I have a script - a linear list of commands - that takes a long time to run sequentially. I would like to create a utility script (Perl, Bash or other available on Cygwin) that can read commands from any linear script and farm them out to a configurable number of parallel workers.
So if myscript is
command1
command2
command3
I can run:
threadpool -n 2 myscript
Two threads would be created, one commencing with command1 and the other command2. Whichever thread finishes its first job first would then run command3.
Before diving into Perl (it's been a long time) I thought I should ask the experts if something like this already exists. I'm sure there should be something like this because it would be incredibly useful both for exploiting multi-CPU machines and for parallel network transfers (wget or scp). I guess I don't know the right search terms. Thanks!
If you need the output not to be mixed up (which xargs -P risks doing), then you can use GNU Parallel:
parallel -j2 ::: command1 command2 command3
Or if the commands are in a file:
cat file | parallel -j2
GNU Parallel is a general parallelizer and makes is easy to run jobs in parallel on the same machine or on multiple machines you have ssh access to.
If you have 32 different jobs you want to run on 4 CPUs, a straight forward way to parallelize is to run 8 jobs on each CPU:
GNU Parallel instead spawns a new process when one finishes - keeping the CPUs active and thus saving time:
Installation
If GNU Parallel is not packaged for your distribution, you can do a personal installation, which does not require root access. It can be done in 10 seconds by doing this:
(wget -O - pi.dk/3 || curl pi.dk/3/ || fetch -o - http://pi.dk/3) | bash
For other installation options see http://git.savannah.gnu.org/cgit/parallel.git/tree/README
Learn more
See more examples: http://www.gnu.org/software/parallel/man.html
Watch the intro videos: https://www.youtube.com/playlist?list=PL284C9FF2488BC6D1
Walk through the tutorial: http://www.gnu.org/software/parallel/parallel_tutorial.html
Sign up for the email list to get support: https://lists.gnu.org/mailman/listinfo/parallel
In Perl you can do this with Parallel::ForkManager:
#!/usr/bin/perl
use strict;
use warnings;
use Parallel::ForkManager;
my $pm = Parallel::ForkManager->new( 8 ); # number of jobs to run in parallel
open FILE, "<commands.txt" or die $!;
while ( my $cmd = <FILE> ) {
$pm->start and next;
system( $cmd );
$pm->finish;
}
close FILE or die $!;
$pm->wait_all_children;
There is xjobs which is better at separating individual job output then xargs -P.
http://www.maier-komor.de/xjobs.html
You could also use make. Here is a very interesting article on how to use it creatively
Source: http://coldattic.info/shvedsky/pro/blogs/a-foo-walks-into-a-bar/posts/7
# That's commands.txt file
echo Hello world
echo Goodbye world
echo Goodbye cruel world
cat commands.txt | xargs -I CMD --max-procs=3 bash -c CMD
Related
I have 16 computation to do and I'd like to launch it in batch in order to use the 16 cores of my machine at the same time.
I'd like to do a shell script of this kind:
#!/bin/ksh
for i in `seq 16`
do
cd directory$i
<batch command>
done
is it possible?
You can. You just have to ensure they run as background tasks, something like:
#!/bin/ksh
for i in `seq 16`
do
cd directory$i
<batch command> &
done
Without that, it will just run the jobs sequentially. You may also want to ensure you wait for them all to finish as well, by using wait:
#!/bin/ksh
for i in `seq 16` ; do
cd directory$i
<batch command> &
done
wait # May depends on shell, bash/ksh waits for all
without the need of backticks (external command)
#!/bin/ksh
for d in dir{1..16}; do
echo $d &
done
wait
echo done
btw schellcheck.net would say:
Use $(..) instead of legacy `..`
I'm working on developing a process that will eventually be resident on a CentOS (latest) virtual machine, I'm developing in Ubuntu 12.04 LTS...
So, I have incron set to monitor my drop folder with IN_CLOSE_WRITE so that when a file is written into it a rather resource intensive script is then run on the file (Images, imagemagick). this all works fine; unless too many files are dropped at once. the script, as I said, is rather resource intensive and if more than 4 or so instances run concurrently my development machine is brought to its knees (the eventual virtual machine will be beefier, but I foresee instances where perhaps HUNDREDS of files will be dropped at once!)
dangerous incrontab:
/path/to/dropfolder IN_CLOSE_WRITE bash /path/to/resourceintensivescript.sh $#/$#
so the question is: how to limit the number of jobs spawned by incrond? I tried using gnu parallel but couldn't figure out how to make that work...
for example:
/path/to/dropfolder IN_CLOSE_WRITE parallel --gnu -j 4 bash /path/to/resourceintensivescript.sh $#/$#
seems to do nothing :/
and:
/path/to/dropfolder IN_CLOSE_WRITE;IN_NO_LOOP bash /path/to/resourceintensivescript.sh $#/$#
ends up missing files :P
Ideas on how to deal with this?
A very basic way to do this is to simply use grep and count the processes... something like:
processName=myprocess
if [ $(ps -ef |grep -v grep|grep ${processName} |wc -l) -le 4 ]
then
do something
fi
With the loop suggestion:
processName=myprocess
while true
do
if [ $(ps -ef |grep -v grep|grep ${processName} |wc -l) -le 4 ]
then
do something
break
fi
sleep 5
done
You can use the sem utility that comes with parallel:
/path/to/dropfolder IN_CLOSE_WRITE sem --gnu --id myjobname -j 4 /path/to/resourceintensivescript.sh $#/$#
I have access to a machine where I have access to 10 of the cores -- and I would like to actually use them. What I am used to doing on my own machine would be something like this:
for f in *.fa; do
myProgram (options) "./$f" "./$f.tmp"
done
I have 10 files I'd like to do this on -- let's call them blah00.fa, blah01.fa, ... blah09.fa.
The problem with this approach is that myProgram only uses 1 core at a time, and doing it like this on the multi-core machine I'd be using 1 core at a time 10 times, so I wouldn't be using my mahcine to its max capability.
How could I change my script so that it runs all 10 of my .fa files at the same time? I looked at Run a looped process in bash across multiple cores but I couldn't get the command from that to do what I wanted exactly.
You could use
for f in *.fa; do
myProgram (options) "./$f" "./$f.tmp" &
done
wait
which would start all of you jobs in parallel, then wait until they all complete before moving on. In the case where you have more jobs than cores, you would start all of them and let your OS scheduler worry about swapping processes in an out.
One modification is to start 10 jobs at a time
count=0
for f in *.fa; do
myProgram (options) "./$f" "./$f.tmp" &
(( count ++ ))
if (( count = 10 )); then
wait
count=0
fi
done
but this is inferior to using parallel because you can't start new jobs as old ones finish, and you also can't detect if an older job finished before you manage to start 10 jobs. wait allows you to wait on a single particular process or all background processes, but doesn't let you know when any one of an arbitrary set of background processes complete.
With GNU Parallel you can do:
parallel myProgram (options) {} {.}.tmp ::: *.fa
From: http://git.savannah.gnu.org/cgit/parallel.git/tree/README
= Full installation =
Full installation of GNU Parallel is as simple as:
./configure && make && make install
If you are not root you can add ~/bin to your path and install in
~/bin and ~/share:
./configure --prefix=$HOME && make && make install
Or if your system lacks 'make' you can simply copy src/parallel
src/sem src/niceload src/sql to a dir in your path.
= Minimal installation =
If you just need parallel and do not have 'make' installed (maybe the
system is old or Microsoft Windows):
wget http://git.savannah.gnu.org/cgit/parallel.git/plain/src/parallel
chmod 755 parallel
cp parallel sem
mv parallel sem dir-in-your-$PATH/bin/
Watch the intro videos to learn more: https://www.youtube.com/playlist?list=PL284C9FF2488BC6D1
# Wait while instance count less than $3, run additional instance and exit
function runParallel () {
cmd=$1
args=$2
number=$3
currNumber="1024"
while true ; do
currNumber=`ps -e | grep -v "grep" | grep " $1$" | wc -l`
if [ $currNumber -lt $number ] ; then
break
fi
sleep 1
done
echo "run: $cmd $args"
$cmd $args &
}
loop=0
# We will run 12 sleep commands for 10 seconds each
# and only five of them will work simultaneously
while [ $loop -ne 12 ] ; do
runParallel "sleep" 10 5
loop=`expr $loop + 1`
done
I have seven licenses of a particular software. Therefore, I want to start 7 jobs simultaneously. I can do that using '&'. Now, 'wait' command waits till the end of all of those 7 processes to be finished to spawn the next 7. Now, I would like to write the shell script where after I start the first seven, as and when a job gets completed I would like to start another. This is because some of those 7 jobs might take very long while some others get over really quickly. I don't want to waste time waiting for all of them to finish. Is there a way to do this in linux? Could you please help me?
Thanks.
GNU parallel is the way to go. It is designed for launching multiples instances of a same command, each with a different argument retrieved either from stdin or an external file.
Let's say your licensed script is called myScript, each instance having the same options --arg1 --arg2 and taking a variable parameter --argVariable for each instance spawned, those parameters being stored in file myParameters :
cat myParameters | parallel -halt 1 --jobs 7 ./myScript --arg1 --argVariable {} --arg2
Explanations :
-halt 1 tells parallel to halt all jobs if one fails
--jobs 7 will launch 7 instances of myScript
On a debian-based linux system, you can install parallel using :
sudo apt-get install parallel
As a bonus, if your licenses allow it, you can even tell parallel to launch these 7 instances amongst multiple computers.
You could check how many are currently running and start more if you have less than 7:
while true; do
if [ "`ps ax -o comm | grep process-name | wc -l`" -lt 7 ]; then
process-name &
fi
sleep 1
done
Write two scripts. One which restarts a job everytime it is finished and one that starts 7 times the first script.
Like:
script1:
./script2 job1
...
./script2 job7
and
script2:
while(...)
./jobX
I found a fairly good solution using make, which is a part of the standard distributions. See here
I have a script that runs some data processing command 10K times.
foreach f (folderName/input*.txt)
mycmd $f
end
I have timed the runtime for each "mycmd $f" to be 0.25 secs.
With 10K runs, it adds up to be more than 1 hr.
I'm running it on a 16 cores nehalem.
It's a huge waste to not run on the remaining 15 cores.
I have tried & with sleep, somehow the script just dies with a warning or error around 3900 iterations, see below. The shorter the sleep, that faster it dies.
foreach f (folderName/input*.txt)
mycmd $f & ; sleep 0.1
end
There has got to be a better way.
Note: I would prefer shell script solutions, let's not wander into C/C++ land.
Thanks
Regards
Pipe the list of files to
xargs -n 1 -P 16 mycmd
For example:
echo folderName/input*.txt | xargs -n 1 -P 16 mycmd
There are a few other solutions possible using one of the following applications:
xjobs
Parallel
PPSS - Parallel Processing Shell Script
runpar.sh
Submit the jobs with batch; that should fix load balancing and resource starvation issues.
for f in folderName/input.*; do
batch <<____HERE
mycmd "$f"
____HERE
done
(Not 100% sure whether the quotes are correct and/or useful.)
With GNU Parallel you can do:
parallel mycmd ::: folderName/input*.txt
From: http://git.savannah.gnu.org/cgit/parallel.git/tree/README
= Full installation =
Full installation of GNU Parallel is as simple as:
./configure && make && make install
If you are not root you can add ~/bin to your path and install in
~/bin and ~/share:
./configure --prefix=$HOME && make && make install
Or if your system lacks 'make' you can simply copy src/parallel
src/sem src/niceload src/sql to a dir in your path.
= Minimal installation =
If you just need parallel and do not have 'make' installed (maybe the
system is old or Microsoft Windows):
wget http://git.savannah.gnu.org/cgit/parallel.git/plain/src/parallel
chmod 755 parallel
cp parallel sem
mv parallel sem dir-in-your-$PATH/bin/
Watch the intro video for a quick introduction:
https://www.youtube.com/playlist?list=PL284C9FF2488BC6D1