On Oct 31, 2011, at 10:27 AM, Weston, Stephen wrote: > 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.
It's okay so long as only one process is being run. Directly launching the MPI procs via rsh/ssh won't work, however, if there is more than one proc in the job. > > 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. That was my next question :-) Your colleague is correct. Alternatively, you can tell OMPI to ignore the psm interface to those cards by either configuring it out (--without-psm) or at run time by setting the envar OMPI_MCA_mtl=^psm > > - 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 > > _______________________________________________ > users mailing list > us...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/users
