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CCPEM  September 2018

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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 09:10:01 +0100

Content-Type:

text/plain

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text/plain (119 lines)

Hi Douglas,

 > Does Relion 2.1 or 3 leverage Unified Memory Architecture

No. (And probably this does not help performance)

Best regards,

Takanori Nakane

On 2018/09/14 21:06, Douglas Duckworth 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 <https://scu.med.cornell.edu>
> 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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