What sort of desktop computer should I get for EMAN2 reconstructions
Suggestion as of 12/1/2011
Obviously for large jobs you're going to need access to a linux cluster, but regardless you will still need a desktop workstation.
A complete answer to the question depends a bit upon your budgetary constraints, or lack thereof. As you are probably aware, at the 'high end', computers become rapidly more expensive for marginal gains in performance. Generally speaking, we tend to build our own Linux boxes in-house rather than purchasing prebuilt ones, both as a cost-saving measure, and to insure future upgradability. Then again, there is nothing wrong with most available commercial pre-build PCs as long as you get the correct components. For a minimal cost-effective workstation, I would suggest:
- Sandy-bridge series processor, the quad core Core i7-2600K is a good choice
- If you can get one of the new 6-core versions, that would be 50% more performance
- note that Sandy-bridge significantly outperforms the previous generation, so going with a 6-core from the pre-sandy bridge series is not a great choice)
- If you can afford a dual processor configuration, with dual 6-core Xeon's you will presently have to go with the previous generation, as the Sandy Bridge Xeons won't be out for a while. This configuration (12 cores last gen) is worthwhile, but expensive.
- RAM - 3-6 GB/core is what I'd recommend for image processing
- This depends a bit on the target application. For large viruses, you may wish to get more RAM/core
- The performance benefit of high-speed RAM is rarely worth the cost. Get the fastest you can without breaking the bank
- Disk - we would generally get something like 4, 2 TB drives for data/user files configured as software RAID 5, with a small (~100gb) SSD as a boot drive, current Intel SSDs are good for this purpose.
- Note that other than the very fastest SSD drives, none of the drives can actually keep up with the latest SATA busses anyway, so going out of your way to get the superfast SATA drive is kind of pointless
Video - Get an NVIDIA card, NOT ATI, particularly if you plan on doing stereo. This will also get you some CUDA capabilities. A reasonably high-end GeForce with a good amount of RAM is generally fine with some caveats below.
- Stereo - This is a tricky and complicated issue. There are 2 main choices:
- Active stereo
- Requires a 120 hz stereo capable 1080P display, AND, importantly, a Quadro series Nvidia graphics card (to do stereo in a window under Linux !). Note that you will have difficulties making most consumer '3D TVs' work with this setup, though some will. The most reliable option is to get a monitor designed for stereo use with Nvidia cards (Acer makes a decent 24"). Note that this also requires a dual-link DVI port.
- By FAR the easiest and cheapest option, which also allows multiple users with cheap passive glasses. It also does NOT require an expensive Quadro video card. Chimera and many other programs have built-in support for 'interleaved' stereo, which they implement without support from the underlying Nvidia driver, so you can do it even with cheap graphics cards. Only disadvantage is that you lose 50% of your vertical resolution. Personally this doesn't bother me overly. The other minor issue is that over the last couple of years these have been hard to find. Finally, LG came out with one which can be easily purchased again, though I confess we haven't purchased one of these new ones yet. Does not require dual-link DVI.
- Active stereo
- Monitor - Dual monitor setups can be very useful for image processing. If you can afford it, I would suggest a high-resolution 30" primary display with a passive stereo secondary display. If you get an active stereo secondary display, you will need 2 dual-link DVI outputs on your graphics card.
hope that helps.
Note that these are just my own personal opinion, and do not represent an official recommendation from anyone other than myself. Your mileage may vary.