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Rmpi and OpenMPI
3 messages · Arash Fard, Hao Yu, Martin Morgan
Rmpi may not be installed properly. During installation, check if you get the flags -DMPI2 and -DOPENMPI. The first flag indicates MPI 2 is supported. The second flag indicates that Rmpi finds OPENMPI mpi. In your case, probably -DMPI2 is missed and MPICH is chosen. Try install Rmpi with --configure-args=--with-mpi=/mpipath. Make sure to modify R to include a line at beginning like LD_LIBRARY_PATH=/usr/lib64/OMPI/gnu/ Hao
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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Department of Statistics & Actuarial Sciences Fax Phone#:(519)-661-3813 The University of Western Ontario Office Phone#:(519)-661-3622 London, Ontario N6A 5B7 http://www.stats.uwo.ca/faculty/yu
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