So I have a situation where I'm running numerous commands with parallel and piping the output to another script that consumes the output. The problem I'm having is that my script that does the processing of output needs to know when a particular command has finished executing.
I'm using the --tag option so that I know what command has generated output but currently I have to wait until parallel is done running all commands before I can know that I'm not going to get anymore output from a particular command. From my understanding of parallel I see the following possible solutions but none really suit me.
I could group the output lines with the --line-buffer option so it
looks like that were ran sequentially. Then whenever I see output
from the next command I know the previous has finished, however
doing it that way slows me up as one command may take 30 seconds to
complete while after it there may 20 other commands that only took
one second and I wish to process them in as close to real-time as
possible.
I could wrap my command in a tiny bash script that outputs 'Process
with some ID DONE' to get the notification the command completed. I
don't really like this because I'm running several hundred commands
at a time and don't really want to add all those extra bash
processes.
I am really hoping that I'm just missing something in the docs and there is a flag in there to do what I'm looking for.
My understanding is that parallel is implemented in perl, which I'm comfortable with, but would rather not have to add the functionality myself unless its completely necessary.
Any help or suggestions are greatly appreciated.
The default behaviour with --tag should work perfectly. It will not output anything until the job is done. And then your postprocessor can simply grab the argument from the start of the line.
Example:
parallel -j3 --tag 'echo Job {} start; sleep {}; echo Job {} ended' ::: 7 1 3 5 2 4 6
If you want to keep the order:
parallel -j3 --keep-order --tag 'echo Job {} start; sleep {}; echo Job {} ended' ::: 7 1 3 5 2 4 6
Notice how the jobs would mix if the output was done immediately. Compare with --ungroup (which you do not want):
parallel -j3 --ungroup 'echo Job {} start; sleep {}; echo Job {} ended' ::: 7 1 3 5 2 4 6
Related
I have a script say parallelise.sh, whose contents are 10 different python calls shown below:
python3.8 script1.py
python3.8 script2.py
.
.
.
python3.8 script10.py
Now, I use GNU parallel
nohup parallel -j 5 < parallellise.sh &
It starts as expected; 5 different processors are being used and the first 5 scripts, script_1.py ... script_5.py are running. Now I notice that some of them (say two of them script_1.py and script_2.py) complete very fast, whereas the others need more time to complete.
Now, there are unused resources (2 processors) while waiting for the remaining 3 scripts (script_3.py, script_4.py, and script_5.py) to complete so that the next 5 can be loaded. Is there a way to use these resources by loading new ones as existing commands get completed?
For information: My OS is CentOS
As #RenaudPacalet says there is nothing else to do.
So there is something in your scripts which causes this not to happen.
To help debug you can use:
parallel --lb --tag < parallellise.sh
and maybe add a "Starting X" line at the beginning of scriptX.py and a "Finishing X" line at the end of scriptX.py so you can see that the scripts are indeed finishing.
Without knowing anything about scriptX.py it is impossible to say what is causing this.
(Instead of nohup consider using tmux or screen so you can have the jobs run in the background but always check in on them and see their output. nohup is not ideal for debugging).
I have a requirement where I need to trigger 10 shell scripts at a time. I may have 200+ shell scripts to be executed.
e.g. if I trigger 10 jobs and two jobs completed, I need to trigger another 2 jobs which will make number of jobs currently executing to 10.
I need your help and suggestion to cater this requirement.
Yes with GNU Parallel like this:
parallel -j 10 < ListOfJobs.txt
Or, if your jobs are called job_1.sh to job_200.sh:
parallel -j 10 job_{}.sh ::: {1..200}
Or. if your jobs are named with discontiguous, random names but are all shell scripts named with .sh suffix in one directory:
parallel -j 10 ::: *.sh
There is a very good overview here. There are lots of questions and answers on Stack Overflow here.
Simply run them as background jobs:
for i in {1..10}; { ./script.sh & }
Adding more jobs if less than 10 are running:
while true; do
pids=($(jobs -pr))
((${#pids[#]}<10)) && ./script.sh &
done &> /dev/null
There are different ways to handle this:
Launch them together as background tasks (1)
Launch them in parallel (1)
Use the crontab (2)
Use at (3)
Explanations:
(1) You can launch the processes exactly when you like (by launching a command, click a button or whatever event you choose)
(2) The processes will be launched at the same time, every (working) day, periodically.
(3) You choose a time when the processes will be launched together once.
I have used below to trigger 10 jobs a time.
max_jobs_trigger=10
while mapfile -t -n ${max_jobs_trigger} ary && ((${#ary[#]})); do
jobs_to_trigger=`printf '%s\n' "${ary[#]}"`
#Trigger script in background
done
I would like to run commands in parallel. So that if one fails, the whole job exists as failure. How can I do that? More specifically, I would like to run aws sync commands in parallel. I have 5 aws sync commands that run sequentially. I would like them to run in parallel so that if one fails, the whole job fails. How can I do that?
GNU Parallel is a really handy and powerful tool that works with anything bash
http://www.gnu.org/software/parallel/
https://www.youtube.com/watch?v=OpaiGYxkSuQ
# run lines from a file, 8 at a time
cat commands.txt | parallel --eta -j 8 "{}"
I need to run many (hundreds) commands in shell, but I only want to have a maximum of 4 processes running (from the queue) at once. Each process will last several hours.
When a process finishes I want the next command to be "popped" from the queue and executed.
I also want to be able to add more process after the beginning, and it will be great if I could remove some jobs from the queue, or at least empty the queue.
I have seen solutions using makefile, but this only work if I have all my list of commands before the beginning. Also tried using mkfifo sjobq, and others, but I never could reach my needs...
Does anyone have code to solve this problem?
Edit: In response to Mark Setchell
The solution with tail -f and parallel is almost perfect, but when I do it, it always keep not launching the last 4 commands until I add more, and so on, I don't know why, and it is quite troublesome...
As for Redis, good solution also, but it takes more time to master all of it.
Thanks !
Use GNU Parallel to make a job queue like this:
# Clear out file containing job queue
> jobqueue
# Start GNU Parallel processing jobs from queue
# -k means "keep" output in order
# -j 4 means run 4 jobs at a time
tail -f jobqueue | parallel -k -j 4
# From another terminal, submit 40 jobs to the queue
for i in {1..40}; do echo "sleep 5;date +'%H:%M:%S Job $i'"; done >> jobqueue
Another option is to use REDIS - see my answer here Run several jobs parallelly and Efficiently
I have a build script, which works very slowly, especially on Solaris. I want to improve its performance by running it in multiple jobs. How can I do that?
Try GNU Parallel, it is quite easy to use:
GNU parallel is a shell tool for executing jobs in parallel using one or more computers. A job can be a single command or a small script that has to be run for each of the lines in the input. The typical input is a list of files, a list of hosts, a list of users, a list of URLs, or a list of tables. A job can also be a command that reads from a pipe. GNU parallel can then split the input and pipe it into commands in parallel.
If you use xargs and tee today you will find GNU parallel very easy to use as GNU parallel is written to have the same options as xargs. If you write loops in shell, you will find GNU parallel may be able to replace most of the loops and make them run faster by running several jobs in parallel.
GNU parallel makes sure output from the commands is the same output as you would get had you run the commands sequentially. This makes it possible to use output from GNU parallel as input for other programs.
For each line of input GNU parallel will execute command with the line as arguments. If no command is given, the line of input is executed. Several lines will be run in parallel. GNU parallel can often be used as a substitute for xargs or cat | bash.
You mentioned that it is a build script. If you are using command line utility make you can parallelize builds using make's -j<N> option:
GNU make knows how to execute several recipes at once. Normally, make will execute only one recipe at a time, waiting for it to finish before executing the next. However, the ‘-j’ or ‘--jobs’ option tells make to execute many recipes simultaneously.
Also, there is distcc which can be used with make to distribute compiling to multiple hosts:
export DISTCC_POTENTIAL_HOSTS='localhost red green blue'
cd ~/work/myproject;
make -j8 CC=distcc
GNU parallel is quite good. #Maxim - good suggestion +1.
For a one off, if you cannot install new software, try this for a slow command that has to run multiple times, run slowcommand 17 times. Change things to fit your needs:
#!/bin/bash
cnt=0
while [ $cnt -le 17 ] # loop 17 times
do
slow_command &
cnt=$(( $cnt + 1 ))
[ $(( $cnt % 5 )) -eq 0 ] && wait # 5 jobs at a time in parallel
done
wait # you will have 2 jobs you di not wait for in the loop 17 % 5 == 2