification?
> At which point of the iteration is the GPU used (or is there another
> way to quickly monitor the GPU usage)?
> (--gpu "0,1:2,3" option does appear in the submitted script, btw)
>
>
> Thanks,
> Best,
> Nicolas
>
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--
Julian Reitz, Dipl.-Biochem.
J.W. Goethe Universität Frankfurt am Main
BMLS - Buchmann Institut for Molecular Life Sciences
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