Trivially Parallel + BASH

Sometimes we have to run an analysis tool on a large number of files, but each analysis is completely independent of the others. This is a trivially parallel application.

We can manage the analysis via a Bash script that looks for available CPUs and starts up jobs as resources become free.

The basic flow is:

• Loop over files

  • Run jobs until all the processors are full

  • Use lockfiles to indicate when a job is running

  • When resources become free, start up the next job

Here’s an implementation:

Listing 97 parallel.sh

#!/bin/bash

# run a bunch of single-processor analysis jobs in parallel.  Lock
# files are used to keep track of how many processors are in use at
# any given time -- this allows for jobs of varying length to be run
# together.

#----------------------------------------------------------------------------
# user modifiable variables:

# number of parallel tasks to run
NCPUS=4

# set the prefix of the datafile to process
data_prefix=plt

# set the full name of the analysis routines (must be in the path)
analysis=echo

# Number of seconds to sleep before checking again.
N=60


#----------------------------------------------------------------------------
# the processing functions
function process_files
{

    # the argument $1 is the name of the datafile

    echo "working on " $1
    root=$(basename $1)
    echo $1 > _process.$root

    if [ -f $1 ]; then

        # do processing
        ${analysis} $1   #>> /dev/null

        # this sleep line is not necessary if the analysis takes any
	    # measurable amount of time
	    sleep 30

    fi   # end test of whether datafile is a file (as it should be)

    rm -f _process.$root
}



#----------------------------------------------------------------------------
# The function freecpus looks counts the _process.XX files to determine how many
# files we are currently processing.  If we are processing < NCPUS, return 1 to
# indicate that there are free CPUs available to do more processing.
function freecpus
{
    num=$(ls -l _process.* 2> /dev/null | wc -l)

    if [ $num -lt $NCPUS ]; then
        return 1
    else
        return 0
    fi
}


#----------------------------------------------------------------------------
# the main loop

# We process NCPUS files at a time.  We loop over files, waiting for free CPUs.
# When a CPU becomes available, we launch the processing job in the background,
# and move to the next file, again waiting for an available CPU.

filelist=$(find . -maxdepth 1 -type f -name "${data_prefix}*" -print | sort)

for file in ${filelist}
do

    # wait for available CPUS
    freecpus
    while [ $? -eq 0 ]
    do
        sleep 1
        freecpus
    done

    process_files ${file} &

    sleep 1
done

This looks for files with the name plt* and then runs an analysis tool on them (for this simple example, it is just echo). You can control the number of processors that are used at the top of the script.

Alternatives

GNU parallel is a similar tool that can be used for trivially parallel jobs.