[gmx-users] REMD in one nodes with two processors

[Dongsheng Zhang]

Thank you, David. I try it as:


mpirun -np 2  n1 /home/brasilia/dong/mdrun_mpi_MC  -replex 500 -reseed
-1 -s replica -v >& zevel 

It gives me the same error message: Can not open file: replica.tpr

Any other suggestions?

Thanks!


Dongsheng


On Thu, 2006-05-04 at 20:17 +0200, David van der Spoel wrote:
> Dongsheng Zhang wrote:
> > Dear David,
> > 
> > I had tried mpirun before, it didn't work either. the command was:
> > mpirun -np 2 n1 /home/brasilia/dong/mdrun_mpi_MC  -replex 500 -reseed -1
> > -multi -s replica -deffnm replica -N 2 -v >& zevel
> 
> remove the -N 2 -multi -deffnm replica options and try again.
> 
> 
> > 
> >  Because the two processors are in one node, so I changed my command to
> > ( and go to the local node n1 to submit the job):
> > 
> > /home/brasilia/dong/mdrun_mpi -np 2 -replex 500 -reseed -1 -multi -s
> > replica -deffnm replica -N 2 -v >& zevel
> > 
> > Could you please tell me if there is any way to check if the program can
> > recognize -multi option?
> > 
> > Thank you!
> > 
> > 
> > Dongsheng
> > 
> > 
> > 
> > On Thu, 2006-05-04 at 19:13 +0200, David van der Spoel wrote:
> >> Dongsheng Zhang wrote:
> >>> Marcus,
> >>>
> >>> Thank you for your suggestion. I try it. The computer gives me the same
> >>> error message. The problem is that the program always looks for
> >>> replica.tpr instead of replica0.tpr and replica1.tpr. I don't know why.
> >>>
> >> use mpirun
> >> search mailinglist
> >>> Best wishes!
> >>>
> >>>
> >>> Dongsheng
> >>>
> >>>
> >>> On Thu, 2006-05-04 at 18:38 +0200, Marcus Kubitzki wrote:
> >>>> If you use the -deffnm option, you do not need -s, b/c it is
> >>>> already accounted for with the -deffnm.
> >>>> Marcus
> >>>>
> >>>> Dongsheng Zhang wrote:
> >>>>> David,
> >>>>>
> >>>>> Thank you for your reply. I have provided replica0.tpr and replica1.tpr,
> >>>>> but the program looks for replica.tpr. It surprises me.
> >>>>>
> >>>>> I have also tried to run 
> >>>>>
> >>>>> /home/brasilia/dong/mdrun_mpi -np 2 -replex 500 -reseed -1 -multi -s
> >>>>> replica0  replica1 -deffnm replica -N 2 -v >& zevel 
> >>>>>  It doesn't work either (complains only one replica: Nothing to exchange
> >>>>> with only one replica). it seems the program does not recognize the
> >>>>> -multi option. 
> >>>>>
> >>>>>
> >>>>> Best wishes!
> >>>>>
> >>>>>
> >>>>> Dongsheng
> >>>>>
> >>>>>
> >>>>> On Thu, 2006-05-04 at 18:11 +0200, David van der Spoel wrote:
> >>>>>
> >>>>>> Dongsheng Zhang wrote:
> >>>>>>
> >>>>>>> Dear gmx users,
> >>>>>>>
> >>>>>>> I have trouble to run REMD on one node with two processors. The command
> >>>>>>> I used is
> >>>>>>> /home/brasilia/dong/mdrun_mpi -np 2 -replex 500 -reseed -1 -multi -s
> >>>>>>> replica -deffnm replica -N 2 -v >& zevel
> >>>>>>>
> >>>>>>> the error message is:
> >>>>>>>
> >>>>>>> Can not open file:
> >>>>>>> replica.tpr
> >>>>>> you need replica0 and replica1.tpr
> >>>>>>
> >>>>>>> This error message looks strange to me. Because I have used -multi, the
> >>>>>>> program should look for replica0.tpr and replica1.tpr. Could anyone
> >>>>>>> point out what's wrong in my command?
> >>>>>>>
> >>>>>>>
> >>>>>>> Thank you in advance!
> >>>>>>>
> >>>>>>>
> >>>>>>> Dongsheng
> >>>>>>> _______________________________________________
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