[gmx-users] Slow Runs

Denny Frost dsfrost at cableone.net
Fri Jan 28 20:38:35 CET 2011 

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:

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> 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 | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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