An introduction to use the parallel computing package "snow"

1. Parallel Computing in R
2010/05/09 Tsukuba.R#7
id:mickey24

2. id: mickey24 (@mickey24)

3. Tsukuba.R

4. Tsukuba.R#4
•R Brainf*ck
• Brainf*ck
> hello <- "+++++++++[>++++++++>++++++++++
+>+++++<<<-]>.>++.+++++++..++
+.>-.------------.<++++++++.--------.++
+.------.--------.>+."
> brainfxxk(hello)
[1] "Hello, world!"
http://www.slideshare.net/mickey24/rbrainfck-1085191

5. Tsukuba.R#5
• Animation with R
• library(animation)
http://d.hatena.ne.jp/mickey24/20090614

6. Tsukuba.R#6
• Extend R with C!!!
• C R (C OpenCV )
http://d.hatena.ne.jp/mickey24/20091123/r_de_extension

8. Tsukuba.R#7

9. •
•n snow
•

10. n

11. •
• CPU
!"#! !"#!
!"#!
!!!!
!!!!
!!!!
!"#!

12. 1CPU
sapply(1:8, function(x){ x^2 })
(function(x){x^2})(1)
(function(x){x^2})(2)
(function(x){x^2})(3)
(function(x){x^2})(4)
!"#! (function(x){x^2})(5)
(function(x){x^2})(6)
(function(x){x^2})(7)
(function(x){x^2})(8)
[1] 1 4 9 16 25 36 49 64

13. 4CPU
sapply(1:8, function(x){ x^2 })
(function(x){x^2})(1) (function(x){x^2})(3) (function(x){x^2})(5) (function(x){x^2})(7)
(function(x){x^2})(2) (function(x){x^2})(4) (function(x){x^2})(6) (function(x){x^2})(8)
!"#! !"#! !"#! !"#!
[1] 1 4 9 16 25 36 49 64

14. •
•
•
• 1CPU 1
→ 100CPU
→ 10

15. R
• snow
• R
• http://cran.r-project.org/web/packages/snow/index.html
• R apply
•
• Socket PVM MPI

16. n
snow

17. snow
• 2CPU
•
• CPU

18. • snow
> install.packages("snow")
•
•

19. matprod.R
• 1000
n <- 1000
A <- matrix(rnorm(n^2), n)
B <- matrix(rnorm(n^2), n)
C <- A %*% B
•

20. clmatprod.R
library(snow)
n <- 1000
A <- matrix(rnorm(n^2), n)
B <- matrix(rnorm(n^2), n)
cpu <- 2
hosts <- rep("localhost", cpu)
cl <- makeCluster(hosts, type="SOCK")
C <- parMM(cl, A, B) # C <- A %*% B
stopCluster(cl)

21. •
> source("clmatprod.R")
•
> head(C)

22. •
• parMM(cl, A, B)
• apply
• parApply(cl, X, MARGIN, fun, ...)
• parLapply(cl, X, fun, ...)
• parSapply(cl, X, fun, ..., simplify=TRUE, USE.NAMES=TRUE)
• etc.
•
• clusterMap(cl, fun, ..., MoreArgs = NULL, RECYCLE = TRUE)
• clusterCall(cl, fun, ...)
• etc.
• help (?parApply, ?clusterMap )

23. snow

24. •
• snow
• mCPU n
• O(n^3)
#!
$!
!"#! !"#! !"#! !!!! !"#!
#!
!! "!

25. • 1CPU( )
system.time(A %*% B)
• mCPU ( )
system.time(parMM(cl, A, B))

26. • @DBCLS
•
• Sun Grid Engine OpenMPI
•

27. @DBCLS
1 8
CPU 8CPU 64CPU
16GB 128GB
!"#$! !"#$!
!"#$! !"#$!
!"#$! !"#$!
!"#$! !"#$!

29. 1000
( )
3.00
2.50
2.00
1.50
1.00
Faster!
0.50
0
1 4 8 16 CPU
4CPU 1.14

30. 3000
( )
40.00
30.00
20.00
10.00 Faster!
0
1 4 8 16 CPU
8CPU 2.70

32. • snow
• C
• C R (40 50 )
www
http://d.hatena.ne.jp/
syou6162/20090117/1232120983

33. • snow
• snow Simplified
http://www.sfu.ca/~sblay/R/snow.html
• RjpWiki - R
http://www.okada.jp.org/RWiki/?R%A4%C7%CA%C2%CE%F3%B7%D7%BB%BB
• RjpWiki - L.Tierney snow
http://www.okada.jp.org/RWiki/?L.%20Tierney%BB%E1%A4%CEsnow
%A5%D1%A5%C3%A5%B1%A1%BC%A5%B8%A4%C7%A5%AF
%A5%E9%A5%B9%A5%BF%B7%D7%BB%BB%A4%F2%B9%D4%A4%A6#scce80a1
• Rmpi + snow + Sun Grid Engine
• Scheduled Parallel Computing with R: R + Rmpi + OpenMPI + Sun Grid Engine
(SGE)
http://blog.nguyenvq.com/2010/01/20/scheduled-parallel-computing-with-r-r-rmpi-
openmpi-sun-grid-engine-sge/

36. R+
Sun Grid Engine +
Open MPI +
snow

37. • @DBCLS
• Sun Grid Engine
• OpenMPI
• mpirun R
• Rmpi snow OpenMPI
•
•

38. •
• Rmpi OpenMPI
• snow Rmpi
> install.packages("Rmpi", configure.args=
"/path/to/mpidir")
> install.packages("snow")

39. gmatprod.R
library(Rmpi)
library(snow)
n <- 1000
A <- matrix(rnorm(n^2), n)
B <- matrix(rnorm(n^2), n)
cl <- makeCluster() #
C <- parMM(cl, A, B) # C <- A %*% B
stopCluster(cl)

40. gmatprod.sh
#!/bin/bash
#$ -S /bin/bash # /bin/bash
#$ -j y # stdout stderr -o
#$ -o gmatprod.log # stdout stderr
#$ -pe openmpi 8 #
export PATH=[path to R & snow_install_dir & mpirun]:$PATH
export LD_LIBRARY_PATH=/path/to/mpidir/lib:$LD_LIBRARY_PATH
MPIRUN_PATH=/path/to/mpirun
MPIRUN_OPTS="-np ${NSLOTS} -machinefile ${TMPDIR}/machines"
RSCRIPT=gmatprod.R
RPATH=/path/to/snow_install_dir/RMPISNOW
CMD="${RPATH} CMD BATCH --no-save ${RSCRIPT}"
${MPIRUN_PATH} ${MPIRUN_OPTS} ${CMD}

41. • qsub Grid Engine
$ qsub gmatprod.sh

42. •
• Scheduled Parallel Computing with R: R + Rmpi + OpenMPI +
Sun Grid Engine (SGE)
http://blog.nguyenvq.com/2010/01/20/scheduled-parallel-
computing-with-r-r-rmpi-openmpi-sun-grid-engine-sge/
• Sun Grid Engine MPI R