How to make bash interpreter stop until a command is finished? - bash

I have a bash script with a loop that calls a hard calculation routine every iteration. I use the results from every calculation as input to the next. I need make bash stop the script reading until every calculation is finished.
for i in $(cat calculation-list.txt)
do
./calculation
(other commands)
done
I know the sleep program, and i used to use it, but now the time of the calculations varies greatly.
Thanks for any help you can give.
P.s>
The "./calculation" is another program, and a subprocess is opened. Then the script passes instantly to next step, but I get an error in the calculation because the last is not finished yet.

If your calculation daemon will work with a precreated empty logfile, then the inotify-tools package might serve:
touch $logfile
inotifywait -qqe close $logfile & ipid=$!
./calculation
wait $ipid
(edit: stripped a stray semicolon)
if it closes the file just once.
If it's doing an open/write/close loop, perhaps you can mod the daemon process to wrap some other filesystem event around the execution? `
#!/bin/sh
# Uglier, but handles logfile being closed multiple times before exit:
# Have the ./calculation start this shell script, perhaps by substituting
# this for the program it's starting
trap 'echo >closed-on-calculation-exit' 0 1 2 3 15
./real-calculation-daemon-program

Well, guys, I've solved my problem with a different approach. When the calculation is finished a logfile is created. I wrote then a simple until loop with a sleep command. Although this is very ugly, it works for me and it's enough.
for i in $(cat calculation-list.txt)
do
(calculations routine)
until [[ -f $logfile ]]; do
sleep 60
done
(other commands)
done

Easy. Get the process ID (PID) via some awk magic and then use wait too wait for that PID to end. Here are the details on wait from the advanced Bash scripting guide:
Suspend script execution until all jobs running in background have
terminated, or until the job number or process ID specified as an
option terminates. Returns the exit status of waited-for command.
You may use the wait command to prevent a script from exiting before a
background job finishes executing (this would create a dreaded orphan
process).
And using it within your code should work like this:
for i in $(cat calculation-list.txt)
do
./calculation >/dev/null 2>&1 & CALCULATION_PID=(`jobs -l | awk '{print $2}'`);
wait ${CALCULATION_PID}
(other commands)
done

Related

Pause script by keyboard input

(Sorry for my bad english.) I would like to pause a running script by pressing the [SPACE] bar. The script must run, until the user not press the [SPACE] bar, then pause 20 seconds, and run forth. How can i continuously watch the keyboard input while the script is running?
One way to do it:
#!/bin/bash -eu
script(){ #a mock for your script
while :; do
echo working
sleep 1
done
}
set -m #use job control
script & #run it in the background in a separate process group
read -sd ' ' #silently read until a space is read
kill -STOP -$! #stop the background process group
sleep 2 #wait 2 seconds (change it to 20 for your case)
kill -CONT -$! #resume the background process group
fg #put it in the forground so it's killable with Ctrl+C
I think the most simple way is to implement a script with checkpoints, which tests if a pause is required. Of course, it means your code never call 'long' running command...
A more complex solution is to use SIGPAUSE signal. You can have the main process that execute the script and the side process that catches [SPACE] and emit SIGPAUSE to the main process. Here I see at least two issues:
- how to share the terminal/keyboard between the 2 process (simple if your main script don't expect input from keyboard),
- if the main script starts several processes, you will have to deal with process group...
So it really depends on the complexity of your script. You may consider to rely only on regular Job control provided by Bash.
I suggest to use a controlling script that freezes you busy script:
kill -SIGSTOP ${PID}
and then
kill -SIGCONT ${PID}
to allow the process to continue.
see https://superuser.com/questions/485884/can-a-process-be-frozen-temporarily-in-linux for more detailed explanation.

How to run a command after a certain time while another command is running?

I have a bash script which will be running a main command, let's say for one hour. I would like to execute another command after a certain time since the main command has been started (at t_x). Something like this:
main starts -------> main ends
|
|
at time t_x, second command is executed
At the moment I have something like this:
mpirun main_command & sleep 1m && second_command
and the problem is that after second command is executed, the main command is killed. Can anyone help me? Thanks!
The first command is failing to lock the console, as another process is also using it. You will need to redirect the standard io pipelines, 0<&- mpirun main_command >/dev/null 2>/dev/null If this still does not work, use shell -c 'mpirun main_command' & sleep 1m;second_command You can use ; instead of &&, unless you need a failing exit code when someone interrupts the sleep.

Introduce timeout in a bash for-loop

I have a task that is very well inside of a bash for loop. The situation is though, that a few of the iterations seem to not terminate. What I'm looking for is a way to introduce a timeout that if that iteration of command hasn't terminated after e.g. two hours it will terminate, and move on to the next iteration.
Rough outline:
for somecondition; do
while time-run(command) < 2h do
continue command
done
done
One (tedious) way is to start the process in the background, then start another background process that attempts to kill the first one after a fixed timeout.
timeout=7200 # two hours, in seconds
for somecondition; do
command & command_pid=$!
( sleep $timeout & wait; kill $command_pid 2>/dev/null) & sleep_pid=$!
wait $command_pid
kill $sleep_pid 2>/dev/null # If command completes prior to the timeout
done
The wait command blocks until the original command completes, whether naturally or because it was killed after the sleep completes. The wait immediately after sleep is used in case the user tries to interrupt the process, since sleep ignores most signals, but wait is interruptible.
If I'm understanding your requirement properly, you have a process that needs to run, but you want to make sure that if it gets stuck it moves on, right? I don't know if this will fully help you out, but here is something I wrote a while back to do something similar (I've since improved this a bit, but I only have access to a gist at present, I'll update with the better version later).
#!/bin/bash
######################################################
# Program: logGen.sh
# Date Created: 22 Aug 2012
# Description: parses logs in real time into daily error files
# Date Updated: N/A
# Developer: #DarrellFX
######################################################
#Prefix for pid file
pidPrefix="logGen"
#output direcory
outDir="/opt/Redacted/logs/allerrors"
#Simple function to see if running on primary
checkPrime ()
{
if /sbin/ifconfig eth0:0|/bin/grep -wq inet;then isPrime=1;else isPrime=0;fi
}
#function to kill previous instances of this script
killScript ()
{
/usr/bin/find /var/run -name "${pidPrefix}.*.pid" |while read pidFile;do
if [[ "${pidFile}" != "/var/run/${pidPrefix}.${$}.pid" ]];then
/bin/kill -- -$(/bin/cat ${pidFile})
/bin/rm ${pidFile}
fi
done
}
#Check to see if primary
#If so, kill any previous instance and start log parsing
#If not, just kill leftover running processes
checkPrime
if [[ "${isPrime}" -eq 1 ]];then
echo "$$" > /var/run/${pidPrefix}.$$.pid
killScript
commands && commands && commands #Where the actual command to run goes.
else
killScript
exit 0
fi
I then set this script to run on cron every hour. Every time the script is run, it
creates a lock file named after a variable that describes the script that contains the pid of that instance of the script
calls the function killScript which:
uses the find command to find all lock files for that version of the script (this lets more than one of these scripts be set to run in cron at once, for different tasks). For each file it finds, it kills the processes of that lock file and removes the lock file (it automatically checks that it's not killing itself)
Starts doing whatever it is I need to run and not get stuck (I've omitted that as it's hideous bash string manipulation that I've since redone in python).
If this doesn't get you squared let me know.
A few notes:
the checkPrime function is poorly done, and should either return a status, or just exit the script itself
there are better ways to create lock files and be safe about it, but this has worked for me thus far (famous last words)

call a separate job/shell file and wait for it to complete execution before continuing further, in ksh

I intend to call a shell script from the main script and wait for it to complete before processing the main script further,
I have tried doing
xyz_Sh &
while [[ $cnt -gt 0 ]] ; do
cnt=`ps -ef| grep "xyz_Sh" |grep -v grep |wc -l`
done
I also tried using wait as
. xyz_Sh &
wait_id=$!
wait $wait_id
but in this case the control does not return back to the main routine, the script stops after executes xyz_Sh, what am I missing here ?
Thanks
Ali
Unless something is put into the background in xyz_Sh then the default shell behavior should do exactly what you want.
In a shell script, a command isn't executed until the previous command has ended, so:
xyz_Sh
//do other stuff
should work exactly as you want it to.
If, on the other hand, xyz_Sh does put things in the background, then you should alter xyz_Sh to wait for all of its processes to finish before exiting. This can be done with the wait command.

Why can't I use job control in a bash script?

In this answer to another question, I was told that
in scripts you don't have job control
(and trying to turn it on is stupid)
This is the first time I've heard this, and I've pored over the bash.info section on Job Control (chapter 7), finding no mention of either of these assertions. [Update: The man page is a little better, mentioning 'typical' use, default settings, and terminal I/O, but no real reason why job control is particularly ill-advised for scripts.]
So why doesn't script-based job-control work, and what makes it a bad practice (aka 'stupid')?
Edit: The script in question starts a background process, starts a second background process, then attempts to put the first process back into the foreground so that it has normal terminal I/O (as if run directly), which can then be redirected from outside the script. Can't do that to a background process.
As noted by the accepted answer to the other question, there exist other scripts that solve that particular problem without attempting job control. Fine. And the lambasted script uses a hard-coded job number — Obviously bad. But I'm trying to understand whether job control is a fundamentally doomed approach. It still seems like maybe it could work...
What he meant is that job control is by default turned off in non-interactive mode (i.e. in a script.)
From the bash man page:
JOB CONTROL
Job control refers to the ability to selectively stop (suspend)
the execution of processes and continue (resume) their execution at a
later point.
A user typically employs this facility via an interactive interface
supplied jointly by the system’s terminal driver and bash.
and
set [--abefhkmnptuvxBCHP] [-o option] [arg ...]
...
-m Monitor mode. Job control is enabled. This option is on by
default for interactive shells on systems that support it (see
JOB CONTROL above). Background processes run in a separate
process group and a line containing their exit status is
printed upon their completion.
When he said "is stupid" he meant that not only:
is job control meant mostly for facilitating interactive control (whereas a script can work directly with the pid's), but also
I quote his original answer, ... relies on the fact that you didn't start any other jobs previously in the script which is a bad assumption to make. Which is quite correct.
UPDATE
In answer to your comment: yes, nobody will stop you from using job control in your bash script -- there is no hard case for forcefully disabling set -m (i.e. yes, job control from the script will work if you want it to.) Remember that in the end, especially in scripting, there always are more than one way to skin a cat, but some ways are more portable, more reliable, make it simpler to handle error cases, parse the output, etc.
You particular circumstances may or may not warrant a way different from what lhunath (and other users) deem "best practices".
Job control with bg and fg is useful only in interactive shells. But & in conjunction with wait is useful in scripts too.
On multiprocessor systems spawning background jobs can greatly improve the script's performance, e.g. in build scripts where you want to start at least one compiler per CPU, or process images using ImageMagick tools parallely etc.
The following example runs up to 8 parallel gcc's to compile all source files in an array:
#!bash
...
for ((i = 0, end=${#sourcefiles[#]}; i < end;)); do
for ((cpu_num = 0; cpu_num < 8; cpu_num++, i++)); do
if ((i < end)); then gcc ${sourcefiles[$i]} & fi
done
wait
done
There is nothing "stupid" about this. But you'll require the wait command, which waits for all background jobs before the script continues. The PID of the last background job is stored in the $! variable, so you may also wait ${!}. Note also the nice command.
Sometimes such code is useful in makefiles:
buildall:
for cpp_file in *.cpp; do gcc -c $$cpp_file & done; wait
This gives much finer control than make -j.
Note that & is a line terminator like ; (write command& not command&;).
Hope this helps.
Job control is useful only when you are running an interactive shell, i.e., you know that stdin and stdout are connected to a terminal device (/dev/pts/* on Linux). Then, it makes sense to have something on foreground, something else on background, etc.
Scripts, on the other hand, doesn't have such guarantee. Scripts can be made executable, and run without any terminal attached. It doesn't make sense to have foreground or background processes in this case.
You can, however, run other commands non-interactively on the background (appending "&" to the command line) and capture their PIDs with $!. Then you use kill to kill or suspend them (simulating Ctrl-C or Ctrl-Z on the terminal, it the shell was interactive). You can also use wait (instead of fg) to wait for the background process to finish.
It could be useful to turn on job control in a script to set traps on
SIGCHLD. The JOB CONTROL section in the manual says:
The shell learns immediately whenever a job changes state. Normally,
bash waits until it is about to print a prompt before reporting
changes in a job's status so as to not interrupt any other output. If
the -b option to the set builtin command is enabled, bash reports
such changes immediately. Any trap on SIGCHLD is executed for each
child that exits.
(emphasis is mine)
Take the following script, as an example:
dualbus#debian:~$ cat children.bash
#!/bin/bash
set -m
count=0 limit=3
trap 'counter && { job & }' CHLD
job() {
local amount=$((RANDOM % 8))
echo "sleeping $amount seconds"
sleep "$amount"
}
counter() {
((count++ < limit))
}
counter && { job & }
wait
dualbus#debian:~$ chmod +x children.bash
dualbus#debian:~$ ./children.bash
sleeping 6 seconds
sleeping 0 seconds
sleeping 7 seconds
Note: CHLD trapping seems to be broken as of bash 4.3
In bash 4.3, you could use 'wait -n' to achieve the same thing,
though:
dualbus#debian:~$ cat waitn.bash
#!/home/dualbus/local/bin/bash
count=0 limit=3
trap 'kill "$pid"; exit' INT
job() {
local amount=$((RANDOM % 8))
echo "sleeping $amount seconds"
sleep "$amount"
}
for ((i=0; i<limit; i++)); do
((i>0)) && wait -n; job & pid=$!
done
dualbus#debian:~$ chmod +x waitn.bash
dualbus#debian:~$ ./waitn.bash
sleeping 3 seconds
sleeping 0 seconds
sleeping 5 seconds
You could argue that there are other ways to do this in a more
portable way, that is, without CHLD or wait -n:
dualbus#debian:~$ cat portable.sh
#!/bin/sh
count=0 limit=3
trap 'counter && { brand; job & }; wait' USR1
unset RANDOM; rseed=123459876$$
brand() {
[ "$rseed" -eq 0 ] && rseed=123459876
h=$((rseed / 127773))
l=$((rseed % 127773))
rseed=$((16807 * l - 2836 * h))
RANDOM=$((rseed & 32767))
}
job() {
amount=$((RANDOM % 8))
echo "sleeping $amount seconds"
sleep "$amount"
kill -USR1 "$$"
}
counter() {
[ "$count" -lt "$limit" ]; ret=$?
count=$((count+1))
return "$ret"
}
counter && { brand; job & }
wait
dualbus#debian:~$ chmod +x portable.sh
dualbus#debian:~$ ./portable.sh
sleeping 2 seconds
sleeping 5 seconds
sleeping 6 seconds
So, in conclusion, set -m is not that useful in scripts, since
the only interesting feature it brings to scripts is being able to
work with SIGCHLD. And there are other ways to achieve the same thing
either shorter (wait -n) or more portable (sending signals yourself).
Bash does support job control, as you say. In shell script writing, there is often an assumption that you can't rely on the fact that you have bash, but that you have the vanilla Bourne shell (sh), which historically did not have job control.
I'm hard-pressed these days to imagine a system in which you are honestly restricted to the real Bourne shell. Most systems' /bin/sh will be linked to bash. Still, it's possible. One thing you can do is instead of specifying
#!/bin/sh
You can do:
#!/bin/bash
That, and your documentation, would make it clear your script needs bash.
Possibly o/t but I quite often use nohup when ssh into a server on a long-running job so that if I get logged out the job still completes.
I wonder if people are confusing stopping and starting from a master interactive shell and spawning background processes? The wait command allows you to spawn a lot of things and then wait for them all to complete, and like I said I use nohup all the time. It's more complex than this and very underused - sh supports this mode too. Have a look at the manual.
You've also got
kill -STOP pid
I quite often do that if I want to suspend the currently running sudo, as in:
kill -STOP $$
But woe betide you if you've jumped out to the shell from an editor - it will all just sit there.
I tend to use mnemonic -KILL etc. because there's a danger of typing
kill - 9 pid # note the space
and in the old days you could sometimes bring the machine down because it would kill init!
jobs DO work in bash scripts
BUT, you ... NEED to watch for the spawned staff
like:
ls -1 /usr/share/doc/ | while read -r doc ; do ... done
jobs will have different context on each side of the |
bypassing this may be using for instead of while:
for `ls -1 /usr/share/doc` ; do ... done
this should demonstrate how to use jobs in a script ...
with the mention that my commented note is ... REAL (dunno why that behaviour)
#!/bin/bash
for i in `seq 7` ; do ( sleep 100 ) & done
jobs
while [ `jobs | wc -l` -ne 0 ] ; do
for jobnr in `jobs | awk '{print $1}' | cut -d\[ -f2- |cut -d\] -f1` ; do
kill %$jobnr
done
#this is REALLY ODD ... but while won't exit without this ... dunno why
jobs >/dev/null 2>/dev/null
done
sleep 1
jobs

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