David, Thank you. My mdrun_mpi has problems with parallel computing. I don't know why. I recompile gromacs, then it works now. I have saved the old Makefile before "make distclean". I find it is the same as the new Makefile, then I don't understand why the old mdrun_mpi didn't work.
Thank you very much for your help! Dongsheng On Thu, 2006-05-04 at 21:52 +0200, David van der Spoel wrote: > Dongsheng Zhang wrote: > > Thank you, David. I try it as: > > > > > > mpirun -np 2 n1 /home/brasilia/dong/mdrun_mpi -replex 500 -reseed > > -1 -s replica -v >& zevel > > > > It gives me the same error message: Can not open file: replica.tpr > > > was mdrun compiled with MPI? are you sure the second copy of mdrun is in > the right directory? try it from your home directory > > > 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 > >>>>>>>>> _______________________________________________ > >>>>>>>>> gmx-users mailing list gmx-users@gromacs.org > >>>>>>>>> http://www.gromacs.org/mailman/listinfo/gmx-users > >>>>>>>>> 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/mailing_lists/users.php > >>>>>>> _______________________________________________ > >>>>>>> gmx-users mailing list gmx-users@gromacs.org > >>>>>>> http://www.gromacs.org/mailman/listinfo/gmx-users > >>>>>>> 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/mailing_lists/users.php > >>>>> _______________________________________________ > >>>>> gmx-users mailing list gmx-users@gromacs.org > >>>>> http://www.gromacs.org/mailman/listinfo/gmx-users > >>>>> 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/mailing_lists/users.php > >>> _______________________________________________ > >>> gmx-users mailing list gmx-users@gromacs.org > >>> http://www.gromacs.org/mailman/listinfo/gmx-users > >>> 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/mailing_lists/users.php > >> > > _______________________________________________ > > gmx-users mailing list gmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > 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/mailing_lists/users.php > > _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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/mailing_lists/users.php
