STASH_UTILS Deployment Guide

Lawrie Rikus, Wenming Lu

21 Jan 2016

Installation of stash_utils ver 0.0.9

1. Installation of stash_utils at /projects/access/apps/

Note: We understand that the following procedures are not standard practice to deploy utilities. Those procedures are illustrated here to record how we deliver the stash_utils at the first time. All these procedures will be updated to follow the agreed common guidelines in the future and this doc will be updated accordingly.

• Prepare the location for stash_utils go to raijin,

cd /projects/access/apps/
mkdir -p stash_utils
cd stash_utils
mkdir -p 0.0.9
cd 0.0.9
mkdir -p python

• Deploy the scripts and codes At the raijin:/projects/access/apps/stash_utils/0.0.9/python

cp -r /home/548/ljr548/python/STASHmasterDB .
cp -r /home/548/ljr548/python/STASHutils .
cp /home/548/ljr548/python/pretty_stash.py .

Note: All of these scripts and codes will be put into SVN and the steps will be updated to check out from the svn repository.

• Deploy the lib prettytable At raijin:$HOME,

~ljr548/anaconda2/bin/pip install prettytable --user

Then prettytable is installed at raijin:$HOME/.local, copy the prettytable to stash_utils,

cp -r $HOME/.local/lib/python2.7/site-packages /projects/access/apps/stash_utils/0.0.9/python

Note: We need to discuss how to install prettytable for general uses.

2. Creation of stash_utils module at /projects/access/modules/stash_utils

At raijin:/projects/access/modules/,

mkdir stash_utils
cd stash_utils
touch 0.0.9

And update the module file 0.0.9 as,

#%Module
source /opt/Modules/extensions/extensions.tcl

set name "stash_utils"
set version "0.0.9"
set install-contact "Wenming Lu <[email protected]>"
set install-date    "21-01-16"
set help "stash utils"
set url https://access-svn.nci.org.au/svn/utils/trunk

set prefix "/projects/access/apps/$name/$version"

prepend-path PATH $prefix/bin
prepend-path PATH $prefix/python

# Add line break after docommon to avoid warnings from module switch

prepend-path PYTHONPATH /projects/access/apps/stash_utils/0.0.9/python/STASHutils/:/projects/access/apps/stash_utils/0.0.9/python/site-packages


source /projects/access/modules/common

Note: This module file should be in SVN repository (to be discussed!)

3. Test of the installation

Open a raijin xterm and,

module load stash_utils/0.0.9
pretty_stash.py

You should see the output as follows,

Usage: pretty_stash.py [options] arg1

Options:
  --version             show program's version number and exit
  -h, --help            show this help message and exit
  -f FILENAME, --file=FILENAME
                        Read in STASH info from FILE  Default: STASHC
  -u USER, --user=USER  User ID (for job location) default: Current user
  -s SECTNUM, --section=SECTNUM
                        Number of section of stash to examine: [0]
  -x EXPT, --expt=EXPT  UMUI experiment ID (for job location)
  -S STASHMASTER, --SMDir=STASHMASTER
                        Location of pythonj stashmaster DBs [default:
                        /home/548/ljr548/python/STASHmasterDB//vUMVer
  -v UMVER, --UMVer=UMVER
                        UM Version of STASHmaster [default: 7.6]