[gmx-users] Nodes problem?
Justin A. Lemkul
jalemkul at vt.edu
Sat Jan 7 05:19:52 CET 2012
Albert wrote:
> Hello:
>
> I am submiting gromacs in cluster and the job ALWAYS terminate with
> following messages:
>
>
> vol 0.75 imb F 5% pme/F 0.52 step 4200, will finish Sat Jan 7
> 09:36:14 2012
> vol 0.77 imb F 6% pme/F 0.52 step 4300, will finish Sat Jan 7
> 09:36:28 2012
>
> step 4389: Water molecule starting at atom 42466 can not be settled.
> Check for bad contacts and/or reduce the timestep if appropriate.
> Wrote pdb files with previous and current coordinates
>
> step 4390: Water molecule starting at atom 42466 can not be settled.
> Check for bad contacts and/or reduce the timestep if appropriate.
> Wrote pdb files with previous and current coordinates
>
> step 4391: Water molecule starting at atom 41659 can not be settled.
> Check for bad contacts and/or reduce the timestep if appropriate.
>
> step 4391: Water molecule starting at atom 42385 can not be settled.
> Check for bad contacts and/or reduce the timestep if appropriate.
> Wrote pdb files with previous and current coordinates
> Wrote pdb files with previous and current coordinates
>
> step 4392: Water molecule starting at atom 32218 can not be settled.
> Check for bad contacts and/or reduce the timestep if appropriate.
> Wrote pdb files with previous and current coordinates
>
> step 4393: Water molecule starting at atom 41659 can not be settled.
> Check for bad contacts and/or reduce the timestep if appropriate.
>
> step 4393: Water molecule starting at atom 32218 can not be settled.
> Check for bad contacts and/or reduce the timestep if appropriate.
> Wrote pdb files with previous and current coordinates
> Wrote pdb files with previous and current coordinates
>
> -------------------------------------------------------
> Program mdrun_mpi_bg, VERSION 4.5.5
> Source code file: ../../../src/mdlib/pme.c, line: 538
>
> Fatal error:
> 3 particles communicated to PME node 4 are more than 2/3 times the
> cut-off out of the domain decomposition cell
> of their charge group in dimension x.
> This usually means that your system is not well equilibrated.
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
> "How Do You Like Your Vacation So Far ?" (Speed 2 - Cruise Control)
>
> Error on node 19, will try to stop all the nodes
> Halting parallel program mdrun_mpi_bg on CPU 19 out of 24
>
> gcq#191: "How Do You Like Your Vacation So Far ?" (Speed 2 - Cruise Control)
>
> Abort(-1) on node 19 (rank 19 in comm 1140850688): application called
> MPI_Abort(MPI_COMM_WORLD, -1) - process 1
> 9
> <Jan 07 05:08:35.964275> BE_MPI (ERROR): The error message in the job
> record is as follows:
> <Jan 07 05:08:35.964330> BE_MPI (ERROR): "killed with signal 6"
>
>
>
>
> -----------here is my scrips to submting jobs----------------
> # @ job_name = I213A
> # @ class = kdm-large
> # @ account_no = G07-13
> # @ error = gromacs.out
> # @ output = gromacs.out
> # @ environment = COPY_ALL
> # @ wall_clock_limit = 12:00:00
> # @ notification = error
> # @ notify_user = albert at icm.edu.pl
> # @ job_type = bluegene
> # @ bg_size = 6
> # @ queue
> mpirun -exe /opt/gromacs/4.5.5/bin/mdrun_mpi_bg -args "-nosum -dlb yes
> -v -s npt.tpr" -mode VN -np 24
>
>
> -----------here is my npt.mdp file--------------------
> title = OPLS Lysozyme NPT equilibration
> define = -DPOSRES ; position restrain the protein
> ; Run parameters
> integrator = md ; leap-frog integrator
> nsteps = 200000 ; 1 * 200000 = 200 ps
> dt = 0.001 ; 1 fs
> ; Output control
> nstxout = 100 ; save coordinates every 0.2 ps
> nstvout = 100 ; save velocities every 0.2 ps
> 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 = 1.0 ; short-range neighborlist cutoff (in nm)
> rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm)
> rvdw = 1.0 ; 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
> tc-grps = Protein Non-Protein ; two coupling groups - more
> accurate
> tau_t = 0.1 0.1 ; time constant, in ps
> ref_t = 300 300 ; reference temperature, one for each
> group, in K
> ; 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 = 1.0 ; 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'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?
>
The error message tells you the problem, and leads you to the helpful
information found at:
http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings
Follow the links therein for more information, and search the list archive for
tips from the several thousand posts with the same problem :)
-Justin
--
========================================
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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