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Posted to commits@airavata.apache.org by er...@apache.org on 2017/02/13 20:56:29 UTC
airavata-docs git commit: Added gaussian configuration steps to run
in comet
Repository: airavata-docs
Updated Branches:
refs/heads/master a31d32a26 -> db4a4c877
Added gaussian configuration steps to run in comet
Project: http://git-wip-us.apache.org/repos/asf/airavata-docs/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata-docs/commit/db4a4c87
Tree: http://git-wip-us.apache.org/repos/asf/airavata-docs/tree/db4a4c87
Diff: http://git-wip-us.apache.org/repos/asf/airavata-docs/diff/db4a4c87
Branch: refs/heads/master
Commit: db4a4c877aa65f8b189da778139a02b26489d987
Parents: a31d32a
Author: Eroma Abeysinghe <er...@gmail.com>
Authored: Mon Feb 13 15:56:25 2017 -0500
Committer: Eroma Abeysinghe <er...@gmail.com>
Committed: Mon Feb 13 15:56:25 2017 -0500
----------------------------------------------------------------------
Admin-Tutorials.md | 124 +++++++++++++++++++++++++++++++++++++++++-------
1 file changed, 107 insertions(+), 17 deletions(-)
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http://git-wip-us.apache.org/repos/asf/airavata-docs/blob/db4a4c87/Admin-Tutorials.md
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diff --git a/Admin-Tutorials.md b/Admin-Tutorials.md
index ff0c6e0..cb69ab2 100644
--- a/Admin-Tutorials.md
+++ b/Admin-Tutorials.md
@@ -2,7 +2,7 @@
This page is dedicated to Gateway Admins!
-### Prior to starting your configurations make sure;
+### Prior to starting your configurations
1. You have admin access to the PGA portal, Admin Dashboard
2. Storage resource ID added to the pga_config.php </br>
3. Credentials generated, updated in PGA and added to authorized_keys file in compute resources
@@ -10,15 +10,13 @@ This page is dedicated to Gateway Admins!
NOTE: If you are using a hosted gateway the 2 and 4 would be taken cared by the SciGaP team.
-### Select Your Quick Start Tutorials
+### Select Your Quick Start Tutorial
1. <a href="#LocalJob">Running Echo on Local Machine</a></br>
2. <a href="#GaussianJob">Gaussian Job Submission to Comet (XSEDE resource)</a></br>
3. <a href="#PrePostCommands">Add Environment Variables, Pre and Post Job Commands for an Application</a></br>
4. <a href="#SampleApp">Samples Application Configurations</a></br>
5. <a href= "#QOS&Reservation">Add Gateway QOS and Reservation for a Cluster</a></br>
6. <a href= "#Preference">Add Storage Resource Preferences</a></br>
-<br>
-</br>
#####<h5 id="LocalJob">Running Echo on Local Machine</h5>
Quickest way to confirm Airavata and PGA setup. This will tell you what you need to do to Echo a simple 'Hello World' in your local machine
@@ -54,16 +52,29 @@ Quickest way to confirm Airavata and PGA setup. This will tell you what you need
- Required in Commandline: True
- Meta Data:
- Provide application outputs
- - Click Add Application Output
- - Name: Echo-Standard-Out
- - Value:
- - Type: STDOUT
- - Application Argument:
- - Data Movement: False
- - Is the Output required?: True
- - Required on command line?: True
- - Location:
- - Search Query:</br>
+ NOTE: 3 application outputs to define.</br>
+ - 1st output
+ - Click Add Application Output
+ - Name: Echo-Standard-Out
+ - Value:
+ - Type: STDOUT
+ - Application Argument:
+ - Data Movement: False
+ - Is the Output required?: True
+ - Required on command line?: True
+ - Location:
+ - Search Query:</br>
+ - 2nd output
+ - Click Add Application Output
+ - Name: Echo-Standard-Error
+ - Value:
+ - Type: STDERR
+ - Application Argument:
+ - Data Movement: False
+ - Is the Output required?: True
+ - Required on command line?: True
+ - Location:
+ - Search Query:</br>
  </br></br>
3. Create the application deployment: Echo on Local Machine
- Navigate to Admin Dashboard → App Catalog → Application Deployment
@@ -72,16 +83,95 @@ Quickest way to confirm Airavata and PGA setup. This will tell you what you need
- Application Compute Host: Local (Local machine has to be added as a compute resource prior to this step)
- Application Executable Path: /home/airavata/ECHO/echo_wrapper.sh (Local to where you have airavata installed)
- Application Parallelism Type: SERIAL
+
4. Echo_wrapper.sh contains;
<pre><code>
#!/bin/bash
- #sleep 4
- echo "Echoed_Output=$1" >> $2 2>> $3
+ #sleep 10
+ echo "Echoed_Output=$*"
</code></pre>
#####<h5 id="GaussianJob">Gaussian Job Submission to Comet (XSEDE resource)</h5>
This is a tutorial to configuring and running an application on XSEDE resource through PGA portal.
+
+1. Create new application module: Gaussian
+ - Navigate to Admin Dashboard → App Catalog → Apllication Module
+ - Click Create a new Application Module
+ - Enter Application Module Name: Gaussian
+ - Enter Application Module Version: Gaussian 09 (Not mandatory)
+ - Enter Description: Gaussian provides capabilities for electronic structure modeling
+ - Create
+ - This create the Gaussian module </br>
+2. Create the application interface: Gaussian
+ - Navigate to Admin Dashboard → App Catalog → Application Interface
+ - Click 'Create new Application Interface'
+ - Add Application Name: Gaussian
+ - Add Application Description: Gaussian provides capabilities for electronic structure modeling
+ - Select Application Module: Gaussian ( If multiple modules are using same interface here you can add multiple modules. Ex: Gaussian 03 and Gaussian 09 modules)
+ - Set 'Enable Archiving Working Directory' to True (Why? - This is set to true when you want to bring back all the files in working directory back to PGA. Caution: If there are very large files they may not be able to SCP)
+ - Set 'Enable Optional File Inputs' to False (Why? - Set to false because there won't be any additional optional inputs for Gaussian)
+ - Provide application inputs
+ - Click Add Application Input
+ - Name: Input-File
+ - Value:
+ - Type: URI (Why - This is the type for file uploads)
+ - Application Arguments:
+ - Standard Input: False (Why? - Futuristic property and not in real use at the moment)
+ - User Friendly Description: Gaussian input file specifying desired calculation type, model chemistry, molecular system and other parameters. (This is information to the user at creating job experiment. Not mandatory)
+ - Input Order: 1
+ - Data is Staged: False
+ - Is the Input Required: True
+ - Required in Commandline: True
+ - Meta Data:
+ - Provide application outputs</br>
+ NOTE: 3 application outputs to define. </br>
+ - 1st Output
+ - Click Add Application Output
+ - Name: Gaussian-Application-Output
+ - Value: Gaussian.log
+ - Type: URI
+ - Application Argument:
+ - Data Movement: True
+ - Is the Output required?: True
+ - Required on command line?: True
+ - Location:
+ - Search Query:</br>
+ - 2nd output
+ - Click Add Application Output
+ - Name: Gaussian-Standard-Out
+ - Value:
+ - Type: STDOUT
+ - Application Argument:
+ - Data Movement: False
+ - Is the Output required?: True
+ - Required on command line?: True
+ - Location:
+ - Search Query:</br>
+ - 3rd output
+ - Click Add Application Output
+ - Name: Gaussian-Standard-Error
+ - Value:
+ - Type: STDERR
+ - Application Argument:
+ - Data Movement: False
+ - Is the Output required?: True
+ - Required on command line?: True
+ - Location:
+ - Search Query:</br>
+   </br></br>
+3. Create the application deployment: Gaussian on Comet
+ - Navigate to Admin Dashboard → App Catalog → Application Deployment
+ - Click 'Create new Application Deployment'
+ - Application Module: Gaussian
+ - Application Compute Host: comet.sdsc.edu (Your comet specific gateway preferences need to be added in 'Gateway Management' prior to this)
+ - Application Executable Path: g09
+ - Application Parallelism Type: SERIAL
+ - Application Deployment Description: Gaussian provides capabilities for electronic structure modeling.
+ - Module Load Commands: module load gaussian
+ - Post Job Commands: mkdir -p "$PWD"_restart; cp *.chk ${pwd}_restart; mv *.rwf* ${pwd}_restart; (Why? - any command you would want to execute after post job execution)
+
+
Work-in-Progress
-Refer <a href="/Gateway-Configurations/#AppCatalog" target="_blank">Application Configuration</a> for more details.
+Refer <a href="/Gateway-Configurations/#AppCatalog" target="_blank">Application Configuration</a> for more generic details.