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MP on 2 Dual Xeon 64bit (Read 4171 times)

tlefebure

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Posts: 36
Cornell University

MP on 2 Dual Xeon 64bit
Aug 24^th, 2006 at 2:41pm

Hello,
I'm trying to run hyphy with Linux (Ubuntu 6.06) on the following box:
Code:

uname -a
Linux babylon 2.6.15-26-amd64-xeon #1 SMP PREEMPT Thu Aug 3 03:58:27 UTC 2006 x86_64 GNU/Linux

So basically I have ~4 processors with hyper-threading (virtually 8 cpus). Compilation works great with ./build.sh MP or ./build.sh MP2. But when I try speedtest.bf, I have quite bad results for the Xeon 3.73GHz processors, and the computation time is almost independent of the number of given cpus:

./HYPHYMP CPU=1 -> 31s
./HYPHYMP CPU=1 -> 22s
./HYPHYMP CPU=1 -> 22s
./HYPHYMP CPU=1 -> 21s
./HYPHYMP CPU=1 -> 22s
./HYPHYMP CPU=1 -> 21s
./HYPHYMP CPU=1 -> 24s
...

I monitored cpus during those runs, and only 1 was used independently of the CPU flag (compiling with MP or MP2 has no effect).

Am I doing something wrong?
Thanks
Tristan

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Sergei

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Re: MP on 2 Dual Xeon 64bit
Reply #1 - Aug 24^th, 2006 at 3:12pm

Dear Tristan,

This is odd (I presume you changed CPU=1 to CPU=2, CPU=3 etc). I just recompiled the latest build on a 4 core Opteron, and I am seeing speedups and appropriate numbers of threads based on the CPU command.

Hyperthreading doesn't actually speed up things much, in my experience (I saw 10-15% gains on older Xeons). My only guess is that the PREEMPT kernel flag may have something to do with thread scheduling...

My box has
Code:

Linux monkeysupreme 2.4.29-295u0001.Scyldsmp #1 SMP Thu Jun 9 17:05:43 PDT 2005 x86_64 x86_64 x86_64 GNU/Linux

and I have not heard of MP issues like yours before.

Sorry I can't be of more help.

Sergei

Associate Professor
Division of Infectious Diseases
Division of Biomedical Informatics
School of Medicine
University of California San Diego

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tlefebure YaBB Newbies Offline Posts: 36 Cornell University	Re: MP on 2 Dual Xeon 64bit Reply #2 - Aug 24^th, 2006 at 3:21pm yep, sorry, it should be written: ./HYPHYMP CPU=1 -> 31s ./HYPHYMP CPU=2 -> 22s ./HYPHYMP CPU=3 -> 22s ./HYPHYMP CPU=4 -> 21s ./HYPHYMP CPU=5 -> 22s ./HYPHYMP CPU=6 -> 21s ./HYPHYMP CPU=7 -> 24s I will look around the PREEMPT flag ...
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Sergei

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Re: MP on 2 Dual Xeon 64bit
Reply #3 - Aug 24^th, 2006 at 3:25pm

Dear Tristan,

You get a decent speed-up from 1 to 2, but then everything levels out, so at least for CPU=2, there is something going on. The test data set is too small to see much improvement past 3 or 4 CPUs, though (that is not suprising). I am a bit puzzled by why the single processor result is so poor, given that my tests on a 3.2 GHz (old) Xeon (under Windows) gave 16 seconds (1 CPU) and 10 seconds (2 CPUs).

Let me make a bigger speedtest example for you to test...

Cheers,
Sergei

Associate Professor
Division of Infectious Diseases
Division of Biomedical Informatics
School of Medicine
University of California San Diego

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tlefebure YaBB Newbies Offline Posts: 36 Cornell University	Re: MP on 2 Dual Xeon 64bit Reply #4 - Aug 24^th, 2006 at 4:28pm I've tried the speedtest_2.bf, and obtained: CPU=1 -> 87 CPU=2 -> 86 CPU=4 -> 92 CPU=6 -> 96 The more cpus we use, the longer hyphy is! (but times may not be significantly different) The problem seems that I can't use multi-threading. I'm now looking for another program to test the multi-threading on this box. Tristan
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Sergei YaBB Administrator Offline Datamonkeys are forever... Posts: 1658 UCSD Gender:	Re: MP on 2 Dual Xeon 64bit Reply #5 - Sep 15^th, 2006 at 4:41pm Dear Tristan, MP builds seem to be working fine on the Xeon, but the standard speedtest.bf example is too small to be effectively parallelized on your machine; a larger example gets 2x speed up as expected from CPU=1 to CPU=2 (it's in my home directory under BatchFiles as speedtest_large.bf) Cheers, Sergei
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tlefebure YaBB Newbies Offline Posts: 36 Cornell University	Re: MP on 2 Dual Xeon 64bit Reply #6 - Sep 19^th, 2006 at 5:44am Thanks ! It works great. So on 64bit Xeon cpus, the compilation flags should be: COMPILER_FLAGS=" -w -c -fsigned-char -O3 -fpermissive -I`pwd`/Source -I`pwd`/Source/SQLite -march=nocona " Tristan
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