Rhpc

Install.

Installation example using mpicc

R -q -e 'dir.create(Sys.getenv("R_LIBS_USER"),rec=T)'
R CMD INSTALL Rhpc_0.yy-yday.tar.gz
  

Special installation example

Maybe need to edit Rhpc/src/worker/Rhpc.in by the different implementation of MPI.

R -q -e 'dir.create(Sys.getenv("R_LIBS_USER"),rec=T)'
mpiexec -n 1 /usr/local1/R-3.0.1.gcc.gotoblas/bin/R CMD INSTALL Rhpc_0.yy-yday.tar.gz \
 --configure-args='--with-mpicc=gcc43
                   --with-mpi-cflags=-I/opt/FJSVplang/include64/mpi/fujitsu
                   --with-mpi-ldflags="-lmpi_f -lfjgmp64 -L/opt/FJSVpnple/lib -ljrm -L/opt/FJSVpnidt/lib -lfjidt -L/opt/FJSVplang/lib64 -lfj90i -lfj90f -lelf -lm -lpthread -lrt -ldl"'
  

Windows installation example

please install MSMpiSetup.exe from https://msdn.microsoft.com/en-us/library/bb524831%28v=vs.85%29.aspx .

> library(Rhpc)
> Rhpc_initialize()
> cl<-Rhpc_getHandle(2)
> Rhpc_worker_call(cl,Sys.getpid)
[[1]]
[1] 10571

[[2]]
[1] 10572

  

Execute.

generate worker by MPI_Comm_Spawn

$ R -q
> library(Rhpc)
> Rhpc_initialize()
> cl<-Rhpc_getHandle(4)
> Rhpc_worker_call(cl,Sys.getpid)
[[1]]
[1] 10571

[[2]]
[1] 10572

[[3]]
[1] 10573

[[4]]
[1] 10574

> Rhpc_finalize()
> q("no")

  

execute by mpirun or mpiexec

# this file name is test.R
library(Rhpc)
Rhpc_initialize()
cl<-Rhpc_getHandle()
Rhpc_lapply(cl, 1:10000, sqrt)
Rhpc_finalize()
  

command Line:

mpiexec -n PROCNUM ~/R/x86_64-unknown-linux-gnu-library/3.0/Rhpc/Rhpc CMD BATCH -q --no-save test.R

Download

	Name	Last modified	Size	Description
	Parent Directory		-
	Documents/	2015-06-26 15:26	-
	RhpcBLASctl_0.20-137.tar.gz	2020-05-16 23:33	39K	- Control the number of threads on BLAS for R
	Rhpc_0.19-276.tar.gz	2019-10-03 12:27	66K	- permits *apply() style dispatch for HPC(source)
	examples/	2016-01-13 20:27	-
	old/	2020-05-16 23:55	-

Benchmark

Export performance

Rhpc_Export

library(Rhpc)
Rhpc_initialize()
cl<-Rhpc_getHandle()
set.seed(123)
N<-4e3
Rhpc_numberOfWorker(cl)
M<-matrix(runif(N^2),N,N)
system.time(Rhpc_Export(cl,"M"))
f<-function()sum(M)
all.equal(rep(sum(M),Rhpc_numberOfWorker(cl)),unlist(Rhpc_worker_call(cl,f)))
Rhpc_finalize()

parallel(Rmpi)::clusterExport

library(parallel)
library(Rmpi)
cl<-makeMPIcluster()
set.seed(123)
N<-4e3
length(cl)
M<-matrix(runif(N^2),N,N)
system.time(clusterExport(cl,"M"))
f<-function()sum(M)
all.equal(rep(sum(M),length(cl)),unlist(clusterCall(cl,f)))
stopCluster(cl)

lapply performance

Rhpc_lapply

library(Rhpc)
Rhpc_initialize()
cl<-Rhpc_getHandle()
system.time(ans<-Rhpc_lapply(cl, 1:10000, sqrt))
all.equal(sqrt(1:10000),unlist(ans))
Rhpc_finalize()

Rhpc_lapplyLB

library(Rhpc)
Rhpc_initialize()
cl<-Rhpc_getHandle()
system.time(ans<-Rhpc_lapplyLB(cl, 1:10000, sqrt))
all.equal(sqrt(1:10000),unlist(ans))
Rhpc_finalize()

parallel(Rmpi)::clusterApply

library(parallel)
library(Rmpi)
cl<-makeMPIcluster()
system.time(ans<-clusterApply(cl,1:10000,sqrt))
all.equal(sqrt(1:10000),unlist(ans))
stopCluster(cl)

parallel(Rmpi)::clusterApplyLB

library(parallel)
library(Rmpi)
cl<-makeMPIcluster()
system.time(ans<-clusterApplyLB(cl,1:10000,sqrt))
all.equal(sqrt(1:10000),unlist(ans))
stopCluster(cl)