From e94a818ec03cc157c7c90439ae2d2ee1f03bcab8 Mon Sep 17 00:00:00 2001
From: Mike Lake <Mike.Lake@uts.edu.au>
Date: Mon, 1 Nov 2021 16:01:14 +1100
Subject: [PATCH] Use docopt and not argparse, use a virtualenv.
---
check_utilisation.py | 68 +++++++++++++++++++++++++-------------------
1 file changed, 39 insertions(+), 29 deletions(-)
diff --git a/check_utilisation.py b/check_utilisation.py
index cc232df..0c52539 100755
--- a/check_utilisation.py
+++ b/check_utilisation.py
@@ -3,14 +3,14 @@
'''
This script checks the utilisation of HPC jobs.
-Run the program to get help on usage.
+Run the program with -h or --help to get help on usage.
Note to installers:
1. This program should be installed on just the login node under /opt/eresearch/
2. The public version of the users database needs to be updated every time the
main database is updated.
-Notes:
+Notes to myself:
Cannot use job key 'euser'from pbs_connect(pbs_server):
At first I was using job['euser'] from the jobs returned from PBS to get the user
running the job. It turns out that this key is only available to PBS admin users
@@ -21,14 +21,20 @@ Cannot use job key 'euser'from pbs_connect(pbs_server):
Author: Mike Lake
Releases:
-2021-04-29 First release.
+ 2021-04-29 First release.
+ 2021-11-01 Use docopt arg parsing instead or argparse. Had to add a virtualenv for this.
'''
-import argparse
+# Load python from this virtual environment and unload the system python.
+activate_this_file = "/opt/eresearch/virtualenvs/hpc_py3/bin/activate_this.py"
+with open(activate_this_file) as f:
+ exec(f.read(), dict(__file__=activate_this_file))
+
import sys, os, re
import pwd
import datetime
+from docopt import docopt
# Append what ever pbs directory is under the directory that this script is located
# in. This ensures that we use /opt/eresearch/pbs for the version used by users and
@@ -68,6 +74,23 @@ from_email = 'YourEmail@example.com'
# Your login nodes mail server.
mail_server = 'postoffice.example.com'
+# The programs usage comes from this string being parsed by docopt.
+usage_doc = '''
+Check Your HPC Utilisation
+
+Usage:
+ check_utilisation.py running [-e <email>] [-u user]
+ check_utilisation.py finished
+ check_utilisation.py all
+ check_utilisation.py -h | --help
+
+Options:
+ -e, --email <email> Email a copy of this report to yourself.
+ -u, --user <user> Only show jobs for this user.
+
+For further help contact the author: Mike.Lake@uts.edu.au
+'''
+
prefix = '''
<p>Hi</p>
@@ -334,23 +357,10 @@ def main():
##################################################
# Check program args and access to required files.
##################################################
-
- # I have replaced the default help's message with a clearer one.
- parser = argparse.ArgumentParser(\
- description='Check Your HPC Utilisation', \
- usage="%(prog)s running|finished|all [-h] [-u USER] [-e EMAIL]", \
- epilog='Contact %s for further help.' % from_email, \
- )
-
- parser.add_argument('state', choices=['running','finished','all'], default='running', \
- help='Select one job state to report on.')
- parser.add_argument('-u', '--user', help='Only show jobs for this user.')
- parser.add_argument('-e', '--email', help='Email a copy of this report to yourself.')
-
- args = parser.parse_args()
- state = args.state
- user_id = args.user
- recipient_email = args.email
+ args = docopt(usage_doc, argv=None, help=True, version=None, options_first=False)
+
+ user_id = None
+ recipient_email = None
# Check that we can access the HPC user database.
dirpath = os.path.dirname(sys.argv[0])
@@ -375,7 +385,7 @@ def main():
conn = pbs.pbs_connect(pbs_server)
- if state == 'running':
+ if args['running']:
# This will get just current jobs; queued, running, and exiting.
# We have added the 't' to also include current array jobs.
jobs = get_jobs(conn, extend='t')
@@ -390,7 +400,7 @@ def main():
# This will also remove array parent jobs as they are state 'B".
jobs = [j for j in jobs if j['job_state'] == 'R']
print('Found %d running jobs out of %d total jobs.' % (len(jobs), total))
- elif state == 'finished':
+ elif args['finished']:
# This will get ALL jobs, current and finished.
jobs = get_jobs(conn, extend='xt')
total = len(jobs)
@@ -416,7 +426,7 @@ def main():
jobs = jobs_tmp
print('Found %d finished jobs from last %d days.' % (len(jobs), past_days))
- elif state == 'all':
+ elif args['all']:
# This will get ALL jobs, current and finished.
jobs = get_jobs(conn, extend='xt')
total = len(jobs)
@@ -440,7 +450,7 @@ def main():
else:
# We should never get here.
- print("Invalid state %s" % state)
+ print("Invalid positional argument.")
sys.exit()
pbs.pbs_disconnect(conn)
@@ -466,17 +476,17 @@ def main():
sys.exit()
fh.write(prefix)
- if state == 'running':
+ if args['running']:
fh.write("<p>Running Jobs</p>")
fh.write(print_table_start())
print_jobs(jobs, fh)
fh.write(print_table_end())
- elif state == 'finished':
+ elif args['finished']:
fh.write("<p>Finished Jobs</p>")
fh.write(print_table_start())
print_jobs(jobs, fh)
fh.write(print_table_end())
- elif state == 'all':
+ elif args['all']:
# Write the running jobs.
fh.write("<a name='finished'/>")
fh.write("<p><b>Finished Jobs</b> - Go to list of <a href='#running'>running jobs</a></p>")
@@ -493,7 +503,7 @@ def main():
fh.write(print_table_end())
else:
# We should never get here.
- print("Invalid state %s" % state)
+ print("Invalid positional argument." )
fh.write(postfix)
fh.close()
--
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