[gmx-users] Slow Runs

Denny Frost dsfrost at cableone.net
Fri Jan 28 20:43:45 CET 2011


gromacs 4.5.1

On Fri, Jan 28, 2011 at 12:40 PM, Erik Marklund <erikm at xray.bmc.uu.se>wrote:

>  PME is still an Ewald sum.
>
> Erik
>
> Denny Frost skrev 2011-01-28 20.38:
>
> 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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>
>
>
> --
> -----------------------------------------------
> Erik Marklund, PhD student
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,    75124 Uppsala, Sweden
> phone:    +46 18 471 4537        fax: +46 18 511 755erikm at xray.bmc.uu.se    http://folding.bmc.uu.se/
>
>
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