[gmx-users] Slow Runs

Justin A. Lemkul jalemkul at vt.edu
Fri Jan 28 20:39:46 CET 2011



Denny Frost wrote:
> I don't have any domain decomposition information like that in my log 
> file.  That's worrisome.  The only other information I could find about 
> PME and Ewald and this set of lines:
> 

What version of Gromacs is this?

-Justin

> Table routines are used for coulomb: TRUE
> Table routines are used for vdw:     FALSE
> Will do PME sum in reciprocal space.
> 
> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> U. Essman, L. Perela, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen 
> A smooth particle mesh Ewald method
> J. Chem. Phys. 103 (1995) pp. 8577-8592
> -------- -------- --- Thank You --- -------- --------
> 
> Will do ordinary reciprocal space Ewald sum.
> Using a Gaussian width (1/beta) of 0.384195 nm for Ewald
> Cut-off's:   NS: 1.2   Coulomb: 1.2   LJ: 1.2
> System total charge: 0.000
> Generated table with 4400 data points for Ewald.
> Tabscale = 2000 points/nm
> Generated table with 4400 data points for LJ6.
> Tabscale = 2000 points/nm
> Generated table with 4400 data points for LJ12.
> Tabscale = 2000 points/nm
> Configuring nonbonded kernels...
> Configuring standard C nonbonded kernels...
> Testing x86_64 SSE2 support... present.
> 
> 
> Why does it say it will do PME on one line, then ordinary Ewald later?
> 
> On Fri, Jan 28, 2011 at 12:26 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     Denny Frost wrote:
> 
>         I just realized that that was a very old mdp file.  Here is an
>         mdp file from my most recent run as well as what I think are the
>         domain decomposition statistics.
> 
>         mdp file:
>         title               =  BMIM+PF6
>         cpp                 =  /lib/cpp
>         constraints         =  hbonds
>         integrator          =  md
>         dt                  =  0.002   ; ps !
>         nsteps              =  4000000   ; total 8ns.
>         nstcomm             =  1
>         nstxout             =  50000
>         nstvout             =  50000
>         nstfout             =  0
>         nstlog              =  5000
>         nstenergy           =  5000
>         nstxtcout           =  25000
>         nstlist             =  10
>         ns_type             =  grid
>         pbc                 =  xyz
>         coulombtype         =  PME
>         vdwtype             =  Cut-off
>         rlist               =  1.2
>         rcoulomb            =  1.2
>         rvdw                =  1.2
>         fourierspacing      =  0.12
>         pme_order           =  4
>         ewald_rtol          =  1e-5
>         ; Berendsen temperature coupling is on in two groups
>         Tcoupl              =  berendsen
>         tc_grps             =  BMI      PF6      tau_t               =
>          0.2  0.2
>         ref_t               =  300  300
>         nsttcouple          =  1
>         ; Energy monitoring
>         energygrps          =  BMI      PF6
>         ; Isotropic pressure coupling is now on
>         Pcoupl              =  berendsen
>         pcoupltype          =  isotropic
>         ;pc-grps             =  BMI      PFF
>         tau_p               =  1.0
>         ref_p               =  1.0
>         compressibility     =  4.5e-5
> 
>         ; Generate velocites is off at 300 K.
>         gen_vel             =  yes
>         gen_temp            =  300.0
>         gen_seed            =  100000
> 
>         domain decomposition
>         There are: 12800 Atoms
>         Max number of connections per atom is 63
>         Total number of connections is 286400
>         Max number of graph edges per atom is 6
>         Total number of graph edges is 24800
> 
> 
>     More useful information is contained at the very top of the .log
>     file, after the citations.  An example from one of my own runs is:
> 
>     Linking all bonded interactions to atoms
>     There are 2772 inter charge-group exclusions,
>     will use an extra communication step for exclusion forces for PME
> 
>     The initial number of communication pulses is: X 2 Y 1
>     The initial domain decomposition cell size is: X 1.05 nm Y 1.58 nm
> 
>     The maximum allowed distance for charge groups involved in
>     interactions is:
>                     non-bonded interactions           1.400 nm
>     (the following are initial values, they could change due to box
>     deformation)
>                two-body bonded interactions  (-rdd)   1.400 nm
>              multi-body bonded interactions  (-rdd)   1.054 nm
>      atoms separated by up to 5 constraints  (-rcon)  1.054 nm
> 
>     When dynamic load balancing gets turned on, these settings will
>     change to:
>     The maximum number of communication pulses is: X 2 Y 2
>     The minimum size for domain decomposition cells is 0.833 nm
>     The requested allowed shrink of DD cells (option -dds) is: 0.80
>     The allowed shrink of domain decomposition cells is: X 0.79 Y 0.53
>     The maximum allowed distance for charge groups involved in
>     interactions is:
>                     non-bonded interactions           1.400 nm
>                two-body bonded interactions  (-rdd)   1.400 nm
>              multi-body bonded interactions  (-rdd)   0.833 nm
>      atoms separated by up to 5 constraints  (-rcon)  0.833 nm
> 
> 
>     Making 2D domain decomposition grid 9 x 6 x 1, home cell index 0 0 0
> 
> 
>     Also, the output under "DOMAIN DECOMPOSITION STATISTICS" (at the
>     bottom of the file) would be useful.  Also look for any notes about
>     performance lost due to imbalance, waiting for PME, etc.  These
>     provide very detailed clues about how your system was treated.
> 
>     -Justin
> 
> 
>     -- 
>     ========================================
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================



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