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<font face="Times New Roman" size=3> Dear David, </font><br>
<font face="Times New Roman" size=3>> </font><br>
<font face="Times New Roman" size=3>> > On Thu, 2004-05-27 at 09:46, B. Nick wrote: </font><br>
<font face="Times New Roman" size=3>> > > Dear gromacs users, </font><br>
<font face="Times New Roman" size=3>> > > </font><br>
<font face="Times New Roman" size=3>> > > I want to rerun a previous job that executed on a </font><br>
<font face="Times New Roman" size=3>> > > different cluster without any problem. But every time </font><br>
<font face="Times New Roman" size=3>> > > the job crashes after few minutes with the following </font><br>
<font face="Times New Roman" size=3>> > > error messages. </font><br>
<font face="Times New Roman" size=3>> > > (Other people simulating different system say that </font><br>
<font face="Times New Roman" size=3>> > > the have no problems.) </font><br>
<font face="Times New Roman" size=3>> > </font><br>
<font face="Times New Roman" size=3>> > Can you be more specific? Is this the same job that ran on four </font><br>
<font face="Times New Roman" size=3>> > processors before? Or is it a mdrun -rerun? </font><br>
<font face="Times New Roman" size=3>> </font><br>
<font face="Times New Roman" size=3>> It is a job of a series of jobs with identical input files </font><br>
<font face="Times New Roman" size=3>> but different structures (always 16 chains of 500 units, which </font><br>
<font face="Times New Roman" size=3>> results in a box of about 6 nm edge length) and the input file worked </font><br>
<font face="Times New Roman" size=3>> on the other cluster for 1, 4 and 6 nodes. In order to test the </font><br>
<font face="Times New Roman" size=3>> speed of my new account, I wanted to run it again. </font><br>
<font face="Times New Roman" size=3>> It just took the old structures and input file and rerun </font><br>
<font face="Times New Roman" size=3>> grompp -np 4 on the new cluster. After submission of the job I </font><br>
<font face="Times New Roman" size=3>> always get the error message. I have also attached the input </font><br>
<font face="Times New Roman" size=3>> file. </font><br>
<font face="Times New Roman" size=3>could you try with pbc = full in the mdp file? </font><br>
<br>
<font face="Times New Roman" size=3>If I try this I get the error message from grompp</font><br>
<br>
<font face="Courier New" size=2>creating statusfile for 4 nodes...</font><br>
<font face="Courier New" size=2>ERROR: invalid enum 'full' for variable pbc, using 'xyz'</font><br>
<font face="Courier New" size=2>Next time use one of: 'xyz' 'no'</font><br>
<br>
<font face="Times New Roman" size=3>I'am using version 3.1.4 as in case of the first runs.</font><br>
<font face="Times New Roman" size=3>But also in the manual of version 3.2 I do not find the option pbc = full.</font><br>
<br>
<font face="Times New Roman" size=3>So the problem is still unsolved.</font><br>
<font face="Times New Roman" size=3>Any further suggestion ?</font><br>
<br>
<font face="Times New Roman" size=3>Thanks again. </font><br>
<br>
<font face="Times New Roman" size=3>> > > </font><br>
<font face="Times New Roman" size=3>> > > Back Off! I just backed up traj.xtc to ./#traj.xtc.1# </font><br>
<font face="Times New Roman" size=3>> > > Fatal error: ci = 2280 should be in 0 .. 2196 [FILE nsgrid.c, LINE 210] </font><br>
<font face="Times New Roman" size=3>> > > Error on node 1, will try to stop all the nodes </font><br>
<font face="Times New Roman" size=3>> > > Fatal error: ci = 2280 should be in 0 .. 2196 [FILE nsgrid.c, LINE 210] </font><br>
<font face="Times New Roman" size=3>> > > Error on node 2, will try to stop all the nodes </font><br>
<font face="Times New Roman" size=3>> > > Fatal error: ci = 2280 should be in 0 .. 2196 [FILE nsgrid.c, LINE 210] </font><br>
<font face="Times New Roman" size=3>> > > Error on node 3, will try to stop all the nodes </font><br>
<font face="Times New Roman" size=3>> > > Fatal error, aborting. </font><br>
<font face="Times New Roman" size=3>> > > Fatal error, aborting. </font><br>
<font face="Times New Roman" size=3>> > > Fatal error, aborting. </font><br>
<font face="Times New Roman" size=3>> > > Job sge.628260 on sunc12.rz.RWTH-Aachen.DE: received signal ABRT. </font><br>
<font face="Times New Roman" size=3>> > > </font><br>
<font face="Times New Roman" size=3>> > > ------------------------------------------------------------------------------ </font><br>
<font face="Times New Roman" size=3>> > > | Execution of Batch-Request stopped at Thu May 27 00:40:58 MEST 2004 </font><br>
<font face="Times New Roman" size=3>> > > | peak memory value: 13.72M </font><br>
<font face="Times New Roman" size=3>> > > | real time used: 00:18:17 </font><br>
<font face="Times New Roman" size=3>> > > ------------------------------------------------------------------------------ </font><br>
<font face="Times New Roman" size=3>> ; </font><br>
<font face="Times New Roman" size=3>> ; MD Input File </font><br>
<font face="Times New Roman" size=3>> ; B. Nick, 20.10.03 </font><br>
<font face="Times New Roman" size=3>> ; </font><br>
<font face="Times New Roman" size=3>> ; </font><br>
<font face="Times New Roman" size=3>> title = Triclinic cell at 200 K </font><br>
<font face="Times New Roman" size=3>> cpp = /lib/cpp </font><br>
<font face="Times New Roman" size=3>> </font><br>
<font face="Times New Roman" size=3>> </font><br>
<font face="Times New Roman" size=3>> ; *** Run control *** </font><br>
<font face="Times New Roman" size=3>> </font><br>
<font face="Times New Roman" size=3>> integrator = md </font><br>
<font face="Times New Roman" size=3>> tinit = 0 </font><br>
<font face="Times New Roman" size=3>> dt = 0.0005 ; in ps </font><br>
<font face="Times New Roman" size=3>> nsteps = 4000000 ; total 1.0 ns. </font><br>
<font face="Times New Roman" size=3>> nstcomm = 1 ; </font><br>
<font face="Times New Roman" size=3>> </font><br>
<font face="Times New Roman" size=3>> </font><br>
<font face="Times New Roman" size=3>> ; *** Output control *** </font><br>
<font face="Times New Roman" size=3>> </font><br>
<font face="Times New Roman" size=3>> nstxout = 0 </font><br>
<font face="Times New Roman" size=3>> nstvout = 0 </font><br>
<font face="Times New Roman" size=3>> nstfout = 0 </font><br>
<font face="Times New Roman" size=3>> nstlog = 5000 </font><br>
<font face="Times New Roman" size=3>> nstenergy = 100 </font><br>
<font face="Times New Roman" size=3>> nstxtcout = 5000 </font><br>
<font face="Times New Roman" size=3>> </font><br>
<font face="Times New Roman" size=3>> </font><br>
<font face="Times New Roman" size=3>> ; *** Neighbor searching *** </font><br>
<font face="Times New Roman" size=3>> </font><br>
<font face="Times New Roman" size=3>> nstlist = 10 </font><br>
<font face="Times New Roman" size=3>> ns_type = grid </font><br>
<font face="Times New Roman" size=3>> pbc = xyz </font><br>
<font face="Times New Roman" size=3>> rlist = 0.8 </font><br>
<font face="Times New Roman" size=3>> </font><br>
<font face="Times New Roman" size=3>> </font><br>
<font face="Times New Roman" size=3>> ; *** Electrostatics and VdW </font><br>
<font face="Times New Roman" size=3>> </font><br>
<font face="Times New Roman" size=3>> coulombtype = Shift </font><br>
<font face="Times New Roman" size=3>> rcoulomb_switch = 0.8 </font><br>
<font face="Times New Roman" size=3>> rcoulomb = 0.9 </font><br>
<font face="Times New Roman" size=3>> epsilon_r = 1.0 </font><br>
<font face="Times New Roman" size=3>> vdwtype = Shift </font><br>
<font face="Times New Roman" size=3>> rvdw_switch = 0.8 </font><br>
<font face="Times New Roman" size=3>> rvdw = 0.9 </font><br>
<font face="Times New Roman" size=3>> DispCorr = EnerPres </font><br>
<font face="Times New Roman" size=3>> </font><br>
<font face="Times New Roman" size=3>> </font><br>
<font face="Times New Roman" size=3>> ; *** Temperature coupling *** </font><br>
<font face="Times New Roman" size=3>> </font><br>
<font face="Times New Roman" size=3>> tcoupl = Nose-Hoover </font><br>
<font face="Times New Roman" size=3>> tc-grps = System </font><br>
<font face="Times New Roman" size=3>> tau_t = 0.1 </font><br>
<font face="Times New Roman" size=3>> ref_t = 200 </font><br>
<font face="Times New Roman" size=3>> </font><br>
<font face="Times New Roman" size=3>> </font><br>
<font face="Times New Roman" size=3>> ; *** Pressure coupling *** </font><br>
<font face="Times New Roman" size=3>> </font><br>
<font face="Times New Roman" size=3>> Pcoupl = Parrinello-Rahman </font><br>
<font face="Times New Roman" size=3>> Pcoupltype = anisotropic </font><br>
<font face="Times New Roman" size=3>> tau_p = 0.1 </font><br>
<font face="Times New Roman" size=3>> compressibility = 4e-5 4e-5 4e-5 4e-5 4e-5 4e-5 </font><br>
<font face="Times New Roman" size=3>> ref_p = 1 1 1 1 1 1 </font><br>
<font face="Times New Roman" size=3>> </font><br>
<font face="Times New Roman" size=3>> </font><br>
<font face="Times New Roman" size=3>> ; *** Velocity gerneration *** </font><br>
<font face="Times New Roman" size=3>> </font><br>
<font face="Times New Roman" size=3>> gen_vel = no </font><br>
<font face="Times New Roman" size=3>> </font><br>
<font face="Times New Roman" size=3>> </font><br>
<font face="Times New Roman" size=3>> ; *** Bonds *** </font><br>
<font face="Times New Roman" size=3>> </font><br>
<font face="Times New Roman" size=3>> constraints = all-bonds </font><br>
<font face="Times New Roman" size=3>> constraint_algorithm = lincs </font><br>
<font face="Times New Roman" size=3>> unconstrained_start = no </font><br>
<font face="Times New Roman" size=3>> lincs_order = 4 </font><br>
<font face="Times New Roman" size=3>> morse = no </font><br>
<font face="Times New Roman" size=3>> </font><br>
<font face="Times New Roman" size=3>> </font><br>
<font face="Times New Roman" size=3>> ; *** User defined thingies *** </font><br>
<font face="Times New Roman" size=3>> </font><br>
<font face="Times New Roman" size=3>> </font><br>
<font face="Times New Roman" size=3>> ---------- </font><br>
<font face="Times New Roman" size=3>> Thank you very much, </font><br>
<font face="Times New Roman" size=3>> Gitta </font><br>
<font face="Times New Roman" size=3>> </font><br>
<font face="Times New Roman" size=3>> </font><br>
<font face="Times New Roman" size=3>> > David. </font><br>
<font face="Times New Roman" size=3>> > ________________________________________________________________________ </font><br>
<font face="Times New Roman" size=3>> > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, </font><br>
<font face="Times New Roman" size=3>> > Dept. of Cell and Molecular Biology, Uppsala University. </font><br>
<font face="Times New Roman" size=3>> > Husargatan 3, Box 596, 75124 Uppsala, Sweden </font><br>
<font face="Times New Roman" size=3>> > phone: +46 18 471 4205 fax: +46 18 511 755 </font><br>
<font face="Times New Roman" size=3>> > spoel@xray.bmc.uu.se spoel@gromacs.org </font><font face="Times New Roman" size=3 color=#0000FF><u><http://xray.bmc.uu.se/></u></font><font face="Times New Roman" size=3 color=#000000>~spoel </font><br>
<font face="Times New Roman" size=3 color=#000000>> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ </font><br>
<font face="Times New Roman" size=3 color=#000000>> > </font><br>
<font face="Times New Roman" size=3 color=#000000>> > </font><br>
<font face="Times New Roman" size=3 color=#000000>> > </font><br>
<font face="Times New Roman" size=3 color=#000000>> > ------------------------------ </font><br>
<font face="Times New Roman" size=3 color=#000000>> > </font><br>
<font face="Times New Roman" size=3 color=#000000>> > _______________________________________________ </font><br>
<font face="Times New Roman" size=3 color=#000000>> > gmx-users mailing list </font><br>
<font face="Times New Roman" size=3 color=#000000>> > gmx-users@gromacs.org </font><br>
<font face="Times New Roman" size=3 color=#000000>> > </font><font face="Times New Roman" size=3 color=#0000FF><u><http://www.gromacs.org/mailman/listinfo/gmx-users></u></font><font face="Times New Roman" size=3 color=#000000> </font><br>
<font face="Times New Roman" size=3 color=#000000>> > </font><br>
<font face="Times New Roman" size=3 color=#000000>-- </font><br>
<font face="Times New Roman" size=3 color=#000000>David. </font><br>
<font face="Times New Roman" size=3 color=#000000>________________________________________________________________________ </font><br>
<font face="Times New Roman" size=3 color=#000000>David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, </font><br>
<font face="Times New Roman" size=3 color=#000000>Dept. of Cell and Molecular Biology, Uppsala University. </font><br>
<font face="Times New Roman" size=3 color=#000000>Husargatan 3, Box 596, 75124 Uppsala, Sweden </font><br>
<font face="Times New Roman" size=3 color=#000000>phone: +46 18 471 4205 fax: +46 18 511 755 </font><br>
<font face="Times New Roman" size=3 color=#000000>spoel@xray.bmc.uu.se spoel@gromacs.org </font><font face="Times New Roman" size=3 color=#0000FF><u><http://xray.bmc.uu.se/></u></font><font face="Times New Roman" size=3 color=#000000>~spoel </font><br>
<font face="Times New Roman" size=3 color=#000000>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ </font><br>
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