[gmx-users] Slow Runs

[Justin A. Lemkul]

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

-- 
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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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