Posts Tagged ‘GAP’

Building a harvester rig

I decided to build a workstation computer, for several reasons. I have access to many different types of computing resources, with differing advantages and disadvantages. The Nectar Grid for instance provides virtual machines with many cores. Very good for coarse-grained parallel processing, like the case when I have 132 million semigroups in a file and I would like to classify them according to their eggbox pictures. I can divide the file into smaller chunks and using GNU Parallel I can easily utilize all available processors. But for single thread calculations these virtual machines are not ideal since they tend to have older/power efficient slower processors. I’m also fed up with laptops, they are fine for writing code, but once under some load they get hot and burn the battery in an hour. Also, PC building is a dying art and I wanted to have one more go, before it disappears.

For most semigroup and group algorithms the bottleneck is the memory. Orbit calculations, or more generally search trees are not trivially parallelizable. So, the requirements for the new rig:

  1. good single-thread performance
  2. large memory bank with error correction
  3. 24/7 energy efficient operation

One fast processor with huge amount of memory. This is of course totally against the post-Moore’s law era’s trends: many slow cores with little local memory.

Why error correction? RAM modules are quite reliable nowadays, but they do fail sometimes. In most cases the buggy software is blamed, as software failures are more frequent and there is no way to tell the difference between software and hardware failure. But they are rare. So, unless you need very precise calculations that run for days, you don’t need ECC RAM. But that’s exactly what we are doing here, sometimes a week long computation where absolute mathematical precision is required, so not even a single bit-flip caused by a malevolent cosmic ray is allowed. It freaks you out if you start thinking about undetected memory failures. It is a bit like the question whether you want to drive with or without the safety belt.

Choices for the components:

Motherboard: For the Intel 22nm Haswell processors, ASUS P9D WS with the Intel C226 chipset which is meant to be a server chipset (so no overclocking), but the board has some fancy features, like the UEFI BIOS.


Memory: 4x8GB low-voltage, 1600MHz ECC modules. 32GB in total, 16GB per channel.


Power supply: Fanless 400W Platinum (Seasonic). The thought of wasting energy when producing power is simply outrageous. That’s why the premium PSU.

Graphics card: No gaming here.

Storage: Another non-issue. Just use whatever drive I have available at the moment.

Processor: Intel Pentium G3420


No pins here. You have to worry about the motherboard, not the CPU.


What?!?!? A budget processor in ‘high-end’ workstation?!? Well, it is enough for the current purpose. For single thread calculations you don’t need many cores/hyper-threading. This Pentium does support ECC, therefore it is more like a crippled Xeon than a dumbed-down i7. The name ‘Pentium’ is very nostalgic. There is an upgrade path to E3 Xeons, so the build is somewhat future-proof.

After reading Inside Intel this company would be my last choice to buy from, but their products are actually superior. Faster and more power efficient. The full system power consumption is 23W when idling. Not that this value matters, since the machine  is only switched on when there is something to calculate. Half-steam takes 40W, while full blast (both cores using all 4 memory modules) requires 51W. Cooling is not an issue. Unlike my desktop with an AMD FX 8320.

Harvester?!? Well, the expression ‘mining rig’ has been taken by the cryptocurrency folks. Not a big problem since an agricultural metaphor seems better fitting anyway. In most search algorithms we grow trees with enormous foliage in order to get the solutions, the fruits. The truth is that I got the word from the science-fiction movie Moon.

Naming is an important issue. Once we named a subversion server ‘mordor’, and it killed three hard drives in a row. Since the motherboard-memory combination exhibits the Aussie national colors (my current place of residence), the name mollymook came as an obvious choice.


My original idea was not to have a case. Just have the pieces on the table. So I ended up with this:

DSC_3456This of course was a very stupid idea. First, an ATX board is a bit bigger than a Raspberry Pi, second the cables are very rigid, so the above configuration was metastable. A little touch at one point and the components started jumping around.

So, a case was needed. As for housing I’m ok with Scandinavian design. No, ikea hasn’t started selling computers cases yet, but Fractal Design has. It was meant to be a joke, but the furniture company is indeed mentioned in the manual.

Impressive 140mm silent cooling fans.

DSC03362In a modern case, installing the components and cable-management is easy.

DSC03381And you end up with a clean build.


For the OS, Ubuntu 14.04 was installed, but this is just an arbitrary choice. For running GAP all you need is a solid UNIX base system and a C-compiler, the details don’t matter.

It is all good, HR mollymook is happily cutting its way through the fabric of the mathematical universe, exploring the unknown, while physically residing in a stylish black&white high airflow box.

Yep, this pseudo-poetic-techno-rubbish metaphor is a good way of ending this buildlog.


GAP on the Pi

August 1, 2013 6 comments












