I have a series of 250 bash scripts which need to be executed in parallel. Each script utilizes approximately 1 core so I do not want to execute them all at the same time. I would like to run 10 scripts at the same time and whenever one finishes execute another script.
I recommend parallel, but I'm going to post this monstrosity for the benefit of having people pick it apart and tune it. :)
#! /bin/env bash
## TODO: this documentation block needs to be expanded.
use="
$0 <#procs> <cmdfile>
Pass the number of desired processes to prespawn as the 1st argument.
Pass the command file with the list of tasks you need done.
Command file format:
KEYSTRING:cmdlist
where KEYSTRING will be used as a unique logfile name
and cmdlist is the base command string to be run
KEYSTRING may not contain whitespace of any sort.
Other lines are not allowed, including blanks or comments.
"
die() { echo "$# $use" >&2; exit 1; }
case $# in
2) case "$1" in
*[^0-9]*) die "INVALID #procs '$1'" ;;
esac
declare -i primer="$1" # a countdown of how many processes to pre-spawn
cmdfile="$2"
[[ -r "$cmdfile" ]] || { die "$cmdfile not readable"; }
grep -v : "$cmdfile" || { die "$cmdfile has invalid lines"; }
declare -i lines=$( grep -c : $cmdfile)
if (( lines < primer ))
then die "Note - command lines in $cmdfile ($lines) fewer than requested process chains ($primer)"
fi ;;
*) die ;;
esac >&2
trap 'echo abort $0#$LINENO; use; exit 1' ERR # make sure any error is fatal
trap ': no-op to ignore' HUP # ignore hangups (built-in nohup without explicit i/o redirection)
spawn() {
IFS="$IFS:" read key cmd && [[ "${cmd:-}" ]] || return
echo "$(date) executing '$cmd'; c.f. $key.log" | tee "$key.log"
echo "# autogenerated by $0 $(date)
{ $cmd
spawn
} >> $key.log 2>&1 &
" >| $key.sh
. $key.sh
rm -f $key.sh
return 0
}
# create a command list based on those designators
declare chains=0
while (( primer-- )) # until we've filled the requested quota
do spawn # create a child process
done < $cmdfile
I've implemented a way to have concurrent jobs in bash, as seen here.
I'm looping through a file with around 13000 lines. I'm just testing and printing each line, as such:
#!/bin/bash
max_bg_procs(){
if [[ $# -eq 0 ]] ; then
echo "Usage: max_bg_procs NUM_PROCS. Will wait until the number of background (&)"
echo " bash processes (as determined by 'jobs -pr') falls below NUM_PROCS"
return
fi
local max_number=$((0 + ${1:-0}))
while true; do
local current_number=$(jobs -pr | wc -l)
if [[ $current_number -lt $max_number ]]; then
echo "success in if"
break
fi
echo "has to wait"
sleep 4
done
}
download_data(){
echo "link #" $2 "["$1"]"
}
mapfile -t myArray < $1
i=1
for url in "${myArray[#]}"
do
max_bg_procs 6
download_data $url $i &
((i++))
done
echo "finito!"
I've also tried other solutions such as this and this, but my issue is persistent:
At a "random" given step, usually between the 2000th and the 5000th iteration, it simply gets stuck. I've put those various echo in the middle of the code to see where it would get stuck but it the last thing it prints is the $url $i.
I've done the simple test to remove any parallelism and just loop the file contents: all went fine and it looped till the end.
So it makes me think I'm missing some limitation on the parallelism, and I wonder if anyone could help me out figuring it out.
Many thanks!
Here, we have up to 6 parallel bash processes calling download_data, each of which is passed up to 16 URLs per invocation. Adjust per your own tuning.
Note that this expects both bash (for exported function support) and GNU xargs.
#!/usr/bin/env bash
# ^^^^- not /bin/sh
download_data() {
echo "link #$2 [$1]" # TODO: replace this with a job that actually takes some time
}
export -f download_data
<input.txt xargs -d $'\n' -P 6 -n 16 -- bash -c 'for arg; do download_data "$arg"; done' _
Using GNU Parallel it looks like this
cat input.txt | parallel echo link '\#{#} [{}]'
{#} = the job number
{} = the argument
It will spawn one process per CPU. If you instead want 6 in parallel use -j:
cat input.txt | parallel -j6 echo link '\#{#} [{}]'
If you prefer running a function:
download_data(){
echo "link #" $2 "["$1"]"
}
export -f download_data
cat input.txt | parallel -j6 download_data {} {#}
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 $foo &
done
This will run all do-somethings at once, but there are a couple downsides, mainly that do-something may also have some significant I/O which performing all at once might slow down a bit. The other problem is that this code block returns immediately, so no way to do other work when all the do-somethings are finished.
How would you write this loop so there are always X do-somethings running at once?
Depending on what you want to do xargs also can help (here: converting documents with pdf2ps):
cpus=$( 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.
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
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 ...
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.
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.
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: $(OUTPUT)
and then just run
make -j<NUMBER>
to run at most NUMBER commands in parallel.
While doing this right in bash is probably impossible, you can do a semi-right fairly easily. bstark gave a fair approximation of right but his has the following flaws:
Word splitting: You can't pass any jobs to it that use any of the following characters in their arguments: spaces, tabs, newlines, stars, question marks. If you do, things will break, possibly unexpectedly.
It relies on the rest of your script to not background anything. If you do, or later you add something to the script that gets sent in the background because you forgot you weren't allowed to use backgrounded jobs because of his snippet, things will break.
Another approximation which doesn't have these flaws is the following:
scheduleAll() {
local job i=0 max=4 pids=()
for job; do
(( ++i % max == 0 )) && {
wait "${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.
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
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
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
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.
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
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
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.
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"
$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.
I'm running a shell script in Linux Mint that calls some processes taking few minutes.
For each process I want to echo a message like this:
echo "Cleaning temporary files... X seconds."
myprocess
where X is the current elapsed time and I would like it to change every second, but not printing a new line.
Is there a good way to do that? I only found ways to print the total time in the end, but not the elapsed time while running the process.
Use this at the beginning of your script, this creates a subprocess which runs in background and keeps on updating the status.
file=$(mktemp)
progress() {
pc=0;
while [ -e $file ]
do
echo -ne "$pc sec\033[0K\r"
sleep 1
((pc++))
done
}
progress &
#Do all the necessary staff
#now when everything is done
rm -f $file
You'll have to run the process in the background with &, otherwise the rest of the script will wait until it finishes. Use backspaces to overwrite your current line, so make sure you don't use newlines.
So, to do what you want:
myproc &
myPid=$! # save process id
tmp=""
while true; do
if kill -0 "$myPid"; then # if the process accepts a signal, keep waiting
for i in {0..${#tmp}..1}; do
printf "%b" "\b" # print backspaces until we have cleared the previous line
done
tmp=$( printf "Cleaning temp files... %t seconds." )
printf "%s" "$tmp"
else
break # drop out of the while loop
fi
sleep 1
done
You can run each command with time:
time <command>
and then use sed/awk to exctract the elapsed time.
Here is a way to have awk print on STDERR every seconds.
You should just add:
when myprocess is over, create a file /tmp/SOMETHING
have awk include a test : it exits when /tmp/SOMETHING appears
The loop part (without the termination test... so "infinite loop" until CTRL-C) is:
ping 127.0.0.1 | awk '
BEGIN{cmd="date +%s"; cmd|getline startup ; close (cmd) }
/bytes from/ { cmd | getline D ; close (cmd) ;
print D-startup | "cat >&2" }'
now you just need to use "printf" and ansi escape sequence to print without a newline, have the ansi-escape go back until the beginning of the number, and flush the output (all descriptors) by invoking system:
ping 127.0.0.1 | awk -v getback4char="$(printf '\033[4D')" '
BEGIN{cmd="date +%s"; cmd|getline startup ; close (cmd) ; printf "Elapsed time: ";}
/bytes from/ { cmd | getline D ; close (cmd) ;
printf "%4d%s" ,(D-startup) , getback4char | "cat >&2"
system("") }'
note: this is compatible with all version of awk I know of, even ANCIENT ones (ie, not gawk/nawk only, but also the venerable awk.)
I need to the following things to make sure my application server is
Tail a log file for a specific string
Remain blocked until that string is printed
However if the string is not printed for about 20 mins quit and throw and exception message like "Server took more that 20 mins to be up"
If string is printed in the log file quit the loop and proceed.
Is there a way to include time outs in a while loop ?
#!/bin/bash
tail -f logfile | grep 'certain_word' | read -t 1200 dummy_var
[ $? -eq 0 ] && echo 'ok' || echo 'server not up'
This reads anything written to logfile, searches for certain_word, echos ok if all is good, otherwise after waiting 1200 seconds (20 minutes) it complains.
You can do it like this:
start_time=$(date +"%s")
while true
do
elapsed_time=$(($(date +"%s") - $start_time))
if [[ "$elapsed_time" -gt 1200 ]]; then
break
fi
sleep 1
if [[ $(grep -c "specific string" /path/to/log/file.log) -ge 1 ]]; then
break
fi
done
You can use signal handlers from shell scripts (see http://www.ibm.com/developerworks/aix/library/au-usingtraps/index.html).
Basically, you'd define a function to be called on, say, signal 17, then put a sub-script in the background that will send that signal at some later time:
timeout(pid) {
sleep 1200
kill -SIGUSR1 $pid
}
watch_for_input() {
tail -f file | grep item
}
trap 'echo "Not found"; exit' SIGUSR1
timeout($$) &
watch_for_input
Then if you reach 1200 seconds, your function is called and you can choose what to do (like signal your tail/grep combo that is watching for your pattern in order to kill it)
time=0
found=0
while [ $time -lt 1200 ]; do
out=$(tail logfile)
if [[ $out =~ specificString ]]; then
found=1
break;
fi
let time++
sleep 1
done
echo $found
The accepted answer doesn't work and will never exit (because althouth read -t exits, the prior pipe commands (tail -f | grep) will only be notified of read -t exit when they try to write to output, which never happens until the string matches).
A one-liner is probably feasible, but here are scripted (working) approaches.
Logic is the same for each one, they use kill to terminate the current script after the timeout.
Perl is probably more widely available than gawk/read -t
#!/bin/bash
FILE="$1"
MATCH="$2"
# Uses read -t, kill after timeout
#tail -f "$FILE" | grep "$MATCH" | (read -t 1 a ; kill $$)
# Uses gawk read timeout ability (not available in awk)
#tail -f "$FILE" | grep "$MATCH" | gawk "BEGIN {PROCINFO[\"/dev/stdin\", \"READ_TIMEOUT\"] = 1000;getline < \"/dev/stdin\"; system(\"kill $$\")}"
# Uses perl & alarm signal
#tail -f "$FILE" | grep "$MATCH" | perl -e "\$SIG{ALRM} = sub { `kill $$`;exit; };alarm(1);<>;"