Building a relatively cheap, silent, small, powerful PC for scientific computing

The topic is not so easy. I wanted to build a system for "cheap", running machine learning computing quickly while it is still small. The main motivation was that I tried to use cloud servers, but they are expensive and their CPU was not so strong (8 cores, Opteron 6128, rated 6128 at www.cpubenchmark.net). I realized that I could quickly spend some hundreds of euro thus why don't I build an own machine from that price to get raw CPU power? (I don't need too much RAM or GPU right now.)

Shopping

1. Looking at the CPU benchmarks and prices, I ended up to AMD processors. They are cheap although running hotter compared to Intel. I bought a used AMD FX 8350 from ebay for ~140 euro with shipping. (This is 200 euro in the retail shops in my city.) This processor is really powerful, rated 9050 at www.cpubenchmark.net, x1.5 faster than the cloud server what I used for a month. The CPU was the biggest part of the computer costs.

2. The computer should be small so I picked a microATX case and one of the cheapest (but good) motherboard for my FX CPU. Case: MS-Tech SLIM LC-02 (43e), motherboard: MSI 760GMA-P34 (52e).

3. The PC should be silent, but on the other side, AMD FX CPU runs hot, so I need the coolest silent cooler for the microATX case. First hit in Google: http://www.frostytech.com/top5_lowprofile_heatsinks.cfm . Looking into the category, I chosen the best: Scythe Shuriken SCSK-1000 (32e).

4. Graphics card: nothing. I use the on-board GPU so far because I don't use GPU for anything yet.

5. Used 2 GB Kingston HyperX DDR3 1800MHZ RAM (15e) can be run nicely on higher frequencies, in my case, I achieved 1680 Mhz. Upgradeable later if needed.

6. Hard drive: Kingspec 32GB SSD JMF606H from aliexpress ($32 -> ~23e) to install a basic Ubuntu system. Upgradeable later if needed.

7. No monitor or peripherals because once the system will be set up and running, I put on shelf and manage remotely with ssh and vnc.

So the complete system is 140+43+52+32+15+23 -> 305 euro (~$423).

Setup

There is no perfect system and it was also right for my case. I installed Ubuntu and everything was fine except the hot AMD FX with inadequate cooling and suspend sometimes did not resume back. The hot CPU was a huge issue by default because the frequency was throttled down to half all the time when the CPU hit 60-65 degrees. The same task completed after 5h 40m when I assembled the machine and it was 4h after I fixed the heating issues:

- Since the shelf of the machine is a closed space, I removed the side of the microATX case permanently.
- I looked at many CPU thermal paste reviews and I found out that Arctic Cooling MX-2 is a cheap while giving one of the best performance, it even beats its successor MX-4. I bought 8g from ebay (6e). I have not expected too much, but the difference is very noticeable compared to the factory thermal paste shipped with Scythe Shuriken SCSK-1000.
- The third step was to undervolt the CPU without loosing performance. I was not so successful like others on the internet (~1.1V), but I was able to go down to 1.275V with tweaking the FSB and multiplier. I share my BIOS settings at the end of this post.

The undervolting (and switching off all unneeded hw in BIOS) has the advantage to lower the power consumption as much as possible. The whole effect was about 30W decrease in my case. Eventually, the system eats 60W in idle, 97W loading one CPU core and 202W on full CPU load.

BIOS screenshots




Edit (26/04/2015)

1. I put an additional 4 GB Kingston HyperX memory module into the PC
2. I experienced instability of the system after a half year. The CPU has been pulled down a bit and the voltage increased. The system become stable and I could put the side back to the microATX case.