[gmx-users] RE: job crashes

[David van der Spoel]

On Thu, 2004-05-27 at 13:49, B. Nick wrote:
> Dear David, 
> 
> > On Thu, 2004-05-27 at 09:46, B. Nick wrote:
> > > Dear gromacs users,
> > > 
> > > I want to rerun a previous job that executed on a
> > > different cluster without any problem. But every time
> > > the job crashes after few minutes with the following
> > > error messages. 
> > > (Other people simulating different system say that
> > > the have no problems.)
> > 
> > Can you be more specific? Is this the same job that ran on four
> > processors before? Or is it a mdrun -rerun?
> 
> It is a job of a series of jobs with identical input files
> but different structures (always 16 chains of 500 units, which
> results in a box of about 6 nm edge length) and the input file worked 
> on the other cluster for 1, 4 and 6 nodes. In order to test the
> speed of my new account, I wanted to run it again.
> It just took the old structures and input file and rerun
> grompp -np 4 on the new cluster. After submission of the job I
> always get the error message. I have also attached the input
> file.
could you try with pbc = full in the mdp file?
> 
> > > 
> > > Any suggestion what is my problem???
> > > 
> > > Back Off! I just backed up traj.xtc to ./#traj.xtc.1#
> > > Fatal error: ci = 2280 should be in 0 .. 2196 [FILE nsgrid.c, LINE 210]
> > > Error on node 1, will try to stop all the nodes
> > > Fatal error: ci = 2280 should be in 0 .. 2196 [FILE nsgrid.c, LINE 210]
> > > Error on node 2, will try to stop all the nodes
> > > Fatal error: ci = 2280 should be in 0 .. 2196 [FILE nsgrid.c, LINE 210]
> > > Error on node 3, will try to stop all the nodes
> > > Fatal error, aborting.
> > > Fatal error, aborting.
> > > Fatal error, aborting.
> > > Job sge.628260 on sunc12.rz.RWTH-Aachen.DE: received signal ABRT.
> > > 
> > > ------------------------------------------------------------------------------
> > > | Execution of Batch-Request stopped at Thu May 27 00:40:58 MEST 2004
> > > | peak memory value: 13.72M
> > > | real time used: 00:18:17
> > > ------------------------------------------------------------------------------
> ;
> ;	MD Input File 
> ;	B. Nick, 20.10.03
> ;	
> ;
> title               =  Triclinic cell at 200 K
> cpp                 =  /lib/cpp
> 
> 
> ; *** Run control ***
> 
> integrator          =  md
> tinit               =  0
> dt                  =  0.0005	; in ps
> nsteps              =  4000000	; total 1.0 ns.
> nstcomm             =  1        ; 
> 
> 
> ; *** Output control ***
> 
> nstxout             =    0
> nstvout             =    0
> nstfout             =    0
> nstlog              = 5000
> nstenergy           =  100
> nstxtcout           = 5000
> 
> 
> ; *** Neighbor searching ***
> 
> nstlist             =  10
> ns_type             =  grid
> pbc                 =  xyz
> rlist               =  0.8
> 
> 
> ; *** Electrostatics and VdW
> 
> coulombtype         =  Shift
> rcoulomb_switch     =  0.8
> rcoulomb            =  0.9
> epsilon_r           =  1.0
> vdwtype             =  Shift
> rvdw_switch         =  0.8
> rvdw                =  0.9
> DispCorr            =  EnerPres
> 
> 
> ; *** Temperature coupling ***
> 
> tcoupl              =  Nose-Hoover
> tc-grps		    =  System
> tau_t               =  0.1
> ref_t               =  200
> 
> 
> ; *** Pressure coupling ***
> 
> Pcoupl              =  Parrinello-Rahman
> Pcoupltype          =  anisotropic
> tau_p               =  0.1
> compressibility     =  4e-5 4e-5 4e-5 4e-5 4e-5 4e-5
> ref_p               =  1 1 1 1 1 1
> 
> 
> ; *** Velocity gerneration ***
> 
> gen_vel             =  no
> 
> 
> ; *** Bonds ***
> 
> constraints          =  all-bonds
> constraint_algorithm =  lincs
> unconstrained_start  =  no
> lincs_order          =  4
> morse                =  no
> 
> 
> ; *** User defined thingies ***
> 
> 
> ---------- 
> Thank you very much,
> Gitta
> 
> 
> > David.
> > ________________________________________________________________________
> > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> > Dept. of Cell and Molecular Biology, Uppsala University.
> > Husargatan 3, Box 596, 75124 Uppsala, Sweden
> > phone:  +46 18 471 4205  fax: +46 18 511 755
> > spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > 
> > 
> > 
> > ------------------------------
> > 
> > _______________________________________________
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> > gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > 
-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone:  +46 18 471 4205  fax: +46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++