[3dem] [External] Seeking advice for RELION cryo-EM workstation

Fri Oct 6 00:00:28 PDT 2023

Hello Tinghai,

At the moment, you need 4 GPUs if you want to use cryoSPARC Live with all its capabilities: two GPUs will be used for preprocessing (= motion correction, CTF estimation, particle picking and extraction), one GPU for streaming 2D classification and one GPU for streaming 3D refinement.

I don’t know whether or not cryoSPARC Live might change in future versions to enable a similar workflow but using fewer GPUs. You also need to consider whether this functionality is helpful to you. It is pretty cool to see the 3D reconstruction getting better in near-real time, and it might make sense to have this setup directly at the microscope (one can then stop collecting when no more improvement is made). But in my experience, this works well only for easy datasets (with minimal heterogeneity, or with purely discrete heterogeneity that can be resolved easily in 2D classification, because the Live workflow doesn’t include heterogeneous refinement nor 3D classification), and for more typical datasets I have to dig in anyway. The most valuable part of cryoSPARC Live, I think, is the real-time motion correction and CTF estimation: this tells you enough about the microscope settings (and whether you need to pause the collection and adjust something). Another sensible way to use Live, not at the microscope, is to preprocess your movies as they are being downloaded (this can save a lot of time depending on the dataset size and download speed).

I haven’t looked at the specs of these two GPUs in details, but I think for single-particle analysis and unless you work with very large box sizes (in this case, choose the GPU with the largest memory), you can’t really go wrong with either. Therefore, I would recommend getting 4 GPUs, because as you say it will make a difference in how many jobs you can run in parallel.

I hope this helps,

Guillaume

On 6 Oct 2023, at 03:46, Xu, Tinghai <Tinghai.Xu at vai.org<mailto:Tinghai.Xu at vai.org>> wrote:

Dear colleagues,

Related to the cryo-EM workstation suggestion.

Regarding the Cryo-EM workstation suggestion, I'm looking for insights from anyone who has experience comparing a setup with 2x 4090 GPUs to one with 4xA4500 GPUs, while keeping all other configurations identical, such as a 32-core CPU and 512GB of RAM. Both options fall within the same price range. I understand that the performance of the 4090 GPUs is significantly better than the A4500 GPUs. However, I'm concerned about the trade-off between having two jobs running concurrently with the 2x 4090 setup versus having the ability to run four jobs simultaneously with the 4xA4500 setup in applications like CryoSPARC.

I would greatly appreciate hearing from anyone who has practical experience with these configurations and any suggestions you might have.
Thank you in advance for your insights.

Tinghai

-----------------------
Tinghai Xu, Ph.D.
Assistant Professor
Edward A. Doisy Research Center, Room 553
Department of Biochemistry and Molecular Biology
Saint Louis University School of Medicine
1100 South Grand Blvd.
St. Louis, MO 63104
Email: TinghaiXu at gmail.com<mailto:TinghaiXu at gmail.com>
Homepage: https://urldefense.com/v3/__http://www.xulaboratory.org__;!!Mih3wA!EGUcXFKmrtQAazZlyeEdzdZuxHRASiPdq0zRJZFK3JRh5SHRJBe_qEejw8BGmjPFmoyupnpmKJmFaOnTRWI6e-xY7jsLAtDb$ <https://urldefense.com/v3/__http://www.xulaboratory.org/__;!!Mih3wA!EGUcXFKmrtQAazZlyeEdzdZuxHRASiPdq0zRJZFK3JRh5SHRJBe_qEejw8BGmjPFmoyupnpmKJmFaOnTRWI6e-xY7lDTwmym$ >

From: 3dem <3dem-bounces at ncmir.ucsd.edu<mailto:3dem-bounces at ncmir.ucsd.edu>> On Behalf Of Guillaume Gaullier
Sent: Wednesday, October 4, 2023 3:44 PM
To: Yingxia Hu <yhu at hexagonbio.com<mailto:yhu at hexagonbio.com>>
Cc: 3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu>
Subject: [External] Re: [3dem] Seeking advice for RELION cryo-EM workstation

Hi Alicia,

60 TB of bulk storage (maybe less usable space, depending on the raid configuration of these HDD) will be barely sufficient for working on one dataset at a time. Storage is the most overlooked of the configuration options (we are all obsessed with computing power, GPUs, etc.), but insufficient storage will be an endless source of problems and frustration down the road (speaking from experience…). You will be wasting GPU time if a significant fraction of the time is spent moving data around because the workstation’s bulk storage is full.

So you should plan for this before buying, and my main recommendation is to get as much bulk storage as you can afford.

I hope this helps,

Guillaume

On 3 Oct 2023, at 23:18, Yingxia Hu <yhu at hexagonbio.com<mailto:yhu at hexagonbio.com>> wrote:

Dear colleagues,

I am seeking advice on building a cryo-EM workstation for data processing using RELION. Here is a draft configuration:

  *   1x Intel Xeon W Series CPU, 12 cores, 3.20 GHz;
  *   8x32GB RAM;
  *   1TB M2 drive for OS, 3.84TB U.2 NVMe drive for scratch disk;
  *   3x20TB Hard Drive (3.5" Internal - SATA/600 - 7200rpm);
  *   2x Nvidia RTX A4500.

Would 2x A4500 be sufficient for RELION jobs? And which one would be better between 4070 (12GB memory, faster clock speed) and A4500 (20GB, slower clock speed)? Any other advice is appreciated. Thanks in advance!

Best,
Alicia

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