Wait for pid end signal

Question

I wrote a script to parallelize matlab (i'm experiencing some trouble with the matlab parallel computing toolbox). The idea is to launch simultaneously matlab on all processors available. At the moment, the script launches more times matlab than there is processors on the machine. I would like to know how to add something to the code which would wait for a signal. That signal would mean, 'yep keep going'.

How to be sure that every task is sent on a different core ?

Moreover, i'm working on a remote computer and i would like to be able to close my terminal while code keeps running. So i use disown, how to be sure that the disown applies to the job that had been launched on the previous line ?

Thanks a lot

#! /bin/bash
#
# parmat.sh   File   Nb_iteration
#
np=$(nproc)
echo "nombre de processeurs disponibles : "$np

nbf=$(( $2 / $np))   #number of loops on all processors
rmd=$(expr $2 % $np) #remainder

# Loop
for var1 in $(seq 1 $nbf)
do
lp=$((var1 * $np - $np + 1))
le=$(($lp + $np - 1))
for var in $(seq $lp $le) 
do
  echo $var
  sed s/pl_id/$var/g <$1 >temp_$var.m
  /applications/matlab/r2013a/bin/matlab -nodesktop -r temp_$var &
  #rm temp_$var.m 
  disown
done
#write something for the loop to wait that all matlabs finished their run.
done

# Remainder
if [ "$rmd" -ne "0" ]
then
   lp=$(($nbf * $np + 1))
   le=$(($lp + $rmd - 1))
   for var in $(seq $lp $le) 
   do
      echo $var
      sed s/pl_id/$var/g <$1 >temp_$var.m
      /usr/local/MATLAB/R2011b/bin/matlab -nodesktop -r temp_$var &
      #rm temp_$var.m 
      disown
   done
 fi

Answer 1

You might try executing each matlab instance in a separate backgrounded subshell, and then just calling wait at the bottom of your outer loop.

Here's an example I came up with that (I think) solves both problems (i.e., how to wait for all instances to finish, and how to run each instance on a specific CPU):

#!/bin/bash
numCpus=$(grep -c ^processor /proc/cpuinfo) # I don't have nproc on my system

for cpu in $(seq 0 $((numCpus-1))); do
  (
    sleepSecs=$(( RANDOM % 10 + 1 ))
    echo "Sleeping for $sleepSecs seconds on CPU $cpu..."
    taskset -c $cpu sleep $sleepSecs
    echo "Done sleeping on CPU $cpu."
  ) &
done

usleep 500 # This is just here to keep the output ordered correctly
echo "Waiting for subshells to finish..."
wait
echo "All subshells completed."

Each subshell is run in the background with the & suffix and sleeps a random amount of time between 1 and 10 seconds. After spawning the subshells, calling wait with no arguments causes the parent shell to wait for all subshells to complete. Note that this assumes you haven't spawned any other subshells prior to this point in the script. If you have, you'll have to keep track of the PIDs or job numbers of each of the subshells you want to wait on, and pass them as arguments to wait.

Running this on my machine, I get something that looks like this:

Sleeping for 2 seconds on CPU 0...
Sleeping for 9 seconds on CPU 1...
Sleeping for 4 seconds on CPU 3...
Sleeping for 8 seconds on CPU 2...
Sleeping for 10 seconds on CPU 4...
Sleeping for 9 seconds on CPU 5...
Waiting for subshells to finish...
Done sleeping on CPU 0.
Done sleeping on CPU 3.
Done sleeping on CPU 2.
Done sleeping on CPU 5.
Done sleeping on CPU 1.
Done sleeping on CPU 4.
All subshells completed.

Edit: Of course, if you want a visual confirmation that each subshell is running on the intended CPU, you should have it do something other than sleep, since sleep (by design) doesn't eat CPU cycles, and so won't show up on your CPU monitor. You can still confirm by printing out the PID of each spawned subshell, and then verifying with ps or top what CPU they're running on. These commands don't show that information by default, but I'm sure there are options to get them to display it. Also, keep in mind that although taskset lets you set a process' CPU affinity, there is no guarantee that the kernel will run it on that CPU, or that the kernel won't switch it over to another CPU. The CPU affinity is more like a suggestion to the kernel regarding which CPU to use.