Changes between Initial Version and Version 1 of Workshops/cypress/JobDependency

Timestamp:

08/22/18 14:59:59 (6 years ago)

Author:

fuji

Comment:

—

Workshops/cypress/JobDependency

@@ +1 @@
+= Job Dependency =
+If you haven't done yet, download Samples by:
+
+{{{svn co file:///home/fuji/repos/workshop ./workshop}}}
+
+Checkout Sample files onto local machine, (linux shell)
+
+{{{svn co svn+ssh://USERID@cypress1.tulane.edu/home/fuji/repos/workshop ./workshop}}}
+
+
+----
+
+Job dependencies are used to defer the start of a job until the specified dependencies have been satisfied. They are specified with the '''--dependency''' option to '''sbatch''' command.
+{{{
+sbatch --dependency=<type:job_id[:job_id][,type:job_id[:job_id]]> ...
+}}}
+
+Dependency types:
+* '''after:jobid[:jobid...]'''  job can begin after the specified jobs have started
+* '''afterany:jobid[:jobid...]'''       job can begin after the specified jobs have terminated
+* '''afternotok:jobid[:jobid...]'''     job can begin after the specified jobs have failed
+* '''afterok:jobid[:jobid...]'''        job can begin after the specified jobs have run to completion with an exit code of zero (see the user guide for caveats).
+
+
+== Submitting Dependent Jobs ==
+Get into '''JobDependencies''' directory under '''workshop''', 
+{{{
+[fuji@cypress1 ~]$ cd workshop/
+[fuji@cypress1 workshop]$ cd JobDependencies
+[fuji@cypress1 JobDependencies]$ ls
+addOne.py  number.dat  script.sh  slurmscript  SubmitDependentJobs.sh
+}}}
+
+Python code addOne.py reads '''number.dat''' and gets an integer number, and then adds one and stores it back to '''number.dat''' .
+{{{
+[fuji@cypress1 JobDependencies]$ cat addOne.py
+# HELLO PYTHON
+import datetime
+import socket
+
+now = datetime.datetime.now()
+print 'Hello, world!'
+print now.isoformat()
+print socket.gethostname()
+#
+with open('number.dat','r') as f:
+        data = f.readline()
+        number = int(data)
+#
+print "Number = %d" % number
+with open('number.dat','w') as f:
+        f.write(str(number + 1))
+#
+}}}
+
+
+'''slurmscipt''' just run the code,
+{{{
+[fuji@cypress1 JobDependencies]$ cat slurmscript
+#!/bin/bash
+#SBATCH --qos=workshop            # Quality of Service
+#SBATCH --partition=workshop      # partition
+#SBATCH --job-name=python       # Job Name
+#SBATCH --time=00:01:00         # WallTime
+#SBATCH --nodes=1               # Number of Nodes
+#SBATCH --ntasks-per-node=1     # Number of tasks (MPI processes)
+#SBATCH --cpus-per-task=1       # Number of threads per task (OMP threads)
+
+module load anaconda
+python addOne.py
+
+sleep 10
+}}}
+
+Let submit one job and then submit anther job that depends on the first jobs as,
+{{{
+[fuji@cypress1 JobDependencies]$ sbatch slurmscript
+Submitted batch job 773997
+[fuji@cypress1 JobDependencies]$ sbatch --dependency=afterok:773997 slurmscript
+Submitted batch job 773998
+}}}
+
+List the jobs,
+{{{
+[fuji@cypress1 JobDependencies]$ squeue -u fuji
+     JOBID    QOS               NAME     USER ST       TIME NO NODELIST(REASON)
+    773998 worksh             python     fuji PD       0:00  1 (Dependency)
+    773997 worksh             python     fuji  R       0:00  1 cypress01-117
+}}}
+
+After the first job completed, the second job begin to run,
+{{{
+[fuji@cypress1 JobDependencies]$ squeue -u fuji
+     JOBID    QOS               NAME     USER ST       TIME NO NODELIST(REASON)
+    773998 worksh             python     fuji  R       0:05  1 cypress01-117
+}}}
+
+The results are:
+{{{
+[fuji@cypress1 JobDependencies]$ ls
+addOne.py  number.dat  script.sh  slurm-773997.out  slurm-773998.out  slurmscript  SubmitDependentJobs.sh
+[fuji@cypress1 JobDependencies]$ cat slurm-773997.out
+Hello, world!
+2018-08-22T14:55:37.421310
+cypress01-117
+Number = 2
+[fuji@cypress1 JobDependencies]$ cat slurm-773998.out
+Hello, world!
+2018-08-22T14:55:47.619183
+cypress01-117
+Number = 3
+}}}