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From er...@apache.org
Subject airavata-docs git commit: Added gaussian configuration steps to run in comet
Date Mon, 13 Feb 2017 20:56:29 GMT
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 <eroma.abeysinghe@gmail.com>
Authored: Mon Feb 13 15:56:25 2017 -0500
Committer: Eroma Abeysinghe <eroma.abeysinghe@gmail.com>
Committed: Mon Feb 13 15:56:25 2017 -0500

----------------------------------------------------------------------
 Admin-Tutorials.md | 124 +++++++++++++++++++++++++++++++++++++++++-------
 1 file changed, 107 insertions(+), 17 deletions(-)
----------------------------------------------------------------------


http://git-wip-us.apache.org/repos/asf/airavata-docs/blob/db4a4c87/Admin-Tutorials.md
----------------------------------------------------------------------
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>
 ![Screenshot](img/AppInterface1.png) ![Screenshot](img/AppInterface2.png) </br></br>
 3. Create the application deployment: Echo on Local Machine
     - Navigate to Admin Dashboard &rarr; App Catalog &rarr; 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
+![Screenshot](img/AppDeployment.png)
 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 &rarr; App Catalog &rarr; 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 &rarr; App Catalog &rarr; 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>
+![Screenshot](img/GauAppInt1.png) ![Screenshot](img/GauAppInt2.png) ![Screenshot](img/GauAppInt3.png)
</br></br>
+3. Create the application deployment: Gaussian on Comet
+    - Navigate to Admin Dashboard &rarr; App Catalog &rarr; 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)
+![Screenshot](img/GauAppDep.png)
+
 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.
 


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