Hi George,
If pmemd.MPI wasn't there, it's surprising you got the output I mentioned
last email instead of "pmemd.MPI: command not found" 4 times. That's what
you would normally get if pmemd.MPI really didn't exist.
To just build pmemd, you can go to $AMBERHOME/src/pmemd and just run "make
parallel". That should do it, but you may run into problems if you've done
a make clean, since that will have gutted netCDF and you'll have trouble
linking to that (I think). After it's built, though, you'll have to move
pmemd.MPI into the $AMBERHOME/bin directory.
Keep an eye out for incompatible MPIs, though, since that will cause the
error you mentioned. Again, if you're using amber11, the only way you would
NOT have pmemd.MPI is if there was an error while it was compiled that you
overlooked or if it was deleted from the bin directory, since it's built by
default.
Hope this helps,
Jason
On Thu, Sep 16, 2010 at 2:27 PM, George Tzotzos <gtzotzos.me.com> wrote:
> Hi Jason,
>
> I retracted the previous message because I realised that pmemd.MPI was not
> found in /bin.
> sander.MPI was installed. The version of amber is 11.
>
> I checked a 2nd machine running OSX in which I've also installed amber11.
> pmemd.MPI is installed in this machine.
>
> Is there a way to install pmemd.MPI without trying to reinstall amber11?
>
> Thanks for the advice
>
> George
>
>
> On Sep 16, 2010, at 7:50 PM, Jason Swails wrote:
>
> > What version of amber are you using? If you're using amber11, pmemd.MPI
> > should be installed automatically alongside sander.MPI. Moreover, if
> > pmemd.MPI was not installed, you'd see something about "command not
> found",
> > not
> >
> > MPI version of PMEMD must be used with 2 or more processors!
> > MPI version of PMEMD must be used with 2 or more processors!
> > MPI version of PMEMD must be used with 2 or more processors!
> > application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
> > application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
> > application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
> > MPI version of PMEMD must be used with 2 or more processors!
> > application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
> >
> > I still think my previous response is the most likely. The above
> messages
> > are basically 4 threads of pmemd.MPI that are unaware of any kind of MPI
> > world. i.e. mpirun from, say, openMPI not playing nice with pmemd.MPI
> > compiled from an mpich2 mpif90. Do you have MPI_HOME set? What is
> > $MPI_HOME/bin/mpirun and `which mpirun` ? Are they different?
> >
> > Good luck!
> > Jason
> >
> > On Thu, Sep 16, 2010 at 1:46 PM, George Tzotzos <gtzotzos.me.com> wrote:
> >
> >> I'd like to retract the previous message.
> >>
> >> It seems that pmemd.MPI was not installed during the installation.
> >> sander.MPI was
> >>
> >> So my question is whether there's a special procedure to install it?
> >>
> >> George
> >>
> >>
> >> On Sep 16, 2010, at 7:35 PM, George Tzotzos wrote:
> >>
> >>> Hi everybody
> >>>
> >>> amber11 parallel has been installed and passed all tests.
> >>>
> >>> I'm running OSX on a 4 Core 2.8 GHz Intel Core i7 machine.
> >>>
> >>> Running: mpirun -np 4 sander.MPI etc. works smoothly
> >>>
> >>> Running: mpirun -np 4 pmemd.MPI produces the following error.
> >>>
> >>> MPI version of PMEMD must be used with 2 or more processors!
> >>> MPI version of PMEMD must be used with 2 or more processors!
> >>> MPI version of PMEMD must be used with 2 or more processors!
> >>> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
> >>> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
> >>> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
> >>> MPI version of PMEMD must be used with 2 or more processors!
> >>> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
> >>>
> >>> Any ideas as to why?
> >>>
> >>> Thanks in advance and regards
> >>>
> >>> George
> >>>
> >>>
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Graduate Student
> > 352-392-4032
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Thu Sep 16 2010 - 12:00:04 PDT
