Template file for Sun Grid Engine (SGE) job submissions

template.qsub

#!/bin/bash -l

# template.qsub - Template file for Sun Grid Engine (SGE) job submissions

# Andrés Bretón, http://andresbreton.com

# Template from https://gist.github.com/bretonics/1dc5d0926aefa7787ebf48a0bad5316b

#-------------------------------------------------------------------------------
# ENVIRONMENTAL VARIABLES AVAILABLE

# JOB_ID                Current job ID
# JOB_NAME              Current job name
# NSLOTS                The number of slots (threads or processors) requested by a job
# HOSTNAME              Name of execution host
# SGE_TASK_ID           Array Job task index number
# SGE_TASK_STEPSIZE     The step size of the array job specification
# SGE_TASK_FIRST        The index number of the first array job task
# SGE_TASK_LAST         The index number of the last array job task
# TMPDIR                The absolute path to the job's temporary working directory

#-------------------------------------------------------------------------------
# COMPUTING DIRECTIVES

# Specify hard time limit for the job
# The job will be aborted if it runs longer than this time
# The default time is 12 hours
#$ -l h_rt=24:00:00

# Memory
# Request a node with at least 32 of memory (4 cores x 8GB per core = 32GB total)
#$ -l mem_total=32G # Request a node that has at least 16G of total memory
#$ -l mem_per_core=8G # Request a node with at least 8 GB of memory per core

# Request a parallel environment with four cores
#$ -pe omp 4

# Request MPI jobs
# The SCC has 2 sets of nodes dedicated to run MPI jobs
# One set has 16-core nodes with 128 GB each
# The other set of nodes has 28-core nodes with 256 GB each
#$ -pe mpi_28_tasks_per_node 224 # 8 nodes with 28 core each

# Request GPU jobs
#$ -pe omp 4 # Request 4 CPUs

# Request 1 GPU (the number of GPUs needed should be divided by the number of CPUs requested above)
#$ -l gpus=0.25

# Specify the minimum GPU compute capability
#$ -l gpu_c=3.5

# Request my job to run on Buy-in Compute group hardware my_project has access to
#$ -l buyin

#-------------------------------------------------------------------------------
# ACTION DIRECTIVES

# Set SCC project
#$ -P project_name

# Job name
#$ -N job_name

# Stdout output
#$ -o "${JOB_NAME}/${JOB_NAME}_stdout.qlog"

# Stderr output
#$ -e "${JOB_NAME}/${JOB_NAME}_stderr.qlog"

# Merge the error and output streams into a single file
#$ -j y

# Specify the output file name
#$ -o "${JOB_NAME}/$JOB_NAME.qlog"

# Send an email (by default no email is sent). The possible values are -
# job begins (b), ends (e), is aborted (a), is suspended (s), or never (n) – default
#$ -m beasn

# Email adress to send email
#$ -M user_email

# All current environment variables should be exported to the batch job
#$ -V

# Set the runtime environment variable env to value
#$ -v env=value

# Setup job dependency list
# job_list is a comma separated list of job ids and/or job names which must complete before this job can run
#$ -hold_jid job_list

# Run in current directory
#$ -cwd

#-------------------------------------------------------------------------------
# JOB

# Load modules
modules=()
module load ${modules[@]}

#- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

# Save environment to file
env > "${JOB_NAME}/${JOB_NAME}.env"

# Keep track of information related to the current job
echo "# ================================================================================"
echo "#    JOB NAME:    $JOB_NAME"
echo "#    USER:        $USER"
echo "#    PWD:         $(pwd)"
echo "#    HOST:        $HOSTNAME"
echo "#    JOB ID:      $JOB_ID"
echo "#    TASK ID:     $SGE_TASK_ID"
echo "#    START:       $(date)"
printf "\n\n#    "
module list
echo "# ================================================================================"
echo ""
echo ""
echo ""

#- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# CALLS

cmd=""
echo "#--------------------------------------------------------------------------------"
echo "#  Running :"
echo "#  $cmd"
echo "#--------------------------------------------------------------------------------"
echo ""
echo ""
$cmd
echo "# ================================================================================"


echo ""
echo ""
cmd=""
echo "#--------------------------------------------------------------------------------"
echo "#  Running :"
echo "#  $cmd"
echo "#--------------------------------------------------------------------------------"
echo ""
echo ""
$cmd
echo "# ================================================================================"

#- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# End job message
echo ""
echo ""
echo ""
echo "# ================================================================================"
echo "#    End: $(date)"
echo "#    User: $USER"
echo "#    Cores/Threads: $NSLOTS"
echo "#    Temporary Directory: $TMPDIR"
echo "# ================================================================================"
echo ""
echo ""
echo ""