1 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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How to Use the SCF in Today’s Environment

June 13, 2007

DMT MeetingLisa Coleman, Scott Zentz

Denise Cooper, Walt Miller

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Topics

• 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 Multiple Mac G5 computers controlled by a single head node

thunder, lightning

(16 processors each)

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

File editing and activities such as email, calendars, etc.

manila,

corregidor

- Compile & test before running on cluster

- Changing Open Directory passwords

- Submitting jobs to the cluster

Mac 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 help@asdsun

• ASDC system malfunctions help@sorcerer

• Cluster job submittal help@asdsun

• NOMAD questions [email protected]

• General “How to” type questions help@asdsun

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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

• Attaching CERES SAN

• Finder

• Darwin Terminal

• Editors

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Attaching SAN Step 1

From Finder, Highlight Go and select Connect to ServerApple K should also bring the next window up

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Selecting SAN

The CERES SAN is cebu.larc.nasa.govNFS mount for old system is belowSA 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 /VolumesCommand for various editors

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Available Editors

• 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”

Orxterm –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/instrument-san/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 documentMake 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/instrument-san/development/denise_area/mac/rcf/jobSubmitter_pThis 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/instrument-san/rcf/joblogs –e /CERES/instrument-san/rcf/joblogs –q processing /CERES/instrument-san/rcf/Ed3_Repro/wrapper.sh 20070613 FM1

– qsub –S /bin/csh –V –o /CERES/instrument-san/rcf/joblogs –j y –q processing /CERES/instrument-san/rcf/Ed3_Repro/wrapper.sh 20070613 FM1