Re: Dual Origin vs dual Alfa from Nathalie Godbout on 2001-02-14 (Amber Archive Feb 2001)

From: Nathalie Godbout <godbout_at_sgihud.hudson.sgi.com>
Date: Wed 14 Feb 2001 08:18:23 -0800

Anton Guliaev wrote:
>
> Dear Amber Users -- I am currently using dual 225MhzR10K Origin 200 for
> my MD simulations. I am looking to upgrade this machine with the dual
> 360MhzR12K ($9K). Does anybody use this configuration and know how much
> would I gain in CPU time (30-40%?)? Also, to my knowledge, dual CPU
> Compaq alfa in general outperform the Origin 200 -- is this really true
> for Amber calculations? I would appreciate any feedback..
> Also, how good is dual 400MhzR12K Octane, compare with dual 225MhzR10K
> Origin...
>
> THanks a lot,
>
> Anton
>
> P.S. The benchmarks on Amber page do not cover new 400Mhz or 360Mhz R12K
> CPUs
>
> --
> ************************************
> * Anton B. Guliaev, Ph.D *
> _ * Life Sciences Division * _
> / )* LBNL, Berkeley CA 94720 *( \
> / / * abguliaev_at_lbl.gov * \ \
> _( (_ * T: 510-486-5773 F:(510)-486-6488 * ) )_
> (((\ \)**/ )**************************( \**(/ /)))
> (\\\\ \_/ / \ \_/ ////)
> \ / \ /
> \ _/ \_ /
> / / \ \
> /___/ \___\

Hi Anton,

I've attached a text file with the latest Amber6 benchmarks on most
sgi platforms. You will notice in the table that I have done the
calculations using two versions of the source code; the original source
code and a modified version of the source code. The modified version is
a version of Amber6 that has been made to run faster by making one of
the most computing intensive part of the code (namely subroutine
short_ene) faster. Because this subroutine is in a parallel part of the
code, the scalability is reduced a little but time to solution is
better.

I don't know what type of run you do but the more time you spend in
this subroutine, the more you will benefit from the improvement. This
version will be available in the Amber7 distribution so you can compare
your 225MhzR10k results with the results using the modified version of
the source code. I don't know if the modified version of the code will
run faster than the original source code on other computer
architectures, I only have access to sgi machines ;-)

Let me know if you have 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 across sgi platforms.
               Nathalie Godbout, sgi 2/14/01
  *on sgi1400: - 4xPIII 500MHz/2048KB L2 cache 
               - Linux
               - PGI compilers
               - MPICH (1.2) and sgi MPI
               - original Amber6 source code
  *on sgi1200: - 16xPIII (8 nodes) 700MHz/256KB L2 cache
               - Linux
               - PGI compilers
               - MPICH (1.2)
               - ethernet (2 jobs/node) and myrinet (1 job/node)
               - original Amber6 source code
  *on Origin200: - 4xR12k IP27 360MHz/4MB L2 cache
                 - Irix 6.5
                 - MIPSpro 7.3.1 compilers
                 - sgi MPI
                 - original and modified Amber6 source code
  *on sgi2800: - 32xR12k IP27 400MHz/8MB L2 cache
               - Irix 6.5
               - MIPSpro 7.3.1 compilers
               - sgi MPI
               - original and modified Amber6 source code
  *on sgi3800: - 128xR12k IP35 400MHz/8MB L2 cache 
               - Irix 6.5.9
               - MIPSpro 7.3.1 compilers
               - sgi MPI
               - original and modified Amber6 source code
PROWAT:
-------
        sgi1400    sgi1400   sgi1200    sgi1200   origin200   origin200
        (500mhz)   (500mhz)  (700mhz)   (700mhz)   (360mhz)    (360mhz)
        mpich      sgi-mpi   ethernet   myrinet   orig code   modif code
------------------------------------------------------------------------
nproc  time spup  time spup  time spup  time spup  time spup  time spup 
  1    278.72     276.80     187.42     186.14     150.21     129.43
  2    148  1.88  145  1.91  103  1.82   99  1.88   79  1.90   68  1.90
  4     87  3.20   84  3.30   64  2.93   55  3.38   45  3.34   39  3.32
  8                           44  4.26   33  5.64
 16                           34  5.51   21  8.86
--------------------------------------------------------------------------------
            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:
-----
       sgi1400    sgi1400   sgi1200    sgi1200   origin200   origin200
       (500mhz)   (500mhz)  (700mhz)   (700mhz)   (360mhz)    (360mhz)
       mpich      sgi-mpi   ethernet   myrinet   orig code   modif code
------------------------------------------------------------------------
nproc  time spup  time spup  time spup  time spup  time spup  time spup
  1    441.21     437.73     331.64     330.49     197.67     170.28                     
  2    254  1.74  241  1.82  203  1.63  183  1.81  110  1.80   96  1.77
  4    157  2.81  146  3.00  146  2.27  101  3.27   61  3.24   55  3.10
  8                          106  3.13   60  5.51  
 16                           79  4.20   41  8.06           
-------------------------------------------------------------------------------
            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:
--------
       sgi1400    sgi1400   sgi1200    sgi1200   origin200   origin200
       (500mhz)   (500mhz)  (700mhz)   (700mhz)   (360mhz)    (360mhz)
       mpich      sgi-mpi   ethernet   myrinet   orig code   modif code
-----------------------------------------------------------------------
nproc  time spup  time spup  time spup  time spup  time spup  time spup
  1    223.14     223.04     166.22     167.95      96.70      80.32                  
  2    126  1.77  121  1.84  106  1.57   94  1.79   56  1.73   47  1.71
  4     79  2.82   71  3.14   80  2.08   53  3.17   31  3.12   28  2.87
  8                           56  2.97   33  5.09
 16                           43  3.86   22  7.63        
-------------------------------------------------------------------------------
             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)
-------------------------------------------------------------------------------

Received on Wed Feb 14 2001 - 08:18:23 PST