How to Use the SCF in Today’s Environment June 13, 2007 DMT Meeting

How to Use the SCF in Today’s
Environment
June 13, 2007
DMT Meeting
Lisa Coleman, Scott Zentz
Denise Cooper, Walt Miller
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Topics
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Currently Accessible SCF Computers
Which Machines to Use for What
Contact information
So Far and What’s Next
Editing SAN Files from Your iMac (Miller)
Tricks & Info (Cooper)
Submitting a Job to the Cluster (Cooper)
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Currently Accessible SCF
Computers
Individual Workstations
iMacs, PCs, SUNs, etc.
manila, corregidor
Mac G5 servers
Mac cluster
thunder, lightning
(16 processors each)
Multiple Mac G5 computers
controlled by a single head node
SGI’s high performance
computer with compiler
Lanina
(36 processors)
SGI’s high performance
computer
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Which Machine to Use for What
Individual
Workstations
manila,
corregidor
Mac cluster
File editing and activities such as email,
calendars, etc.
- Compile & test before running on cluster
- Changing Open Directory passwords
- Submitting jobs to the cluster
Simultaneously execute multiple jobs
thunder,
lightning
Editing, compiling, and executing software
lanina
Executing compiled software
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Contact Information
• SCF system malfunctions
[email protected]
• ASDC system malfunctions
[email protected]
• Cluster job submittal
[email protected]
• NOMAD questions
[email protected]
• General “How to” type questions
[email protected]
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So Far and What’s Next
• Recently accomplished goals (CERES DMT)
Deployment of the iMacs
Migration to the san
• Near term goals
Maximize use of cluster as intended
Move off of thunder and lightning
• Long term
Move off of lanina
Make use of Intel machines on cluster
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Editing SAN Files from your iMac
Walter Miller
SSAI
June 13, 2007
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Overview
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Attaching CERES SAN
Finder
Darwin Terminal
Editors
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Attaching SAN Step 1
From Finder, Highlight Go and select Connect to Server
Apple K should also bring the next window up
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Selecting SAN
The CERES SAN is cebu.larc.nasa.gov
NFS mount for old system is below
SA needs to set this portion up
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Logging into SAN
Change the name from alias to Manila user name,
i.e. miller not Walt Miller
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Select Correct Volume
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Next Window
Select your folder (directory)
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Reaching it from Finder
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Opening File with Default
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Selecting Editor
A couple of other editors are shown
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Darwin Terminal
Mounted file systems under /Volumes
Command for various editors
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Available Editors
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Carbon Emacs
Nedit
TextEditor
TextWrangler
Xcode
Can use file open menu to get to SAN
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TextWrangler
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Quirks
• Some editors will open new file on desktop that
the editor is already open, not where terminal is.
• TextWrangler will save line numbers to file if
using option.
• Nedit does not appear as an option from finder.
• In Nedit, need to hit enter after selecting folder to
list next level.
• Different hot keys between editors.
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Tricks & Info
Denise Cooper
SSAI
June 13, 2007
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Tricks & Info
• To log into a different system, eg. Warlock
In X11 menu –
Select Customize
Select Duplicate for Terminal
Edit the new Terminal line by double clicking each field
Change Terminal to warlock
Change the command xterm to the following:
xterm –geometry 155x50+130+150 –title WARLOCK –bg “midnight blue” –fg white –fa Monaco –fs
12 –sb –sl 1000 –e sh –c “ssh –Y warlock –p 250 –l cooper”
Or
xterm –geometery 155x50+130+150 –title WARLOCK –bg “#154031” –fg white –fa Monaco –fs 12 –
sb –sl 1000 –e sh –c “ssh –Y warlock –p250 –l cooper”
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Tricks & Info
• To see color numbers such as “#154031” go
to the following:
URL://http:houseof3d.com/pete/applets/tools/colors
• The above URL was discovered by Taiping Zhang and allows you to
move a set of sliders to select color numbers for background and
foreground. The colors must be surrounded by quotes and have a #
before the six digits as shown above.
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Tricks & Info
• To mount the SAN disk to your machine:
Select Finder
In the Finder menu select Go - Connect to Server
Make sure to change the name listed to your login name for
manila/corregidor and fill in your password and click Connect.
A Finder window will appear and you should then select CERES
An icon with a globe and CERES underneath will appear on your desktop
and you now have access to your directories on the SAN.
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Tricks & Info
• To edit a file using CarbonEmacs
In your .cshrc file add the following line:
alias emacs ‘open –a /Applications/Emacs.app’
This will allow you to open emacs directly from a terminal
window on your machine.
Open a new X11 terminal window on your machine
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Tricks & Info
cd /Volumes/CERES/instrumentsan/development/denise_area/rel4/rcf
emacs CER1.1P3_input_find.csh
This will bring up an emacs window, remember that the
normal menu you are used to seeing on emacs on thunder
will be up at the top of your screen on your iMac. You will
also notice if you try to emacs the same file on thunder it
will tell you that the file is locked.
You may also use nedit or any other editor that you prefer,
even vi.
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Tricks & Info
• Editing a FrameMaker document
Make sure the FrameMaker document resides on your iMac
Open up dingo using the Citrix server on your iMac
Select Start – Programs – Adobe – FrameMaker 7.0 – Adobe FrameMaker
7.0
In FrameMaker select File – Open – C$ on ‘Client’ (V:) – select file you
want to edit
If the Start button does not show up on your dingo server, select
MyComputer from the desktop and then select the FrameMaker file
from there starting from C$ on ‘Client’ (V: )
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Submitting a Job to the Cluster
• You may want to look at an example of a script that submits a set
of jobs to the cluster where each creates the PCFin, PCF and runs
the job on a Node:
/CERES/instrumentsan/development/denise_area/mac/rcf/jobSubmitter_p
This script requires that you have a couple of directories and other
scripts in your rcf area: joblogs/ & Ed3_Repro/
You can copy this script and those in Ed3_Repro and edit them to work
in your area. Remember that you must source your environment when
you submit a job to a cluster node – it does not have the environment
that you have on manila carried over to the cluster node, it is a NEW
machine, so nothing is set up until you do it in your script. This is the
same as how it works in production at ASDC.
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Submitting a Job to the Cluster
• Things you will need:
– Account on manila/corregidor, at this time you can only
submit jobs from these two machines
– wrapper script
– joblogs directory – for your wrapper.sh.oxxxxx &
wrapper.sh.exxxxx files
• Command to submit a job:
– qsub –S /bin/csh –V –o <output_file_directory> –e
<error_file_directory> –q <queue_name> <wrapper_script_name>
<script variables> OR
– qsub –S /bin/csh –V –o <output file directory> -j y –q <queue
name> <wrapper script name> <script variables>
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Submitting a Job to the Cluster
• Examples:
– qsub –S /bin/csh –V –o /CERES/instrumentsan/rcf/joblogs –e /CERES/instrument-san/rcf/joblogs –
q processing /CERES/instrumentsan/rcf/Ed3_Repro/wrapper.sh 20070613 FM1
– qsub –S /bin/csh –V –o /CERES/instrumentsan/rcf/joblogs –j y –q processing /CERES/instrumentsan/rcf/Ed3_Repro/wrapper.sh 20070613 FM1
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