On Mar 5, 2010, at 8:52 AM, abc def wrote:
> Hello,
> From within the MPI fortran program I run the following command:
>
> CALL SYSTEM("cd " // TRIM(dir) // " ; mpirun -machinefile ./machinefile -np 1
> /home01/group/Execute/DLPOLY.X > job.out 2> job.err ; cd - > /dev/null")
That is guaranteed not to work. The problem is that mpirun sets environmental
variables for the original launch. Your system call carries over those envars,
causing mpirun to become confused.
>
> where "dir" is a process-number-dependent directory, to ensure the processes
> don't over-write each other, and machinefile is written earlier by using
> hostname to obtain the node of the current process, so this new program
> launches using the same node as the one that launches it.
>
> In fortran, the program automatically waits until the system call is complete.
>
> Since you mentioned MPI_COMM_SPAWN, I looked into this. I read that it's
> non-blocking, so somehow I'd have to prevent the program from moving forwards
> until it was complete, and secondly, I need to "cd" into the directory I
> mentioned above, before running the external command, and I don't know how
> one would achieve this with this command.
>
> Do you think MPI_COMM_SPAWN can help?
It's the only method supported by the MPI standard. If you need it to block
until this new executable completes, you could use a barrier or other MPI
method to determine it.
> I appreciate your time.
>
> From: r...@open-mpi.org
> Date: Fri, 5 Mar 2010 07:55:59 -0700
> To: us...@open-mpi.org
> Subject: Re: [OMPI users] running external program on same
> processor (Fortran)
>
> How are you trying to start this external program? With an MPI_Comm_spawn? Or
> are you just fork/exec'ing it?
>
> How are you waiting for this external program to finish?
>
> On Mar 5, 2010, at 7:52 AM, abc def wrote:
>
> Hello,
>
> Thanks for the comments. Indeed, until yesterday, I didn't realise the
> difference between MVAPICH, MVAPICH2 and Open-MPI.
>
> This problem has moved from mvapich2 to open-mpi now however, because I now
> realise that the production environment uses Open-MPI, which means my
> solution for mvapich2 doesn't work now. So if I may ask your kind assistance:
>
> Just to re-cap, I have an MPI fortran program, which runs on N nodes, and
> each node needs to run an external program. This is external program was
> written for MPI, although I want to run it in serial as part of the process
> on each node.
>
> Is there any way at all to launch this external MPI program so it's treated
> simply as a (serial) extension of the current node's processes? As I say, the
> MPI originating program simply waits for the external program to finish
> before continuing, so it it's essentially a bit like a "subroutine", in that
> sense.
>
> I'm having problems launching this external program from within my MPI
> program, under the open-mpi system, even without worrying about node
> assignment, and I think this might be because the system detects that I'm
> trying to launch another process from one of the nodes, and stops it. I'm
> guessing here, but it simply stops with an error saying the MPI process was
> stopped.
>
> Any help is very much appreciated; I have been going at this for more than a
> day now and don't seem to be getting anywhere.
>
> Thank you!
>
> From: r...@open-mpi.org
> Date: Wed, 3 Mar 2010 07:24:32 -0700
> To: us...@open-mpi.org
> Subject: Re: [OMPI users] running external program on same processor
> (Fortran)
>
> It also would have been really helpful to know that you were using MVAPICH
> and -not- Open MPI as this mailing list is for the latter. We could have
> directed you to the appropriate place if we had known.
>
>
> On Mar 3, 2010, at 5:17 AM, abc def wrote:
>
> I don't know (I'm a little new to this area), but I figured out how to get
> around the problem:
>
> Using SGE and MVAPICH2, the "-env MV2_CPU_MAPPING 0:1....." option in mpiexec
> seems to do the trick.
>
> So when calling the external program with mpiexec, I map the called process
> to the current core rank, and it seems to stay distributed and separated as I
> want.
>
> Hope someone else finds this useful in the future.
>
> > Date: Wed, 3 Mar 2010 13:13:01 +1100
> > Subject: Re: [OMPI users] running external program on same processor
> > (Fortran)
> >
> > Surely this is the problem of the scheduler that your system uses,
> > rather than MPI?
> >
> >
> > On Wed, 2010-03-03 at 00:48 +0000, abc def wrote:
> > > Hello,
> > >
> > > I wonder if someone can help.
> > >
> > > The situation is that I have an MPI-parallel fortran program. I run it
> > > and it's distributed on N cores, and each of these processes must call
> > > an external program.
> > >
> > > This external program is also an MPI program, however I want to run it
> > > in serial, on the core that is calling it, as if it were part of the
> > > fortran program. The fortran program waits until the external program
> > > has completed, and then continues.
> > >
> > > The problem is that this external program seems to run on any core,
> > > and not necessarily the (now idle) core that called it. This slows
> > > things down a lot as you get one core doing multiple tasks.
> > >
> > > Can anyone tell me how I can call the program and ensure it runs only
> > > on the core that's calling it? Note that there are several cores per
> > > node. I can ID the node by running the hostname command (I don't know
> > > a way to do this for individual cores).
> > >
> > > Thanks!
> > >
> > > ====
> > >
> > > Extra information that might be helpful:
> > >
> > > If I simply run the external program from the command line (ie, type
> > > "/path/myprogram.ex <enter>"), it runs fine. If I run it within the
> > > fortran program by calling it via
> > >
> > > CALL SYSTEM("/path/myprogram.ex")
> > >
> > > it doesn't run at all (doesn't even start) and everything crashes. I
> > > don't know why this is.
> > >
> > > If I call it using mpiexec:
> > >
> > > CALL SYSTEM("mpiexec -n 1 /path/myprogram.ex")
> > >
> > > then it does work, but I get the problem that it can go on any core.
> > >
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> >
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