Profile

User private default request files are processed under the locations \(HOME/.sge_request and \)cwd/.sge_request. The working directory local default request file has the highest precedence

E-mail

send email when the job ends:

-m e
-M your@email

sge template

#$ -S /bin/bash
#$ -cwd
#$ -V
#$ -b y
#$ -j yes
#$ -N sge_example
#$ -o /tmp/

sge script

job.sge

# IMPORTANT: specifies the interpreting shell for this job to be the Bash shell
#$ -S /bin/bash

# execute the job for the current working directory.
#$ -cwd

# set the required cpu time of your job
# HH:MM:SS
#$ -l h_cpu=20:00:00

# set the required memory:
# normal:3.7 GB, 72 h, 4 slots per host.
# bigmem: 7.7 GB, 72 h, 2 slots per host.
# hugemem: 15.7 GB, 72 h, 1 slot per host.
#$ -l h_vmem=7000M

# don't flood myself with e-mail
#$ -m n

# join the error and standard output streams
#$ -j yes

# Defines or redefines the path used for the standard error  stream 
# and the standard output stream of the job. 
#$ -o ~/tmp/sge/$(date +"%b%d.%H%M")

# name of the job
#$ -N mapping_simulation

# all environment variables active within the qsub utility be exported to  the  context of the job.
#$ -V

# If the value of -b is 'y', then command  may be a binary or script. If  the  value  of -b is 'n' then command needs to be a script and it will be handled as script.
#$ -b y

echo $1 | ./job.Rf

submit script

for i in `seq 1 100`; do qsub job.sge $i; done

Other tips

SGE command

• submit jobs

  qsub
  

• check the state of jobs

  qstat
  

• check the state of a particular job

  qstat -j JOB_ID
  

• check the state of severs

  qstat -g c
  

• delete jobs

  qdel -u augix