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 `..`
Related
For example, I want to run one command every 10 seconds and the other command every 5 minutes. I can only get the first one to log properly to a text file. Below is the shell script I am working on:
echo "script Running. Press CTRL-C to stop the process..."
while sleep 10;
do
curl -s -I --http2 https://www.ubuntu.com/ >> new.txt
echo "------------1st command--------------------" >> logs.txt;
done
||
while sleep 300;
do
curl -s -I --http2 https://www.google.com/
echo "-----------------------2nd command---------------------------" >> logs.txt;
done
I would advise you to go with #Marvin Crone's answer, but researching cronjobs and back-ground processes doesn't seem like the kind of hassle I would go through for this little script. Instead, try putting both loops into separate scripts; like so:
script1.sh
echo "job 1 Running. Type fg 1 and press CTRL-C to stop the process..."
while sleep 10;
do
echo $(curl -s -I --http2 https://www.ubuntu.com/) >> logs.txt;
done
script2.sh
echo "job 2 Running. Type fg 2 and press CTRL-C to stop the process..."
while sleep 300;
do
echo $(curl -s -I --http2 https://www.google.com/) >> logs.txt;
done
adding executable permissions
chmod +x script1.sh
chmod +x script2.sh
and last but not least running them:
./script1.sh & ./script2.sh &
this creates two separate jobs in the background that you can call by typing:
fg (1 or 2)
and stop them with CTRL-C or send them to background again by typing CTRL-Z
I think what is happening is that you start the first loop. Your first loop needs to complete before the second loop will start. But, the first loop is designed to be infinite.
I suggest you put each curl loop in a separate batch file.
Then, you can run each batch file separately, in the background.
I offer two suggestions for you to investigate for your solution.
One, research the use of crontab and set up a cron job to run the batch files.
Two, research the use of nohup as a means of running the batch files.
I strongly suggest you also research the means of monitoring the jobs and knowing how to terminate the jobs if anything goes wrong. You are setting up infinite loops. A simple Control C will not terminate jobs running in the background. You are treading in areas that can get out of control. You need to know what you are doing.
Hi all/ I'm trying to make something like parallel tool for shell simply because the functionality of parallel is not enough for my task. The reason is that I need to run different versions of compiler.
Imagine that I need to compile 12 programs with different compilers, but I can run only 4 of them simultaneously (otherwise PC runs out of memory and crashes :). I also want to be able to observe what's going on with each compile, therefore I execute every compile in new window.
Just to make it easier here I'll replace compiler that I run with small script that waits and returns it's process id sleep.sh:
#!/bin/bash
sleep 30
echo $$
So the main script should look like parallel_run.sh :
#!/bin/bash
for i in {0..11}; do
xfce4-terminal -H -e "./sleep.sh" &
pids[$i]=$!
pstree -p $pids
if (( $i % 4 == 0 ))
then
for pid in ${pids[*]}; do
wait $pid
done
fi
done
The problem is that with $! I get pid of xfce4-terminal and not the program it executes. So if I look at ptree of 1st iteration I can see output from main script:
xfce4-terminal(31666)----{xfce4-terminal}(31668)
|--{xfce4-terminal}(31669)
and sleep.sh says that it had pid = 30876 at that time. Thus wait doesn't work at all in this case.
Q: How to get right PID of compiler that runs in subshell?
Maybe there is the other way to solve task like this?
It seems like there is no way to trace PID from parent to child if you invoke process in new xfce4-terminal as terminal process dies right after it executed given command. So I came to the solution which is not perfect, but acceptable in my situation. I run and put compiler's processes in background and redirect output to .log file. Then I run tail on these logfiles and I kill all tails which belongs to current $USER when compilers from current batch are done, then I run the other batch.
#!/bin/bash
for i in {1..8}; do
./sleep.sh > ./process_$i.log &
prcid=$!
xfce4-terminal -e "tail -f ./process_$i.log" &
pids[$i]=$prcid
if (( $i % 4 == 0 ))
then
for pid in ${pids[*]}; do
wait $pid
done
killall -u $USER tail
fi
done
Hopefully there will be no other tails running at that time :)
I'm trying to schedule a series of mpi jobs on an Ubuntu 14.04 LTS machine using a bash script. Basically, I want a simulation to run on every core for a certain amount of time, then terminate and move on to the next case once that time has elapsed.
My issue arises when mpi exits at the end of the first job - it breaks the loop and returns the terminal to my control instead of heading onto the next iteration of the loop.
My script is included below. The file "case_names" is just a text file of directory names. I've tested the script with other commands and it works fine until I uncomment the mpirun call.
#!/bin/bash
while read line;
do
# Access case dierctory
cd $line
echo "Case $line accessed"
# Start simulation
echo "Case $line starting: $(date)"
mpirun -q -np 8 dsmcFoamPlus -parallel > log.dsmcFoamPlus &
# Wait for 10 hour runtime
sleep 36000
# Kill job
pkill mpirun > /dev/null
echo "Case $line terminated: $(date)"
# Return to parent directory
cd ..
done < case_names
Does anyone know of a way to stop mpirun from breaking the loop like this?
So far I've tried GNOME task scheduler and task-spooler, but neither have worked (likely due to aliases that have to be invoked before the commands I use become available). I'd really rather not have to resort to setting up slurm. I've also tried using the disown command to separate the mpi process from the shell I'm running the scheduling script in, and have even written a separate script just to kill processes which the scheduling script runs remotely.
Many thanks in advance!
I've managed to find a workaround that allows me to schedule tasks with a bash script like I wanted. Since this solves my issue, I'm posting it as an answer (although I would still welcome an explanation as to why mpi behaves in this way in loops).
The solution lay in writing a separate script for both calling and then killing mpi, which would itself be called by the scheduling script. Since this child bash process has no loops in it, there are no issues with mpi breaking them after being killed. Also, once this script has exited, the scheduling loop can continue unimpeded.
My (now working) code is included below.
Scheduling script:
while read line;
do
cd $line
echo "CWD: $(pwd)"
echo "Case $line accessed"
bash ../run_job
echo "Case $line terminated: $(date)"
cd ..
done < case_names
Execution script (run_job):
mpirun -q -np 8 dsmcFoamPlus -parallel > log.dsmcFoamPlus &
echo "Case $line starting: $(date)"
sleep 600
pkill mpirun
I hope someone will find this useful.
I have a bash script with a loop of processes that I want to run in parallel:
for i in {1..5}
do
echo Running for simulation $i
python script.py $i > ./outlogs/$i.log 2>&1 &
done
But when I do this the file redirection doesn't work, so $i.log just stays empty. The redirection only works when I do not use the & at the end, but then the script waits for each process to finish before starting the next one, which I don't want.
I tried a solution using script -c, but this does not update in realtime, only once the process ends. Does anyone have better suggestions, where the file redirection works in this script but it still updates in realtime?
You need simply add -u option so it will look like this:
python -u script.py $i > ./outlogs/$i.log 2>&1 &
Option -u is for unbuffered binary stdout and stderr
I would like to make a .sh that runs multiple other ones .sh in new tabs/windows.
something like inside main.sh
"sh1.sh"
wait 5 seconds to load
"sh2.sh"
wait 5 seconds
"sh3.sh"
You could try xterm -e ~/sh1.sh as your command. It'll close as soon as the script has finished though.
If you need to run them in separate windows simultaneously, you need to background each process.
xterm -e sh1.sh &
sleep 5 # why do you want to pause between invocations?
xterm -e sh2.sh &
sleep 5
xterm -e sh3.sh &
This should probably be refactored to use a loop and/or a wrapper function.
for prog in sh1.sh sh2.sh sh3.sh; do
xterm -e $prog &
sleep 5
done