Hello, So far as I can tell Numeric.dot(), which uses innerproduct() from multiarraymodule.c doesn't call the BLAS, even if Numeric was compiled against native BLAS. This means (at least on my machine) that X = ones((150, 16384), 'd') C = dot(X, tranpose(X)) is about 15 times as slow as the comparable operations in Matlab (v6), which does, I think, use the native BLAS. I guess that multiarray.c is not particularly optimised to use the BLAS because of the difficulties of coping with all sorts of types (float32, int64 etc), and with non-contiguous arrays. The innerproduct is so basic to most of the work I use Numeric for that a speed up here would make a big difference. I'm thinking of patching multiarray.c to use the BLAS when it can, but before I start are there good reasons for doing something different? Any advice gratefully received! Cheers, Richard. -- Department of Computer Science, Exeter University Voice: +44 1392 264065 R.M.Everson@exeter.ac.uk Secretary: +44 1392 264061 http://www.dcs.ex.ac.uk/people/reverson Fax: +44 1392 264067
Hi, Thanks to Jon Saenz and Chris Baker for helping out with fast linear algebra and statistical distribution routines. Again, I have a tangential question. I am hitting the physical limit of the CPU (meaning things have been optimized down to assembly level), in order to achieve even higher performance, the only way to go is hardware. Is there any recommendation for fast machines at the price range of a few thousand dollars? (I cannot afford supercomputers or connection machines.) My purpose is to run Monte Carlo simulation. This means that a lot of scenarios can be run in parallel fashion. Of course I can just use regular cheap Pentium boxes... but they are kind of bulky, and I don't need any of the video, audio, USB features (I think 10 machines at 1GHz each would be the size of calculation power I need, or equivalently, a single machine at an equivalent 10GHz. Heck, if there are some specialized racks/boxes, I can wire the motherboards myself.) I am wondering what you people do for heavy number crunching? Are there any cheap yet specialized machines? What about machines with dual processor? I would imagine a lot of people in the number crunching world run into my situation, and since the number crunching machines don't require much beyond a motherboard and a small hard-drive, maybe there are already some cheap solutions out there. thanks! Hung Jung __________________________________________________ Do You Yahoo!? Yahoo! GeoCities - quick and easy web site hosting, just $8.95/month. http://geocities.yahoo.com/ps/info1
"HJL" == Hung Jung Lu <hungjunglu@yahoo.com> writes:
HJL> Again, I have a tangential question. I am hitting the HJL> physical limit of the CPU (meaning things have been optimized HJL> down to assembly level), in order to achieve even higher HJL> performance, the only way to go is hardware. HJL> Is there any recommendation for fast machines at the price HJL> range of a few thousand dollars? (I cannot afford HJL> supercomputers or connection machines.) My purpose is to run HJL> Monte Carlo simulation. This means that a lot of scenarios HJL> can be run in parallel fashion. Of course I can just use HJL> regular cheap Pentium boxes... but they are kind of bulky, HJL> and I don't need any of the video, audio, USB features (I HJL> think 10 machines at 1GHz each would be the size of HJL> calculation power I need, or equivalently, a single machine HJL> at an equivalent 10GHz. Heck, if there are some specialized HJL> racks/boxes, I can wire the motherboards myself.) I am HJL> wondering what you people do for heavy number crunching? Are HJL> there any cheap yet specialized machines? What about machines HJL> with dual processor? I would imagine a lot of people in the HJL> number crunching world run into my situation, and since the HJL> number crunching machines don't require much beyond a HJL> motherboard and a small hard-drive, maybe there are already HJL> some cheap solutions out there. The usual way is to build some "blackboxes", i.e. mobo/cpu/memory/NIC, diskless or nearly diskless (you don't want to maintain machines :-). Connect them using 100bT or faster networks (though 100bT should be fine). Do such things exist? Sort of -- they tend to be more expensive than building them yourself, but if you've got a reliable local supplier, they can build them fairly cheaply for you. I'd go with single or dual athlons, myself :-). If power and maintenance is an issue, duals, and if not, maybe singles. We use MOSIX (www.mosix.org) for transparent load balancing between linux machines, and it could be used on the machines I described (using a floppy or CD to boot). The next question is whether some form of parallel RNG will help. The answer is "maybe". I worked with a student who evaluated coupled chains, and we couldn't do too much better. And then after that, is whether you want to figure out how to post-process the results. If you want to automate the whole thing (and it isn't clear that it would be worth it, but...), you could use PyPVM to front-end the sub-processes distributed on the network, load-balanced at the system level by MOSIX. Now for the problems -- MOSIX seems to have difficulties with Python. Severe difficulties. I don't know if it still holds true for recent MOSIX releases. (note that I use R (www.r-project.org) for most of my simulation work these days, but am looking at Python for stat analyses, of which MCMC tools are of interest). best, -tony -- A.J. Rossini Rsrch. Asst. Prof. of Biostatistics U. of Washington Biostatistics rossini@u.washington.edu FHCRC/SCHARP/HIV Vaccine Trials Net rossini@scharp.org -------------- http://software.biostat.washington.edu/ -------------- FHCRC: M-W: 206-667-7025 (fax=4812)|Voicemail is pretty sketchy/use Email UW: T-Th: 206-543-1044 (fax=3286)|Change last 4 digits of phone to FAX Rosen: (Mullins' Lab) Fridays, and I'm unreachable except by email.
Hung Jung Lu wrote:
Is there any recommendation for fast machines at the price range of a few thousand dollars? (I cannot afford supercomputers or connection machines.) My purpose is to run Monte Carlo simulation. This means that a lot of scenarios can be run in parallel fashion. Of course I can just use regular cheap Pentium boxes... but they are kind of bulky, and I don't need any of the video, audio, USB features (I
I've been looking into setting up a system to do similar work, and it looks to me like the best bang for the buck right now are dual Athlon systems. If space is an important consideration, you can get dual Athlon 1U rack mount systems for less than $2000. I'm pretty sure the only dual Athlon board currently available (Tyan K7 thunder) has on board video, ethernet and SCSI, which means it cost a little more than it could, but these systems are still a pretty good deal if you get one without a hard drive (or a very cheap one). I just did quick web search, and epox is supposed to be coming out with a dual board as well, so there may be cheaper options soon. -Chris -- Christopher Barker, Ph.D. ChrisHBarker@home.net --- --- --- http://members.home.net/barkerlohmann ---@@ -----@@ -----@@ ------@@@ ------@@@ ------@@@ Oil Spill Modeling ------ @ ------ @ ------ @ Water Resources Engineering ------- --------- -------- Coastal and Fluvial Hydrodynamics -------------------------------------- ------------------------------------------------------------------------
At 10:46 AM 11/27/2001 -0800, Chris Barker wrote:
Hung Jung Lu wrote:
Is there any recommendation for fast machines at the price range of a few thousand dollars? (I cannot afford supercomputers or connection machines.) My purpose is to run Monte Carlo simulation. This means that a lot of scenarios can be run in parallel fashion. Of course I can just use regular cheap Pentium boxes... but they are kind of bulky, and I don't need any of the video, audio, USB features (I
I've been looking into setting up a system to do similar work, and it looks to me like the best bang for the buck right now are dual Athlon systems. If space is an important consideration, you can get dual Athlon 1U rack mount systems for less than $2000. I'm pretty sure the only dual Athlon board currently available (Tyan K7 thunder) has on board video, ethernet and SCSI, which means it cost a little more than it could, but these systems are still a pretty good deal if you get one without a hard drive (or a very cheap one). I just did quick web search, and epox is supposed to be coming out with a dual board as well, so there may be cheaper options soon.
-Chris
There is a cheaper dual CPU Tyan board which uses the same motherboard chipset. Its the Tyan Tiger-MP S2460, which doesn't have SCSI, onboard video, or Ethernet, but is half the price (around $200). -willryu
participants (5)
-
Chris Barker -
Hung Jung Lu -
R.M.Everson＠exeter.ac.uk -
rossini＠blindglobe.net -
William Ryu