Want to Build a Research Server?

Final Thoughts

This article is very long, and may not be applicable to everyone’s needs, so below is a summary of my points.

  1. Intel Xeon processors have a larger cache than standard Intel Core processors and allow for better multiprocessing for HPC applications.
  2. The number of cores dictates the number of simultaneous processes that can be executed at any given time, so a CPU with more cores can do more work simultaneously.
  3. Clock speed (GHz) is not a huge factor for HPC, except for perhaps 3D rendering, fluid dynamics, gaming etc.
  4. For big datasets, large amounts of RAM can be a lifesaver, and Registered RAM can enhance performance.
  5. RAM is not all about GB, as the clock speed is also very important for fast retrieval and storage.
  6. Hard disks are slow, and every effort should be made to prevent them from being a bottleneck.
  7. Solid State Drives are a great way to expand “memory” without having to purchase more RAM and provide a great alternative to hard disk swap.
  8. Choice of motherboard, case and power supply should be dictated by CPU model and other devices.

Comparison of my Previous System to my Current System

  batcave workhorse
CPU Intel Core 2 Duo 6600 2.40GHz (2 total cores)
2x Intel Xeon E5645 2.40GHz 6HT cores (12 total cores, 24 threads)
Memory 2GB DDR2 667MHz
24GB (4x6GB) Kingston DDR3 1333MHz
Hard Disk 1 2TB Hitachi Deskstar 7K2000 7200rpm SATA II 2TB Hitachi Deskstar 7K2000 7200rpm SATA II
Hard Disk 2 2TB Deskstar 5K3000 5900rpm SATA III 2TB Deskstar 5K3000 5900rpm SATA III
System Board ASUS P5NSLI ASUS Z8PE-D18
Case Unknown; from 2001! Cooler Master HAF X
Built November 2007 June 2011
Decommissioned June 2011 (repurposed)

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13 comments to Want to Build a Research Server?

  • Jay

    So how much did this set you back?

    • About $2500, which isn’t too bad for me. A MacPro would have been close to $3000 for a low end. I was eyeing the MacPro…but I am kind of over Mac. I am still not settled on ALL of the hardware in this purchase. I’ve considered exchanging for a faster CPU clock speed, or a different motherboard, but we will see.

  • I kinda read this as “just buy top of the line everything except maybe the motherboard and you’ll be good.” Any experience with tradeoffs? How would you prioritize cpu vs ram vs disk io speed?

    In my experience multiple cores don’t necessarily give a huge boost in HPC if you aren’t writing for it. I don’t tend to write multithreaded code because of the complexity and debugging issues that go with it. In that case, more cores won’t help my code finish faster; it’ll only help if there are multiple jobs running at once. Xeons are great if you’re switching between a boatload of threads like a web server might or you’re concerned about power/overheating, but in my experience they aren’t worth the extra cash you pay. In that situation, clock speed can be a lot more important than you give it credit for here.

    • Well, to be frank, this upgrade has been way overdue, and I did a bit of “throwing money” around. The purpose of the post was to document the decisions I made and what else was out there. Of course it will come across that way, because in an ideal world, if everyone could afford the top of the line hardware, we would all be good computing-wise. It would be too difficult to tailor this post to everyone’s needs.

      In terms of priority, *for my research use* I put RAM as the most important, followed closely behind by the CPU and the number of threads it can run concurrently (not so much the clock speed), followed by disk I/O. I find that for my work investing in more or better RAM gives the best bang for the buck, followed by the CPU. Although a lot of my work is disk bound (crawling), faster disks are so much more expensive and are out of my budget. Because of this, I had to make the tradeoff to favor upgrading RAM over disks. At least there are some tricks that can be done with RAM to prevent overuse of disks.

      To me “high performance computing” goes hand in hand with parallelism. Of course if the code has not been written to take advantage of the cores, the extra cores are useless. I would expect that if someone is buying a multicore processor, they intend to program to use the cores. For my research, not programming to take advantage of these extra cores would qualify as *not* high performance computing. I never suggested that CPUs with more cores will make things run faster; just that more work is done at a time. Hadoop is the most trivial example I can give where code takes advantage of multiple cores, OpenMP is another.

      Everyone will have their own opinion, but for my use, based on experiences I have had using servers containing Xeons, and the issues I faced without a higher-end processor, the Xeons were the way to go without a question.

  • buster highmann

    why wouldn’t you drop that money on several cheap computers, instead of one expensive one?

    for $2500 you could have got 14 motherboards, 14 AMD Phenom quad-core CPUs and 14 x 1 GB ram

    • Sigh. I’ve heard that. While a cluster would be cool, I tend to use AWS when I need a cluster setup. Also just too much of a pain to have to build that many systems. I don’t spend money often, so I was ok with putting out a one time large purchase ;). This machine really serves two purposes: for development of jobs to be shipped to AWS (time = $), and to prevent me from having to use AWS for high-memory, high-speed applications.

      Over the past 20 years though, I have collected a lot of old machines that might an ok cluster, just obviously not high end.

  • Heya

    Is SATA3 Working on this motherboard?

    I cant find any info saying that this Motherboard can support SATA3. Only Sata 2 in official notes.

    Let me know if u got Sata 3 to work.

    Thanks bye

    I got D18 too, works like dream so far!

  • Btw forgot to say, U might be better off with EVGA Server motherboard- They can OC CPU = 12 cores x 4-5 ghz after OC…. That would be pretty much power…

    • I am having trouble receiving the D18. It seems to be a rare beast. It’s taken almost a month now. Considering cancelling. If I do I will probably go with the EVGA or Supermicro.

  • I can sell u mine D18 and jump to EVGA tbh. I could use some extra OC for my work 😀

  • Steven

    Which OS do you plan on running?

    • I finished the system 🙂

      I put in the same HD that was running on my old server. I am running 64bit Ubuntu 10.04 (Lucid). Runs great!
      Considering upgrading to 11.04, or switching to CentOS, but I really don’t have too much of a reason to switch to CentOS.

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