Parallelize Bash script with maximum number of processes

Question

Lets say I have a loop in Bash:

for foo in `some-command`
do
   do-something $foo
done

do-something is cpu bound and I have a nice shiny 4 core processor. I'd like to be able to run up to 4 do-something's at once.

The naive approach seems to be:

for foo in `some-command`
do
   do-something $foo &
done

This will run all do-somethings at once, but there are a couple downsides, mainly that do-something may also have some significant I/O which performing all at once might slow down a bit. The other problem is that this code block returns immediately, so no way to do other work when all the do-somethings are finished.

How would you write this loop so there are always X do-somethings running at once?

Answer 1

Depending on what you want to do xargs also can help (here: converting documents with pdf2ps):

cpus=$( ls -d /sys/devices/system/cpu/cpu[[:digit:]]* | wc -w )

find . -name \*.pdf | xargs --max-args=1 --max-procs=$cpus  pdf2ps

From the docs:

--max-procs=max-procs
-P max-procs
       Run up to max-procs processes at a time; the default is 1.
       If max-procs is 0, xargs will run as many processes as  possible  at  a
       time.  Use the -n option with -P; otherwise chances are that only one
       exec will be done.

Answer 2

With GNU Parallel http://www.gnu.org/software/parallel/ you can write:

some-command | parallel do-something

GNU Parallel also supports running jobs on remote computers. This will run one per CPU core on the remote computers - even if they have different number of cores:

some-command | parallel -S server1,server2 do-something

A more advanced example: Here we list of files that we want my_script to run on. Files have extension (maybe .jpeg). We want the output of my_script to be put next to the files in basename.out (e.g. foo.jpeg -> foo.out). We want to run my_script once for each core the computer has and we want to run it on the local computer, too. For the remote computers we want the file to be processed transferred to the given computer. When my_script finishes, we want foo.out transferred back and we then want foo.jpeg and foo.out removed from the remote computer:

cat list_of_files | \
parallel --trc {.}.out -S server1,server2,: \
"my_script {} > {.}.out"

GNU Parallel makes sure the output from each job does not mix, so you can use the output as input for another program:

some-command | parallel do-something | postprocess

See the videos for more examples: https://www.youtube.com/playlist?list=PL284C9FF2488BC6D1

Answer 3

maxjobs=4
parallelize () {
        while [ $# -gt 0 ] ; do
                jobcnt=(`jobs -p`)
                if [ ${#jobcnt[@]} -lt $maxjobs ] ; then
                        do-something $1 &
                        shift  
                else
                        sleep 1
                fi
        done
        wait
}

parallelize arg1 arg2 "5 args to third job" arg4 ...

Answer 4

Instead of a plain bash, use a Makefile, then specify number of simultaneous jobs with make -jX where X is the number of jobs to run at once.

Or you can use wait ("man wait"): launch several child processes, call wait - it will exit when the child processes finish.

maxjobs = 10

foreach line in `cat file.txt` {
 jobsrunning = 0
 while jobsrunning < maxjobs {
  do job &
  jobsrunning += 1
 }
wait
}

job ( ){
...
}

If you need to store the job's result, then assign their result to a variable. After wait you just check what the variable contains.

Answer 5

Here an alternative solution that can be inserted into .bashrc and used for everyday one liner:

function pwait() {
    while [ $(jobs -p | wc -l) -ge $1 ]; do
        sleep 1
    done
}

To use it, all one has to do is put & after the jobs and a pwait call, the parameter gives the number of parallel processes:

for i in *; do
    do_something $i &
    pwait 10
done

It would be nicer to use wait instead of busy waiting on the output of jobs -p, but there doesn't seem to be an obvious solution to wait till any of the given jobs is finished instead of a all of them.

Answer 6

Maybe try a parallelizing utility instead rewriting the loop? I'm a big fan of xjobs. I use xjobs all the time to mass copy files across our network, usually when setting up a new database server. http://www.maier-komor.de/xjobs.html

Answer 7

While doing this right in bash is probably impossible, you can do a semi-right fairly easily. bstark gave a fair approximation of right but his has the following flaws:

• Word splitting: You can't pass any jobs to it that use any of the following characters in their arguments: spaces, tabs, newlines, stars, question marks. If you do, things will break, possibly unexpectedly.
• It relies on the rest of your script to not background anything. If you do, or later you add something to the script that gets sent in the background because you forgot you weren't allowed to use backgrounded jobs because of his snippet, things will break.

Another approximation which doesn't have these flaws is the following:

scheduleAll() {
    local job i=0 max=4 pids=()

    for job; do
        (( ++i % max == 0 )) && {
            wait "${pids[@]}"
            pids=()
        }

        bash -c "$job" & pids+=("$!")
    done

    wait "${pids[@]}"
}

Note that this one is easily adaptable to also check the exit code of each job as it ends so you can warn the user if a job fails or set an exit code for scheduleAll according to the amount of jobs that failed, or something.

The problem with this code is just that:

• It schedules four (in this case) jobs at a time and then waits for all four to end. Some might be done sooner than others which will cause the next batch of four jobs to wait until the longest of the previous batch is done.

A solution that takes care of this last issue would have to use kill -0 to poll whether any of the processes have disappeared instead of the wait and schedule the next job. However, that introduces a small new problem: you have a race condition between a job ending, and the kill -0 checking whether it's ended. If the job ended and another process on your system starts up at the same time, taking a random PID which happens to be that of the job that just finished, the kill -0 won't notice your job having finished and things will break again.

A perfect solution isn't possible in bash.

Answer 8

If you're familiar with the make command, most of the time you can express the list of commands you want to run as a a makefile. For example, if you need to run $SOME_COMMAND on files *.input each of which produces *.output, you can use the makefile

INPUT  = a.input b.input
OUTPUT = $(INPUT:.input=.output)

%.output : %.input
    $(SOME_COMMAND) $< $@

all: $(OUTPUT)

and then just run

make -j<NUMBER>

to run at most NUMBER commands in parallel.

Answer 9

function for bash:

parallel ()
{
    awk "BEGIN{print \"all: ALL_TARGETS\\n\"}{print \"TARGET_\"NR\":\\n\\t@-\"\$0\"\\n\"}END{printf \"ALL_TARGETS:\";for(i=1;i<=NR;i++){printf \" TARGET_%d\",i};print\"\\n\"}" | make $@ -f - all
}

using:

cat my_commands | parallel -j 4

Answer 10

The project I work on uses the wait command to control parallel shell (ksh actually) processes. To address your concerns about IO, on a modern OS, it's possible parallel execution will actually increase efficiency. If all processes are reading the same blocks on disk, only the first process will have to hit the physical hardware. The other processes will often be able to retrieve the block from OS's disk cache in memory. Obviously, reading from memory is several orders of magnitude quicker than reading from disk. Also, the benefit requires no coding changes.

Answer 11

This might be good enough for most purposes, but is not optimal.

#!/bin/bash

n=0
maxjobs=10

for i in *.m4a ; do
    # ( DO SOMETHING ) &

    # limit jobs
    if (( $(($((++n)) % $maxjobs)) == 0 )) ; then
        wait # wait until all have finished (not optimal, but most times good enough)
        echo $n wait
    fi
done

Answer 12

Really late to the party here, but here's another solution.

A lot of solutions don't handle spaces/special characters in the commands, don't keep N jobs running at all times, eat cpu in busy loops, or rely on external dependencies (e.g. GNU parallel).

With inspiration for dead/zombie process handling, here's a pure bash solution:

function run_parallel_jobs {
    local concurrent_max=$1
    local callback=$2
    local cmds=("${@:3}")
    local jobs=( )

    while [[ "${#cmds[@]}" -gt 0 ]] || [[ "${#jobs[@]}" -gt 0 ]]; do
        while [[ "${#jobs[@]}" -lt $concurrent_max ]] && [[ "${#cmds[@]}" -gt 0 ]]; do
            local cmd="${cmds[0]}"
            cmds=("${cmds[@]:1}")

            bash -c "$cmd" &
            jobs+=($!)
        done

        local job="${jobs[0]}"
        jobs=("${jobs[@]:1}")

        local state="$(ps -p $job -o state= 2>/dev/null)"

        if [[ "$state" == "D" ]] || [[ "$state" == "Z" ]]; then
            $callback $job
        else
            wait $job
            $callback $job $?
        fi
    done
}

And sample usage:

function job_done {
    if [[ $# -lt 2 ]]; then
        echo "PID $1 died unexpectedly"
    else
        echo "PID $1 exited $2"
    fi
}

cmds=( \
    "echo 1; sleep 1; exit 1" \
    "echo 2; sleep 2; exit 2" \
    "echo 3; sleep 3; exit 3" \
    "echo 4; sleep 4; exit 4" \
    "echo 5; sleep 5; exit 5" \
)

# cpus="$(getconf _NPROCESSORS_ONLN)"
cpus=3
run_parallel_jobs $cpus "job_done" "${cmds[@]}"

The output:

1
2
3
PID 56712 exited 1
4
PID 56713 exited 2
5
PID 56714 exited 3
PID 56720 exited 4
PID 56724 exited 5

For per-process output handling $$ could be used to log to a file, for example:

function job_done {
    cat "$1.log"
}

cmds=( \
    "echo 1 \$\$ >\$\$.log" \
    "echo 2 \$\$ >\$\$.log" \
)

run_parallel_jobs 2 "job_done" "${cmds[@]}"

Output:

1 56871
2 56872

Answer 13

You can use a simple nested for loop (substitute appropriate integers for N and M below):

for i in {1..N}; do
  (for j in {1..M}; do do_something; done & );
done

This will execute do_something N*M times in M rounds, each round executing N jobs in parallel. You can make N equal the number of CPUs you have.

Answer 14

Here is how I managed to solve this issue in a bash script:

 #! /bin/bash

 MAX_JOBS=32

 FILE_LIST=($(cat ${1}))

 echo Length ${#FILE_LIST[@]}

 for ((INDEX=0; INDEX < ${#FILE_LIST[@]}; INDEX=$((${INDEX}+${MAX_JOBS})) ));
 do
     JOBS_RUNNING=0
     while ((JOBS_RUNNING < MAX_JOBS))
     do
         I=$((${INDEX}+${JOBS_RUNNING}))
         FILE=${FILE_LIST[${I}]}
         if [ "$FILE" != "" ];then
             echo $JOBS_RUNNING $FILE
             ./M22Checker ${FILE} &
         else
             echo $JOBS_RUNNING NULL &
         fi
         JOBS_RUNNING=$((JOBS_RUNNING+1))
     done
     wait
 done

Answer 15

My solution to always keep a given number of processes running, keep tracking of errors and handle ubnterruptible / zombie processes:

function log {
    echo "$1"
}

# Take a list of commands to run, runs them sequentially with numberOfProcesses commands simultaneously runs
# Returns the number of non zero exit codes from commands
function ParallelExec {
    local numberOfProcesses="${1}" # Number of simultaneous commands to run
    local commandsArg="${2}" # Semi-colon separated list of commands

    local pid
    local runningPids=0
    local counter=0
    local commandsArray
    local pidsArray
    local newPidsArray
    local retval
    local retvalAll=0
    local pidState
    local commandsArrayPid

    IFS=';' read -r -a commandsArray <<< "$commandsArg"

    log "Runnning ${#commandsArray[@]} commands in $numberOfProcesses simultaneous processes."

    while [ $counter -lt "${#commandsArray[@]}" ] || [ ${#pidsArray[@]} -gt 0 ]; do

        while [ $counter -lt "${#commandsArray[@]}" ] && [ ${#pidsArray[@]} -lt $numberOfProcesses ]; do
            log "Running command [${commandsArray[$counter]}]."
            eval "${commandsArray[$counter]}" &
            pid=$!
            pidsArray+=($pid)
            commandsArrayPid[$pid]="${commandsArray[$counter]}"
            counter=$((counter+1))
        done


        newPidsArray=()
        for pid in "${pidsArray[@]}"; do
            # Handle uninterruptible sleep state or zombies by ommiting them from running process array (How to kill that is already dead ? :)
            if kill -0 $pid > /dev/null 2>&1; then
                pidState=$(ps -p$pid -o state= 2 > /dev/null)
                if [ "$pidState" != "D" ] && [ "$pidState" != "Z" ]; then
                    newPidsArray+=($pid)
                fi
            else
                # pid is dead, get it's exit code from wait command
                wait $pid
                retval=$?
                if [ $retval -ne 0 ]; then
                    log "Command [${commandsArrayPid[$pid]}] failed with exit code [$retval]."
                    retvalAll=$((retvalAll+1))
                fi
            fi
        done
        pidsArray=("${newPidsArray[@]}")

        # Add a trivial sleep time so bash won't eat all CPU
        sleep .05
    done

    return $retvalAll
}

Usage:

cmds="du -csh /var;du -csh /tmp;sleep 3;du -csh /root;sleep 10; du -csh /home"

# Execute 2 processes at a time
ParallelExec 2 "$cmds"

# Execute 4 processes at a time
ParallelExec 4 "$cmds"

Answer 16

$DOMAINS = "list of some domain in commands" for foo in some-command do

eval `some-command for $DOMAINS` &

    job[$i]=$!

    i=$(( i + 1))

done

Ndomains=echo $DOMAINS |wc -w

for i in $(seq 1 1 $Ndomains) do echo "wait for ${job[$i]}" wait "${job[$i]}" done

in this concept will work for the parallelize. important thing is last line of eval is '&' which will put the commands to backgrounds.