Dear Dr.Mark Thank you very much you are right I understood your mean exactly,
On Sun, Apr 10, 2011 at 12:44 PM, Mark Abraham <[email protected]>wrote: > On 10/04/2011 6:04 PM, mohsen ramezanpour wrote: > > Dear Dr.Mark > > On Sun, Apr 10, 2011 at 12:20 PM, Mark Abraham <[email protected]>wrote: > >> On 10/04/2011 5:40 PM, mohsen ramezanpour wrote: >> >>> Dear All >>> I used the following commands accoring to Extending Simulation in >>> gromacs/Documentation/how-tos/Extending Simulation >>> to extend my simulation. >>> I entered: >>> >>> tpbconv -s npt-1.tpr -extend 100 -o npt-1-extend.tpr >>> >>> nohup mpirun -np 4 mdrun -s npt-1-extend.tpr -cpi npt-1.cpt >>> >>> Ii run this command on a node with 4 cpu. >>> the result was these files: >>> confout.gro , state.cpt ,md.log , traj.trr ,state_prev.cpt ,ener.edr >>> , >>> #confout.gro.1# ,#confout.gro.2# ,#confout.gro.3# ,# ener.edr.1# >>> ,#ener.edr.2# ,#md.log.1 #,#traj.trr.1# ,#traj.trr.2# , >>> >>> I extended 4 files on 4 distinct nodes! >>> >> >> That's not the behaviour you were looking for. You've run the same .tpr >> four times, once on each CPU. This is because mdrun was not compiled with >> MPI. See the installation instructions. >> >> I think I explained bad.let me explain it more: > Suppose I entered the above commands on just one node(with 4 cpu) for > npt-1.tpr (just one time I entered these commands) > > > You seem to have used mpirun to run four different mdrun processes, each > using the same .tpr, one on each cpu. You should be trying to run one > mdrun_mpi using that .tpr, but all four cpus working on the same run. > > Look at the top few lines of your .log. That will tell you how many nodes > mdrun thought it was running on. I think you will see "NNODES=1". If so, > don't use this mdrun with mpirun. > > > besides if you were right it would result the same outputs when I run it > on different nodes with the same commands,please see below! > > > Not strictly true. See > http://www.gromacs.org/Documentation/Terminology/Reproducibility > > > > >> it is excellent,because the number of outputs was different, for example >>> one node produced 3 md.log and 4 confout.gro ! >>> >>> The main question is: >>> which one of the resulted outputs are the main result? on wich do I must >>> analyse? >>> >> >> They should all be equivalent, but not necessarily binary identical. >> > Actually I checked all of them,they are different,with different averages > of quantities, > and all of them show a final text that means the program finished > succesfully! > > > The averages being the same or different merely reflect whether your run > was reproducible. Assuming there was no output files in your working > directory to start with, you've run the same irreproducible run four times, > because you're using a non-MPI mdrun. > > Mark > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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