Hi R HPC people:
 
This is probably really easy but here it is. 
 
I'm trying to use Rmpi on a cluster at last.  So I'm using the simple example file:
 
[hodgess@grid bin]$ cat Rtest1.R
# Load the R MPI package if it is not already loaded.
if (!is.loaded("mpi_initialize")) {
    library("Rmpi")
    }
# Spawn as many slaves as possible
mpi.spawn.Rslaves()
# In case R exits unexpectedly, have it automatically clean up
# resources taken up by Rmpi (slaves, memory, etc...)
.Last <- function(){
    if (is.loaded("mpi_initialize")){
        if (mpi.comm.size(1) > 0){
            print("Please use mpi.close.Rslaves() to close slaves.")
            mpi.close.Rslaves()
        }
        print("Please use mpi.quit() to quit R")
        .Call("mpi_finalize")
    }
}
# Tell all slaves to return a message identifying themselves
mpi.remote.exec(paste("I am",mpi.comm.rank(),"of",mpi.comm.size()))
# Tell all slaves to close down, and exit the program
mpi.close.Rslaves()
mpi.quit()
[hodgess@grid bin]$ mpirun -machinefile Machinefile ./R CMD BATCH Rtest1.R      ssh_exchange_identification: Connection closed by remote host
ssh_exchange_identification: Connection closed by remote host
ssh_exchange_identification: Connection closed by remote host
ssh_exchange_identification: Connection closed by remote host
ssh_exchange_identification: Connection closed by remote host
ssh_exchange_identification: Connection closed by remote host
ssh_exchange_identification: Connection closed by remote host
ssh_exchange_identification: Connection closed by remote host
ssh_exchange_identification: Connection closed by remote host
ssh_exchange_identification: Connection closed by remote host
ssh_exchange_identification: Connection closed by remote host
ssh_exchange_identification: Connection closed by remote host
ssh_exchange_identification: Connection closed by remote host
ssh_exchange_identification: Connection closed by remote host
ssh_exchange_identification: Connection closed by remote host
ssh_exchange_identification: Connection closed by remote host
ssh_exchange_identification: Connection closed by remote host
ssh_exchange_identification: Connection closed by remote host
ssh_exchange_identification: Connection closed by remote host
ssh_exchange_identification: Connection closed by remote host
ssh_exchange_identification: Connection closed by remote host
ssh_exchange_identification: Connection closed by remote host
ssh_exchange_identification: Connection closed by remote host
ssh_exchange_identification: Connection closed by remote host
[grid.uhd.edu:26277] ERROR: A daemon on node compute-3-0 failed to start as expected.
[grid.uhd.edu:26277] ERROR: There may be more information available from
[grid.uhd.edu:26277] ERROR: the remote shell (see above).
[grid.uhd.edu:26277] ERROR: The daemon exited unexpectedly with status 255.
[grid.uhd.edu:26277] ERROR: A daemon on node compute-3-0 failed to start as expected.
[grid.uhd.edu:26277] ERROR: There may be more information available from
[grid.uhd.edu:26277] ERROR: the remote shell (see above).
[grid.uhd.edu:26277] ERROR: The daemon exited unexpectedly with status 255.
[grid:26277] *** Process received signal ***
[grid:26277] Signal: Segmentation fault (11)
[grid:26277] Signal code: Address not mapped (1)
[grid:26277] Failing at address: 0x100000000
[grid:26277] [ 0] /lib64/libpthread.so.0 [0x39be20e4c0]
[grid:26277] [ 1] /lib64/libc.so.6(strlen+0x30) [0x39bd678d70]
[grid:26277] [ 2] /lib64/libc.so.6(__strdup+0x16) [0x39bd678aa6]
[grid:26277] [ 3] /opt/openmpi/lib/libopen-rte.so.0(orte_schema_base_get_node_tokens+0xdf) [0x2ae9315f7c7f]
[grid:26277] [ 4] /opt/openmpi/lib/libopen-rte.so.0(orte_pls_base_store_active_daemons+0xad) [0x2ae9315d2e3d]
[grid:26277] [ 5] /opt/openmpi/lib/libopen-rte.so.0(orte_pls_rsh_launch+0xd7e) [0x2ae9315d81de]
[grid:26277] [ 6] /opt/openmpi/lib/libopen-rte.so.0(orte_pls_base_recv+0x47e) [0x2ae9315d254e]
[grid:26277] [ 7] /opt/openmpi/lib/libopen-rte.so.0 [0x2ae9315c777e]
[grid:26277] [ 8] /opt/openmpi/lib/libopen-rte.so.0(mca_oob_tcp_msg_recv_complete+0x205) [0x2ae9315cd675]
[grid:26277] [ 9] /opt/openmpi/lib/libopen-rte.so.0 [0x2ae9315cedda]
[grid:26277] [10] /opt/openmpi/lib/libopen-pal.so.0(opal_event_base_loop+0x4b7) [0x2ae931835fa7]
[grid:26277] [11] /opt/openmpi/lib/libopen-pal.so.0(opal_progress+0x8b) [0x2ae931830e0b]
[grid:26277] [12] /opt/openmpi/lib/libopen-rte.so.0(orte_pls_rsh_launch+0xdaa) [0x2ae9315d820a]
[grid:26277] [13] /opt/openmpi/lib/libopen-rte.so.0(orte_pls_base_recv+0x47e) [0x2ae9315d254e]
[grid:26277] [14] /opt/openmpi/lib/libopen-rte.so.0 [0x2ae9315c777e]
[grid:26277] [15] /opt/openmpi/lib/libopen-rte.so.0(mca_oob_tcp_msg_recv_complete+0x205) [0x2ae9315cd675]
[grid:26277] [16] /opt/openmpi/lib/libopen-rte.so.0 [0x2ae9315cedda]
[grid:26277] [17] /opt/openmpi/lib/libopen-pal.so.0(opal_event_base_loop+0x4b7) [0x2ae931835fa7]
[grid:26277] [18] /opt/openmpi/lib/libopen-pal.so.0(opal_progress+0x8b) [0x2ae931830e0b]
[grid:26277] [19] /opt/openmpi/lib/libopen-rte.so.0(orte_pls_rsh_launch+0xdaa) [0x2ae9315d820a]
[grid:26277] [20] /opt/openmpi/lib/libopen-rte.so.0(orte_pls_base_recv+0x47e) [0x2ae9315d254e]
[grid:26277] [21] /opt/openmpi/lib/libopen-rte.so.0 [0x2ae9315c777e]
[grid:26277] [22] /opt/openmpi/lib/libopen-rte.so.0(mca_oob_tcp_msg_recv_complete+0x205) [0x2ae9315cd675]
[grid:26277] [23] /opt/openmpi/lib/libopen-rte.so.0 [0x2ae9315cedda]
[grid:26277] [24] /opt/openmpi/lib/libopen-pal.so.0(opal_event_base_loop+0x4b7) [0x2ae931835fa7]
[grid:26277] [25] /opt/openmpi/lib/libopen-pal.so.0(opal_progress+0x8b) [0x2ae931830e0b]
[grid:26277] [26] /opt/openmpi/lib/libopen-rte.so.0(orte_pls_rsh_launch+0xdaa) [0x2ae9315d820a]
[grid:26277] [27] /opt/openmpi/lib/libopen-rte.so.0(orte_pls_base_recv+0x47e) [0x2ae9315d254e]
[grid:26277] [28] /opt/openmpi/lib/libopen-rte.so.0 [0x2ae9315c777e]
[grid:26277] [29] /opt/openmpi/lib/libopen-rte.so.0(mca_oob_tcp_msg_recv_complete+0x205) [0x2ae9315cd675]
[grid:26277] *** End of error message ***
Segmentation fault
[hodgess@grid bin]$

Does this make any sense, please?
 
Thanks,
Erin
 
 
 
Erin M. Hodgess, PhD
Associate Professor
Department of Computer and Mathematical Sciences
University of Houston - Downtown
mailto: hodgesse@uhd.edu
 

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