AMBER Archive (2001)

Subject: Re: opinions on supercomputer platforms

From: Nathalie Godbout (godbout_at_sgihud.hudson.sgi.com)
Date: Fri Apr 06 2001 - 14:57:37 CDT

Jake Isaacs wrote:
>
> Our Center for Computational Sciences is looking into purchasing a new
> supercomputer and would like to know how the current state-of-the-art
> platforms (HP, IBM, Compaq, etc.) rank with regards to parallelized AMBER
> programs, especially sander. Any and all insight is welcome.
>
> Thank you.
>
> .-. .-. .-. .-. .------------------------. .-. .-. .-. .-.
> /|||X|||\ /|||X|||\ / Jake Isaacs \ /|||X|||\ /|||X|||\
> X|||/ \|||X|||/ \|||X Department of Molecular X|||/ \|||X|||/ \|||X
> `-' `-' `-' `-' \ & Cellular Biochemistry / `-' `-' `-' `-'
> .-. .-. .-. .-. / University of Kentucky \ .-. .-. .-. .-.
> X|||\ /|||X|||\ /|||X 800 Rose St. X|||\ /|||X|||\ /|||X
> \|||X|||/ \|||X|||/ \ Lexington, KY 40536-0084 / \|||X|||/ \|||X|||/
> `-' `-' `-' `-' `------------------------' `-' `-' `-' `-'

Hi Jake,

Here are the timings for the dhfr, prowat and 4096wat runs on sgi
platforms. I have included the sgi2800 series (aka Origin2000) and
sgi3800 series (aka Origin3000). I will soon include the sgi3800
R14k/500Mhz data.

Let me know if you have any questions.

Nathalie 

-- 
------------------------------------------------------------------------
Nathalie Godbout, Ph.D.       SGI 
godbout_at_hudson.sgi.com        Chemistry and Biology Applications Group
(781)839-2147                 One Cabot Road, Suite 250
(978)562-7450 fax             Hudson, MA     
vnet:483-2147                 01749, USA
------------------------------------------------------------------------
Amber6/sander benchmarks on sgi platforms.

               Nathalie Godbout, sgi 2/14/01

  *on sgi2800: - 32xR12k IP27 400MHz/8MB L2 cache
               - Irix 6.5
               - MIPSpro 7.3.1 compilers
               - sgi MPI
               - original (Amber6) and modified (Amber7) source code

  *on sgi3800: - 128xR14k IP35 400MHz/8MB L2 cache 
               - Irix 6.5.9
               - MIPSpro 7.3.1 compilers
               - sgi MPI
               - original (Amber6) and modified (Amber7) source code

   * Times are reported as follows: for single processor runs, times 
     are in cpu seconds for the nonsetup part of the calculation and 
     for multiple processor runs, nonsetup wallclock times (in seconds) 
     are reported.

PROWAT:
-------
--------------------------------------------------------------------------------
            sgi2800           sgi2800            sgi3800          sgi3800
            (400mhz)          (400mhz)           (400mhz)         (400mhz)
code:       original          modified           original         modified
--------------------------------------------------------------------------------
nproc   time spup  %P      time  spup  %P     time spup  %P     time spup  %P
  1     136.20             115.94             133.82            114.96
  2      71  1.92(95.83)    61  1.90(94.74)    69  1.94(96.91)    60  1.92(95.83)
  4      39  3.49(95.13)    33  3.52(95.45)    38  3.52(95.45)    32  3.59(96.19)
  8      22  6.19(95.82)    19  6.10(95.55)    20  6.69(97.20)    18  6.39(96.40)
 16      13 10.48(96.49)    12  9.67(95.64)    14  9.56(95.51)    11 10.45(96.46)
 32      11 12.38(94.89)    10 11.60(94.33)     8 16.73(97.06)     8 14.37(96.04)
 64                                             6 22.30(97.03)     6 19.16(96.29)
--------------------------------------------------------------------------------

DHFR:
-----
-------------------------------------------------------------------------------
            sgi2800          sgi2800             sgi3800           sgi3800
            (400mhz)         (400mhz)            (400mhz)          (400mhz)
code:       original          modified          original           modified
-------------------------------------------------------------------------------
nproc   time spup  %P     time  spup  %P    time spup  %P      time spup  %P
  1     166.47            142.39            163.20             138.97
  2      94  1.77(87.01)   82   1.73(84.39)  88  1.85(91.89)    75  1.85(91.89)
  4      51  3.26(92.43)   45   3.16(91.14)  47  3.47(94.91)    41  3.39(94.00)
  8      30  5.55(93.69)   27   5.26(92.56)  26  6.28(96.09)    23  6.04(95.36)
 16      20  8.32(93.85)   18   7.89(93.15)  17  9.60(95.56)    16  8.68(94.38)
 32      18  9.25(92.07)   18   7.89(90.14)  13 12.55(95.00)    11 12.63(95.05)
 64                                          11 14.84(94.74)    11 12.63(93.54)
-------------------------------------------------------------------------------

4096WAT:
--------
-------------------------------------------------------------------------------
             sgi2800           sgi2800           sgi3800           sgi3800
            (400mhz)           (400mhz)          (400mhz)          (400mhz)
code:       original            modified         original           modified
-------------------------------------------------------------------------------
nproc   time spup  %P      time  spup  %P     time spup  %P      time spup  %P
  1     85.44              70.53              84.18              69.17      
  2     45  1.90(94.74)    37  1.91(95.29)    45  1.87(93.05)    37  1.87(93.05)
  4     24  3.56(95.88)    21  3.36(93.65)    24  3.51(95.35)    20  3.46(94.80)
  8     14  6.10(95.55)    12  5.88(94.85)    14  6.01(95.27)    12  5.76(94.44)
 16     10  8.54(94.18)     9  7.84(93.06)    10  8.42(94.00)     8  8.65(94.34)
 32      9  9.49(92.35)     8  8.82(91.52)     7 12.02(94.64)     6 11.53(94.27)
 64                                            7 12.02(93.14)     6 11.53(92.78)
-------------------------------------------------------------------------------