pbdRPC (version 0.2-1)

rpc_cs_example: Example Functions of RPC Related to pbdCS

Description

Example functions of RPC related to pbdCS

Usage

check_cs(machine, cmd = .pbd_env$RPC.CS$check)
kill_cs(machine, cmd = .pbd_env$RPC.CS$kill)
start_cs(machine, cmd = .pbd_env$RPC.CS$start,
  preload = .pbd_env$RPC.CS$preload)

Arguments

machine

A machine configuration. See ?machine.

cmd

the main command to be executed on the server.

preload

further commands preloaded before the main command is executed.

Value

Mainly the message received at the command line will be printed, but may not be captured by R.

Details

Using either ssh or plink to launch a pbdCS R cluster.

NO further input from stdin is expected. Outputs or errors may not be captured by R.

start_cs() starts a pbdCS R cluster on remote servers. Typical commands to launch a pbdCS R cluster is given in the example. The linux/unix commands are as the following:

• 1)nohup is for the non-stop call after disconnection.

• 2)mpiexec -np 4 is for launching 4 MPI instances.

• 3)Rscript -e 'pbdCS::pbdserver()' is for R to start the pbdCS R cluster within MPI in batch.

• 4)> .rrlog is to direct the stdout to a file .rrlog

• 5)2>&1 is to turn stderr to stdout which is the file .cslog.

• 6)< /dev/null is to get stdin from /dev/null which is nothing happen.

• 7)& is to put the batch command for the pbdCS R cluster in background.

check_cs() checks if there is a pbdCS R cluster on a remote server. Lunix/unix commands ps and grep are used.

kill_cs() kills the pbdCS R cluster if found. Lunix/unix commands ps, grep, awk, and kill are used.

Examples

# NOT RUN {
library(pbdRPC, quietly = TRUE)
# rpcopt_set(user = "snoweye", hostname = "192.168.56.101")
m <- machine(user = "snoweye", hostname = "192.168.56.101")

check_cs(m)    # pid 2857 (may differ)
kill_cs(m)     # all pbdCS pids are killed
check_cs(m)    # make sure no pbdCS R cluster is running

### use "; " to bypass multiple commands
preload <- "source ~/work-my/00_set_devel_R; "

### start a new pbdCS R cluster
start_cs(m, preload = preload)
check_cs(m)
kill_cs(m)

### Example: for module load on supercomputers
preload <- "module load r; "    # e.g. via module load r
start_cs(m, preload = preload)
check_cs(m)
kill_cs(m)
# }
# NOT RUN {

# }