[R-sig-hpc] fork() warning from mpi
j.maas at uea.ac.uk
Sat May 19 16:11:13 CEST 2012
I get the following message when running a job using R 2.15.0, Rmpi,
doMPI, and a cluster system that uses a LSF operating system and
infiniband connections. I'm just a user and know little about the
workings of such networks but the warning unsettles me a little. I've
asked people who write and maintain open-mpi and they are suggesting
that something has changed in the latest version of R that causes this.
I'm wondering if there has been a change or if we have done something
incorrectly when installing Rmpi on the system, not sure here but this
might have to be built/compiled against open-mpi libraries. The
open-mpi people have suggested that R must be doing some king of fork
after the call MPI-Init.
Could anyone tell me if this is a new problem, or have we done something
incorrectly? I have a toy model file that creates it and am happy to
Thanks a bunch,
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: cn149.private.dns.zone (PID 27492)
MPI_COMM_WORLD rank: 21
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.
University of East Anglia
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