[gmx-users] RE: job crashes

[B. Nick]

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.

> > 
> > 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
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> 
> 
> 
> ------------------------------
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> 

-- 
Dr. Birgitta Nick
DWI, Veltmanplatz8
52062 Aachen, Germany