Sign in with
Sign up | Sign in
Your question

Computer for scientific numerical work

Last response: in Systems
Share
October 22, 2006 8:27:21 PM

Hi,
I am ready to upgrade my computer. I am giving the current one to the kids, so I need a new case and everything. My budget is around 1500$ (us dollars) +/- slop. Most of my usage is either numerical work with moderately large data sets and some visualization and imageprocessing. So of primary interest is FPU and data movement from ram to processor. I don't think the gaming rigs suggested quite meet my needs. I don't really need a high end graphics card. I run linux, since I loathe programming on windows so that is also a consideration, I don't want to do too much fussing with drivers if hardware is not well supported in the linux kernel. So with all that said I am thinking about a dual core 6700e, 2gb ram (pc 800). I don't know if dual core is the way to go for me, though the clock speeds seem impressive and with two processors I could try parralelizing some computations. Anyhow I would welcome some suggestions, I am just beginning my research and good leads on information would be much appreciated.

Thanks
Nicholas
October 22, 2006 10:06:28 PM

Have you checked to see what chipsets are supported by the latest kernel? If I was building machinery for a Linux box that was going to be critical in my work I'd consider going with hardware that's been out for awhile. Even if it is slightly slower, I'd lean toward the stability that comes with some maturity. Besides, the cost savings can be put into massive and fast RAM and HDD's. I just hate a fast machine that impresses off the start, but then crashes half way through something. I do some art and audio with my machines and have lost entire unreplicatable ideas due to general flakiness of too new of hardware/driver issues...I guess if your data is replaceable or replicatable that is another issue, but for capturing spontaniaty and creativity, I'll stick with reliability over speed. I'm still the slowest part of my relatively cheap opteron dual core box most of the time, to be honest.
October 23, 2006 6:37:08 AM

For bioinformatics (ie combinations and permutations in DNA) we just use Apple.

I have a P4 Dual Core oced to 4.8 with 2GB of XMS2 and a WD Raptor. I took my PC to uni and I set both the Apple and my PC to do exactly the same task. (A dist tree of 1000 DNA sequences from a microarray chip)

Basically the program just looks for who is most related to who and ranks them in order. So twins with the same DNA sequence will be ranked next to each other etc etc.

Apple can complete the bioinformatic task in about 4.2 hrs

My pc with exaclty the same task took 5.5 hrs.

For scientific and number crunching just get an apple. You wont need to oc it and it will still chomp the numbers faster...

In terms of cost both are about the same price...
Related resources
November 5, 2006 1:25:09 PM

That is very interesting. Is the speed difference due to Apple's software optimization? Or is it the actual hardware? Also in your application, which incidentally is similar to a lot of the work I do, were you using linux on both computers? When I compile programs I tend to focus a lot on the optimization,
especially things that require iterative optimization. Lastly was that an apple G5?

Thanks
Nicholas
November 5, 2006 2:09:06 PM

In terms of sheer number crunching there is hardly a CPU that can compete with an ATI GPU. Check it out here:

http://www.anandtech.com/video/showdoc.aspx?i=2849&p=1

Basically, GPU's with stream processing perform FP calculations far faster than CPU's. Downside is you'd have to write your own code to exploit this, or find someone who could do it for you.

Pentium D's are pretty much garbage for FP, even with a massive overclock. (4.8? what do you cool that thing with?) A Core 2 Duo is far superior in this category, and I'd put money on one outstripping an Apple though I haven't seen this sort of comparison yet, and probably by a wider margin than that Apple beat the Pen. D. And they're plenty stable, rumors of instability had more to do with the 965 chipset being rolled out a bit prematurely to support the C2D than the CPU itself.

Basically I'd recommend a 6600 or 6700 coupled with a 965 chipset and some good DDR2-800 modules. (965 is superior in memory bandwidth to 975 and has more SATA options). Investigate using ATI's stream processing though, if you can code it, your results will be quite impressive.
November 5, 2006 2:13:44 PM

Ok, the compatability problems with the 965 chipset were all pretty much cleared up with kernel 9.6.18. Hope this helps
November 5, 2006 3:17:53 PM

I just built a computer for numerical work (I am a computing science grad student) and it goes like this:

Core 2 Duo E6600 (has the 4M cache, much, much cheaper than the E6700 for a bit less speed)
MSI P965 Platinum (although Asus P5B-E would be a good choice (I don't like the MSI utilities as much as the ones on my older asus board)
2GB PC6400 OCZ EL Platinum XTC Edition Rev2 (DDR2-800 for barely more $ than DDR2-533)
4xWD 250GB Caviar 16M cache (I really like RAID 10 for speed and safety)
Sapphire Radeon x1800 GTO (I am trying to make use of my friend's card but it is not working well; I would not recommend this card at all - go with an XFX geforce 7600 GT or actually any make of 7600GT)
Enermax Noisetaker 485W (impressive psu, has worked much better than my sister's antec truepower 2.0)
Antec P165 case (makes building & modifying very easy)
DVD burners are hit & miss, pick whatever works but not the cheapest one (my Benq & my sister's almost never work).

Also consider the high end Athlon X2's (get the 2x1M cache ones) as they seem to be good for floating point. Either way dual cores are the way to go even if your programs only currently use 1 core - they will max out that one & you can still work as if nothing was going on (+ in the near future, apps will be designed for multi-core architectures).

Jo
November 5, 2006 5:19:14 PM

i agree with wun911, just get an apple preferably a mac pro. those duel 2.66ghz woodcrests will definatly help with anything extremely processor or FP intensive. they cost $2499 but the price is well worth it.
November 5, 2006 6:08:18 PM

Yeah, Ive always been a fan of apple for laptops, i have on old 12" PB G4 and a new 15" MBP the old one is still working like it was the day i bought it (its just old and too slow for what i want to use it for now). For a desktop in a UNIX like environment such as OS X or Linux, i would always say go with Linux only if you know precisely what you are doing. That being said, it would seem that you do know what you are doing and therefore wont have a problem configuring the Linux box. With that in mind, you can get the same performance out of a Linux computer for less money than out of a MAC. The build from the CS major a few posts up looks really good except you will need a nVidia G-Card due to superior driver support.
November 5, 2006 6:39:33 PM

Thanks This thread is starting to get very helpful indeed.
It's good to hear that the 2.16.18 kernel clears up the motherboard and sata
problems I have been hearing about. I am leaning toward an intel dual core
and an asus p65 motherboard (or msi) provided I can find drivers for everything.

I looked at the Apples, and while one of my first computer was an apple II, since
grad school I have worked mostly on unix servers. Now I find I am doing more work at home. Anyhow, while tiger 10.4 is nice and the apple 30in monitor is enticing, it is all out of budget for me. Especially since upgrading is much harder with an apple, and I will probably be thinking about upgrades in 2-3 years, maybe sooner.

Computing on the GPU, that is an interesting idea. One could probably do something really fun with some good parallel code and a bunch of old graphics cards, ...., wish I had more spare time. In the mean time it will probably be challenging enough getting two cores working efficiently :wink:

By the way anyone have any thoughts on LCD vs CRT monitors? it seems as if CRT is still much more bang for buck.

Nicholas
November 5, 2006 7:12:43 PM

I have been a fan of CRTs for a while but I think LCDs are finally reaching the point where they are worth buying over a CRT. You cant skimp on a LCD though, if you buy a cheap one you will regret it.
November 5, 2006 8:37:18 PM

CRT's cost a ton to ship.
November 5, 2006 8:39:23 PM

lol good point
November 5, 2006 8:56:01 PM

Hahaha, I got a 22" NEC multisync diamondtron from this sleazy monitor repair place, I swear the guys running the place were russian mafia. 127 bucks, no shipping. The manager seriously had an old soviet flag hanging on the wall of his office. 20.1" seems to be the magic number for a good, inexpensive LCD, anything above that and the prices rise exponentially. as long as the response time is <12ms and the contrast ratio is >500:1 should be fine.
November 5, 2006 8:59:00 PM

For a good 965 mobo just go for the ASUS P5B-E. Not too expensive and seems to have the most support out of the bunch.
!