Shell Script for Multithreading a Process

Multithreading semaphore for bash script (sub-processes)

Following recommendation by @Mark Setchell, using GNU Parallel to replace the loop (in a simulated cron environment (see https://stackoverflow.com/a/2546509/8236733)) with

bcpexport() {
    filename=$1
    TO_SERVER_ODBCDSN=$2
    DB=$3 
    TABLE=$4 
    USER=$5
    PASSWORD=$6
    RECOMMEDED_IMPORT_MODE=$7
    DELIMITER=$8 # DO NOT use format like "'\t'", nested quotes seem to cause hard-to-catch error
    <same code from original loop>
}
export -f bcpexport
parallel -j 10 bcpexport \
    ::: $DATAFILES/$TARGET_GLOB \
    ::: "$TO_SERVER_ODBCDSN" \
    ::: $DB \
    ::: $TABLE \
    ::: $USER \
    ::: $PASSWORD \
    ::: $RECOMMEDED_IMPORT_MODE \
    ::: $DELIMITER

to run at most 10 threads at a time, where $DATAFILES/$TARGET_GLOB is a glob string to return all of the files in the desired dir. (eg. "$storagedir/tsv/*.tsv") that we want to go through (and adding the remaining fixed args with each of the elements returned by that glob as the remaining parallel inputs shown) (The $TO_SERVER_ODBCDSN variable is actually "-D -S <some ODBC DSN>", so needed to add quotes to pass as single arg). So if the $DATAFILES/$TARGET_GLOB glob returns files A, B, C, ..., we end up running the commands

bcpexport A "$TO_SERVER_ODBCDSN" $DB ...
bcpexport B "$TO_SERVER_ODBCDSN" $DB ...
bcpexport C "$TO_SERVER_ODBCDSN" $DB ...
...

in parallel. An additionally nice thing about using parallel is

GNU parallel makes sure output from the commands is the same output as you would get had you run the commands sequentially.

How to create Multiple Threads in Bash Shell Script

That's not a thread, but a background process. They are similar but:

So, effectively we can say that threads and light weight processes are same.

The main difference between a light weight process (LWP) and a normal process is that LWPs share same address space and other resources like open files etc. As some resources are shared so these processes are considered to be light weight as compared to other normal processes and hence the name light weight processes.

NB: Redordered for clarity

What are Linux Processes, Threads, Light Weight Processes, and Process State

You can see the running background process using the jobs command. E.g.:

nick@nick-lt:~/test/npm-test$ sleep 10000 &
[1] 23648
nick@nick-lt:~/test/npm-test$ jobs
[1]+  Running    

You can bring them to the foreground using fg:

nick@nick-lt:~/test/npm-test$ fg 1
sleep 1000

where the cursor will wait until the sleep time has elapsed. You can pause the job when it's in the foreground (as in the scenario after fg 1) by pressing CTRL-Z (SIGTSTP), which gives something like this:

[1]+  Stopped                 sleep 1000

and resume it by typing:

bg 1    # Resumes in the background
fg 1    # Resumes in the foreground

and you can kill it by pressing CTRL-C (SIGINT) when it's in the foreground, which just ends the process, or through using the kill command with the % affix to the jobs ID:

kill %1 # Or kill <PID>

Onto your implementation:

BROWSERS=

for i in "${@}"; do
    case $i in
        -b) 
           shift
           BROWSERS="$1"
           ;;
         *)
           ;;
    esac
done

IFS=',' read -r -a SPLITBROWSERS <<< "$BROWSERS"

for browser in "${SPLITBROWSERS[@]}"
do
    echo "Running ${browser}..."
    $browser &
done

Can be called as:

./runtests.sh -b firefox,chrome,ie

Tadaaa.

Multithreading in Bash

Sure, just add & after the command:

read_cfg cfgA &
read_cfg cfgB &
read_cfg cfgC &
wait

all those jobs will then run in the background simultaneously. The optional wait command will then wait for all the jobs to finish.

Each command will run in a separate process, so it's technically not "multithreading", but I believe it solves your problem.

How do I use parallel programming/multi threading in my bash script?

The simplest way is to execute the commands in the background, by adding & to the end of the command:

#!/bin/bash
#script to loop through directories to merge fastq files
sourcedir=/path/to/source
destdir=/path/to/dest

for f in $sourcedir/*
do
    fbase=$(basename "$f")
    echo "Inside $fbase"
    zcat $f/*R1*.fastq.gz | gzip > $destdir/"$fbase"_R1.fastq.gz &
    zcat $f/*R2*.fastq.gz | gzip > $destdir/"$fbase"_R2.fastq.gz &
done

From the bash manual:

If a command is terminated by the control operator ‘&’, the shell executes the command asynchronously in a subshell. This is known as executing the command in the background. The shell does not wait for the command to finish, and the return status is 0 (true). When job control is not active (see Job Control), the standard input for asynchronous commands, in the absence of any explicit redirections, is redirected from /dev/null.

bash while loop threading

You can send tasks to the background by &
If you intend to wait for all of them to finish you can use the wait command:

process_to_background &
echo Processing ...
wait
echo Done

You can get the pid of the given task started in the background if you want to wait for one (or few) specific tasks.

important_process_to_background &
important_pid=$!
while i in {1..10}; do
    less_important_process_to_background $i &
done

wait $important_pid
echo Important task finished

wait
echo All tasks finished

On note though: the background processes can mess up the output as they will run asynchronously. You might want to use a named pipe to collect the output from them.

edit

As asked in the comments there might be a need for limiting the background processes forked. In this case you can keep track of how many background processes you've started and communicate with them through a named pipe.

mkfifo tmp # creating named pipe

counter=0
while read ip
do
  if [ $counter -lt 10 ]; then # we are under the limit
    { check $ip; echo 'done' > tmp; } &
    let $[counter++];
  else
    read x < tmp # waiting for a process to finish
    { check $ip; echo 'done' > tmp; } &
  fi
done
cat /tmp > /dev/null # let all the background processes end

rm tmp # remove fifo

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