Here's what I've got: M E G A - F L O P S A C C O U N T I N G
RF=Reaction-Field FE=Free Energy SCFE=Soft-Core/Free Energy T=Tabulated W3=SPC/TIP3p W4=TIP4p (single or pairs) NF=No Forces Computing: M-Number M-Flops % Flops ----------------------------------------------------------------------------- Coul(T) + VdW(T) 1219164.751609 82903203.109 80.6 Outer nonbonded loop 25980.879385 259808.794 0.3 Calc Weights 37138.271040 1336977.757 1.3 Spread Q Bspline 792283.115520 1584566.231 1.5 Gather F Bspline 792283.115520 4753698.693 4.6 3D-FFT 119163.856212 953310.850 0.9 Solve PME 2527.465668 161757.803 0.2 NS-Pairs 47774.705001 1003268.805 1.0 Reset In Box 371.386080 1114.158 0.0 Shift-X 24758.847360 148553.084 0.1 CG-CoM 1237.953600 3713.861 0.0 Angles 18569.135520 3119614.767 3.0 Propers 14855.308416 3401865.627 3.3 Impropers 3094.855920 643730.031 0.6 Virial 1242.417375 22363.513 0.0 Stop-CM 1237.953600 12379.536 0.0 P-Coupling 12379.423680 74276.542 0.1 Calc-Ekin 12379.436160 334244.776 0.3 Lincs 11760.476208 705628.572 0.7 Lincs-Mat 245113.083072 980452.332 1.0 Constraint-V 23520.928704 188167.430 0.2 Constraint-Vir 11760.452496 282250.860 0.3 ----------------------------------------------------------------------------- Total 102874947.133 100.0 ----------------------------------------------------------------------------- R E A L C Y C L E A N D T I M E A C C O U N T I N G Computing: Nodes Number G-Cycles Seconds % ----------------------------------------------------------------------- Neighbor search 1 99195 8779.027 3300.3 3.8 Force 1 991941 188562.885 70886.8 81.7 PME mesh 1 991941 18012.830 6771.6 7.8 Write traj. 1 41 16.835 6.3 0.0 Update 1 991941 2272.379 854.3 1.0 Constraints 1 991941 11121.146 4180.8 4.8 Rest 1 2162.628 813.0 0.9 ----------------------------------------------------------------------- Total 1 230927.730 86813.1 100.0 ----------------------------------------------------------------------- ----------------------------------------------------------------------- PME spread/gather 1 1983882 17065.384 6415.4 7.4 PME 3D-FFT 1 1983882 503.340 189.2 0.2 PME solve 1 991941 427.136 160.6 0.2 ----------------------------------------------------------------------- Does that mean it's only using 1 node? That would explain the speed issues. On Fri, Jan 28, 2011 at 12:46 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > 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 <er...@xray.bmc.uu.se<mailto: >> er...@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 >>> <jalem...@vt.edu <mailto:jalem...@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 >>> >>> ======================================== >>> -- gmx-users mailing list gmx-users@gromacs.org >>> <mailto:gmx-users@gromacs.org> >>> >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/Search before >>> posting! >>> Please don't post (un)subscribe requests to the list. Use the >>> www interface or send it to gmx-users-requ...@gromacs.org >>> <mailto:gmx-users-requ...@gromacs.org>. >>> >>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> >>> >> >> -- ----------------------------------------------- >> 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 >> er...@xray.bmc.uu.se <mailto:er...@xray.bmc.uu.se> >> http://folding.bmc.uu.se/ >> >> >> >> -- >> gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>. >> >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> > -- > ======================================== > > 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 > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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