I'm just running it directly from a shell. That may sound crazy,
but my original problem was trying to install the Rmpi package,
which is the R interface to MPI. The Rmpi package calls
MPI_Init when it is loaded, and the package is loaded when it
is installed, so the installation failed until I installed the package
using the mpirun command.
But even after installing Rmpi, it is common for R users to run
Rmpi programs from an interactive R session using spawned
workers. And in that case, they aren't using mpirun.
A colleague who reads this list pointed out to me that the
problem is probably because the cluster that I'm using has
QLogic infiniband cards that apparently require
OMPI_MCA_orte_precondition_transports to be set. That
may be the answer to my question.
From: users-bounces_at_[hidden] [users-bounces_at_[hidden]] on behalf of Ralph Castain [rhc_at_[hidden]]
Sent: Monday, October 31, 2011 12:02 PM
To: Open MPI Users
Subject: Re: [OMPI users] Error when calling MPI_Init
How are you running the job without mpirun? Is this under slurm or some other RM?
On Oct 31, 2011, at 9:46 AM, Weston, Stephen wrote:
> I'm seeing an error on one of our clusters when executing the
> MPI_Init function in a program that is _not_ invoked using the
> mpirun command. The error is:
> Error obtaining unique transport key from ORTE
> (orte_precondition_transports not present in the environment).
> followed by "It looks like MPI_INIT failed for some reason; your
> parallel process is likely to abort.", etc. Since mpirun sets
> this environment variable, it's not surprising that it isn't
> set, but in our other Open MPI installations it doesn't seem
> necessary for this environment variable to be set.
> I can work around the problem by setting the
> "OMPI_MCA_orte_precondition_transports" environment variable
> before running the program using the command:
> % eval "export `mpirun env | grep OMPI_MCA_orte_precondition_transports`"
> But I'm very curious what is causing this error, since it only
> happens on one of our clusters. Could this indicate a problem
> with the way we configured Open MPI when we installed it?
> Any pointers on how to further investigate this issue would be
> - Steve Weston
> P.S. I'm using Open MPI 1.4.3 on a Linux cluster using CentOS
> release 5.5. It happens in any MPI program that I execute
> without mpirun.
> users mailing list
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