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Script almost works... one error

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# 1  
Old 02-28-2015
Script almost works... one error
Helo, i have written a bash script for running my calculations. anyway, according to shellcheck the error is somewhere in the while loop or in the if condition.

so the idea of this script is:
submit a job with a name.
while it is in the queue it has a job ID number.
after the job is done i want to proceed with further ORDERS, for this i need a while loop and a if condition

the script:

Code:
#!/bin/bash -l

#Name of the job gets defined
my_job_name='NEB3'
#Name of the folder is defined.
calcname='3rd_NEB-NH-off_to_BHNH-ortho'


[
#creating job directories etc.
]

cd /job_path/NEB_jobs/jobf_${my_job_name}
sbatch job_${my_job_name}

#Id of the job in the queue is registered
my_id=squeue -u myname | sed -n "/${my_job_name}/ {s/[\ ].*//; p}"


while sleep 30; do
        if [ "${my_id}" != squeue -u myname | sed -n "/${my_job_name}/ {s/[\ ].*//; p}" ]; then
        break
done


#cp folders 
#further ORDERS


with this order:
Code:
squeue -u myname | sed -n "/${my_job_name}/ {s/[\ ].*//; p}"

i receive the job id in numbers when i type in the shell. yet i dont know if these numbers are stored as a string or integers.

with regards

---------- Post updated at 08:41 AM ---------- Previous update was at 07:40 AM ----------

so now i've changed the while loop and it works almost:
Code:
#!/bin/bash -l

#Name of the job gets defined
my_job_name='NEB3'
#Name of the folder is defined.
calcname='3rd_NEB-NH-off_to_BHNH-ortho'


[
#creating job directories etc.
]

cd /job_path/NEB_jobs/jobf_${my_job_name}
sbatch job_${my_job_name}

#Id of the job in the queue is registered
my_id=squeue -u myname | sed -n "/${my_job_name}/ {s/[\ ].*//; p}"


while sleep 30; do
        temp_id=&(squeue -u myname | sed -n "/${my_job_name}/ {s/[\ ].*//; p}")
                if [ "${my_id}" != "${temp_id}" ]; then
                        break
                fi
done


FOLLOWING_ORDERS


what does not work, are the FOLOWING_ORDERDS. Does "break" in the while loop terminate the wole bashscrpit?
Last edited by carborane; 02-28-2015 at 08:47 AM..
# 2  
Old 02-28-2015
Quote:
Originally Posted by carborane
what does not work, are the FOLOWING_ORDERDS. Does "break" in the while loop terminate the wole bashscrpit?
No, but - regardless of wether it works or not - i suggest not to use break anyway. It is a concealed GOTO and you shouldn't need it nor use it. Do it like this:

Code:
typeset -i flag=0
while [ $flag -eq 0 ] ; do
     if [ <some condition> ] ; then
          flag=1
     else
          sleep 30
     fi
done

And, by the way:
Code:
temp_id=&(squeue -u myname | sed -n "/${my_job_name}/ {s/[\ ].*//; p}")

what is this supposed to do? I can understand most of it, but what should:

Code:
variable=&(command)

do?

I hope this helps.

bakunin
This User Gave Thanks to bakunin For This Post:
carborane
# 3  
Old 02-28-2015
Code:
variable=&(command)

oh yes i messed this up.

it should be: $ instead of &.

yeah i'll try the while loop, thank you
Last edited by carborane; 02-28-2015 at 11:20 AM..
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