Page tree

Versions Compared


  • This line was added.
  • This line was removed.
  • Formatting was changed.


Code Block
#!/bin/bash -l
##Defining the needed resources with SLURM parameters (modify as needed)
#SBATCH --account=[your-project]
#SBATCH --job-name=iterativeJob
#SBATCH --ntasks=xx
#SBATCH --ntasks-per-node=yy
#SBATCH --time=00:05:00
#SBATCH --export=NONE

##Setting modules
#Add the needed modules (uncomment and adapt the follwing lines)
#module swap the-module-to-swap the-module-i-need
#module load the-modules-i-need

##Setting the variables for controlling recursion
#job iteration counter. It's default value is 1 (as for the first submission). For a subsequent submission, it will receive it value through the "sbatch --export" command from the "parent job".
: ${job_iteration:="1"}

#Maximum number of job iterations. It is always good to have a reasonable number here

echo "This jobscript is calling itself in recursively. This is iteration=${this_job_iteration}."
echo "The maximum number of iterations is set to job_iteration_max=${job_iteration_max}."
echo "The slurm job id is: ${SLURM_JOB_ID}"

##Defining the name of the dependent script.
#This "dependentScript" is the name of the next script to be executed in workflow logic. The most common and more utilised is to re-submit the same script:
thisScript=`squeue -h -j $SLURM_JOBID -o %o`
export dependentScript=${thisScript}

##Safety-net checks before proceding to the execution of this script

#Check 1: If the file with the exact name 'stopSlurmCycle' exists in the submission directory, then stop execution.
#         Users can create a file with this name if they need to interrupt the submission cycle by using the following command:
#             touch stopSlurmCycle
#         (Remember to remove the file before submitting this script again.)
if [[ -f stopSlurmCycle ]]; then
   echo "The file \"stopSlurmCycle\" exists, so the script \"${thisScript}\" will exit."
   echo "Remember to remove the file before submitting this script again, or the execution will be stopped."
   exit 1

#Check 2: If the number of output files has reached a limit, then stop execution.
#         The existence of a large number of output files could be a sign of an infinite recursive loop.
#         In this case we check for the number of "slurm-XXXX.out" files.
#         (Remember to check your output files regularly and remove the not needed old ones or the execution may be stoppped.)
slurmyBaseName="slurm" #Use the base name of the output file
slurmies=$(find . -maxdepth 1 -name "${slurmyBaseName}*" | wc -l)
if [ $slurmies -gt $maxSlurmies ]; then
   echo "There are slurmies=${slurmies} ${slurmyBaseName}-XXXX.out files in the directory."
   echo "The maximum allowed number of output files is maxSlurmies=${maxSlurmies}"
   echo "This could be a sign of an infinite loop of slurm resubmissions."
   echo "So the script ${thisScript} will exit."
   exit 2

#Check 3: Add some other adequate checks to guarantee the correct execution of your workflow
#Check 4: etc.

##Setup/Update of parameters/input for the current script

#The following variables will receive a value with the "sbatch --export" submission from the parent job.
#If this is the first time this script is called, then they will start with the default values given here:
: ${var_start_time:="0"}
: ${var_end_time:="10"}
: ${var_increment:="10"}

#Replacing the current values in the parameter/input file used by the executable:
cp $templateFile $paramFile
sed -i "s,VAR_START_TIME,$var_start_time," $paramFile
sed -i "s,VAR_END_TIME,$var_end_time," $paramFile

#Creating the backup of the parameter file utilised in this job
cp $paramFile $paramFile.$SLURM_JOB_ID

##Verify that everything that is needed is ready
#This section is IMPORTANT. For example, it can be used to verify that the results from the parent submission are there. If not, stop execution.

##Submitting the dependent job
#IMPORTANT: Never use cycles that could fall into infinite loops. Numbered cycles are the best option.

#The following variable needs to be "true" for the cycle to proceed (it can be set to false to avoid recursion when testing):

#Check if the current iteration is within the limits of the maximum number of iterations, then submit the dependent job:
if [ "$useDependentCycle" = "true" ] && [ ${job_iteration} -lt ${job_iteration_max} ]; then
   #Update the counter of cycle iterations
   (( job_iteration++ ))
   #Update the values needed for the next submission
   (( var_end_time += $var_increment ))
   #Dependent Job submission:
   #                         (Note that next_jobid has the ID given by the sbatch)
   #                         For the correct "--dependency" flag:
   #                         Use "afterok" when each job is expected to properly finish.
   #                         Use "afterany" when each job is expected to reach walltime.
   #                         Check documentation for other flags available.
   #IMPORTANT: The --export="list_of_exported_vars" guarantees that values are inherited to the dependent job
   next_jobid=$(sbatch --export="job_iteration=${job_iteration},var_start_time=${var_start_time},var_end_time=${var_end_time},var_increment=${var_increment}" --dependency=afterok:${SLURM_JOB_ID} ${dependentScript} | awk '{print $4}')
   echo "Dependent with slurm job id ${next_jobid} was submitted"
   echo "If you want to stop the submission chain it is recommended to use scancel on the dependent job first"
   echo "Or create a file named: \"stopSlurmCycle\""
   echo "And then you can scancel this job if needed too"
   echo "This is the last iteration of the cycle, no more dependent jobs will be submitted"

##Run the main executable.
#(Modify as needed)
#Syntax should allow restart from a checkpoint