[gmx-users] Slow Runs
Erik Marklund
erikm at xray.bmc.uu.se
Fri Jan 28 20:40:27 CET 2011
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
> <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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--
-----------------------------------------------
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 18 511 755
erikm at xray.bmc.uu.se http://folding.bmc.uu.se/
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