remove snow

master
glmdev 5 years ago
parent 7aafde5fd1
commit 6a2cc5f8ff

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#!/bin/bash
mpiexec --allow-run-as-root -n 1 --hostfile /kube-openmpi/generated/hostfile R --vanilla -f snow-hello.R > mpi.out

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#!/bin/bash
#SBATCH --ntasks=5
cd $SLURM_SUBMIT_DIR
mpiexec -n 1 R --vanilla -f snow-hello.R

@ -1,95 +0,0 @@
### Paul Johnson
### 2017-07-20
### Garrett Mills
### 2019-05-02
### Demonstration of SNOW "Simple Network of Workstations" using MPI
### "Message Passing Interface" (OpenMPI implementation)
library(snow)
p <- rnorm(123, m = 33)
## Sub script asks for 18 cores, here cluster must
## be one smaller
CLUSTERSIZE <- Rmpi::mpi.universe.size()-1
cl <- makeCluster(CLUSTERSIZE, type = "MPI")
## One way to send function to each system.
## Could send identical arguments to nodes
clusterCall(cl, function() {
Sys.info()[c("nodename","machine")]
date()
}
)
timeFn <- function(){
y1 <- Sys.info()[c("nodename","machine")]
y2 <- date()
list(y1, y2)
}
## Send function to each node
clusterExport(cl, c("timeFn"))
## Evaluates a string on a node
x1 <- clusterEvalQ(cl, timeFn())
print(x1)
clusterCall(cl, function() rnorm(1, 33, 1) )
myNorms <- matrix(rnorm(100*CLUSTERSIZE), ncol = CLUSTERSIZE)
## goes column by column
mypapply <- parApply(cl, myNorms, 2, print)
attributes(mypapply)
mypapply <- parApply(cl, myNorms, 2, mean )
mypapply
myNorms <- matrix(rnorm(100*CLUSTERSIZE), ncol = CLUSTERSIZE)
mySum <- function( v ){
s <-Sys.info()[c("nodename")]
s[2] <- date()
ms <- sum(v)
list(s, ms)
}
mypcapply <- parApply(cl, myNorms, 2, mySum)
mypcapply
myNorms <- matrix(rnorm(2500*CLUSTERSIZE), ncol = CLUSTERSIZE)
## Add the system date (includes time) before and after
## calculations to vector s
myMeans <- function(v){
s <- Sys.info()[c("nodename")]
s[2] <- date()
ms <- mean(v)
## want to slow this down so you can study the cluster? uncomment this:
## x <- rnorm(50000000); x <- log(50+x); sum(x); mean(x); quantile(x); gg <- cut(x, quantile(x))
s[3] <- date()
list(s, ms)
}
mypcapply <- parApply(cl, myNorms, 2, myMeans )
mypcapply
library(snow)
stopCluster(cl)
Rmpi::mpi.quit()
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