[gmx-users] something wrong with BlueGene/P
Bao Kai
paeanball at gmail.com
Wed Sep 26 13:51:26 CEST 2012
Hi, all,
I did many simulations with Gromacs on CO2 Water mixtures on my
workstation with 8 cores in parallel, the results are pretty good.
For bigger simulations, I turned to the BlueGene machine. The problem
is that with exactly the same configuration files and same number of
MPI tasks( 8 here) , I always got the following problems.
1773
1774 step 6870: Water molecule starting at atom 1375 can not be settled.
1775 Check for bad contacts and/or reduce the timestep if appropriate.
1776 Wrote pdb files with previous and current coordinates
1777
1778 Step 6871, time 6.871 (ps) LINCS WARNING
1779 relative constraint deviation after LINCS:
1780 rms 0.139809, max 0.559153 (between atoms 10 and 11)
1781 bonds that rotated more than 30 degrees:
1782 atom 1 atom 2 angle previous, current, constraint length
1783 10 11 78.5 0.1210 0.1813 0.1163
1784 10 12 90.0 0.1523 0.1152 0.1163
1785
1786 step 6871: Water molecule starting at atom 4576 can not be settled.
1787 Check for bad contacts and/or reduce the timestep if appropriate.
1788
1789 step 6871: Water molecule starting at atom 5794 can not be settled.
1790 Check for bad contacts and/or reduce the timestep if appropriate.
1791 Wrote pdb files with previous and current coordinates
1792 Wrote pdb files with previous and current coordinates
1793
1794 -------------------------------------------------------
1795 Program mdrun_bgp_d, VERSION 4.5.5
1796 Source code file: pme.c, line: 538
1797
1798 Fatal error:
1799 3 particles communicated to PME node 1 are more than 2/3 times
the cut-off out of the domain decomposition cell of their charge group
in dimension y.
1800 This usually means that your system is not well equilibrated.
1801 For more information and tips for troubleshooting, please
check the GROMACS
1802 website at http://www.gromacs.org/Documentation/Errors
When I do the energy minimization or the NVT equilibration, Gromacs
worked pretty well.
The problem happened when I turned to the NPT equilibration. The
pressure and temperature were set to be 100bar and 318K respectively.
When during the NPT equlibration, the temperature and pressure keep
increasing before the program halt.
1161
1162 DD step 6499 load imb.: force 6.9%
1163
1164 Step Time Lambda
1165 6500 6.50000 0.00000
1166
1167 Energies (kJ/mol)
1168 Angle LJ (SR) Disper. corr. Coulomb (SR)
Coul. recip.
1169 4.50025e+01 2.21540e+04 -7.02187e+02 -1.23033e+05
-1.27743e+04
1170 Potential Kinetic En. Total Energy Temperature
Pres. DC (bar)
1171 -1.14310e+05 1.50736e+04 -9.92368e+04 3.74677e+02
-3.36430e+02
1172 Pressure (bar) Constr. rmsd
1173 1.53825e+03 1.53151e-06
1174
1175 DD step 6599 load imb.: force 5.1%
1176
1177 Step Time Lambda
1178 6600 6.60000 0.00000
1179
1180 Energies (kJ/mol)
1181 Angle LJ (SR) Disper. corr. Coulomb (SR)
Coul. recip.
1182 5.41207e+01 2.32123e+04 -7.01221e+02 -1.23852e+05
-1.27349e+04
1183 Potential Kinetic En. Total Energy Temperature
Pres. DC (bar)
1184 -1.14022e+05 1.50532e+04 -9.89688e+04 3.82147e+02
-3.35505e+02
1185 Pressure (bar) Constr. rmsd
1186 2.37940e+03 1.40409e-06
1187
1188 DD step 6699 load imb.: force 4.8%
1189
1190 Step Time Lambda
1191 6700 6.70000 0.00000
1192
1193 Energies (kJ/mol)
1194 Angle LJ (SR) Disper. corr. Coulomb (SR)
Coul. recip.
1195 4.70219e+01 2.37867e+04 -6.99910e+02 -1.24021e+05
-1.26862e+04
1196 Potential Kinetic En. Total Energy Temperature
Pres. DC (bar)
1197 -1.13574e+05 1.54884e+04 -9.80852e+04 4.03537e+02
-3.34252e+02
1198 Pressure (bar) Constr. rmsd
1199 3.01172e+03 1.56366e-06
1200
1201 DD step 6799 load imb.: force 6.7%
1202
1203 Step Time Lambda
1204 6800 6.80000 0.00000
1205
1206 Energies (kJ/mol)
1207 Angle LJ (SR) Disper. corr. Coulomb (SR)
Coul. recip.
1208 3.79031e+01 2.70730e+04 -6.97586e+02 -1.24088e+05
-1.24549e+04
1209 Potential Kinetic En. Total Energy Temperature
Pres. DC (bar)
1210 -1.10129e+05 3.49837e+04 -7.51454e+04 1.00845e+03
-3.32036e+02
1211 Pressure (bar) Constr. rmsd
1212 9.09741e+03 3.89773e-06
The input file for the NPT equilibration is as follows.
define = -DPOSRES ; position restrain the protein
; Run parameters
integrator = md ; leap-frog integrator
; integrator = md-vv ; leap-frog integrator
nsteps = 100000 ; 2 * 50000 = 100 ps
dt = 0.002 ; 2 fs
; Output control
nstxout = 100 ; save coordinates every 0.2 ps
nstvout = 100 ; save velocities every 0.2 ps
; ; no nstxtcout
nstenergy = 100 ; save energies every 0.2 ps
nstlog = 100 ; update log file every 0.2 ps
; Bond parameters
continuation = yes ; <--- Restarting after NVT
constraint_algorithm = lincs ; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid ; search neighboring grid cells
nstlist = 5 ; 10 fs
rlist = 0.9 ; short-range neighborlist cutoff (in nm)
rcoulomb = 0.9 ; short-range electrostatic cutoff (in nm)
; rcoulomb = 1.5 ; short-range electrostatic cutoff (in nm)
rvdw = 0.9 ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT
; Temperature coupling is on
tcoupl = V-rescale ; modified Berendsen thermostat
; tcoupl = nose-hoover ; modified Berendsen thermostat
; tc-grps = CO2 SOL ; two coupling groups - more accurate
tc-grps = System ; two coupling groups - more accurate
tau_t = 0.1 ; time constant, in ps
ref_t = 318 ; reference temperature, one for each group, in K
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
; turning on pressure coupling
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
; <-- Pressure coupling is on
pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT
pcoupltype = isotropic ; uniform scaling of box vectors
tau_p = 2.0 ; time constant, in ps
ref_p = 100.0 ; reference pressure, in bar
compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Dispersion correction
DispCorr = EnerPres ; account for cut-off vdW scheme
; Velocity generation
gen_vel = no ; <-- Velocity generation is off
;
;
I do not know what to do. This is really kind of the worst things can
happen. I can not understand why it work on the workstation while can
not work on the BlueGene machine.
The thing is a little urgent now. If I could not go over the problem,
my project will be dead.
Any suggestions will be much appreciated.
Thank you very much.
Best Regards,
Kai
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