PROBLEM DEFINITION --

Master:

- AMD_64
- Ubuntu 9.04 64-bit
- OpenMPI 1.3.2 (to avoid the problem in v1.3 where OpenMPI tries to connect
to the localhost via ssh to run local jobs) - manually downloaded source and
compiled
- Rmpi 0.5-7 - package installed using R install.packages()
- R 2.9.0 - installed using apt-get

Slave:

- Intel Pentium 4 32-bit
- Ubuntu 9.04 32-bit
- OpenMPI 1.3.2 (to avoid the problem in v1.3 where OpenMPI tries to connect
to the localhost via ssh to run local jobs) - manually downloaded source and
compiled
- Rmpi 0.5-7 - package installed using R install.packages()
- R 2.9.0 - installed using apt-get

When executing the following command from the master:

--> mpirun --hostfile <some file> -np 1 R CMD BATCH <some program>.R

the following trace results on the master node (lines 18 and 19 are from my
particular R program):

*** caught segfault ***
address 0x10333e4d8, cause 'memory not mapped'

Traceback:
 1: .Call("mpi_recv", x, as.integer(type), as.integer(source),
as.integer(tag),     as.integer(comm), as.integer(status), PACKAGE = "Rmpi")
 2: mpi.recv(x = raw(charlen), type = 4, srctag[1], srctag[2], comm,
status)
 3: typeof(connection)
 4: unserialize(obj)
 5: .mpi.unserialize(mpi.recv(x = raw(charlen), type = 4, srctag[1],
srctag[2], comm, status))
 6: mpi.recv.Robj(node$rank, node$RECVTAG, node$comm)
 7: recvData.MPInode(con)
 8: recvData(con)
 9: FUN(X[[6L]], ...)
10: lapply(cl[1:jobs], recvResult)
11: staticClusterApply(cl, fun, length(x), argfun)
12: clusterApply(cl, splitList(x, length(cl)), lapply, fun, ...)
13: is.vector(X)
14: lapply(args, enquote)
15: do.call("fun", lapply(args, enquote))
16: docall(c, clusterApply(cl, splitList(x, length(cl)), lapply,     fun,
...))
17: snow::parLapply(snow::getMPIcluster(), object, FUN, ..., DMetaData =
DMetaData(object))
18: tmMap(corpuscleanrand, replacePatterns, ("real estate"), by =
"realestate")
19: tmMap(corpuscleanrand, replacePatterns, ("real estate"), by =
"realestate")
aborting ...
Segmentation fault

CONFIGURATION STEPS TAKEN --

- There is no common/shared file system mounted for the cluster.

- All PATH and LD_LIBRARY_PATH environment variables for OpenMPI are
properly set on each node (including the master).

- OpenMPI was configured and built on each node with the
--enable-heterogeneous configuration flag to account for the AMD-64 and
Intel-32 architectures.

- The R_SNOW_LIB environment variable is set properly and the RunSnowNode
and RunSnowWorker scrips are located in the PATH (and set to executable) on
all nodes (including the master).

- All of the OpenMPI settings as documented in the OpenMPI FAQs to allow for
remote execution (i.e. rsh/ssh, .rhosts) are in place.

Any insight or assistance will be greatly appreciated.

Sincerely,
Mark

	[[alternative HTML version deleted]]

