[3dem] Multi CPU desktop
Penczek, Pawel A
Pawel.A.Penczek at uth.tmc.edu
Tue Apr 8 07:32:57 PDT 2014
Hi,
this is quite interesting. However, I would say 5,000 particles only go so far.
I heard that one could get a box with 64 CPUs (I am not sure about threads) and significant memory
for ~10k. I was thinking about getting two of those and hooking them up the have a mini-cluster.
I would of course skip monitors.
My believe is that with such a modest investment one could do decent projects "at home".
Is it really feasible?
Regards,
—
Pawel A. Penczek, Ph.D.
Professor
Structural Biology Imaging Center, Director
The University of Texas
phone: 713-500-5416
fax: 713-500-0652
http://www.uth.tmc.edu/bmb/faculty/pawel-penczek.html
On Apr 8, 2014, at 9:24 AM, Steven Ludtke <sludtke at bcm.edu> wrote:
> 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.
>>> https://urldefense.proofpoint.com/v1/url?u=http://www.thinkmate.com/system/hpx-qs5-4410&k=yYSsEqip9%2FcIjLHUhVwIqA%3D%3D%0A&r=2aNbZJh6eMzYI7ecrNAUvrma%2F0vaXYG%2BIjyWZafay%2BU%3D%0A&m=B%2FjgPQI8mbbsJ99SWBZi%2BF4G1VUWDVs8XI%2BLBj8wCR0%3D%0A&s=30604f55c16402e5ff3c9035c82fc9fd296582ea6759d7d9d5a8932b90ac4661) . 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
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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
>>> ________________
>>> _______________________________________________
>>> 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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