[3dem] Workstation

Steven Ludtke sludtke at bcm.edu
Fri Nov 7 17:24:13 PST 2014

1 core on AMD is NOT equivalent to 1 core on Intel. For the sort of number crunching we do in image processing (floating point math), AMD is way behind per core. AMD was the clear leader about 10 years ago, but since Intel’s core 2 duo series, AMD has been playing catch-up. They can still be cost effective for web services, etc, but for number crunching, even if you get fewer cores you will get more bang for the buck with Intel. Generally the companies understand this, so it takes 1.5-2x more AMD cores to equal the compute power of a Xeon, and Xeon system costs will be close to 1.5 to 2x more expensive per core for an assembled computer.

I keep a page for EMAN users with current computer recommendations. My group manages about 2000 cores of cluster computing (5 different generations), so we pay fairly careful attention to these things. I expect in terms of computer purchasing, advice for EMAN will hold quite well for Relion, Frealign, etc.

http://blake.bcm.edu/emanwiki/EMAN2/FAQ/Computer <http://blake.bcm.edu/emanwiki/EMAN2/FAQ/Computer>

There is very little reason to pay the significant premium for a Quadro card. You can get much better bang for the buck if you want to do GPU computation. The ONLY thing that the Quadro can do that consumer-grade cards cannot is Windowed frame-interleaved stereo 3D. If you buy a passive stereo monitor (using unpowered polarized glasses) many programs can do very effective stereo with any graphics card at all (like Chimera). 

The biggest thing to take into account in the movie-mode era is disk performance. Many compute operations can become disk speed limited quite easily. A single traditional hard drive can give ~150 MB/sec. A single SSD can give as high as 500-600 MB/sec for mainstream cards, but they are more expensive, and have somewhat poor durability for heavy write loads. A good inexpensive solution is to put 8 traditional 4TB drives in a case supporting hot-swapping with a PCIE RAID controller. This can give throughputs of ~1.5 GB/sec to the local computer, for a very modest cost.

See the page above for more...
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

> On Nov 7, 2014, at 6:07 PM, Hernando J Sosa <hernando.sosa at einstein.yu.edu> wrote:
> Dear EM users,
> We have some money to spend  (<10K) in a personal  workstation mainly to be used for number crunching  and single particle analysis. I came across  this system (see below) made by a company called Thinkmate.
> Does anybody have experience with this company?   
> Any comments on the system ?
> As configured it has 64 cores (4 x 16) and 128 GB of RAM
> I chose AMD Opteron  over Intel as it seems to produce the best price/performance but I may be wrong.
> Any comments suggestions are welcomed.
> Thanks
> Hernando
> <image001.png>
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