[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. 
could you try with pbc = full in the mdp file? 

If I try this I get the error message from grompp

creating statusfile for 4 nodes...
ERROR: invalid enum 'full' for variable pbc, using 'xyz'
Next time use one of: 'xyz' 'no'

I'am using version 3.1.4 as in case of the first runs.
But also in the manual of version 3.2 I do not find the option pbc = full.

So the problem is still unsolved.
Any further suggestion ?

Thanks again. 

> > > 
> > > 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> 
> > 
-- 
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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