[R-sig-hpc] Rmpi and OpenMPI

[Martin Morgan]

Hi Arash --

In terms of diagnosis, probably during your installation Rmpi decided to 
not set the -DMPI2 directive.

In terms of solution, it likely involves inspection of Rmpi/configure.ac 
to understand why this is not set, followed either by setting 
appropriate environment variables or editing configure.ac then cd Rmpi/ 
&& autoconf && cd .. and then R CMD INSTALL --clean Rmpi.

Martin

Arash Fard wrote:
> Hi,
> 
> I have recently installed Rmpi using OpenMPI, but I receive some wired
> errors at run time . For example, when I use "orterun R --vanilla
> --interactive" for interactive mode, then call mpi.universe.size() function,
> I receive this error: "This function is not supported under MPI 1.2". While,
> OpenMPI should be based on MPI-2. As another example, after calling
> mpi.spawn.Rslaves(), I recieve : "You cannot use MPI_Comm_spawn API".
> Moreover, when I try make a cluster using snow, I receive:
> Error in mpi.comm.spawn(slave = mpitask, slavearg = args, nslaves = count,
> :
>   MPI_Comm_spawn is not supported.
> Calls: makeCluster -> switch -> makeMPIcluster -> mpi.comm.spawn
> 
> Please be informed that linked libraries to Rmpi.so are as follows:
> [root at furcatus bin]# R CMD ldd /usr/local/lib64/R/library/Rmpi/libs/Rmpi.so
>         libmpi.so.0 => /usr/lib64/OMPI/gnu/libmpi.so.0 (0x0000002a9569b000)
>         libutil.so.1 => /lib64/libutil.so.1 (0x0000002a958e8000)
>         libpthread.so.0 => /lib64/tls/libpthread.so.0 (0x0000002a959eb000)
>         libc.so.6 => /lib64/tls/libc.so.6 (0x0000002a95b01000)
>         libdat.so.1 => /usr/lib64/libdat.so.1 (0x0000002a95d3a000)
>         libibverbs.so.1 => /usr/lib64/libibverbs.so.1 (0x0000002a95e43000)
>         librt.so.1 => /lib64/tls/librt.so.1 (0x0000002a95f50000)
>         libopen-rte.so.0 => /usr/lib64/OMPI/gnu/libopen-rte.so.0
> (0x0000002a9606a000)
>         libtorque.so.2 => /usr/lib64/libtorque.so.2 (0x0000002a96230000)
>         libopen-pal.so.0 => /usr/lib64/OMPI/gnu/libopen-pal.so.0
> (0x0000002a96388000)
>         libnuma.so.1 => /usr/lib64/libnuma.so.1 (0x0000002a964de000)
>         libdl.so.2 => /lib64/libdl.so.2 (0x0000002a965e2000)
>         libnsl.so.1 => /lib64/libnsl.so.1 (0x0000002a966e6000)
>         libm.so.6 => /lib64/tls/libm.so.6 (0x0000002a967fe000)
>         /lib64/ld-linux-x86-64.so.2 (0x000000552aaaa000)
> 
> Please also be informed that MPICH and LAM/MPI are also installed on our
> system. Is it possible that there is a confusion between different MPI
> implementations? In this case, what is the solution.
> 
> I highly appreciate your kind attention.
> Best regards,
> 
> Arash
> Odum School of Ecology
> The University of Georgia
> 
> 	[[alternative HTML version deleted]]
> 
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793