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Subject: Re: [OMPI users] call to fork() error
From: Jeff Squyres (jsquyres_at_[hidden])
Date: 2012-05-10 08:00:47


I'm afraid I don't know the inner workings of R at all. They must have changed something between 2.13 and 2.15 such that they're now calling fork() after MPI_Init()...

The problem is that OpenFabrics-based networks do things that make fork()... unstable (for lack of a longer description). That's why you're getting this warning message.

Note, too, that this is only a warning message. It's possible that everything will be fine. If so, you can set the MCA param to disable this warning message. We just erred on the side of caution (after too many users complained that they called fork() after MPI_Init() when they were using OpenFabrics-based networks, and then Bad Things Happened).

On May 10, 2012, at 4:10 AM, Jim Maas wrote:

> I'm getting the following error when running an open-mpi job on a LSF cluster using a new version of R 2.15. I didn't get the error message when running previously using R 2.13. Could anyone point me to the possible cause, or how to find the offending code? I'm not a sysop, just a user.
>
> Thanks
>
> Jim
> --------------------------------------------------------------------------
> An MPI process has executed an operation involving a call to the
> "fork()" system call to create a child process. Open MPI is currently
> operating in a condition that could result in memory corruption or
> other system errors; your MPI job may hang, crash, or produce silent
> data corruption. The use of fork() (or system() or other calls that
> create child processes) is strongly discouraged.
>
> The process that invoked fork was:
>
> Local host: cn159.private.dns.zone (PID 12792)
> MPI_COMM_WORLD rank: 7
>
> If you are *absolutely sure* that your application will successfully
> and correctly survive a call to fork(), you may disable this warning
> by setting the mpi_warn_on_fork MCA parameter to 0.
>
> --
> Dr. Jim Maas
> University of East Anglia
>
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-- 
Jeff Squyres
jsquyres_at_[hidden]
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