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listlurker June 1, 2010 08:40 PM

Linux Server For Quantum Physics Lab Use?
 
A friend of mine who's an American quantum physicist is looking to put together a Linux server for lab use, and wanted my opinion on his parts choices. I immediately realized that this sort of feedback was better solicited from the Hardware Canucks, as much of what I know, I learned here. Go to the source, as it were ...

My friend's budget cap is around $1800 US, and he writes that "the finished system will include a 2 port 10G network card which isn't part of the 1800; it is a pricy little puppy".

I'm pasting his tentative parts list below, and would welcome feedback. Most the parts are from NewEgg because he's in the US, so he'll be using US sources.

Last thing, if you feel like explaining your recommendations, by all means do. He'll understand the intricacies of what you're saying, even if I don't :-) A quantum physicist, after all ...

His parts, and comments, follow. Thanks much, all:


=====

The parts list for the Linux server I mentioned on Saturday
Motherboard: ASUS Z8NA-D6C Dual LGA 1366

Newegg.com - ASUS Z8NA-D6C Dual LGA 1366 Intel 5500 ATX Dual Intel Xeon 5500 and 5600 Series Server/Workstation Motherboard

CPU: Intel Xeon E5520 Nehalem 2.26GHz x 2

http://www.newegg.com/Product/Product.aspx?Item=N82E16819117185 383 x 2 USD

RAM: Patriot Signature 6GB (3 x 2GB) 240-Pin DDR3 SDRAM x 2
Newegg.com - Patriot Signature 6GB (3 x 2GB) 240-Pin DDR3 SDRAM ECC Registered DDR3 1333 (PC3 10600) Server Memory Model PSD36G1333ERK
255 x 2 USD

PSU: iStarUSA TC-2U/50-80 24Pin 500W Single 2U

http://www.newegg.com/Product/Product.aspx?Item=N82E16817147084&cm_re=2u_supply-_-17-147-084-_-Product 100 + 7 USD shipping

Cooling: Intel BXSTS100C Thermal Solution LGA1366 for 2-Socket Servers/Workstations

http://www.amazon.com/Intel-BXSTS100C-Solution-2-Socket-Workstations/dp/B001GVISF6/ref=sr_1_1?ie=UTF8&s=electronics&qid=1274222480&sr =8-1 34 x 2 USD

One slightly tricky bit is that is has to fit in a 2U rack mount case that we already have. (The power supply "fits" after some adjustments.) Since video performance is irrelevant (it's OK, you can breath now) we are just using the mother board video --- this will only have a monitor connected very rarely, mostly during setup. There is no system disk speficied, it will likely be two mirrored 160GB SATA drives.

This systems is for 3-D visualization (among other things) so fast is good, but it has to be cheap also (otherwise not worth building it).

A second project is a 20TB disk array to be connected to this server (eSATA + port-multipliers) to be scratch work space for the cluster --- the disk system is all pretty straightforward. It will have to live in a separate box due to power and space considerations.

This is not the fastest possible system; part of the reason to look at building it (which we usually don't do) it to see what the options are. It's going to be used headless; all the access will be remote via command-line (and some web apps we are putting together).

We've not done this before --- no particular need. Some of the 3D visualization software we want to use is happier on Linux than OS X, so it made some sense to try building a linux server. Speaking of scavenging, we were given an old cluster whose disk array had failed. That's where the 2U cases came from. Probably going to use some of the old systems (they're AMD CPUs from 2000-2001) for monitoring my cluster (power, temp, disk usage etc); all it has to do is run a web server. I've got quite a pile of spare parts. Probably will rebuild the disk array sometime but not right now. The AMD servers are _very_ noisy but since they are in a machine room, doesn't really matter (at least not to me).

No graphics card, and only 2 SATA drives for the system. The only PCI cards will be a 2-port 10Gb NIC (12.5 watts) and possibly a 4-port SATA (1 watt). The total load looks to be just under 400W, that's why the 500W supply. The box is a 2U rackmount server enclosure, so the power supply is not the typical ATX shape, it needs to be the shape (more or less) of a aluminum foil box. Most of the usual ATX power supply manufactures don't make server supplies. This will be sitting in a room that is _always_ < 70F so heating is not a problem (the cooling in the machine room is pretty remarkable).

The quad-cores are hyper-threaded; it looks like 16 cores... (we are also getting 25 Mac systems with the same CPUs, so the cluster will have just under 700 CPUs total).

We'll probably go with the CentOS 5 Linux distribution; since this is not a workstation, I want the distribution with the least amount of junk. It's only going to run custom visualization software and a server for a distributed filesystem. Not sure if this is over-kill or not since we don't have a good comparison. We'll only know after building it.

shaw June 1, 2010 09:01 PM

Here's my server, very similar.

Supermicro X8DAi
dual E5520s
Patriot 12Gb

I would choose a server-grade board over the Asus (Tyan being another choice). I had one before the SM, and once I set up the X8DAi I never looked back. PSU-wise I run a PCP&C Silencer 910W since it's up 24/7. Didn't want to load the PSU with a lower-wattage model. The board also required dual 8-pin EPS connectors, which the Silencer has.


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