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<font size="+1"><font face="WenQuanYi WenQuanYi Bitmap Song">Hello:<br>
<br>
I am submiting gromacs in cluster and the job ALWAYS terminate
with following messages:<br>
<br>
<br>
vol 0.75 imb F 5% pme/F 0.52 step 4200, will finish Sat Jan 7
09:36:14 2012<br>
vol 0.77 imb F 6% pme/F 0.52 step 4300, will finish Sat Jan 7
09:36:28 2012<br>
<br>
step 4389: Water molecule starting at atom 42466 can not be
settled.<br>
Check for bad contacts and/or reduce the timestep if
appropriate.<br>
Wrote pdb files with previous and current coordinates<br>
<br>
step 4390: Water molecule starting at atom 42466 can not be
settled.<br>
Check for bad contacts and/or reduce the timestep if
appropriate.<br>
Wrote pdb files with previous and current coordinates<br>
<br>
step 4391: Water molecule starting at atom 41659 can not be
settled.<br>
Check for bad contacts and/or reduce the timestep if
appropriate.<br>
<br>
step 4391: Water molecule starting at atom 42385 can not be
settled.<br>
Check for bad contacts and/or reduce the timestep if
appropriate.<br>
Wrote pdb files with previous and current coordinates<br>
Wrote pdb files with previous and current coordinates<br>
<br>
step 4392: Water molecule starting at atom 32218 can not be
settled.<br>
Check for bad contacts and/or reduce the timestep if
appropriate.<br>
Wrote pdb files with previous and current coordinates<br>
<br>
step 4393: Water molecule starting at atom 41659 can not be
settled.<br>
Check for bad contacts and/or reduce the timestep if
appropriate.<br>
<br>
step 4393: Water molecule starting at atom 32218 can not be
settled.<br>
Check for bad contacts and/or reduce the timestep if
appropriate.<br>
Wrote pdb files with previous and current coordinates<br>
Wrote pdb files with previous and current coordinates<br>
<br>
-------------------------------------------------------<br>
Program mdrun_mpi_bg, VERSION 4.5.5<br>
Source code file: ../../../src/mdlib/pme.c, line: 538<br>
<br>
Fatal error:<br>
3 particles communicated to PME node 4 are more than 2/3 times
the cut-off out of the domain decomposition cell<br>
of their charge group in dimension x.<br>
This usually means that your system is not well equilibrated.<br>
For more information and tips for troubleshooting, please check
the GROMACS<br>
website at <a class="moz-txt-link-freetext" href="http://www.gromacs.org/Documentation/Errors">http://www.gromacs.org/Documentation/Errors</a><br>
-------------------------------------------------------<br>
<br>
"How Do You Like Your Vacation So Far ?" (Speed 2 - Cruise
Control)<br>
<br>
Error on node 19, will try to stop all the nodes<br>
Halting parallel program mdrun_mpi_bg on CPU 19 out of 24<br>
<br>
gcq#191: "How Do You Like Your Vacation So Far ?" (Speed 2 -
Cruise Control)<br>
<br>
Abort(-1) on node 19 (rank 19 in comm 1140850688): application
called MPI_Abort(MPI_COMM_WORLD, -1) - process 1<br>
9<br>
<Jan 07 05:08:35.964275> BE_MPI (ERROR): The error message
in the job record is as follows:<br>
<Jan 07 05:08:35.964330> BE_MPI (ERROR): "killed with
signal 6"<br>
<br>
<br>
<br>
<br>
-----------here is my scrips to submting jobs----------------<br>
# @ job_name = I213A<br>
# @ class = kdm-large<br>
# @ account_no = G07-13 <br>
# @ error = gromacs.out<br>
# @ output = gromacs.out<br>
# @ environment = COPY_ALL<br>
# @ wall_clock_limit = 12:00:00<br>
# @ notification = error<br>
# @ notify_user = <a class="moz-txt-link-abbreviated" href="mailto:albert@icm.edu.pl">albert@icm.edu.pl</a><br>
# @ job_type = bluegene<br>
# @ bg_size = 6<br>
# @ queue<br>
mpirun -exe /opt/gromacs/4.5.5/bin/mdrun_mpi_bg -args "-nosum
-dlb yes -v -s npt.tpr" -mode VN -np 24<br>
<br>
<br>
-----------here is my npt.mdp file--------------------<br>
title = OPLS Lysozyme NPT equilibration <br>
define = -DPOSRES ; position restrain the protein<br>
; Run parameters<br>
integrator = md ; leap-frog integrator<br>
nsteps = 200000 ; 1 * 200000 = 200 ps<br>
dt = 0.001 ; 1 fs<br>
; Output control<br>
nstxout = 100 ; save coordinates every 0.2 ps<br>
nstvout = 100 ; save velocities every 0.2 ps<br>
nstenergy = 100 ; save energies every 0.2 ps<br>
nstlog = 100 ; update log file every 0.2 ps<br>
; Bond parameters<br>
continuation = yes ; Restarting after NVT <br>
constraint_algorithm = lincs ; holonomic constraints <br>
constraints = all-bonds ; all bonds (even heavy atom-H
bonds) constrained<br>
lincs_iter = 1 ; accuracy of LINCS<br>
lincs_order = 4 ; also related to accuracy<br>
; Neighborsearching<br>
ns_type = grid ; search neighboring grid cells<br>
nstlist = 5 ; 10 fs<br>
rlist = 1.0 ; short-range neighborlist cutoff (in
nm)<br>
rcoulomb = 1.0 ; short-range electrostatic cutoff (in
nm)<br>
rvdw = 1.0 ; short-range van der Waals cutoff (in
nm)<br>
; Electrostatics<br>
coulombtype = PME ; Particle Mesh Ewald for long-range
electrostatics<br>
pme_order = 4 ; cubic interpolation<br>
fourierspacing = 0.16 ; grid spacing for FFT<br>
; Temperature coupling is on<br>
tcoupl = V-rescale ; modified Berendsen thermostat<br>
tc-grps = Protein Non-Protein ; two coupling groups -
more accurate<br>
tau_t = 0.1 0.1 ; time constant, in ps<br>
ref_t = 300 300 ; reference temperature, one for
each group, in K<br>
; Pressure coupling is on<br>
pcoupl = Parrinello-Rahman ; Pressure coupling on in
NPT<br>
pcoupltype = isotropic ; uniform scaling of box vectors<br>
tau_p = 2.0 ; time constant, in ps<br>
ref_p = 1.0 ; reference pressure, in bar<br>
compressibility = 4.5e-5 ; isothermal compressibility of
water, bar^-1<br>
; Periodic boundary conditions<br>
pbc = xyz ; 3-D PBC<br>
; Dispersion correction<br>
DispCorr = EnerPres ; account for cut-off vdW scheme<br>
; Velocity generation<br>
gen_vel = no ; Velocity generation is off <br>
<br>
<br>
I've also try to change the number of nodes to fix it but it
doesn't work. would you please give me some advices to fix this?<br>
<br>
Thank you very much<br>
<br>
best<br>
Shuguang<br>
<br>
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