[gmx-users] Slow Runs
Justin A. Lemkul
jalemkul at vt.edu
Fri Jan 28 20:46:05 CET 2011
Denny Frost wrote:
> gromacs 4.5.1
>
Ah, what I posted was from 4.0.7. I wonder why that sort of output was
eliminated in 4.5; it's quite useful. Sorry for leading you astray on that. No
matter, the end of the .log file will still contain statistics about what's
eating up all your simulation time.
-Justin
> On Fri, Jan 28, 2011 at 12:40 PM, Erik Marklund <erikm at xray.bmc.uu.se
> <mailto: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 <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 <mailto:erikm at xray.bmc.uu.se> http://folding.bmc.uu.se/
>
>
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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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