AMBER Archive (2009)

Subject: Re: [AMBER] pmemd running very slow in amber10

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Thu May 14 2009 - 05:09:11 CDT

I suspect the thermostat, but to find out more you should look at one
of the scaling benchmark runs that you did (hopefully) and check the
bottom of the file where pmemd prints out the time used for various
tasks. that will be very helpful.

On Thu, May 14, 2009 at 1:41 AM, Vijay Manickam Achari
<vjrajamany_at_yahoo.com> wrote:
>
> Dear amber users,
>
> I have installed amber10 and pmemd in altix4700.
> All the installation went well without error after guidance from amber mailing list.
>
> If I run sander.MPI in amber10, it runs fine, but if I run pmemd it run very slow. I run my script not using PBS but directly.
>
>
> Here I give my *.in file and the *.out file contents.
>
> *in file
> =========Dynamic Simulation with Constant Pressure
>  &cntrl
>   imin=0,
>   irest=1, ntx=7,
>   iwrap = 1, ntxo=1,
>   scnb=1.0, scee=1.0,
>   ntt=3, gamma_ln = 1.0,
>   tempi = 300.0, temp0=300.0, tautp=0.2,
>   ntb = 2, ntp=1, taup=0.2,
>   ntf=2,ntc=2,
>   nstlim=100000, dt=0.001,
>   ntwe=100, ntwx=100, ntpr=100, ntwr=-50000,
>   ntr=0,
>  /
>
>
>
> *.out
> ============
>
>          -------------------------------------------------------
>          Amber 10 SANDER                              2008
>          -------------------------------------------------------
>
> | PMEMD implementation of SANDER, Release 10
>
> | Run on 05/14/2009 at 13:32:03
>
>  [-O]verwriting output
>
> File Assignments:
> |   MDIN: MD-betaMalto-lowLyo.in
> |  MDOUT: betaMalto-lowLyo-MD00-run0000.out
> | INPCRD: e2malto-lowLyo-equi21.rst_100000
> |   PARM: maltose-lowLyo.top
> | RESTRT: betaMalto-lowLyo-MD01-run0100.rst
> |   REFC: refc
> |  MDVEL: mdvel
> |   MDEN: mden
> |  MDCRD: betaMalto-lowLyo-MD00-run0000.traj
> | MDINFO: mdinfo
> |LOGFILE: logfile
>
>
>  Here is the input file:
>
> Dynamic Simulation with Constant Pressure
>  &cntrl
>   imin=0,
>   irest=1, ntx=7,
>   iwrap = 1, ntxo=1,
>   scnb=1.0, scee=1.0,
>   ntt=3, gamma_ln = 1.0,
>   tempi = 300.0, temp0=300.0, tautp=0.2,
>   ntb = 2, ntp=1, taup=0.2,
>   ntf=2,ntc=2,
>   nstlim=100000, dt=0.001,
>   ntwe=100, ntwx=100, ntpr=100, ntwr=-50000,
>   ntr=0,
>  /
>
>
>
>
>
> | Conditional Compilation Defines Used:
> | MPI
> | SLOW_INDIRECTVEC
> | PUBFFT
> | MKL
>
> | Largest sphere to fit in unit cell has radius =    24.102
>
> | New format PARM file being parsed.
> | Version =    1.000 Date = 06/23/08 Time = 17:06:22
> | Duplicated    0 dihedrals
>
> | Duplicated    0 dihedrals
>
> --------------------------------------------------------------------------------
>   1.  RESOURCE   USE:
> --------------------------------------------------------------------------------
>
>  getting new box info from bottom of inpcrd
>
>  NATOM  =   23736 NTYPES =       9 NBONH =   14776 MBONA  =    9216
>  NTHETH =   27648 MTHETA =   12032 NPHIH =   45312 MPHIA  =   21248
>  NHPARM =       0 NPARM  =       0 NNB   =  123552 NRES   =    1256
>  NBONA  =    9216 NTHETA =   12032 NPHIA =   21248 NUMBND =       9
>  NUMANG =      14 NPTRA  =      20 NATYP =       9 NPHB   =       1
>  IFBOX  =       1 NMXRS  =      81 IFCAP =       0 NEXTRA =       0
>  NCOPY  =       0
>
> | Coordinate Index Table dimensions:    18    9   10
> | Direct force subcell size =     5.1696    5.3561    5.0569
>
>     BOX TYPE: RECTILINEAR
>
> --------------------------------------------------------------------------------
>   2.  CONTROL  DATA  FOR  THE  RUN
> --------------------------------------------------------------------------------
>
>
>
> General flags:
>     imin    =       0, nmropt  =       0
>
> Nature and format of input:
>     ntx     =       7, irest   =       1, ntrx    =       1
>
> Nature and format of output:
>     ntxo    =       1, ntpr    =     100, ntrx    =       1, ntwr    =  -50000
>     iwrap   =       1, ntwx    =     100, ntwv    =       0, ntwe    =     100
>     ioutfm  =       0, ntwprt  =       0, idecomp =       0, rbornstat=      0
>
> Potential function:
>     ntf     =       2, ntb     =       2, igb     =       0, nsnb    =      25
>     ipol    =       0, gbsa    =       0, iesp    =       0
>     dielc   =   1.00000, cut     =   8.00000, intdiel =   1.00000
>     scnb    =   1.00000, scee    =   1.00000
>
> Frozen or restrained atoms:
>     ibelly  =       0, ntr     =       0
>
> Molecular dynamics:
>     nstlim  =    100000, nscm    =      1000, nrespa  =         1
>     t       =   0.00000, dt      =   0.00100, vlimit  =  20.00000
>
> Langevin dynamics temperature regulation:
>     ig      =   71277
>     temp0   = 300.00000, tempi   = 300.00000, gamma_ln=   1.00000
>
> Pressure regulation:
>     ntp     =       1
>     pres0   =   1.00000, comp    =  44.60000, taup    =   0.20000
>
> SHAKE:
>     ntc     =       2, jfastw  =       0
>     tol     =   0.00001
>
> | Intermolecular bonds treatment:
> |     no_intermolecular_bonds =       1
>
> | Energy averages sample interval:
> |     ene_avg_sampling =     100
>
> Ewald parameters:
>     verbose =       0, ew_type =       0, nbflag  =       1, use_pme =       1
>     vdwmeth =       1, eedmeth =       1, netfrc  =       1
>     Box X =   93.053   Box Y =   48.205   Box Z =   50.569
>     Alpha =   90.000   Beta  =   90.000   Gamma =   90.000
>     NFFT1 =   96       NFFT2 =   50       NFFT3 =   54
>     Cutoff=    8.000   Tol   =0.100E-04
>     Ewald Coefficient =  0.34864
>     Interpolation order =    4
>
> | PMEMD ewald parallel performance parameters:
> |     block_fft =    1
> |     fft_blk_y_divisor =    4
> |     excl_recip =    0
> |     excl_master =    0
> |     atm_redist_freq =  320
>
> --------------------------------------------------------------------------------
>   3.  ATOMIC COORDINATES AND VELOCITIES
> --------------------------------------------------------------------------------
>
>
>  begin time read from input coords =  4012.500 ps
>
>  Number of triangulated 3-point waters found:     1000
>
>     Sum of charges from parm topology file =   0.00000000
>     Forcing neutrality...
>
> | Dynamic Memory, Types Used:
> | Reals              908174
> | Integers          1893246
>
> | Nonbonded Pairs Initial Allocation:  168376
>
> | Running AMBER/MPI version on   64 nodes
>
>
> --------------------------------------------------------------------------------
>   4.  RESULTS
> --------------------------------------------------------------------------------
>
>  ---------------------------------------------------
>  APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
>  using   5000.0 points per unit in tabled values
>  TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
> | CHECK switch(x): max rel err =   0.3338E-14   at   2.509280
> | CHECK d/dx switch(x): max rel err =   0.8261E-11   at   2.768360
>  ---------------------------------------------------
>
>  NSTEP =      100   TIME(PS) =    4012.600  TEMP(K) =   301.34  PRESS =   -45.6
>  Etot   =     72323.5211  EKtot   =     16896.3909  EPtot      =     55427.1302
>  BOND   =      4331.7919  ANGLE   =     12660.8451  DIHED      =      3557.8100
>  1-4 NB =      5543.6944  1-4 EEL =    112668.1311  VDWAALS    =    -10250.7744
>  EELEC  =    -73084.3679  EHBOND  =         0.0000  RESTRAINT  =         0.0000
>  EKCMT  =      1136.7441  VIRIAL  =      1359.7065  VOLUME     =    226657.6514
>                                                    Density    =         1.0897
>  Ewald error estimate:   0.1325E-03
>  ------------------------------------------------------------------------------
>
>
>  NSTEP =      200   TIME(PS) =    4012.700  TEMP(K) =   300.36  PRESS =    51.9
>  Etot   =     72308.4304  EKtot   =     16841.3962  EPtot      =     55467.0342
>  BOND   =      4223.5093  ANGLE   =     12742.0334  DIHED      =      3598.7024
>  1-4 NB =      5569.0962  1-4 EEL =    112679.4301  VDWAALS    =    -10228.2235
>  EELEC  =    -73117.5137  EHBOND  =         0.0000  RESTRAINT  =         0.0000
>  EKCMT  =      1124.6180  VIRIAL  =       870.8898  VOLUME     =    226443.8438
>                                                    Density    =         1.0907
>  Ewald error estimate:   0.8322E-04
>  ------------------------------------------------------------------------------
>
>
>
> I dont know what is the error.
> Can anyone help?
>
> Thank you in advance.
>
>
>
> Vijay Manickam Achari
> (Phd Student c/o Prof Rauzah Hashim)
> Chemistry Department,
> University of Malaya,
> Malaysia
>  vjramana_at_gmail.com
>
>
>
>
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>

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