AMBER Archive (2000)

Subject: Re: CCL:Performance of Compaq ES vs IBM or ORIGIN servers

From: Nathalie Godbout (godbout_at_sgihud.hudson.sgi.com)
Date: Tue Nov 28 2000 - 16:09:51 CST

Sam Andersen wrote:
>
> Hi,
> Does anybody have Compaq/DEC multiprocessor ALPHA servers that
> are being used for MD simulations by AMBER or CHARMM using MPI
> or any other parallel arch.? We are planning to buy 4 or 8 processor
> ES40 or GS60 DEC server. This is for dedicated parallel processing
> on all processors for MD simulations of large protein systems
> (sizes of about 100K atoms). We have been using SGI-ORIGIN series
> of machines for MD simulations and have NO experience with compaq
> systems (for parallel jobs).
>
> Are there people in chemistry community using these servers
> (under Tru64 UNIX and MPI/OPEMMP) for MD or other apps?. I would
> appreciate if somebody comment on their efficeincy in parallel
> jobs (particulalry SANDER or GIBBS of AMBER6). Also, if people
> out there use other systems like multiprocessor SGI-ORIGIN or
> IBM-SP2, Could you please comment on relative performance of
> parallel execution of AMBER codes on these systems? If people
> have expereinced particular probelms in running parallel jobs
> (particularly AMBER6 MD simulations)on multiprocessor ES40 or
> GS60 compaq/DEC systems, Please share your experience.
>
> I will post summary.
> Thanks and happy thanksgiving weekend.
> Sam
>
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Hi Sam,

I've attached a text file with the timings for the prowat, dhfr and
4096wat Amber6 runs on sgi platforms including Origin architecture with
up to 32 processors. Let me know if you have questions about these
results.

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 11/28/00

  *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 6.5.9
                 - MIPSpro 7.3.1 compilers
                 - sgi MPI

  *on sgi2800: - 32xR12k IP27 400MHz/8MB L2 cache
               - Irix 6.5.9
               - MIPSpro 7.3.1 compilers
               - sgi MPI

  *on sgi3800: - 128xR12k 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)   26  6.28(96.09)
 16      20  8.32(93.85)   17  9.60(95.56)
 32      18  9.25(92.07)   13 12.55(95.00)
-------------------------------------------

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)
------------------------------------------
spup is the abbreviation for speedup and %P is percentage of parallelism 
according to Amdhal's law.