After some trials, I was able to install Rmpi package on my computer using the following code:
R CMD INSTALL -l /storage/home/***/.R Rmpi_0.6-7.tar.gz --configure-args="--with-Rmpi-type=OPENMPI --disable-dlopen --with-Rmpi-include=/gpfs/group/RISE/sw7/openmpi_4.1.4_gcc-9.3.1/include --with-Rmpi-libpath=/gpfs/group/RISE/sw7/openmpi_4.1.4_gcc-9.3.1/lib"
I tried to run the following test code:
# Load the R MPI package if it is not already loaded.
if (!is.loaded("mpi_initialize")) {
library("Rmpi")
}
ns <- mpi.universe.size() - 1
mpi.spawn.Rslaves(nslaves=ns)
#
# 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.bcast.cmd( id <- mpi.comm.rank() )
mpi.bcast.cmd( ns <- mpi.comm.size() )
mpi.bcast.cmd( host <- mpi.get.processor.name() )
mpi.remote.exec(paste("I am",mpi.comm.rank(),"of",mpi.comm.size()))
# Test computations
x <- 5
x <- mpi.remote.exec(rnorm, x)
length(x)
x
# Tell all slaves to close down, and exit the program
mpi.close.Rslaves(dellog = FALSE)
mpi.quit()
On my HPC I run the following:
qsub -A open -l walltime=6:00:00 -l nodes=4:ppn=4:stmem -I
module use /gpfs/group/RISE/sw7/modules
module load openmpi/4.1.4-gcc.9.3.1 r/4.0.3
mpirun -np 4 Rscript "codes/test/test4.R"
But then I get the following error indicating that I only have 1 number of slaves:
--------------------------------------------------------------------------
By default, for Open MPI 4.0 and later, infiniband ports on a device
are not used by default. The intent is to use UCX for these devices.
You can override this policy by setting the btl_openib_allow_ib MCA parameter
to true.
Local host: comp-sc-0222
Local adapter: mlx4_0
Local port: 1
--------------------------------------------------------------------------
--------------------------------------------------------------------------
By default, for Open MPI 4.0 and later, infiniband ports on a device
are not used by default. The intent is to use UCX for these devices.
You can override this policy by setting the btl_openib_allow_ib MCA parameter
to true.
Local host: comp-sc-0222
Local adapter: mlx4_0
Local port: 1
--------------------------------------------------------------------------
--------------------------------------------------------------------------
By default, for Open MPI 4.0 and later, infiniband ports on a device
are not used by default. The intent is to use UCX for these devices.
You can override this policy by setting the btl_openib_allow_ib MCA parameter
to true.
Local host: comp-sc-0222
Local adapter: mlx4_0
Local port: 1
--------------------------------------------------------------------------
--------------------------------------------------------------------------
By default, for Open MPI 4.0 and later, infiniband ports on a device
are not used by default. The intent is to use UCX for these devices.
You can override this policy by setting the btl_openib_allow_ib MCA parameter
to true.
Local host: comp-sc-0222
Local adapter: mlx4_0
Local port: 1
--------------------------------------------------------------------------
--------------------------------------------------------------------------
WARNING: There was an error initializing an OpenFabrics device.
Local host: comp-sc-0222
Local device: mlx4_0
--------------------------------------------------------------------------
--------------------------------------------------------------------------
WARNING: There was an error initializing an OpenFabrics device.
Local host: comp-sc-0222
Local device: mlx4_0
--------------------------------------------------------------------------
--------------------------------------------------------------------------
WARNING: There was an error initializing an OpenFabrics device.
Local host: comp-sc-0222
Local device: mlx4_0
--------------------------------------------------------------------------
--------------------------------------------------------------------------
WARNING: There was an error initializing an OpenFabrics device.
Local host: comp-sc-0222
Local device: mlx4_0
--------------------------------------------------------------------------
Error in mpi.comm.spawn(slave = system.file("Rslaves.sh", package = "Rmpi"), :
Choose a positive number of slaves.
Calls: mpi.spawn.Rslaves -> mpi.comm.spawn
Execution halted
Error in mpi.comm.spawn(slave = system.file("Rslaves.sh", package = "Rmpi"), :
Choose a positive number of slaves.
Calls: mpi.spawn.Rslaves -> mpi.comm.spawn
Execution halted
Error in mpi.comm.spawn(slave = system.file("Rslaves.sh", package = "Rmpi"), :
Choose a positive number of slaves.
Calls: mpi.spawn.Rslaves -> mpi.comm.spawn
Execution halted
Error in mpi.comm.spawn(slave = system.file("Rslaves.sh", package = "Rmpi"), :
Choose a positive number of slaves.
Calls: mpi.spawn.Rslaves -> mpi.comm.spawn
Execution halted
I have tried specifying different number of np's but still get the same error. What could be the cause here?
============================================================
(EDIT)
It seems that my original command to load the modules also load intel/19.1.2 and mkl/2020.3. If I unload them, I do see that OMPI_UNIVERSE_SIZE=4.
[****@comp-sc-0220 work]$ module purge
[****@comp-sc-0220 work]$ module load openmpi/4.1.4-gcc.9.3.1 r/4.0.3
[****@comp-sc-0220 work]$ module list
Currently Loaded Modules:
1) openmpi/4.1.4-gcc.9.3.1 2) intel/19.1.2 3) mkl/2020.3 4) r/4.0.3
[****@comp-sc-0220 work]$ mpirun -np 4 env | grep OMPI_UNIVERSE_SIZE
[****@comp-sc-0220 work]$ type mpirun; mpirun --version; mpirun -np 1 env | grep OMPI
mpirun is /opt/aci/intel/compilers_and_libraries_2020.2.254/linux/mpi/intel64/bin/mpirun
Intel(R) MPI Library for Linux* OS, Version 2019 Update 8 Build 20200624 (id: 4f16ad915)
Copyright 2003-2020, Intel Corporation.
LMOD_FAMILY_COMPILER_VERSION=19.1.2
LMOD_FAMILY_COMPILER=intel
[****@comp-sc-0220 work]$ module purge
[****@comp-sc-0220 work]$ module load openmpi/4.1.4-gcc.9.3.1 r/4.0.3
[****@comp-sc-0220 work]$ module unload intel mkl
[****@comp-sc-0220 work]$ module list
Currently Loaded Modules:
1) openmpi/4.1.4-gcc.9.3.1 2) r/4.0.3
[****@comp-sc-0220 work]$ mpirun -np 4 env | grep OMPI_UNIVERSE_SIZE
OMPI_UNIVERSE_SIZE=4
OMPI_UNIVERSE_SIZE=4
OMPI_UNIVERSE_SIZE=4
OMPI_UNIVERSE_SIZE=4
[****@comp-sc-0220 work]$ type mpirun; mpirun --version; mpirun -np 1 env | grep OMPI
mpirun is /gpfs/group/RISE/sw7/openmpi_4.1.4_gcc-9.3.1/bin/mpirun
mpirun (Open MPI) 4.1.4
Report bugs to http://www.open-mpi.org/community/help/
OMPI_MCA_pmix=^s1,s2,cray,isolated
OMPI_COMMAND=env
OMPI_MCA_orte_precondition_transports=954e2ae0a9569e46-2223294369d728a3
OMPI_MCA_orte_local_daemon_uri=4134338560.0;tcp://10.102.201.220:58039
OMPI_MCA_orte_hnp_uri=4134338560.0;tcp://10.102.201.220:58039
OMPI_MCA_mpi_oversubscribe=0
OMPI_MCA_orte_app_num=0
OMPI_UNIVERSE_SIZE=4
OMPI_MCA_orte_num_nodes=1
OMPI_MCA_shmem_RUNTIME_QUERY_hint=mmap
OMPI_MCA_orte_bound_at_launch=1
OMPI_MCA_ess=^singleton
OMPI_MCA_orte_ess_num_procs=1
OMPI_COMM_WORLD_SIZE=1
OMPI_COMM_WORLD_LOCAL_SIZE=1
OMPI_MCA_orte_tmpdir_base=/tmp
OMPI_MCA_orte_top_session_dir=/tmp/ompi.comp-sc-0220.26954
OMPI_MCA_orte_jobfam_session_dir=/tmp/ompi.comp-sc-0220.26954/pid.8212
OMPI_NUM_APP_CTX=1
OMPI_FIRST_RANKS=0
OMPI_APP_CTX_NUM_PROCS=1
OMPI_MCA_initial_wdir=/storage/work/k/****
OMPI_MCA_orte_launch=1
OMPI_MCA_ess_base_jobid=4134338561
OMPI_MCA_ess_base_vpid=0
OMPI_COMM_WORLD_RANK=0
OMPI_COMM_WORLD_LOCAL_RANK=0
OMPI_COMM_WORLD_NODE_RANK=0
OMPI_MCA_orte_ess_node_rank=0
OMPI_FILE_LOCATION=/tmp/ompi.comp-sc-0220.26954/pid.8212/0/0
But if I run the same test4.R again, I get the following error:
/gpfs/group/RISE/sw7/R-4.0.3-intel-19.1.2-mkl-2020.3/R-4.0.3/../install/lib64/R/bin/exec/R: error while loading shared libraries: libiomp5.so: cannot open shared object file: No such file or directory
--------------------------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
/gpfs/group/RISE/sw7/R-4.0.3-intel-19.1.2-mkl-2020.3/R-4.0.3/../install/lib64/R/bin/exec/R: error while loading shared libraries: libiomp5.so: cannot open shared object file: No such file or directory
/gpfs/group/RISE/sw7/R-4.0.3-intel-19.1.2-mkl-2020.3/R-4.0.3/../install/lib64/R/bin/exec/R: error while loading shared libraries: libiomp5.so: cannot open shared object file: No such file or directory
/gpfs/group/RISE/sw7/R-4.0.3-intel-19.1.2-mkl-2020.3/R-4.0.3/../install/lib64/R/bin/exec/R: error while loading shared libraries: libiomp5.so: cannot open shared object file: No such file or directory
--------------------------------------------------------------------------
mpirun detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:
Process name: [[63743,1],0]
Exit code: 127
--------------------------------------------------------------------------
============================================================
(EDIT 2)
I changed my module load command again to module load openmpi/4.1.4-gcc.9.3.1 r/4.0.5-gcc-9.3.1. With this newer version of R I ran my test4.R script again with mpirun -np 4 Rscript "codes/test/test4.R". It is now returning a new error message as follows:
[1] "/storage/home/k/kxk5678/.R"
[2] "/gpfs/group/RISE/sw7/R-4.0.5-gcc-9.3.1/install/lib64/R/library"
[1] "/storage/home/k/kxk5678/.R"
[2] "/gpfs/group/RISE/sw7/R-4.0.5-gcc-9.3.1/install/lib64/R/library"
[1] "/storage/home/k/kxk5678/.R"
[2] "/gpfs/group/RISE/sw7/R-4.0.5-gcc-9.3.1/install/lib64/R/library"
[1] "/storage/home/k/kxk5678/.R"
[2] "/gpfs/group/RISE/sw7/R-4.0.5-gcc-9.3.1/install/lib64/R/library"
[1] 4
[1] 4
[1] 4
[1] 4
--------------------------------------------------------------------------
All nodes which are allocated for this job are already filled.
--------------------------------------------------------------------------
Error in mpi.comm.spawn(slave = system.file("Rslaves.sh", package = "Rmpi"), :
MPI_ERR_SPAWN: could not spawn processes
Calls: mpi.spawn.Rslaves -> mpi.comm.spawn
Execution halted
Error in mpi.comm.spawn(slave = system.file("Rslaves.sh", package = "Rmpi"), :
MPI_ERR_SPAWN: could not spawn processes
Calls: mpi.spawn.Rslaves -> mpi.comm.spawn
Execution halted
Error in mpi.comm.spawn(slave = system.file("Rslaves.sh", package = "Rmpi"), :
MPI_ERR_SPAWN: could not spawn processes
Calls: mpi.spawn.Rslaves -> mpi.comm.spawn
Execution halted
Error in mpi.comm.spawn(slave = system.file("Rslaves.sh", package = "Rmpi"), :
MPI_ERR_SPAWN: could not spawn processes
Calls: mpi.spawn.Rslaves -> mpi.comm.spawn
Execution halted
--------------------------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpirun detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:
Process name: [[62996,1],1]
Exit code: 1
--------------------------------------------------------------------------
Install the package pbdMPI in an R session on the login node and run the following translation of the Rmpi test code into the use of pbdMPI:
library(pbdMPI)
ns <- comm.size()
# Tell all R sessions to return a message identifying themselves
id <- comm.rank()
ns <- comm.size()
host <- system("hostname", intern = TRUE)
comm.cat("I am", id, "on", host, "of", ns, "\n", all.rank = TRUE)
# Test computations
x <- 5
x <- rnorm(x)
comm.print(length(x))
comm.print(x, all.rank = TRUE)
finalize()
You run it the same way you used for the Rmpi version: mpirun -np 4 Rscript your_new_script_file.
Spawning MPI (as in the Rmpi example) was appropriate when running on clusters of workstations but on an HPC cluster the prevalent way to program with MPI is SPMD - single program multiple data. SPMD means that your code is a generalization of a serial code that is able to have several copies of itself cooperate with each other.
In the above example, cooperation happens only with printing (the comm... functions). There is no manager/master, just several R sessions running the same code (usually computing something different based on comm.rank()) and cooperating/communicating via MPI. This is the prevalent way of large scale parallel computing on HPC clusters.