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. - Steve ________________________________________ From: users-boun...@open-mpi.org [users-boun...@open-mpi.org] on behalf of Ralph Castain [r...@open-mpi.org] 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: > Hello, > > 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 > appreciated. > > - 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 > us...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/users _______________________________________________ users mailing list us...@open-mpi.org http://www.open-mpi.org/mailman/listinfo.cgi/users
