We've had a few reports of this - it looks like someone made a change to R that can cause problems. Basically, the open fabrics driver for Infiniband doesn't support "fork" operations - it can lead to memory corruption issues if you inadvertently do the "wrong thing" at some point after the fork. Hence, we emit a warning if we see a "fork" operation when Infiniband is being used with the OFED verbs driver.
You can suppress the warning by setting -mca mpi_warn_on_fork 0 on your cmd line. You will probably be okay, but just be aware you could hit issues. On May 16, 2012, at 6:17 AM, Jim Maas wrote: > I'm getting the following error with a new version of R, using Rmpi and a few > other modules. I've already had a couple of good suggestions from this group > about how to diagnose the cause of the fork error using "strace" but we don't > have it on our LSF Linux cluster. This is my first use of R/mpi/parallel etc > so am a bit naive. Also the code I'm running involves random number > generation so will always give slightly different answers. > > My normal routine is to : > a) try the code with a small number of iterations on my own > Linux/R/open-mpi pc using 8 cores, then > b) make the job bigger and run it to the cluster. > > I only get the warning on the cluster which suggests that it caused by > something related to R and/or Rmpi and/or LSF and/or open MPI ??? > > Could someone suggest some rigorous R test-code that I could run on my pc, > ok if it takes some time, and then rerun it on cluster to confirm that I get > the same results, and thus the warning in inconsequential? > > 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 > _______________________________________________ > users mailing list > us...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/users
