[3dem] Multi CPU desktop

Steven Ludtke sludtke at bcm.edu
Tue Apr 8 07:24:58 PDT 2014


Here is the system I was referring to:

Supermicro SC743-TQ-865B-SQ tower case (supports 8 hot-swap drives plus 3 fixed), MUCH quieter than similar cases, and very well designed
SUPERMICRO X9DAE motherboard - supports 2 processors, 16 DIMMs (up to 1 TB of RAM)
2x Xeon E5-2650 (2.6 Ghz)
128 GB DDR3 - registered PC12800
LSI MegaRAID SAS 9271-8i - Hardware RAID controller
8x4TB WD Black drives
Any GeForce card (really no benefit in the Quadros)

Total cost of this config is ~$8k, and would be higher if you got higher clocked processors, but:

- 16 cores -> 32 threads - A few years ago threads were useless, but now you can get ~ 25% performance boost in image processing by using 24 or 32 rather than 16
- 128 GB RAM - suitable for very large projects and tomography processing
- 24 TB of usable RAID6 storage, which can read/write at ~1GB/sec, VERY useful with direct-detector data (note that 6TB drives are just emerging now, so if 24 TB isn't quite enough for you, wait a couple of months, and you can put 36 TB in the same form factor)

For many image processing projects, I can skip the cluster and just do the processing on this machine. I can use our old GroEL test data set (5000 particles) and get a 7.6 Å gold standard resolution structure out of this machine from scratch in under 1 hour.

On Apr 8, 2014, at 9:05 AM, rkhayat at ccny.cuny.edu wrote:

> Hi Steve,
> 
> What motherboard and CPU chipsets are you using? Thanks.
> 
> Best wishes,
> Reza
> 
> Reza Khayat, PhD
> Assistant Professor
> The City College of New York
> Department of Chemistry, MR-1135
> 160 Convent Avenue
> New York, NY  10031
> Tel. (212) 650-6070
> www.khayatlab.org
> 
> 
> ---- Original message ----
>> Date: Tue, 8 Apr 2014 09:02:25 -0500
>> From: 3dem-bounces at ncmir.ucsd.edu (on behalf of Steven Ludtke 
> <sludtke at bcm.edu>)
>> Subject: Re: [3dem] Multi CPU desktop  
>> To: Hernando J Sosa <hernando.sosa at einstein.yu.edu>
>> Cc: "3dem at ncmir.ucsd.edu" <3dem at ncmir.ucsd.edu>
>> 
>>  I'm using a 16 core (2x8) Xeon setup at the moment,
>>  which is quite good for a wide range of problems,
>>  particularly if you equip it with a fast internal
>>  RAID. The Opteron processors have remained pretty
>>  sluggish per-core compared to the Intel processors
>>  in recent years. That is, 16 opteron cores vs 16
>>  Xeon cores at the same clock speed still has a
>>  substantial performance difference for floating
>>  point math. For most image processing applications,
>>  performance within a specific chip series will scale
>>  pretty linearly with clock speed, so 8x3 ghz cores
>>  will be equivalent to 12x2 ghz cores in the same
>>  series.  If you're thinking about the opterons, I
>>  would definitely suggest seeing if you can run a
>>  benchmark before purchasing, and make sure the $$$
>>  you're forking out for a large number of cores is
>>  going to get you a real advantage.
>>  On Apr 8, 2014, at 7:58 AM, Hernando J Sosa
>>  <hernando.sosa at einstein.yu.edu> wrote:
>> 
>>    Dear All,
>> 
>>    I am considering getting a desktop for  image
>>    processing and was looking into some 4  CPU ones
>>     (Opteron  16 cores each e.g.
>>     http://www.thinkmate.com/system/hpx-qs5-4410) . I
>>    was wondering  if anybody has any particular
>>    suggestion or better alternatives (apart from
>>    submitting your jobs to a central computing
>>    facility).
>> 
>> 
>>    Thanks
>> 
>>    Hernando
>>    _______________________________________________
>>    3dem mailing list
>>    3dem at ncmir.ucsd.edu
>>    https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem
>> 
>>  ----------------------------------------------------------
> ------------------
>>  Steven Ludtke, Ph.D.
>>  Professor, Dept of Biochemistry and Mol. Biol.
>>    (www.bcm.edu/biochem)
>>  Co-Director National Center For Macromolecular
>>  Imaging        (ncmi.bcm.edu)
>>  Co-Director CIBR Center
>>    (www.bcm.edu/research/cibr)
>>  Baylor College of Medicine
>> 
>>  sludtke at bcm.edu
>> ________________
>> _______________________________________________
>> 3dem mailing list
>> 3dem at ncmir.ucsd.edu
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----------------------------------------------------------------------------
Steven Ludtke, Ph.D.
Professor, Dept of Biochemistry and Mol. Biol.         (www.bcm.edu/biochem)
Co-Director National Center For Macromolecular Imaging        (ncmi.bcm.edu)
Co-Director CIBR Center                          (www.bcm.edu/research/cibr)
Baylor College of Medicine                             
sludtke at bcm.edu







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