I'm looking for advice on the classic build vs buy question.

We need a new linux server to run Matlab computation on in our lab (academic). Matlab parallel computing toolbox licence allows up to 12 local workers so we are aiming at a 12 core server with 4GB memory per core (total of 48gb). The system will have an SSD for the OS and a raid-5 (4x2tb) for data.

I looked around and found a (relatively) cheap vendor, Silicon Mechanics, that offers a system to our liking (specs below) for $6732. However, buying the components from newegg cost only $4464!

The difference is $2268 which is 50% of the base cost. If buying from a company can be thought of as a sort of insurance, basically my premiums are of 50% of the base cost which to me sounds like a lot.

Of course any downtime is bad, but the work is not "mission critical", i.e. if it takes a few days to fix it when it breaks its no the end of the world. If it takes weeks to months then its a problem. If it breaks 2-3 times in 3 years, not too bad. If it breaks every month not good.

In term of build experience, I set up a linux cluster in grad school (from existing computers) and I build my home pcs but I never built a server before.

The server components I'm thinking about:

1 x SUPERMICRO SYS-7046T-6F 4U Tower Server Barebone Dual LGA 1366 Intel 5520 DDR3 1333/1066/800 ($1,050)

12 x Kingston 4GB 240-Pin DDR3 SDRAM DDR3 1333 (PC3 10600) ECC Unbuffered Server Memory ($420)

2 x Intel Xeon E5645 Westmere-EP 2.4GHz LGA 1366 80W Six-Core ($1,116)

4 x Seagate Constellation ES 2TB 7200 RPM SATA 6.0Gb/s 3.5" ($1,040)

1 x SAMSUNG Internal DVD Writer Black SATA ($20)

1 x Intel 520 Series 2.5" 180GB SATA III MLC SSD $300

1 x LSI LSI00281 PCI-Express 2.0 x8 MD2 Low profile SATA / SAS MegaRAID SAS 9260CV-4i Controller Card, $695