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Thread: DF and kernels

  1. 04-13-2003, 03:09 AM #1
    Kosh
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    DF and kernels

    Hey, I thought I'd post something here before my final exams hit and you never hear from me again.

    Something to note before you read all the stuff below: these are not well controlled tests nor are they conclusive, I noticed some trends and decide to post because I thought the results were interesting. After reading a thread in the gentoo forums I decided to go and try the 2.5.67 kernel (my computer was getting a bit too complacent ... thought it could start slacking off in its folding duties ). So after a while I got the idea of comparing the folding capabilities of the 2.5.67 kernel against its 2.4.20 predecessor. So I ran a few tests.

    All testing was done using Gentoo linux 1.4rc3. The client used was the regular client (not the beta) and with the current (89aa) protein. All kernels were compiled with a minimum number of extra features enabled (e.g. no framebuffer console, no extra networking options, no unecessary filesystems, no usb), ALSA drivers were used, DRM was enabled, and ReiserFS was used on all systems (mounted with noatime and notail options) DMA was enabled.

    A comparison on my sister's computer, usually has X running on two virtual screens, this test was not very well controlled at all:
    This is a development-sources 2.5.67 kernel
    Code:
    ------------------------------------------------------------
Distributed Folding Linux Benchmark Script V1.0

Sample Size: 15870 structures over 19800 seconds.

Structures Per Second:			0.80
Structures Per Minute:			48.09
Structures Per Hour:			2885.45
Structures Per Day:			69250.80

Linux OS - Running Kernel Version 2.5.67
Intel(R) Pentium(R) III CPU family      1266MHz @ 1272mhz (512 KB cache)
------------------------------------------------------------
    This is a gentoo-sources 2.4.19 kernel (not 2.4.20 like mine)
    Code:
    ------------------------------------------------------------
Distributed Folding Linux Benchmark Script V1.0

Sample Size: 15475 structures over 19800 seconds.

Structures Per Second:			0.78
Structures Per Minute:			46.89
Structures Per Hour:			2813.64
Structures Per Day:			67527.36

Linux OS - Running Kernel Version 2.4.19-gentoo-r10
Intel(R) Pentium(R) III CPU family      1266MHz @ 1273mhz (512 KB cache)
------------------------------------------------------------
    A 2.55% increase from the older kernel (note that this is the only test where I had the good sense to let cron start the clients so they would be logged at exactly the same time ).

    Continued in next post due to post size limit (I'm sure you will have lots of fun reading through all this :sleepy: ).
    Last edited by Kosh; 04-13-2003 at 03:33 AM.
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  2. 04-13-2003, 03:11 AM #2
    Kosh
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    A comparison on my computer with X loaded, running gaim, phoenix, xmms, fluxbox, pan -- I was actively using the computer during this time. The test was done with some control, but the time period was shorter and there may have been some variation:

    This is a development-sources 2.5.67 kernel
    Code:
    ------------------------------------------------------------
Distributed Folding Linux Benchmark Script V1.0

Sample Size: 13710 structures over 16098 seconds.

Structures Per Second:			0.85
Structures Per Minute:			51.10
Structures Per Hour:			3065.97
Structures Per Day:			73583.28

Linux OS - Running Kernel Version 2.5.67
AMD Athlon(TM) XP1600+ @ 1410mhz (256 KB cache)
------------------------------------------------------------
    This is a development-sources 2.5.67 kernel (WITH elevator=cfq passed as a boot option)
    Code:
    ------------------------------------------------------------
Distributed Folding Linux Benchmark Script V1.0

Sample Size: 13730 structures over 16606 seconds.

Structures Per Second:			0.83
Structures Per Minute:			49.61
Structures Per Hour:			2976.51
Structures Per Day:			71436.24

Linux OS - Running Kernel Version 2.5.67
AMD Athlon(TM) XP1600+ @ 1410mhz (256 KB cache)
------------------------------------------------------------
    This is a gentoo-sources 2.4.20 kernel
    Code:
    ------------------------------------------------------------
Distributed Folding Linux Benchmark Script V1.0

Sample Size: 12785 structures over 15593 seconds.

Structures Per Second:			0.82
Structures Per Minute:			49.20
Structures Per Hour:			2951.71
Structures Per Day:			70841.04

Linux OS - Running Kernel Version 2.4.20-gentoo-r2
AMD Athlon(TM) XP1600+ @ 1410mhz (256 KB cache)
------------------------------------------------------------
    Here I was playing with the elevator option in the 2.5 kernel, the improvement with the regular elevator algorithm is 3.87%, with the cfq elevator algorithm it drops to 0.840% (of course this might just be to random variations, again these tests are not well controlled).
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  3. 04-13-2003, 03:13 AM #3
    Kosh
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    A comparison on my computer with no other programs loaded, this test is the best controlled of the lot, the only varation here should be the luck of the folding algorithm, and I managed a longer time period to get a better average:

    This is a development-sources 2.5.67 kernel
    Code:
    ------------------------------------------------------------
Distributed Folding Linux Benchmark Script V1.0

Sample Size: 22650 structures over 24449 seconds.

Structures Per Second:			0.93
Structures Per Minute:			55.59
Structures Per Hour:			3335.11
Structures Per Day:			80042.64

Linux OS - Running Kernel Version 2.5.67
AMD Athlon(TM) XP1600+ @ 1410mhz (256 KB cache)
------------------------------------------------------------
    This is a gentoo-sources 2.4.20 kernel
    Code:
    ------------------------------------------------------------
Distributed Folding Linux Benchmark Script V1.0

Sample Size: 22640 structures over 25055 seconds.

Structures Per Second:			0.90
Structures Per Minute:			54.22
Structures Per Hour:			3253.00
Structures Per Day:			78072.00

Linux OS - Running Kernel Version 2.4.20-gentoo-r2
AMD Athlon(TM) XP1600+ @ 1410mhz (256 KB cache)
------------------------------------------------------------
    Here are the processes running for each test above:

    This is a gentoo-sources 2.4.20 kernel
    Code:
    USER       PID %CPU %MEM   VSZ  RSS TTY      STAT START   TIME COMMAND
root         1  0.0  0.0  1328  480 ?        S    08:02   0:04 init
root         2  0.0  0.0     0    0 ?        SW   08:02   0:00 [keventd]
root         3  0.0  0.0     0    0 ?        SWN  08:02   0:00 [ksoftirqd_CPU0]
root         4  0.0  0.0     0    0 ?        SW   08:02   0:00 [kswapd]
root         5  0.0  0.0     0    0 ?        SW   08:02   0:00 [bdflush]
root         6  0.0  0.0     0    0 ?        SW   08:02   0:00 [kupdated]
root         8  0.0  0.0     0    0 ?        SW   08:02   0:00 [kreiserfsd]
root        69  0.0  0.1  1636  844 ?        S    08:02   0:00 /sbin/devfsd /dev
root       678  0.0  0.1  1388  544 ?        S    08:02   0:00 metalog [MASTER] 
root       681  0.0  0.0  1360  452 ?        S    08:02   0:00 metalog [KERNEL] 
at         682  0.0  0.1  1436  588 ?        S    08:02   0:00 [atd]
root       717  0.0  0.1  1488  636 ?        S    08:02   0:00 /usr/sbin/fcron
root       884  0.0  0.0  1328  440 ?        S    08:02   0:00 /sbin/dhcpcd eth0
root       955  0.0  0.2  2804 1360 ?        S    08:02   0:00 /usr/sbin/sshd
root       972  0.0  0.3  3904 1664 ?        S    08:02   0:00 /sbin/mount.smbfs
root      1007  0.0  0.1  2220 1012 tty2     S    08:02   0:00 login -- root    
root      1008  0.0  0.0  1308  472 tty3     S    08:02   0:00 /sbin/agetty 3840
root      1009  0.0  0.0  1308  472 tty4     S    08:02   0:00 /sbin/agetty 3840
root      1010  0.0  0.0  1308  472 tty5     S    08:02   0:00 /sbin/agetty 3840
root      1011  0.0  0.0  1308  472 tty6     S    08:02   0:00 /sbin/agetty 3840
root      1012  0.0  0.2  2568 1492 tty2     S    08:02   0:00 -bash
root      1018  0.0  0.2  2236 1132 tty1     S    08:03   0:00 [login]
qed       1028  0.0  0.2  2568 1508 vc/1     S    08:05   0:00 -bash
qed       2535  0.0  0.1  2636  740 vc/1     R    15:24   0:00 ps aux
    This is a development-sources 2.5.67 kernel
    Code:
    USER       PID %CPU %MEM   VSZ  RSS TTY      STAT START   TIME COMMAND
root         1  0.0  0.0  1328  476 ?        S    Apr11   0:04 init
root         2  0.0  0.0     0    0 ?        SWN  Apr11   0:00 [ksoftirqd/0]
root         3  0.0  0.0     0    0 ?        SW<  Apr11   0:00 [events/0]
root         4  0.0  0.0     0    0 ?        SW   Apr11   0:00 [pdflush]
root         5  0.0  0.0     0    0 ?        SW   Apr11   0:01 [pdflush]
root         6  0.0  0.0     0    0 ?        SW   Apr11   0:00 [kswapd0]
root         7  0.0  0.0     0    0 ?        SW<  Apr11   0:00 [aio/0]
root         8  0.0  0.0     0    0 ?        SW   Apr11   0:00 [kseriod]
root         9  0.0  0.0     0    0 ?        SW<  Apr11   0:00 [reiserfs/0]
root        70  0.0  0.1  1664  872 ?        S    Apr11   0:00 /sbin/devfsd /dev
root       589  0.0  0.1  1412  588 ?        S    Apr11   0:00 metalog [MASTER] 
root       590  0.0  0.0  1360  452 ?        S    Apr11   0:00 metalog [KERNEL] 
at         593  0.0  0.1  1440  580 ?        S    Apr11   0:00 /usr/sbin/atd
root       628  0.0  0.1  1488  632 ?        S    Apr11   0:00 /usr/sbin/fcron
root       795  0.0  0.0  1328  444 ?        S    Apr11   0:00 /sbin/dhcpcd eth0
root       866  0.0  0.2  2804 1356 ?        S    Apr11   0:00 /usr/sbin/sshd
root       883  0.0  0.3  3968 1720 ?        S    Apr11   0:00 /sbin/mount.smbfs
root       885  0.0  0.0     0    0 ?        SW   Apr11   0:00 [smbiod]
root       897  0.0  0.0  1308  472 vc/3     S    Apr11   0:00 /sbin/agetty 3840
root       898  0.0  0.0  1308  472 vc/4     S    Apr11   0:00 /sbin/agetty 3840
root       899  0.0  0.0  1308  472 vc/5     S    Apr11   0:00 /sbin/agetty 3840
root       900  0.0  0.0  1308  472 vc/6     S    Apr11   0:00 /sbin/agetty 3840
qed       2432  0.0  0.1  2300  984 ?        SN   03:42   0:00 /bin/sh ./foldit
qed       2436 99.8 24.5 134852 126340 ?     RN   03:42 609:05 ./foldtrajlite -f
root      2708  0.0  0.2  2240 1132 vc/2     S    05:09   0:00 login -- qed     
root      2709  0.0  0.1  2232 1008 vc/1     S    05:09   0:00 login -- root    
root      4058  0.0  0.2  2572 1496 vc/1     R    13:48   0:00 -bash
qed       4063  0.0  0.2  2568 1492 vc/2     S    13:48   0:00 -bash
root      4095  0.0  0.1  2640  744 vc/1     R    13:52   0:00 ps aux
    Here the new kernel improves on the old by 2.52%, this test might actually be reproducable (I'm going try and do this at some point), but first I'm going to have a look at how the cfq elevator performs under the same conditions.
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  4. 04-13-2003, 03:30 AM #4
    Kosh
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    From my folding logs, no control even attempted, but the time period is quite a bit longer so I am posting it. This is also the data where I first got the idea that 2.5.67 might have a noticable folding improvement over the 2.4.20 kernel:

    This is a development-sources 2.5.67 kernel
    Code:
    ------------------------------------------------------------
Distributed Folding Linux Benchmark Script V1.0

Sample Size: 35750 structures over 40389 seconds.

Structures Per Second:			0.89
Structures Per Minute:			53.11
Structures Per Hour:			3186.51
Structures Per Day:			76476.24

Linux OS - Running Kernel Version 2.5.67
AMD Athlon(TM) XP1600+ @ 1410mhz (256 KB cache)
------------------------------------------------------------
    This is a gentoo-sources 2.4.19 kernel (This was my old kernel, it had lots of stuff compiled into it and so it was not streamlined for the test)
    Code:
    ------------------------------------------------------------
Distributed Folding Linux Benchmark Script V1.0

Sample Size: 32885 structures over 40862 seconds.

Structures Per Second:			0.80
Structures Per Minute:			48.29
Structures Per Hour:			2897.22
Structures Per Day:			69533.28

Linux OS - Running Kernel Version 2.4.19-gentoo-r9
AMD Athlon(TM) XP1600+ @ 1410mhz (256 KB cache)
------------------------------------------------------------
    Before you look at the numbers and become shocked ... this was not controlled ... I was quite likely doing something like compiling the 2.5.67 kernel while the 2.4.19 was running :P . Also note that it is a 2.4.19 kernel and not 2.4.20.

    I should also note that all of the 2.4 series kernels I used are from the gentoo-sources package in Gentoo, they will obviously have different targets from the raw 2.5.67 kernel or something like wolk-sources or mm-sources. It is entirely possible that selecting a proper set of patches for a 2.4 kernel it could reduce the advantage the 2.5 kernel appears to have. It is also possible that with a proper patch set a 2.4 kernel could outperform a 2.5 kernel (it is a developmental kernel remember). It might be interesting to hear what Chinasaur has to say about this, since in his recent review of Mandrake 9.1 he noted that he was getting 186K per CPU (XP1800 with PC2700), his hardware is better than mine (XP1600 with PC2100), but I was getting 151K so maybe the Mandrake kernel is making up part of the 35K difference.

    I hope this was of interest to some of you, I do think there is a reasonable possibility that the 2.5 kernel will outperform the 2.4 but at this point it is still a lot closer to hypothesis than proven conclusion. If some of you want to run off and install a 2.5 kernel thats great, just remember that things can AND WILL break, and don't be dissappointed if you don't get any performance increase (but please add to this thread -- or at least tell me if no one else is interested). In any case this little review has done wonders for my post count .

    Happy folding
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  5. 04-13-2003, 06:30 AM #5
    TheOtherPhil
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    Very interesting...thanks! I run Gentoo on a few boxen so I might have a play when I get the time
    Train hard, fight easy

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  6. 04-21-2003, 01:30 PM #6
    Chinasaur
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    Kosh:





    Agent Smith was right!: "I hate this place. This zoo. This prison. This reality, whatever you want to call it, I can't stand it any longer. It's the smell! If there is such a thing. I feel saturated by it. I can taste your stink and every time I do, I fear that I've somehow been infected by it."
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  7. 06-09-2003, 01:56 AM #7
    GHOST
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    On the 157 protien, with a pentium 4 1.6

    windows xp gave me 60,000 structures a day.

    mandrake 9.1 gave me 70,000 structures a day

    redhat 9 gives me 75,000 structures a day
    GHOST
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