Waiting for all files to finish writing before continuing

klmcguire · 03-11-2022, 02:05 AM

I am automating a certain process using Linux Bash. Let's say I submit 5 jobs to 5 separate nodes and they write certain output files. I want to wait for all of those output files to finish writing before moving on to the next process in my program. However, each job takes a different amount of time to finish. The current version of my "wait" code is below. Each filename includes an integer starting at one (i.e. job1, job2, job3, job4, job5, etc). $k is the last file in that list, in this example and code below, it would be equilibration5.check. Ok, so the problem is equilibration5.check could be be created before, let's say, equilibration3.check depending if equilibration5 got a faster node than equilibration3. Well, in my code it would move on to the next part before allowing equilibration3 to finish and write equilibration3.check. The next code snippet would then check all of the existing equilibration.check files for "DONE" and then move on to the next process, possibly before some of the other .check files exist.

So, what is the best way to make my program wait until all of the .check files exist, regardless of what order they finish?

FILE=~/$a/MinAnnealEquilMD/Restart_Junk/equilibration$k.check
while test ! -f $FILE
do
sleep 2;
done

until false | grep -q "DONE" ~/$a/MinAnnealEquilMD/Restart_Junk/equilibration*.check
do
sleep 2
done

Turbocapitalist · 03-11-2022, 02:19 AM

There are several ways. The wait command, which is built-in, will pause until all processes finish before proceeding. If you combine that with functions, it could be structured like this:

Code:

#!/bin/sh

aaa() {
        sleep 10
        echo AAA done
}

bbb() {
        sleep 10
        echo BBB done
}

ccc() {
        sleep 10
        echo CCC done
}

aaa &
bbb &
ccc &

echo Waiting 
wait
echo Finished waiting 

exit 0

The built-in wait command found in Bash has additional capabilities. See "man sh" and "man bash". Both manual pages are quite long so to maximize their utility, get comfortable navigating them and using the shortcuts available in the man utility.

klmcguire · 03-11-2022, 04:01 AM

Thanks for the reply. What if I'm sending the jobs off through sbatch and I want them to all run at the same time, but wait for all of them to finish?

pan64 · 03-11-2022, 04:33 AM

is it this sbatch?
you can get job details with scontrol.

klmcguire · 03-11-2022, 04:36 AM

Yes it is that sbatch. How would I use scontrol in this context?

ondoho · 03-12-2022, 06:51 AM

Quote:

Originally Posted by klmcguire

Yes it is that sbatch. How would I use scontrol in this context?

Is it this scontrol?

sundialsvcs · 03-12-2022, 09:13 AM

Also the sync command. (Or the sync() system call.) This forces all pending disk-writes to be completed.

A simple way to handle this would be to write a program or script which "forks" a set of child processes to perform each task, then waits for all of them to finish. Each process ends with a "sync" call to make sure that all physical I/O is completed before it ends.

pan64 · 03-12-2022, 10:09 AM

Quote:

Originally Posted by ondoho

Is it this scontrol?

yes, they belong to this slurm suite: https://slurm.schedmd.com/overview.html
I don't think someone can use it properly without knowing it (like me).