Re: [scipion-users] CPU acceleration in Relion installed via Scipion

[Jose M. de la R. T. <del...@gm...>]

Hi again,

You could in principle have both and alternate...but in your case I think
it is not worth.
Even if you have 2GPU, you can use more than 1 MPI per GPU and also threads.
So the 16 cores will be busy if you want to get the GPU busy as well.

Yes, any consideration about the combination of MPI/threads/cores and GPUs
that are valid for Relion, also apply when using Relion within Scipion.

Best,
Jose Miguel


On Wed, Nov 27, 2019 at 3:04 PM Derek Logan <der...@bi...>
wrote:

> Hi Jose Miguel,
>
> Thanks for your rapid reply! I'll try what you suggest. It wasn't clear to
> me from a first read of the Relion 3.0 paper in eLife whether GPU and CPU
> acceleration were mutually exclusiveonly  at run time or at the time of
> compilation. I assumed it was at run time only. Basically we are looking
> for a way to use our 14 idle CPU cores when 2 of them are running processes
> using the GPUs, so the GPU/CPU optimisation conflict would not matter.
>
> No, we don't have the icc compiler and anyway our CPUs are AMD, so I don't
> know if icc would offer any benefits? I haven't had to think so much about
> hardware and compilation for the past 10-15 years as a protein
> crystallographer ;-)
>
> Maybe these questions are better asked on a Relion forum anyway...
>
> /Derek
>
> On 27 Nov 2019, at 14:53, Jose Miguel de la Rosa Trevin <
> del...@gm...> wrote:
>
> Hi Derek,
>
> If you want to have more control about Relion installation (and
> compilation flags)
> probably is a better idea to do it outside Scipion and then create the
> proper link
> in scipion/software/em/relion-3.0 -> /path/to/relion-3.0
>
> Regarding CPU optimization, remember that this is exclusive with GPU
> acceleration,
> which I assume you want. Moreover, I'm not completely sure if for the
> complete CPU
> optimization, you need the Intel compiler (not GCC) which is not free.
>
> Kind regards,
> Jose Miguel
>
>
>
> On Wed, Nov 27, 2019 at 2:21 PM Derek Logan <
> der...@bi...> wrote:
>
>> Hi,
>>
>> I recently installed scipion 2.0 from source on a machine with an AMD
>> 2950X 16-core CPU and two RTX 2080 Ti GPUs. I then installed Relion 3.0
>> using the plugin interface and gcc 7.4.0. How can I be sure that Relion has
>> been compiled with the CPU acceleration that was introduced in Relion 3.0?
>> I was not attentive to this aspect during the installation and now I don't
>> know where to find the log files that might give me a clue. If Relion was
>> not compiled with CPU acceleration, how can I redo things so that it is?
>> Finally, when running e.g. 3D refinement, do we have to explicitly write
>> "--cpu" in the "Additional arguments" box?
>>
>> Thanks in advance
>> Derek
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
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