linux-helper

#!/bin/bash

## linux-helper: Helper for the multicore and SSH cluster functions of the BatchJobs R
##   package.
##
## Requires the following Unix command line utilities:
##
##  * grep, wc, ps, kill, uptime, echo, cat, possibly setsid
##
## The following commands are implemented. First argument is always the command name.
## For other arguments see below. Each command returns a character vector.
## 
## number-of-cpus
##  Return the number of PEs on worker.
##
## start-job RHOME NICE ROPTIONS RFILE OUTFILE
##   Start an R CMD BATCH process running $RFILE and log
##   the output in $OUTFILE. 
##   RHOME is the path to the R installation.
##   Returns: PID of sh process which spawned R. We use that as batch.job.id. 
##
## kill-job PID
##   Kill the R job with PPID $PID. The PPID is the PID of 
##   the sh process returned by start-job.
##   First a TERM is sent, then 1 sec delay, then KILL. 
## 
##  status FILEDIR
##   Return 4 numbers:
##    - load average of last 1 min, as given by e.g. uptime
##    - number of R processes by _all_ users
##    - number of R processes by _all_ users which have a load of >= 50%
##    - number of R processes by current user 
##      which match $FILEDIR/jobs in the cmd call of R
##
##  list-jobs FILEDIR
##   Return the PPIDs of running R jobs operating on $FILEDIR/jobs.

### efficient [ -n `which [prog]` ]
command_exists () {
    hash "$1" 2> /dev/null;
}

CMD="$1"; shift
export LC_ALL=C ### Avoid any localization issues.
shopt -s nocasematch ### Case insensitive regular expressions

case $CMD in
    number-of-cpus)
        if [[ `uname` =~ "Linux" ]]; then
          cat /proc/cpuinfo | grep '^processor' | wc -l
        else  
          sysctl -n hw.ncpu ## darwin
        fi  
        ;;
    start-job)
        RCMD="R"
        if [ -n "$1" ]; then
            RCMD="${1}/bin/R"
        fi
        # only use setsid on linux, not on darwin (not available there)
 		if [[ `uname` =~ "Linux" ]] && command_exists setsid; then
            RCMD="setsid $RCMD"
        fi          
        if [ -n "$2" ] && command_exists nice; then
            RCMD="nice -n ${2} $RCMD"
        fi
        shift 2
        # nothing should be on all 3 streams except maybe a segfault. throw away. 
        # see comment also in cfLocal
        # we use setsid to start the process in a different session. other ctrl+C in the master
        # session leads to killing of child processes in multicore mode as the SIGINT is passed down
        # $@ 
        ${RCMD} CMD BATCH $@ \
            > /dev/null 2> /dev/null < /dev/null &
        echo $!
        ;;
    kill-job)
        RPPID=$1 
        # find R process whose ppid is the batch.job.id, i.e. the one of the sh process
        # we must list all processes (without terminal) for SSH
        RPID=$(ps -e -o pid= -o ppid= | awk -v j=$RPPID '$2 == j {print $1}')
        kill -TERM $RPID > /dev/null 2> /dev/null
        sleep 1
        kill -KILL $RPID > /dev/null 2> /dev/null
        exit 0
        ;;
    status)
        # remove everyting till load average(s):
        # then delete commas
        LOAD=$(uptime | awk '{gsub(/.*:/,""); {gsub(/,/,"")}; print $1}')
        JOBDIR="$1/jobs"
        # print 3 columns for all processes       
        # use ww for unlimited width in ps for command output
        # we count all R procs, all R50, and all where JOBDIR was in the call args
        ps -e -ww -o pcpu= -o ucomm= -o command= | \
        awk -v j=$JOBDIR -v sysload=$LOAD '
          BEGIN {rprocs=0;rprocs_50=0;njobs=0} 
          $2 != "R" {next} 
          {rprocs++} 
          $1 > 50.0 {rprocs_50++} 
          $0 ~ j {njobs++} 
          END {print sysload " " rprocs " " rprocs_50 " " njobs}'
        ;;
    list-jobs)
        JOBDIR="$1/jobs"
        ps -e -ww -o ppid= -o ucomm= -o command= | \
        awk -v j=$JOBDIR '$2 == "R" && $0 ~ j { print $1 }'
        ;;
    *)
esac