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Subject:

Re: Relion GPU mem

From:

Takanori Nakane <[log in to unmask]>

Reply-To:

Takanori Nakane <[log in to unmask]>

Date:

Sat, 15 Sep 2018 14:10:47 +0100

Content-Type:

text/plain

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text/plain (124 lines)

Hi,

 > Does Relion-3 still use the CPU and system memory for the final 
converged expectation and maximisation iteration? It used to be this way 
to get double precision on these calculations I recall.

Maximisation (gridding) is done on CPU for ALL iterations.
Expectation is performed on GPU even for the final iteration.

These are the same as RELION 2.1.

 > If so, may I ask what are the requirements on the system memory for a 
1000px box and with what refine command options? That’s a big box!

32 or 64 GB should be enough.

Best regards,

Takanori Nakane

On 2018/09/15 12:21, Kyle Morris wrote:
> Hi Takanori,
> 
> Does Relion-3 still use the CPU and system memory for the final converged expectation and maximisation iteration? It used to be this way to get double precision on these calculations I recall.
> 
> If so, may I ask what are the requirements on the system memory for a 1000px box and with what refine command options? That’s a big box!
> 
> Best wishes,
> Kyle
> 
> P.s. Douglas, apologies for hijacking!
> 
>> On 14 Sep 2018, at 21:06, Douglas Duckworth <[log in to unmask]> wrote:
>>
>> Does Relion 2.1 or 3 leverage Unified Memory Architecture thus enabling GPU over subscription as described:
>>
>> https://devblogs.nvidia.com/beyond-gpu-memory-limits-unified-memory-pascal/
>>
>> Thanks,
>>
>> Douglas Duckworth, MSc, LFCS
>> HPC System Administrator
>> Scientific Computing Unit
>> Weill Cornell Medicine
>> 1300 York Avenue
>> New York, NY 10065
>> E: [log in to unmask]
>> O: 212-746-6305
>> F: 212-746-8690
>>
>>
>>
>>> On Fri, Sep 14, 2018 at 12:51 PM, Hansen, Bryan (NIH/NIAID) [E] <[log in to unmask]> wrote:
>>> We've had trouble with a 512 box and our GPU has 16GB of RAM.  I didn't think of the padding for some reason.  Thanks we'll definitely give that a try.
>>>
>>> Bryan
>>>
>>> -----Original Message-----
>>> From: Takanori Nakane <[log in to unmask]>
>>> Sent: Friday, September 14, 2018 10:45 AM
>>> To: Hansen, Bryan (NIH/NIAID) [E] <[log in to unmask]>
>>> Cc: [log in to unmask]
>>> Subject: Re: [ccpem] Relion GPU mem
>>>
>>> Hi,
>>>
>>> What is the box size and how much GPU memory do you have in ONE card?
>>>
>>> Anyway, you can set 'Skip padding: Yes'. With GTX 1080 Ti (11 GB RAM), you can refine up to 1000 px box with this option.
>>>
>>> Best regards,
>>>
>>> Takanori Nakane
>>>
>>>> Hi All,
>>>>
>>>> We've been having some issues in the final steps of 3D refinement with
>>>> our larger box sizes of running out of memory on our GPUs.  I was
>>>> curious if anyone had any suggestions on how to get around this issue.
>>>> Thanks for any tips.  I'm sure this is probably a 'easy' fix that we
>>>> are just missing.
>>>>
>>>>
>>>> Bryan Hansen
>>>> Computational Biologist / Electron Microscopist NIH/NIAID/RTB/RML/EMU
>>>> Rocky Mountain Laboratories
>>>> 903 S. 4th St
>>>> Hamilton, MT 59840
>>>> 406.363.9202
>>>>
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