Call for Benchmarks

**pfb** · 12-20-2003, 06:49 AM

Originally posted by Grumpy
Here is my Dual 2400 MP

Summary
-------
Usr time Sys time
-------- --------
Maketrj 9.266 0.484
Foldtraj 59.859 11.875

My Dual 2400MP (@2600+ speeds):

Code:

Summary
-------
          Usr time  Sys time
          --------  --------
Maketrj      8.016     0.500
Foldtraj    58.078    11.531

Not much difference...

**Grumpy** · 12-20-2003, 08:41 AM

I run Win 2 K Prioity 0

**iggy** · 12-20-2003, 10:20 AM

Barton @ 2226 MHz, WinXP:

Code:

          Usr time  Sys time
          --------  --------
Maketrj      5.984     0.203
Foldtraj    34.234     5.906

AXP1700+ @2205 MHz:

Code:

          Usr time  Sys time
          --------  --------
Maketrj      6.703    0.391
Foldtraj    36.234    5.859

AXP2000+ (1667 MHz), Win2K3:

Code:

          Usr time  Sys time
          --------  --------
Maketrj      9.859     0.594
Foldtraj    59.813     9.344

AXP2000+ (1667MHz), Knoppix 3.3:

Code:

          Usr time  Sys time
          --------  --------
Maketrj      4.850     1.010
Foldtraj    56.470     17.800

**gistech1978** · 12-20-2003, 11:02 AM

2100+ oced to 2600+
2139 (186*11.5)

Maketraj Usr Time = 7.078
Maketraj Sys Time = .422
Foldtraj Usr Time = 37.641
Foldtraj Sys Time = 6.719

**TazAmdmb** · 12-20-2003, 02:03 PM

Opteron 146 @ 2 GHz
Summary
-------
Usr time / Sys time
-------- --------
Maketrj 5.672 / 1.031

Foldtraj 28.719 / 4.641

**hega** · 12-20-2003, 04:08 PM

Intel P4 CPU 2.60GHz, 800MHz FSB
Linux 2.4.23

Usr time Sys time
-------- --------
Maketrj 2.590 0.610
Foldtraj 28.330 9.620

**dano** · 12-20-2003, 04:33 PM

Athlon 64 3200+

Mandrake 9.2 64bit

Usr time / Sys time

Maketrj 3.220 / 0.490

Foldtraj 31.900 / 5.010

**Lucus Maximus** · 12-23-2003, 07:32 AM

AXP2500+ @ 2.4GHz with 200Mhz FSB (RAM sync w/ CAS2.0-2-2-11)
WinXP Pro

Summary
-------
Usr time / Sys time
-------- / --------
Maketrj 5.703 / 0.438
Foldtraj 34.453 / 6.453

------------------------------

AXP2500+ @ 2.5GHz with 200Mhz FSB (RAM sync w/ CAS2.0-2-2-11)
WinXP Pro

Summary
-------
Usr time / Sys time
-------- / --------
Maketrj 5.672 / 0.203
Foldtraj 33.813 / 6.078

-Lucus

**Gortok** · 12-23-2003, 09:39 PM

Barton 2500+@2260 2x256 HyperX 3500@205 2.0-3-3-6 NF7-S v2

One moment, opening rotamer library...
Predicting secondary structure and generating trajectory distribution...
Folding protein...
Benchmark complete.

Summary
-------
Usr time Sys time
-------- --------
Maketrj 6.266 0.953
Foldtraj 34.609 6.688

**pharm24** · 12-27-2003, 11:32 PM

AMD,Athlon XP, 2224,Win2K,6.578,1.141,37.188,8.234

**AAdjuster** · 01-08-2004, 07:49 PM

Barton 2800 @ 2400mhz-10.5x228
2x256 Corsair 11-2-2-2
NF7 v2.0

usr time system time

Maketrj / 5.538 0.250
Foldtraj / 31.976 4.717

**TheOtherPhil** · 01-15-2004, 04:52 PM

AMD FX-51, 1GB Corsair XMS3200RPT - completely stock (for now

). WinXP Pro SP1

Summary
-------
Usr time Sys time
-------- --------
Maketrj 5.266 0.219
Foldtraj 26.766 3.781

**Lucus Maximus** · 01-17-2004, 03:59 AM

Update:
AXP2500+ @ 2.456GHz with 223Mhz FSB (RAM sync w/ CAS2.0-2-2-11)
WinXP Pro

Summary
-------
Usr time / Sys time
-------- / --------
Maketrj 5.508 / 0.250
Foldtraj 32.627 / 5.708

-Lucus

**erk** · 01-23-2004, 05:35 PM

Anyone got -bench results for an overlcocked A64 yet?

**Grumpy** · 01-23-2004, 09:14 PM

I have seen a 3200 Athlon 64 OCed to more than 2.1 Ghz I believe it got something like..

5.656_____ 0.141
30.313____ 4.828

**JohnyDog** · 01-30-2004, 12:56 AM

AMD Tbird 1333 Mhz, Linux 2.4.21

Usr time Sys time
-------- --------
Maketrj 8.260 0.520
Foldtraj 75.340 11.080

**TheOtherPhil** · 01-30-2004, 05:58 AM

FX51 @ 2.46GHz, WinXP Pro SP1, 1Gb Corsair Reg. PC3200:

Code:

Summary
-------
          Usr time  Sys time
          --------  --------
Maketrj      4.750     0.219
Foldtraj    24.391     3.438

**HaloJones** · 01-30-2004, 12:35 PM

The Genome Collective gets the fastest cruncher

**frmky** · 01-31-2004, 07:49 PM

One more...

Opteron 144 running at 1.8GHz
1GB PC3200 Reg. ECC Dual Channel RAM
Windows Server 2003 AMD64

Code:

          Usr time  Sys time
          --------  --------
Maketrj      6.328     0.219
Foldtraj    30.141     6.844

Greg

**Grumpy** · 01-31-2004, 08:23 PM

What Motherboard is that frmky

Nice result

**frmky** · 02-01-2004, 03:19 PM

It's an ASUS SK8V.

I also tried the Linux version of the client. The ICC version gives a slower time for foldtraj:
2.49 0.41
35.95 5.08

and the gcc version won't run since it depends on ncurses-4 I don't have a 32-bit version of it installed.

Greg

**bwkaz** · 02-01-2004, 05:03 PM

You can ln -s libncurses.so.5 libncurses.so.4 to use the gcc client, at least on a 32-bit system. I suppose that might not work on a 64-bit one, but I don't see why it wouldn't.

If you have a working libncurses.so.5 for the icc version, you can just use it, in other words.

**frmky** · 02-01-2004, 06:54 PM

Yeah...that'll probably work once I figure out where the 32-bit libraries are stored. I've have a look at that later.
Greg

**bwkaz** · 02-01-2004, 07:42 PM

I think it's just plain /lib and /usr/lib. I think that /lib64 and /usr/lib64 are for the 64-bit libraries.

However, I don't know for sure, since I have no Opteron / Athlon64 hardware.

**frmky** · 02-01-2004, 09:53 PM

/lib and /usr/lib are 64-bit, /lib32 and /usr/lib32 are the 32 bit libraries. I created the link and followed up with env-update, but it still claims it can't find libncurses.so.4. I checked to make sure those paths were in /etc/env.d, and they are. Even ran ldconfig manually just to make sure. Not sure what's up. Oh well...and I was hoping to break the 30 second barrier.

BTW, I noticed that there are 64-bit binaries for a few other platforms. Is it a simple recompile? Are they faster than the 32-bit ones? If so, I'm willing to make my machine available to make linux-amd64 and freebsd-amd64 binaries.

Greg

**bwkaz** · 02-01-2004, 09:59 PM

Maybe /sbin/ldconfig?

I'm not sure what env-update is supposed to do, nor am I sure what /etc/env.d is for; they sound like distro-magic tools to me.

Though it's always possible that they're for glibc on x86-64...

IIRC from the past, the DF people need a machine that they have physical access to before they can make binaries for that architecture. I don't remember why for sure, though...

But I think that with one of them (Solaris or IRIX) the 32-bit and 64-bit versions are about the same speed anyway. No idea if the same will hold true on Intel, but it might.

**frmky** · 02-01-2004, 10:20 PM

Nope...still no go. I give up on it.

OK..back on topic now....sorry about that!

**gistech1978** · 02-05-2004, 09:44 AM

im having a strange problem...
so the benchmark is completely independent of the current protein?
the reason i ask this is because earlier in this thread i have posted some benches where my maketraj sys time was .422 (186x12) for my current setup or .359 running stock.

well now i have some pc3200 and running a 2100+ at 200x10.5
i benched and got some results basically on par with the results before.

this past weekend i reformatted my hdd and reinstalled xp. everything is essentially the same, and now my maketraj sys time is well over 2 and the others have noticably slowed as well, im at the office right now but i got something like 2.xxx. i tried various ram timings and its all basically the same. right now i have found the timings 2.0-2-3-11 or 2.0-3-3-11 to give me the most memory bandwidth on the nforce2 chipset.

im confused.

**Bionic_Redneck** · 02-08-2004, 10:19 PM

XP1800+
256mb ddr
Gentoo linux
ICC client
Note: 3 different kernels ran benchmark 3 time on each for accuracy

Code:

              Kernel 2.4.22
		   
		   Summary
                    -------
              Usr time  Sys time
              --------    --------
Maketrj      5.960     0.510
Foldtraj    72.220     9.010

                  Kernel 2.6.1

		   Summary
		   -------
             Usr time  Sys time
              --------  --------
Maketrj      6.050     0.490
Foldtraj    71.720    11.220
  
                   Kernel 2.62
		   
                    Summary
              Usr time        Sys time
                --------             --------
Maketrj      5.190             0.890
Foldtraj      59.200            15.970

**Bionic_Redneck** · 02-08-2004, 10:50 PM

kde 3.2 konsole uses 3-5% of cpu by using aterm instead I dropped times a little

Code:

Summary
-------
          Usr time  Sys time
          --------  --------
Maketrj      5.130     0.900
Foldtraj    58.860    15.730

**Thor** · 02-09-2004, 08:50 AM

@ Bionic_Redneck
buy another 256MB RAM ....

My benches on an XP2800 using W2K, 512MB RAM @166Mhz:

usr time: sys time:
10.045 1.512
54.759 9.854

That's about a 4second difference....

Greets Thor

**junky** · 02-10-2004, 05:18 AM

gonna ask a stupid question:
whats these args ?
Maketrj usr, Maketrj sys,Foldtr\
aj usr, Foldtraj sys

i see a lot of number there, how to get these numbers.
thanks.

**bwkaz** · 02-10-2004, 08:36 AM

You get those numbers by running ./foldtrajlite -bench (or .\foldtrajlite -bench on Windows).

I'm not sure what the difference between Maketrj and Foldtraj is (I think the first one is what the client does at the end of a generation, and the second one is what the client does most of the time otherwise), but the difference between "usr" and "sys" time is that "sys" time is spent running kernel code (that the DF program calls). "usr" time is spent running code in the DF program itself.

**Grumpy** · 02-10-2004, 04:57 PM

Thor, that is a very slow result for your computer specs...did you have other stuff running at the time

**iggy** · 02-10-2004, 05:51 PM

Probably a typo - I guess it should have been AXP1800+...

**Thor** · 02-10-2004, 06:29 PM

Thats right, my mistake...it was late at night over here when I wrote that. 12hour learning session isn't any good for a brain

But maybe I was just thinking again about getting myself a new XP2500 and wished there would be enough money for a 2800+

But as always , students never ever have enough money...need a new job to be able to spend some money again

Greets Thor

**Grumpy** · 02-11-2004, 05:17 PM

:sleepy: Oops, sleep deprivation is evil....

**Bionic_Redneck** · 02-11-2004, 09:16 PM

Ok Thor I was using ICC client switched to GCC

Summary
-------
Usr time Sys time
-------- --------
Maketrj 6.010 0.890
Foldtraj 52.470 15.720

**isp** · 02-18-2004, 03:50 PM

So I'm seeing these numbers but would like to ask a question...

If someone wanted to build a mini farm of folders for df, what would you guess would yield the most output...

3x 2.4c @ 3.2 w/ ht on
or
5x amd 2500 or 2600+ at stock

TIA

**doritos** · 03-17-2004, 02:05 AM

HP PA-8500 (440Mhz)

Summary
-------
Usr time Sys time
-------- --------
Maketrj 11.470 0.520
Foldtraj 145.640 3.330

HP PA-8700 (875Mhz)

Summary
-------
Usr time Sys time
-------- --------
Maketrj 7.110 0.430
Foldtraj 79.680 1.730

Thread: Call for Benchmarks

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