Hi again Berk,
I know that this particular run used no more than 1:40 hours (( I was
following it), but I am not able to cough up the complete log as it was
accidentally overwritten by a new run.
I do however have the same phenomenon in a shorter annealing trial. I
enclose the entire log in this mail, and show excerpts below.
My startup script for this run looked like this:
------------------------------
#!/bin/bash
#PBS -A fysisk
#PBS -N pmf_hydanneal_anneal2
#PBS -o pmf_hydanneal.o
#PBS -e pmf.hydanneal.err
#PBS -l walltime=1:00:00,mppwidth=50,mppnppn=4
cd /work/bjornss/pmf/structII/hydrate_annealing/anneal2
source $HOME/gmx_latest_250908/bin/GMXRC
aprun -n 50 parmdrun -s topol.tpr -maxh 1 -npme 18
exit $?
--------------------------
Now this should stop after 0.99hours = 59:24
But as you can see:
----------------------------------------------
head md.log
Log file opened on Mon Sep 29 20:11:42 2008
Host: nid00039 pid: 16507 nodeid: 0 nnodes: 50
The Gromacs distribution was built Mon Sep 29 13:25:26 CEST 2008 by
[EMAIL PROTECTED] (Linux 2.6.16.54-0.2.5-ss x86_64)
:-) G R O M A C S (-:
Groningen Machine for Chemical Simulation
:-) VERSION 4.0_rc1 (-:
---------------------------------------------
tail md.log -n 300 (excerpt)
Step 518975: Run time exceeded 0.990 hours, will terminate the run
............................
,,,
Parallel run - timing based on wallclock.
NODE (s) Real (s) (%)
Time: 1426.000 1426.000 100.0
23:46
(Mnbf/s) (GFlops) (ns/day) (hour/ns)
Performance: 100.149 29.098 242.356 0.099
Finished mdrun on node 0 Mon Sep 29 20:35:28 2008
--------------------------
That is. I got about 40% of the allotted walltime also here.
Peculiarly 1:35 / 4:00 (hexagesimally) ~ 41%. That is the relation
betweem scheduled walltime, and actually obtained time is about the same
in both cases.
Regards
Bjørn
On Wed, 2008-10-01 at 13:25 +0200, Berk Hess wrote:
> Hi,
>
> The Cray XT4 has a torus network, but you don't get access to it as a
> torus.
> You will get assigned processors which can be anywhere in the machine
> and they are usually never in a nice cube, but there are always some
> missing.
> Therefore software, such as Gromacs, can not make use of proper
> Cartesian
>
> (torus) communication as one can for instance on a Blue Gene.
>
> I have no clue about the wallclock issue.
> Can you find out if the run took 1.35 or 4 hours?
> The start time is somewhere at the beginning of the log file.
>
> Berk
>
>
> ______________________________________________________________________
Log file opened on Mon Sep 29 20:11:42 2008
Host: nid00039 pid: 16507 nodeid: 0 nnodes: 50
The Gromacs distribution was built Mon Sep 29 13:25:26 CEST 2008 by
[EMAIL PROTECTED] (Linux 2.6.16.54-0.2.5-ss x86_64)
:-) G R O M A C S (-:
Groningen Machine for Chemical Simulation
:-) VERSION 4.0_rc1 (-:
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2008, The GROMACS development team,
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) parmdrun (-:
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl
GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable
molecular simulation
J. Chem. Theory Comput. 4 (2008) pp. 435-447
-------- -------- --- Thank You --- -------- --------
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C.
Berendsen
GROMACS: Fast, Flexible and Free
J. Comp. Chem. 26 (2005) pp. 1701-1719
-------- -------- --- Thank You --- -------- --------
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
E. Lindahl and B. Hess and D. van der Spoel
GROMACS 3.0: A package for molecular simulation and trajectory analysis
J. Mol. Mod. 7 (2001) pp. 306-317
-------- -------- --- Thank You --- -------- --------
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
H. J. C. Berendsen, D. van der Spoel and R. van Drunen
GROMACS: A message-passing parallel molecular dynamics implementation
Comp. Phys. Comm. 91 (1995) pp. 43-56
-------- -------- --- Thank You --- -------- --------
parameters of the run:
integrator = md
nsteps = 2000000
init_step = 0
ns_type = Grid
nstlist = 5
ndelta = 2
nstcomm = 1
comm_mode = Linear
nstcheckpoint = 1000
nstlog = 100000
nstxout = 20000
nstvout = 20000
nstfout = 20000
nstenergy = 100
nstxtcout = 1000
init_t = 0
delta_t = 0.002
xtcprec = 1000
nkx = 54
nky = 36
nkz = 36
pme_order = 6
ewald_rtol = 1e-05
ewald_geometry = 0
epsilon_surface = 0
optimize_fft = TRUE
ePBC = xyz
bPeriodicMols = FALSE
bContinuation = FALSE
bShakeSOR = FALSE
etc = Berendsen
epc = Berendsen
epctype = Isotropic
tau_p = 2
ref_p (3x3):
ref_p[ 0]={ 1.00000e+01, 0.00000e+00, 0.00000e+00}
ref_p[ 1]={ 0.00000e+00, 1.00000e+01, 0.00000e+00}
ref_p[ 2]={ 0.00000e+00, 0.00000e+00, 1.00000e+01}
compress (3x3):
compress[ 0]={ 1.00000e-06, 0.00000e+00, 0.00000e+00}
compress[ 1]={ 0.00000e+00, 1.00000e-06, 0.00000e+00}
compress[ 2]={ 0.00000e+00, 0.00000e+00, 1.00000e-06}
refcoord_scaling = All
posres_com (3):
posres_com[0]= 0.00000e+00
posres_com[1]= 0.00000e+00
posres_com[2]= 0.00000e+00
posres_comB (3):
posres_comB[0]= 0.00000e+00
posres_comB[1]= 0.00000e+00
posres_comB[2]= 0.00000e+00
andersen_seed = 815131
rlist = 0.9
rtpi = 0.05
coulombtype = PME
rcoulomb_switch = 0
rcoulomb = 0.9
vdwtype = Cut-off
rvdw_switch = 0
rvdw = 0.9
epsilon_r = 1
epsilon_rf = 1
tabext = 1
implicit_solvent = No
gb_algorithm = Still
gb_epsilon_solvent = 80
nstgbradii = 1
rgbradii = 2
gb_saltconc = 0
gb_obc_alpha = 1
gb_obc_beta = 0.8
gb_obc_gamma = 4.85
sa_surface_tension = 2.092
DispCorr = EnerPres
free_energy = no
init_lambda = 0
sc_alpha = 0
sc_power = 0
sc_sigma = 0.3
delta_lambda = 0
nwall = 0
wall_type = 9-3
wall_atomtype[0] = -1
wall_atomtype[1] = -1
wall_density[0] = 0
wall_density[1] = 0
wall_ewald_zfac = 3
pull = no
disre = No
disre_weighting = Conservative
disre_mixed = FALSE
dr_fc = 1000
dr_tau = 0
nstdisreout = 100
orires_fc = 0
orires_tau = 0
nstorireout = 100
dihre-fc = 1000
em_stepsize = 0.01
em_tol = 10
niter = 20
fc_stepsize = 0
nstcgsteep = 1000
nbfgscorr = 10
ConstAlg = Lincs
shake_tol = 1e-04
lincs_order = 6
lincs_warnangle = 30
lincs_iter = 2
bd_fric = 0
ld_seed = 1993
cos_accel = 0
deform (3x3):
deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
userint1 = 0
userint2 = 0
userint3 = 0
userint4 = 0
userreal1 = 0
userreal2 = 0
userreal3 = 0
userreal4 = 0
grpopts:
nrdf: 12957
ref_t: 400
tau_t: 0.5
anneal: Single
ann_npoints: 16
ann. times [0]: 0.0 100.0 200.0 300.0 400.0 500.0 600.0 700.0 800.0 900.0 1000.0 1100.0 1150.0 1200.0 1250.0 1300.0
ann. temps [0]: 400.0 390.0 380.0 370.0 360.0 350.0 340.0 330.0 320.0 310.0 300.0 290.0 280.0 270.0 260.0 250.0
acc: 0 0 0
nfreeze: N N N
energygrp_flags[ 0]: 0
efield-x:
n = 0
efield-xt:
n = 0
efield-y:
n = 0
efield-yt:
n = 0
efield-z:
n = 0
efield-zt:
n = 0
bQMMM = FALSE
QMconstraints = 0
QMMMscheme = 0
scalefactor = 1
qm_opts:
ngQM = 0
Initializing Domain Decomposition on 50 nodes
Dynamic load balancing: auto
Will sort the charge groups at every domain (re)decomposition
Initial maximum inter charge-group distances:
two-body bonded interactions: 0.321 nm
multi-body bonded interactions: 0.321 nm
Minimum cell size due to bonded interactions: 0.353 nm
Using 18 separate PME nodes
Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
Optimizing the DD grid for 32 cells with a minimum initial size of 0.441 nm
The maximum allowed number of cells is: X 14 Y 9 Z 9
Domain decomposition grid 4 x 4 x 2, separate PME nodes 18
Interleaving PP and PME nodes
This is a particle-particle only node
Domain decomposition nodeid 0, coordinates 0 0 0
Using two step summing over 13 groups of on average 2.5 processes
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 --- -------- --------
Using a Gaussian width (1/beta) of 0.288146 nm for Ewald
Cut-off's: NS: 0.9 Coulomb: 0.9 LJ: 0.9
System total charge: -0.000
Generated table with 950 data points for Ewald.
Tabscale = 500 points/nm
Generated table with 950 data points for LJ6.
Tabscale = 500 points/nm
Generated table with 950 data points for LJ12.
Tabscale = 500 points/nm
Enabling TIP4p water optimization for 1632 molecules.
Configuring nonbonded kernels...
Testing x86_64 SSE support... present.
Removing pbc first time
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
S. Miyamoto and P. A. Kollman
SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid
Water Models
J. Comp. Chem. 13 (1992) pp. 952-962
-------- -------- --- Thank You --- -------- --------
Linking all bonded interactions to atoms
There are 3744 inter charge-group exclusions,
will use an extra communication step for exclusion forces for PME
The initial number of communication pulses is: X 1 Y 1 Z 1
The initial domain decomposition cell size is: X 1.56 nm Y 1.04 nm Z 2.07 nm
The maximum allowed distance for charge groups involved in interactions is:
non-bonded interactions 0.900 nm
(the following are initial values, they could change due to box deformation)
two-body bonded interactions (-rdd) 0.900 nm
multi-body bonded interactions (-rdd) 0.900 nm
When dynamic load balancing gets turned on, these settings will change to:
The maximum number of communication pulses is: X 2 Y 2 Z 1
The minimum size for domain decomposition cells is 0.679 nm
The requested allowed shrink of DD cells (option -dds) is: 0.80
The allowed shrink of domain decomposition cells is: X 0.44 Y 0.65 Z 0.43
The maximum allowed distance for charge groups involved in interactions is:
non-bonded interactions 0.900 nm
two-body bonded interactions (-rdd) 0.900 nm
multi-body bonded interactions (-rdd) 0.679 nm
Making 3D domain decomposition grid 4 x 4 x 2, home cell index 0 0 0
Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
0: rest
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
H. J. C. Berendsen, J. P. M. Postma, A. DiNola and J. R. Haak
Molecular dynamics with coupling to an external bath
J. Chem. Phys. 81 (1984) pp. 3684-3690
-------- -------- --- Thank You --- -------- --------
There are: 5952 Atoms
There are: 1632 VSites
Charge group distribution at step 0: 69 70 69 68 69 69 68 69 68 69 69 70 69 70 70 69 69 69 69 68 69 70 69 69 69 69 69 68 69 68 69 70
Grid: 4 x 4 x 5 cells
Constraining the starting coordinates (step 0)
Constraining the coordinates at t0-dt (step 0)
RMS relative constraint deviation after constraining: 0.00e+00
Initial temperature: 399.113 K
Started mdrun on node 0 Mon Sep 29 20:11:42 2008
Step Time Lambda
0 0.00000 0.00000
Long Range LJ corr.: <C6> 2.4553e-04
Long Range LJ corr.: Epot -378.689, Pres: -117.387, Vir: 378.688
Current ref_t for group System: 400.0
Energies (kJ/mol)
Bond Angle Ryckaert-Bell. LJ (SR) Disper. corr.
1.73269e+03 2.20684e+03 3.74754e+02 -3.27568e+03 -3.78689e+02
Coulomb (SR) Coul. recip. Position Rest. Potential Kinetic En.
-4.82547e+04 -7.72684e+03 2.31557e-07 -5.53217e+04 2.20631e+04
Total Energy Temperature Pressure (bar)
-3.32586e+04 4.09595e+02 -8.54846e+03
DD step 4 load imb.: force 35.5% pme mesh/force 3.660
At step 23500 the performance loss due to force load imbalance is 5.0 %
NOTE: Turning on dynamic load balancing
DD load balancing is limited by minimum cell size in dimension Y
DD step 99999 vol min/aver 0.371! load imb.: force 16.1% pme mesh/force 2.535
Step Time Lambda
100000 200.00002 0.00000
Current ref_t for group System: 380.0
Energies (kJ/mol)
Bond Angle Ryckaert-Bell. LJ (SR) Disper. corr.
1.47364e+03 2.28074e+03 4.00472e+02 1.96449e+04 -6.36542e+02
Coulomb (SR) Coul. recip. Position Rest. Potential Kinetic En.
-1.07598e+05 -8.67264e+03 7.41091e+03 -8.56965e+04 2.05206e+04
Total Energy Temperature Pressure (bar)
-6.51759e+04 3.80960e+02 2.48454e+01
DD load balancing is limited by minimum cell size in dimension Y
DD step 199999 vol min/aver 0.381! load imb.: force 17.6% pme mesh/force 2.553
Step Time Lambda
200000 400.00003 0.00000
Current ref_t for group System: 360.0
Energies (kJ/mol)
Bond Angle Ryckaert-Bell. LJ (SR) Disper. corr.
1.58099e+03 2.16785e+03 3.75851e+02 2.00742e+04 -6.39581e+02
Coulomb (SR) Coul. recip. Position Rest. Potential Kinetic En.
-1.08897e+05 -8.72925e+03 7.24469e+03 -8.68226e+04 1.93058e+04
Total Energy Temperature Pressure (bar)
-6.75168e+04 3.58407e+02 -1.19701e+02
DD load balancing is limited by minimum cell size in dimension Y
DD step 299999 vol min/aver 0.379! load imb.: force 14.7% pme mesh/force 2.410
Step Time Lambda
300000 600.00000 0.00000
Current ref_t for group System: 340.0
Energies (kJ/mol)
Bond Angle Ryckaert-Bell. LJ (SR) Disper. corr.
1.45103e+03 1.98849e+03 3.24295e+02 2.05537e+04 -6.41958e+02
Coulomb (SR) Coul. recip. Position Rest. Potential Kinetic En.
-1.10331e+05 -8.75171e+03 7.10619e+03 -8.83013e+04 1.84445e+04
Total Energy Temperature Pressure (bar)
-6.98568e+04 3.42418e+02 1.82660e+02
DD load balancing is limited by minimum cell size in dimension Y
DD step 399999 vol min/aver 0.382! load imb.: force 14.0% pme mesh/force 2.537
Step Time Lambda
400000 800.00006 0.00000
Current ref_t for group System: 320.0
Energies (kJ/mol)
Bond Angle Ryckaert-Bell. LJ (SR) Disper. corr.
1.35018e+03 2.08202e+03 3.34279e+02 2.03256e+04 -6.44543e+02
Coulomb (SR) Coul. recip. Position Rest. Potential Kinetic En.
-1.10919e+05 -8.77606e+03 6.85087e+03 -8.93969e+04 1.72371e+04
Total Energy Temperature Pressure (bar)
-7.21598e+04 3.20003e+02 -4.56519e+02
DD load balancing is limited by minimum cell size in dimension Y
DD step 499999 vol min/aver 0.376! load imb.: force 18.8% pme mesh/force 2.388
Step Time Lambda
500000 1000.00006 0.00000
Current ref_t for group System: 300.0
Energies (kJ/mol)
Bond Angle Ryckaert-Bell. LJ (SR) Disper. corr.
1.30653e+03 1.71956e+03 3.25504e+02 2.11512e+04 -6.46719e+02
Coulomb (SR) Coul. recip. Position Rest. Potential Kinetic En.
-1.12531e+05 -8.80744e+03 6.66688e+03 -9.08157e+04 1.63261e+04
Total Energy Temperature Pressure (bar)
-7.44896e+04 3.03090e+02 -3.13115e+02
Step 518970: Run time exceeded 0.990 hours, will terminate the run
Step Time Lambda
518975 1037.95007 0.00000
Writing checkpoint, step 518975 at Mon Sep 29 20:35:28 2008
Step 518975: Run time exceeded 0.990 hours, will terminate the run
Current ref_t for group System: 296.2
Energies (kJ/mol)
Bond Angle Ryckaert-Bell. LJ (SR) Disper. corr.
1.22521e+03 1.81342e+03 3.17521e+02 2.10303e+04 -6.47331e+02
Coulomb (SR) Coul. recip. Position Rest. Potential Kinetic En.
-1.12463e+05 -8.78273e+03 6.52752e+03 -9.09795e+04 1.60481e+04
Total Energy Temperature Pressure (bar)
-7.49314e+04 2.97929e+02 -2.05323e+01
<====== ############### ==>
<==== A V E R A G E S ====>
<== ############### ======>
Current ref_t for group System: 296.2
Energies (kJ/mol)
Bond Angle Ryckaert-Bell. LJ (SR) Disper. corr.
1.52134e+03 2.06043e+03 3.45924e+02 1.85691e+04 -6.25727e+02
Coulomb (SR) Coul. recip. Position Rest. Potential Kinetic En.
-1.06220e+05 -8.68896e+03 7.20831e+03 -8.58295e+04 1.87523e+04
Total Energy Temperature Pressure (bar)
-6.70772e+04 3.48132e+02 -9.96384e+02
Box-X Box-Y Box-Z Volume Density (SI)
5.27291e+00 3.51663e+00 3.51663e+00 6.54401e+01 8.61378e+02
pV
-5.01842e+03
Total Virial (kJ/mol)
8.89941e+03 -6.05882e+01 1.76660e+02
-6.05462e+01 8.60539e+03 1.01817e+02
1.76695e+02 1.01826e+02 8.77513e+03
Pressure (bar)
-1.07276e+03 3.35659e+01 -9.80458e+01
3.35454e+01 -9.19485e+02 -5.36507e+01
-9.80639e+01 -5.36561e+01 -9.96906e+02
Total Dipole (Debye)
6.82511e+01 3.83409e+01 -5.55213e+01
<====== ############################### ==>
<==== R M S - F L U C T U A T I O N S ====>
<== ############################### ======>
Current ref_t for group System: 296.2
Energies (kJ/mol)
Bond Angle Ryckaert-Bell. LJ (SR) Disper. corr.
1.50237e+02 1.93586e+02 4.54909e+01 5.19727e+03 5.06925e+01
Coulomb (SR) Coul. recip. Position Rest. Potential Kinetic En.
1.18168e+04 1.75503e+02 3.23500e+02 7.36325e+03 1.62427e+03
Total Energy Temperature Pressure (bar)
8.49753e+03 3.01541e+01 2.74825e+03
Box-X Box-Y Box-Z Volume Density (SI)
1.77904e-01 1.18649e-01 1.18649e-01 7.45690e+00 6.97835e+01
pV
1.43641e+04
Total Virial (kJ/mol)
7.47239e+03 6.47161e+02 6.43280e+02
6.47107e+02 7.52105e+03 6.45987e+02
6.43250e+02 6.45972e+02 7.58821e+03
Pressure (bar)
2.75038e+03 3.35543e+02 3.33900e+02
3.35518e+02 2.77877e+03 3.34875e+02
3.33886e+02 3.34868e+02 2.79918e+03
Total Dipole (Debye)
1.91505e+01 1.98672e+01 1.55464e+01
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
-----------------------------------------------------------------------
LJ 19459.205432 642153.779 1.5
Coul(T) 58377.616296 2451859.884 5.9
Coul(T) + LJ 10371.553492 570435.442 1.4
Coul(T) + LJ [W4] 21914.882607 3462551.452 8.3
Coul(T) + LJ [W4-W4] 32688.860990 13140922.118 31.7
Outer nonbonded loop 31695.078814 316950.788 0.8
Calc Weights 11807.741952 425078.710 1.0
Spread Q Bspline 850157.420544 1700314.841 4.1
Gather F Bspline 850157.420544 10201889.047 24.6
3D-FFT 657627.704064 5261021.633 12.7
Solve PME 19168.897536 1226809.442 3.0
NS-Pairs 40312.528423 846563.097 2.0
Reset In Box 229.181568 687.545 0.0
CG-CoM 787.196448 2361.589 0.0
Bonds 498.216960 29394.801 0.1
Angles 896.790528 150660.809 0.4
RB-Dihedrals 896.790528 221507.260 0.5
Pos. Restr. 996.433920 49821.696 0.1
Virial 4683.239424 84298.310 0.2
Update 3935.913984 122013.334 0.3
Stop-CM 3935.913984 39359.140 0.1
P-Coupling 3935.913984 23615.484 0.1
Calc-Ekin 3935.921568 106269.882 0.3
Constraint-V 2540.911392 20327.291 0.0
Constraint-Vir 2540.906496 60981.756 0.1
Settle 846.972096 273571.987 0.7
Virtual Site 3 1693.937664 62675.694 0.2
-----------------------------------------------------------------------
Total 41494096.810 100.0
-----------------------------------------------------------------------
D O M A I N D E C O M P O S I T I O N S T A T I S T I C S
av. #atoms communicated per step for force: 2 x 30471.9
Average load imbalance: 17.2 %
Part of the total run time spent waiting due to load imbalance: 3.2 %
Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % Y 19 % Z 0 %
Average PME mesh/force load: 2.526
Part of the total run time spent waiting due to PP/PME imbalance: 34.1 %
NOTE: 34.1 % performance was lost because the PME nodes
had more work to do than the PP nodes.
You might want to increase the number of PME nodes
or increase the cut-off and the grid spacing.
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 %
-----------------------------------------------------------------------
Domain decomp. 32 103796 6377.120 2773.8 3.9
Vsite constr. 32 518976 98.045 42.6 0.1
Send X to PME 32 518976 360.643 156.9 0.2
Comm. coord. 32 518976 5913.609 2572.2 3.6
Neighbor search 32 103796 4024.003 1750.3 2.5
Force 32 518976 19683.677 8561.7 12.0
Wait + Comm. F 32 518976 13897.790 6045.0 8.5
PME mesh 18 518976 51164.638 22254.7 31.2
Wait + Comm. X/F 18 518976 7844.120 3411.9 4.8
Wait + Recv. PME F 32 518976 47918.787 20842.9 29.2
Vsite spread 32 1037952 189.185 82.3 0.1
Write traj. 32 520 5.476 2.4 0.0
Update 32 518976 1003.153 436.3 0.6
Constraints 32 518976 649.861 282.7 0.4
Comm. energies 32 518976 3908.464 1700.0 2.4
Rest 32 883.281 384.2 0.5
-----------------------------------------------------------------------
Total 50 163921.851 71300.0 100.0
-----------------------------------------------------------------------
Parallel run - timing based on wallclock.
NODE (s) Real (s) (%)
Time: 1426.000 1426.000 100.0
23:46
(Mnbf/s) (GFlops) (ns/day) (hour/ns)
Performance: 100.149 29.098 242.356 0.099
Finished mdrun on node 0 Mon Sep 29 20:35:28 2008
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