Re: SGI_MP and sander 6 from Nathalie Godbout on 2000-10-03 (Amber Archive Oct 2000)

From: Nathalie Godbout <godbout_at_sgihud.hudson.sgi.com>
Date: Tue 03 Oct 2000 11:24:52 -0700

Jarrod Smith wrote:
>
> I just noticed that the shared memory parallel option is no longer
> supported in sander version 6. Does using MPI on SGI Origin machines
> introduce a performance hit vs. the old method? For example, if you
> were able to run a calculation on an Origin using both sander classic
> with SGI_MP turned on and using sander 6 with MPI, would you see a
> performance difference?
>
> --
> Jarrod A. Smith
> Research Asst. Professor, Biochemistry
> Asst. Director, Center for Structural Biology
> Computation and Molecular Graphics
> Vanderbilt University
>
> jsmith_at_structbio.vanderbilt.edu

Hi Jarrod,

MPI codes typically perform as well as OpenMP (or sgi $doacross
directives) codes on shared memory systems such as Origin for moderate
number of processors. There is the potential for OpenMP codes to perform
better on shared memory systems because OpenMP offers the ability to do
fine grain parallelism which is difficult to achieve with MPI. But
having said that, it's a difficult question to answer because there are
many factors which can influence the comparison such as the actual
implementation of these parallel paradigms, the size of the calculation,
the type of run etc.

I hope I've answered your questions. I've attached a text file with the
current results I have for the three standard Amber benchmark runs on
sgi platforms running Irix and Linux.

Nathalie

P.S. If you plan on running sander_classic, I've found a bug in one of
the subroutines. Please check-out the following to make the necessary
changes: http://amber.ch.ic.ac.uk/bugfixes/6.0/bugfix.20

-- 
------------------------------------------------------------------------
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 (original source code) benchmarks across sgi platforms.
               Nathalie Godbout, sgi 09/29/00
  *on sgi1400: - 4xPIII 500MHz/2048KB L2 cache 
               - Linux
               - PGI compilers
               - MPICH (1.2) and sgi MPI
  *on sgi1200: - 16xPIII (8 nodes) 700MHz/256KB L2 cache
               - Linux
               - PGI compilers
               - MPICH (1.2)
               - ethernet (2 jobs/node) and myrinet (1 job/node)
  *on Origin200: - 4xR12k IP27 360MHz/4MB L2 cache
                 - Irix 6.5
                 - MIPSpro 7.3.1 compilers
                 - sgi MPI
  *on sgi2800: - 32xR12k IP27 400MHz/8MB L2 cache
               - Irix 6.5
               - MIPSpro 7.3.1 compilers
               - sgi MPI
  *on sgi3100: - 8xR12k IP35 400MHz/8MB L2 cache 
               - Irix 6.5.9
               - MIPSpro 7.3.1 compilers
               - sgi MPI
PROWAT:
-------
        sgi1400    sgi1400   sgi1200    sgi1200   origin200
        (500mhz)   (500mhz)  (700mhz)   (700mhz)   (360mhz)
        mpich      sgi-mpi   ethernet   myrinet   
------------------------------------------------------------
nproc  time spup  time spup  time spup  time spup  time spup
  1    278.72     276.80     187.42     186.14     150.21  
  2    148  1.88  145  1.91  103  1.82   99  1.88   79  1.90
  4     87  3.20   84  3.30   64  2.93   55  3.38   45  3.34
  8                           44  4.26   33  5.64
 16                           34  5.51   21  8.86
------------------------------------------------------------
            sgi2800           sgi3100
            (400mhz)          (400mhz)
--------------------------------------------
nproc   time spup  %P      time spup  %P   
  1     136.20             133.82         
  2      71  1.92(95.83)    69  1.94(96.91)
  4      39  3.49(95.13)    38  3.52(95.45)
  8      22  6.19(95.82)    20  6.69(97.20)
 16      13 10.48(96.49)    14  9.56(95.51)
 32      11 12.38(94.89)     8 16.73(97.06)
--------------------------------------------
DHFR:
-----
       sgi1400     sgi1400   sgi1200    sgi1200   origin200
       (500mhz)    (500mhz)  (700mhz)   (700mhz)   (360mhz)
       mpich       sgi-mpi   ethernet   myrinet   
------------------------------------------------------------
nproc  time spup  time spup  time spup  time spup  time spup
  1    441.21     437.73     331.64     330.49     197.67             
  2    254  1.74  241  1.82  203  1.63  183  1.81  110  1.80
  4    157  2.81  146  3.00  146  2.27  101  3.27   61  3.24
  8                          106  3.13   60  5.51  
 16                           79  4.20   41  8.06           
------------------------------------------------------------
            sgi2800           sgi3100 
            (400mhz)          (400mhz)
-------------------------------------------
nproc   time spup  %P     time  spup  %P  
  1     166.47            163.20          
  2      94  1.77(87.01)   88  1.85(91.89)
  4      51  3.26(92.43)   47  3.47(94.91)
  8      30  5.55(93.69)   27  6.04(95.36)
 16      20  8.32(93.85)   20  8.16(93.59)
 32      18  9.25(92.07)   16 10.20(93.11)
-------------------------------------------
4096WAT:
--------
       sgi1400     sgi1400   sgi1200    sgi1200  origin200
       (500mhz)    (500mhz)  (700mhz)   (700mhz)   (360mhz)
       mpich       sgi-mpi   ethernet   myrinet
------------------------------------------------------------
nproc  time spup  time spup  time spup  time spup  time spup
  1    223.14     223.04     166.22     167.95      96.70          
  2    126  1.77  121  1.84  106  1.57   94  1.79   56  1.73 
  4     79  2.82   71  3.14   80  2.08   53  3.17   31  3.12
  8                           56  2.97   33  5.09
 16                           43  3.86   22  7.63        
------------------------------------------------------------
             sgi2800          sgi3100 
            (400mhz)          (400mhz)
------------------------------------------
nproc   time spup  %P      time spup  %P 
  1     85.44              84.18        
  2     45  1.90(94.74)    45  1.87(93.05)
  4     24  3.56(95.88)    24  3.51(95.35)
  8     14  6.10(95.55)    14  6.01(95.27)
 16     10  8.54(94.18)    10  8.42(94.00)
 32      9  9.49(92.35)     7 12.02(94.64)
------------------------------------------

Received on Tue Oct 03 2000 - 11:24:52 PDT