Repository: airavata-docs Updated Branches: refs/heads/master 79b99846b -> eed63a29f
adding airavata documentation contributed by Eroma on github scigap docs folder Project: http://git-wip-us.apache.org/repos/asf/airavata-docs/repo Commit: http://git-wip-us.apache.org/repos/asf/airavata-docs/commit/eed63a29 Tree: http://git-wip-us.apache.org/repos/asf/airavata-docs/tree/eed63a29 Diff: http://git-wip-us.apache.org/repos/asf/airavata-docs/diff/eed63a29 Branch: refs/heads/master Commit: eed63a29f423a5e20c60958287537b7c90b91339 Parents: 79b9984 Author: smarru <[email protected]> Authored: Wed Mar 2 16:41:52 2016 -0500 Committer: smarru <[email protected]> Committed: Wed Mar 2 16:41:52 2016 -0500 ---------------------------------------------------------------------- Airavata-Installation.md | 159 +++++++++++++++++++++++++ AiravataApi.md | 7 ++ Application-CookBook.md | 121 +++++++++++++++++++ Contact-Us.md | 12 ++ FAQ.md | 83 +++++++++++++ Gateway-Configurations.md | 126 ++++++++++++++++++++ PGA-Installation.md | 198 ++++++++++++++++++++++++++++++++ User-Profiles.md | 43 +++++++ WSO2-IS-Configuration.md | 38 ++++++ airavata-properties.md | 68 +++++++++++ css/extra.css | 14 +++ img/MultipleWaystoUseAiravata.png | Bin 0 -> 72711 bytes img/MultipleWaystoUseAiravata1.png | Bin 0 -> 129098 bytes img/PGAMenu&SubMenu.png | Bin 0 -> 102694 bytes img/UserProfiles.png | Bin 0 -> 78923 bytes img/UserProfilesOLD.png | Bin 0 -> 101847 bytes mkdocs.yml | 23 ++++ 17 files changed, 892 insertions(+) ---------------------------------------------------------------------- http://git-wip-us.apache.org/repos/asf/airavata-docs/blob/eed63a29/Airavata-Installation.md ---------------------------------------------------------------------- diff --git a/Airavata-Installation.md b/Airavata-Installation.md new file mode 100644 index 0000000..008378c --- /dev/null +++ b/Airavata-Installation.md @@ -0,0 +1,159 @@ + +## Install Airavata +<b>NOTE: Below instructions are for users who host Airavata by themselves. +<br>For communities who require SciGaP to host the gateway can contact through <a href="http://docs.scigap.org/en/latest/Contact-Us/"; target="_blank">SciGaP - Contact Us</a></b> +<br></br> +<br><b>Click your option;</b></br> + +[<button type="button" style="color:#3232ff;text-align:center;font-weight:bold;background-color:darkgray;width:200px;border-radius:4px">Airavata Prerequisites</button>](#Airavata) +[<button type="button" style="color:#3232ff;text-align:center;font-weight:bold;background-color:darkgray;width:200px;border-radius:4px">Airavata on CentOS 7</button>](#AiravataCent) <br></br> + + +### <h3 id="Airavata">General Airavata Prerequisites</h3> +1. JAVA 8 or above is required + - Java installation on CentOS, Mac, Windows, etc.. - <a href="https://docs.oracle.com/javase/8/docs/technotes/guides/install/install_overview.html"; target="_blank">Oracle JAVA Installation</a> +2. RabbitMQ + - <a href="https://www.rabbitmq.com/download.html"; target="_blank">Download the RabbitMQ Binary</a><br>Select the download file as per the operating system of your machine/server. + - Same link has installing guide documentation as well. E.g.:<a href="https://www.rabbitmq.com/install-standalone-mac.html"; target="_blank">MAC Installation Guide</a> + - For detailed information on getting RabbitMQ started, stopped, etc please visit <a href="https://www.rabbitmq.com/documentation.html"; target="_blank">RabbitMQ Documentation</a> +3. Maven + - <a href="http://maven.apache.org/download.cgi"; target="_blank">Download Maven</a> (java based code building tool). +4. MySQL Database + +### <h3 id="AiravataCent">Airavata Installation on CentOS 7</h3> +<b>NOTE: Airavata installation on other operating systems are similar with minor changes.</b></br> +#### Prerequisites +1. CentOS 7 Default open JDK 1.8.0. (minimum) is sufficient. +2. Download RabbitMQ binary for CentOS 7 +<a href="https://https://www.rabbitmq.com/install-generic-unix.html"; target="_blank">Download RabbitMQ Binary for CentOS</a><br> +3. Prerequisite for RabbitmQ Erlang can be installed using yum +<pre><code>yum install Erlang</code></pre> +4. Unzip the downloaded RabbitMQ tar file into a folder in your local machine. +<pre><code>tar -xvf rabbitmq-server-mac-standalone-3.4.1.tar.gz</code></pre> +5. Start the RabbitMQ server in the bin folder using; + <pre><code>./sbin/rabbitmq-server start</code></pre> +6. Install Maven using yum install. ((install the latest maven 3.3.9. Default Maven default of centOS 7). +<pre><code>yum install maven</code></pre> +7. Install MySQL database +<pre><code>yum install mariadb-server</code></pre> +8. Start maria DB with; +<pre><code>systemstl start mariadb</code><pre> +9. While maria DB is running run +<pre><code>mysql _secure_installation</code></pre> +When executing above it will ask you for root password; provide it. +10. Create databases required for Airavata +<pre><code>create database airavata_appcatalog;</code></pre> +<pre><code>create database airavata_expcatalog;</code></pre> +<pre><code>create database airavata_datacatalog;</code></pre> +<pre><code>create database airavata_credentialstore;</code></pre> +<pre><code>create database airavata_wfcatalog;</code></pre> +11. Grant permission to these databases for Airavata<br> +Command syntax: <pre><code>grant all privileges on 'DB-Name'.<p>⁎ to 'username'@'%' identified by 'passwordâ;</code></pre> +E.g.: <pre><code>grant all privileges on airavata_appcatalog.<p>⁎ to 'airavatadb'@'%' identified by 'airavatadbâ;</code></pre> +NOTE: Grant permission to every databased created above. % can be replaced by 'localhost' (if DB is also in the same server as airavata). If DB is in a different server give the server name. +<br> + +#### Install Airavata +1. Create a folder in your local machine (E.g.: mkdir LocalAiravata).<br> +2. Clone the master source (If you have not taken a clone prior) code from github to the created folder.<br> +<pre><code>git clone https://github.com/apache/airavata.git</code></pre> +3. After cloning is completed, build the source code by executing following maven command (In LocalAiravata directory you made); +<pre><code>mvn clean install</code></pre> +Hint: To avoid tests (recommended for first time users) use +<pre><code>mvn clean install -Dmaven.test.skip=true</code></pre> +4. Locate the tar file in target directory +Path: +<pre><code>cd airavata/distribution/target/</code></pre> +5. Navigate to locally created directory (LocalAiravata) copy the tar file +<pre><code>cp airavata/distribution/target/apache-airavata-server-0.16-SNAPSHOT-bin.tar.gz ./</code></pre> +OR +<pre><code>cp airavata/distribution/target/apache-airavata-server-0.16-SNAPSHOT-bin.tar.zip ./</code></pre> +6. Now unzip either the tar or zip file of Airavata server distribution; +<pre><code>unzip apache-airavata-server-0.16-SNAPSHOT-bin.zip</code></pre> +OR +<pre><code>tar xvzf apache-airavata-server-0.16-SNAPSHOT-bin.tar.gz</code></pre> +7. Generate Credential store keystore file in the created local directory. +<pre><code> keytool -genseckey -alias airavata -keyalg AES -keysize 128 -storetype jceks -keystore airavata_sym.jks</code></pre> +For more information visit <a href="https://cwiki.apache.org/confluence/display/AIRAVATA/Credential+Store+Configuration+Guide/"; target="_blank">Credential Store Configuration Documentation</a> +8. Go and put mysql.jar in to lib of Airavata. navigate to lib; + <pre><code>cd /LocalFolderPath/apache-airavata-server-0.16-SNAPSHOT/lib</code></pre> +9. Navigate to bin folder which contains file airavata-server.properties and open it; +<pre><code>vi apache-airavata-server-0.16-SNAPSHOT/bin</code></pre> +10. Update relevant necessary properties to run Airavata locally.<br> +Change as required. Refer for more details;<a href="../Installations/airavata-properties.md"> Airavata Property File</a>. + - API Server Registry Configuration + - Comment out the derby DB properties + - Change MySQL configurations + - registry.jdbc.url=jdbc:mysql://localhost:3306/airavata_expcatalog (replace 'localhost' with correct server name if the DB is in a different server) + - registry.jdbc.user=airavata + - registry.jdbc.password=airavata + - default.registry.gateway=php_reference_gateway (give the gateway name you prefer. Default exists in the file) + - Application Catalog DB Configuration + - Comment out the derby DB properties + - Change MySQL configurations + - appcatalog.jdbc.url=jdbc:mysql://localhost:3306/airavata_appcatalog + - appcatalog.jdbc.user=airavata + - appcatalog.jdbc.password=airavata + - Data Catalog DB Configuration + - Comment out the derby DB properties + - Change MySQL configurations + - datacatalog.jdbc.url=jdbc:mysql://localhost:3306/airavata_datacatalog + - datacatalog.jdbc.user=airavata + - datacatalog.jdbc.password=airavata + - Workflow Catalog DB Configuration + - Comment out the derby DB properties + - Change MySQL configurations + - workflowcatalog.jdbc.url=jdbc:mysql://localhost:3306/airavata_wfcatalog + - workflowcatalog.jdbc.user=airavatadb + - workflowcatalog.jdbc.password=airavatadb + - Server module Configuration + - Make sure all servers required to start are added as given + - servers=apiserver,orchestrator,gfac,credentialstore + - API Server SSL Configurations + - Give the correct path for key generation file. This is in the bin directtory and it is shipped defualt with Airavata. + - apiserver.keystore=/home/airavata/LocalAiravata/apache-airavata-server-0.16-SNAPSHOT/bin/airavata.jks + - Credential Store module Configuration + - Make sure its'true' in + - start.credential.store=true + - Add the path to SSH key generation file + - E.g.: credential.store.keystore.url=/home/airavata/LocalAiravata/airavata-sym.jks + - Comment out the derby DB properties + - Change MySQL configurations + - credential.store.jdbc.url=jdbc:mysql://localhost:3306/airavata_credentialstore + - credential.store.jdbc.user=airavatadb + - credential.store.jdbc.password=airavatadb + - credential.store.keystore.url=/home/airavata/production-deployment/airavata_sym.jks + - API Security Configuration + - Make sure + - api.secured=false + - TLS.enabled=false + - Monitoring Module Configuration + - Add your email address, username and password for email monitoring. This is the email account the job status change emails will be received from compute resources. + email.based.monitor.host=imap.gmail.com + [email protected] + email.based.monitor.password=SamplePassword + - Zookeeper Server Configuration + - For 'Production' scenario make; + - embedded.zk=false + - AMQP Notification Configuration + - Users can use RabbitMQ as 'Guest' users. This is the easy method. For this uncomment + - rabbitmq.broker.url=amqp://localhost:5672 + - To use as a 'Production' user + - Navigate to RabbitMQ bin folder. + - Make sure the RabbitMQ server is running. For production use <pre><code>rabbitmq-server -detached</code></pre> to start. + - Create a virtual-host and user with a password. Follow documentation in <a href="http://blog.dtzq.com/2012/06/rabbitmq-users-and-virtual-hosts.html"; target="_blank">RabbitMQ Users & VirtualHost</a> + - To create a user; <pre><code>rabbitmqctl add_user Username Password</code></pre> + - To create a vitrual-host <pre><code>rabbitmqctl add_vhost vhostauthvhost</code></pre> + - Provide permission to created 'Username' to the created vhost <pre><code>rabbitmqctl set_permissions -p messaging airavata ".*" ".*" ".*â</code></pre> + - Uncomment rabbitmq.broker.url=amqp://Username:Password@localhost:5672/Vhost. Add the created username, password and Vhost in the URL. + - If you need to stop RabbitMQ use <pre><code>rabbitmqctl stop</code></pre> + If the RabbitMQ server stopped then the above user creation, vhost cretion and permission granting commmands need to run again after restarting the servers. +11. Download and install Zookeeper. Use <a href=" http://www.us.apache.org/dist/zookeeper/zookeeper-3.4.8/"; target="_blank">Download Zookeeper</a> <br> You can downlaod and install Zookeeper in the above created local folder; LocalAiravata +12. Navigate to the Zookeeper bin directory and start zookeeper <pre><code>zkServer.sh start</code></pre> +13. In bin start the Airavata server and monitor log messages; This may require JAVA_HOME to be defined. Some configurations such as in bin/zoo.cfg and bin/airavata-server.properties may have to be adjusted if some ports are already in use. Ports need to be open as well. +<pre><code>sh airavata-server.sh start</code></pre> (This will run the airavata server in the background in demon mode)<br> +14. If you are in the target folder use given to start Airavata server;<br> +<pre><code>sh apache-airavata-server-0.16-SNAPSHOT/bin/airavata-server.sh start</code></pre> +15. To monitor the server starting up, view the airavata server log;<br> +<pre><code>tail -f airavata-server.out</code></pre> +16. For subsequent Airavata copies; in the local Airavata folder where source code is cloned do a git clone https://github.com/apache/airavata.git for the latest trunk. \ No newline at end of file http://git-wip-us.apache.org/repos/asf/airavata-docs/blob/eed63a29/AiravataApi.md ---------------------------------------------------------------------- diff --git a/AiravataApi.md b/AiravataApi.md new file mode 100644 index 0000000..5e9f0e7 --- /dev/null +++ b/AiravataApi.md @@ -0,0 +1,7 @@ +## Airavata API + +For Airavata API documentation please visit <a href="http://airavata.staging.apache.org/documentation/api-docs/0.16/"; target="_blank">Airavata 0.16 API Documentation</a> + +If any questions or clarification regarding the API documentation please contact us through; +<a href="http://airavata.apache.org/community/mailing-lists.html"; target="_blank"><br>Airavata Mailing List</a> <br> OR<br> +<a href="https://www.hipchat.com/gMDHyN1KM"; target="_blank">HipChat</a> http://git-wip-us.apache.org/repos/asf/airavata-docs/blob/eed63a29/Application-CookBook.md ---------------------------------------------------------------------- diff --git a/Application-CookBook.md b/Application-CookBook.md new file mode 100644 index 0000000..5dbeeae --- /dev/null +++ b/Application-CookBook.md @@ -0,0 +1,121 @@ +## Application Cookbook Recipes + +### Airavata Applications and Available Resource List +| Application | Resource List | +|:----------------- |:--------------------------| +| Abinit | BigRed2 | +| Amber_Sander | BigRed2, Stampede, Comet | +| AutoDock | BigRed2 | +| CP2K | BigRed2 | +| Echo | BigRed2, Stampede, Comet | +| Gamess | BigRed2, Gordon | +| Gaussian | BigRed2, Comet, Gordon | +| Gromacs | BigRed2, Stampede | +| Lammps | BigRed2, Stampede, Comet | +| NEK5000 | BigRed2 | +| NWChem | Stampede, Comet | +| Phasta_P | Stampede | +| Quantum_Espresso | Stampede, Comet | +| Tinker_Monte | Stampede | +| WRF | Stampede | + + + +### Application Inputs +Inputs for all applications currently available in Airavata can be found in +https://iu.box.com/s/9ztdby709kso8siachz16svn2y511nn7 + + + +### Sample Application Recipes +#### Abinit +###### Module +- Name: Abinit +- Description: A package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT) +###### Interface +- Inputs: + - Pspgth-Input-File + - Tbase-Input-File-1 + - Tbase-Input-File-2 +- Outputs: + - Application-Out + - Standard-Error + - Standard-Out +###### Deployment + +| Resource | Executable Path | Application Parallelism | Module Load Commands | +|:------------------|:------------------------------------------|:--------------------------|:----------------------------------------------------------------------------------| +|bigred2.uits.iu.edu| /N/soft/cle4/abinit/cpu/7.6.4/bin/abinit | CRAY_MPI | module swap PrgEnv-cray/5.2.40 PrgEnv-gnu/5.2.40; module load netcdf fftw abinit | + + +#### Amber_sander +- Name: Amber_Sander +- Description: Assisted Model Building with Energy Refinement MD Package +- Inputs: + - Heat-Restart-File + - Parameter-Topology-File + - Production-Control-File +- Outputs: + - Amber-Execution-log + - Amber-Execution-Summary + - Amber-Restart-File + - Amber-Trajectory-File + - Standard-Error + - Standard-Out +- Deployment + +| Resource | Executable Path | Application Parallelism | Module Load Commands | +|:------------------ |:---------------------------------------------------------- |:--------------------------|:-----------------------------------------------------------------| +| bigred2.uits.iu.edu | /N/soft/cle4/amber/gnu/mpi/12/amber12/bin/sander.MPI -O | MPI | module load amber/gnu/mpi/12; module swap PrgEnv-cray PrgEnv-gnu | +| stampede.tacc.xsede.org| /opt/apps/intel13/mvapich2_1_9/amber/12.0/bin/sander.MPI -O | MPI | module load amber | +| comet.sdsc.edu | /opt/amber/bin/sander.MPI | MPI | module load amber | + + +#### AutoDock +- Name: AutoDock +- Description: AutoDock suite of automated docking tools +- Inputs: + - HSG1-Maps-FLD + - Input-File-DAT + - Input-File-DPF +- Outputs: + - Standard-Error + - Standard-Out +- Deployment + +| Resource | Executable Path | Application Parallelism | Module Load Commands | +|:------------------ |:---------------------------------------------|:--------------------------|:----------------------------| +| bigred2.uits.iu.edu | /N/soft/cle4/autodock/4.2/bin/autodock4 | MPI | module load autodock/4.2 | + + +##### CP2K +- Name: CP2K +- Description: CP2K Test Application Module +- Inputs: + - Input-File-INP +- Outputs: + - CP2K-Application-Output + - Standard-Error + - Standard-Out +- Deployment + +| Resource | Executable Path | Application Parallelism | Module Load Commands | +|:----------------- |:-----------------------------|:--------------------------|:------------------------| +| comet.sdsc.edu | /opt/cp2k/bin/cp2k.popt | MPI | module load cp2k | + + +##### Echo +- Name: CP2K +- Description: A Simple Echo Application +- Inputs: + - Input-to-Echo +- Outputs: + - Standard-Error + - Standard-Out +- Deployment + +| Resource | Executable Path | Application Parallelism | Module Load Commands | +|:------------------ |:---------------------------------------------------------- |:--------------------------|:-------------------------------| +| bigred2.uits.iu.edu | /N/u/seagrid/BigRed2/production/app_wrappers/echo_wrapper.sh | SERIAL | | +| stampede.tacc.xsede.org| /home1/02731/scigap/apps/echo_wrapper.sh | SERIAL | | +| comet.sdsc.edu | /home/scigap/apps/echo_wrapper.sh | SERIAL | | http://git-wip-us.apache.org/repos/asf/airavata-docs/blob/eed63a29/Contact-Us.md ---------------------------------------------------------------------- diff --git a/Contact-Us.md b/Contact-Us.md new file mode 100644 index 0000000..0209d14 --- /dev/null +++ b/Contact-Us.md @@ -0,0 +1,12 @@ +##Contact Us +For your clarifications, Questions and Suggestions please contact us through +<a href="http://airavata.apache.org/community/mailing-lists.html"; target="_blank">Airavata mailing list</a> + +OR + +<a href="https://www.hipchat.com/gMDHyN1KM"; target="_blank">HipChat</a> + +Issue Reporting +Any issue encounterered with Airavata or our gateway please log through; +<a href="https://issues.apache.org/jira/browse/AIRAVATA-1889?jql=project%20%3D%20AIRAVATA"; target="_blank">Airavata JIRA</a> +NOTE: If you don't have an account in Apache JIRA you have to create one prior to submitting issues. http://git-wip-us.apache.org/repos/asf/airavata-docs/blob/eed63a29/FAQ.md ---------------------------------------------------------------------- diff --git a/FAQ.md b/FAQ.md new file mode 100644 index 0000000..0fb3bcc --- /dev/null +++ b/FAQ.md @@ -0,0 +1,83 @@ +## Troubleshooting FAQ +<br><b class="blue"> Q1.</b> I have setup my own gateway and Airavata. When I log into the gateway I cannot create Compute resources. What should I do?</br> +<b class="blue">Answer: </b> In your pga_config.php (in folder .../testdrive/app/config) under heading 'Portal Related Configurations' set 'super-admin-portal' => false, to true.</br> +<br><b class="darkred">Q2.</b> I don't get notifications when users create new accounts in my gateway. Why?</br> +<b class="lred">Answer: </b> That's because you have not defined an email address in <br>'admin-emails' => ['[email protected]','[email protected]']. Here you can add one or many.</br> +<br><br><b class="darkred"> Q3.</b> I am not receiving email notifications from compute resoures for job status changes. What should I do?</br> +<b class="lred">Answer: </b> In airavata-server.properties please locate and set your email account information. +<pre><code>email.based.monitor.host=imap.gmail.com [email protected] +email.based.monitor.password=zzzz +email.based.monitor.folder.name=INBOX +email.based.monitor.store.protocol=imaps (either imaps or pop3)</pre></code> +<br><br><b class="darkred"> Q4.</b> In my Airavata log I have error messages like +<br>ERROR org.apache.airavata.api.server.handler.AiravataServerHandler - Error occurred while retrieving SSH public keys for gateway +<br>ERROR org.apache.airavata.credential.store.server.CredentialStoreServerHandler - Error occurred while retrieving credentials +<br>What should I do? +<br><b class="lred">Answer: </b> This could be due to missing tables in your credential store database. Check whether CREDENTIALS and COMMUNITY_USER tables exits. If not create then using +<pre><code>CREATE TABLE COMMUNITY_USER +( + GATEWAY_ID VARCHAR(256) NOT NULL, + COMMUNITY_USER_NAME VARCHAR(256) NOT NULL, + TOKEN_ID VARCHAR(256) NOT NULL, + COMMUNITY_USER_EMAIL VARCHAR(256) NOT NULL, + PRIMARY KEY (GATEWAY_ID, COMMUNITY_USER_NAME, TOKEN_ID) +); +</pre></code> +<pre><code>CREATE TABLE CREDENTIALS +( + GATEWAY_ID VARCHAR(256) NOT NULL, + TOKEN_ID VARCHAR(256) NOT NULL, + CREDENTIAL BLOB NOT NULL, + PORTAL_USER_ID VARCHAR(256) NOT NULL, + TIME_PERSISTED TIMESTAMP DEFAULT NOW() ON UPDATE NOW(), + PRIMARY KEY (GATEWAY_ID, TOKEN_ID) +); +</pre></code> +<br><br><b class="darkred"> Q5.</b> I cannot login to my Compute Resource and launch jobs from Airavata using the SSH key I generated. What should I do? +<br><b class="lred">Answer: </b> Steps to use generated SSH key<br> + - Generate SSH key + token using Credential Store<br> + - Add the generated token to your resource through PGA --> Admin Dashboard --> Gateway Preferences<br> + - Add the generated SSH key<br> + +<br><b class="darkred"> Q6.</b> When installing PGA in MAC i got below error after updating the composer. + <br>- Error<br> + Mcrypt PHP extension required.<br> + Script php artisan clear-compiled handling the post-update-cmd event returned with an error<br> + [RuntimeException]<br> + Error Output: +<br><b class="lred">Answer: </b> + Install mcrypt installation; + <a href="http://coolestguidesontheplanet.com/install-mcrypt-php-mac-osx-10-10-yosemite-development-server/"; target="_blanks">mcrypt Installation Steps</a> + +<br><b class="darkred"> Q7.</b> After following the required steps only the home page is working and some images are not shown properly. + <br><b class="lred">Answer: </b>If you are facing this behavior first check whether you have enabled mod_rewrite module in apache webserver. + <br>And also check whether you have set AllowOverride All in the Vhost configuration file in apache web server. <br>(e.g file location is /etc/apache2/sites-available/default and there should be two places where you want to change) +<br><pre><code> + <VirtualHost *:80> + ServerAdmin [email protected] + DocumentRoot /var/www/html/portal/public + ServerName pga.example.com + <Directory "/var/www/html/portal/public"> + AllowOverride all + </Directory> + ErrorLog logs/pga_error_log + CustomLog logs/pga--access_log common + </VirtualHost></code></pre> + <br> +<br><b class="darkred"> Q8.</b> I get the Error message Permission Denied to app/storage directory.<br> + <br><b class="lred">Answer: </b>Execute the following command and grant all permissions; <pre><code> sudo chmod -R 777 app/storage</code></pre> + +<br><b class="darkred"> Q9.</b> In Ubuntu environment when executing sudo composer update it fails with message "Mcrypt PHP extension required". + <br><b class="lred">Answer: </b>To fix this install PHP mcrypt extension by following the below steps; + <pre><code>sudo apt-get install php5-mcrypt</code></pre> + use locate mcrypt.so ,to get its locaton + locate mcrypt.ini and open the mcrypt.ini file + sudo pico /etc/php5/mods-available/mcrypt.ini + change the at line a extension=<location of e mcrypt.so file> eg:/usr/lib/php5/20121212/mcrypt.so + save changes. + execute the command: sudo php5enmod mcrypt + Now restart the apache server again and test PGA web-interface. + +<br><b class="darkred"> Q10.</b> When tried to login or create a new user account an Error is thrown which is similar to PHP Fatal error: SOAP-ERROR: Parsing WSDL: Couldn't load from... + <br><b class="lred">Answer: </b> If you face this kind of an error first check whether you have enabled PHP SOAP and OpenSSL extensions. If even after enabling them the issue is still occurring try updating the PHP OpenSSL extension. (Using command like yum update openssl) \ No newline at end of file http://git-wip-us.apache.org/repos/asf/airavata-docs/blob/eed63a29/Gateway-Configurations.md ---------------------------------------------------------------------- diff --git a/Gateway-Configurations.md b/Gateway-Configurations.md new file mode 100644 index 0000000..ccf39e4 --- /dev/null +++ b/Gateway-Configurations.md @@ -0,0 +1,126 @@ +## PGA Configurations +### You Need to Have +1. Airavata & PGA installed and running +2. Tenant created in WSO2 IS hosted by you or SGG +3. Administrator privileges to the gateway with username and password +<br> +<br> +### Airavata Component Configuration +1. For this we use 'Admin Dashboard' +2. Gateway Admin need to configure;<br> + - <a href="#CompResource">Compute Resources</a><br> + - <a href="#CompResource">Compute Resources</a><br> + - <a href="#StoreResource">Storage Resources</a><br> + - <a href= "#Preference">Resource Preferences</a><br> + - <a href= "#AppCatalog">Application Catalog</a><br> + - Application Module<br> + - Application Interface<br> + - Application Deployment<br> + - <a href= "#Credentials">Credential Store</a> + - Generate Credential Store Token + SSH Key. + - Add these to authorized key files and into preferences. +<br> +<br> +###<h3 id="CompResource">Compute Resources</h3> +1. Navigate to Admin Dashboard --> Compute Resources --> Register +2. Add Host Name, Description and create the resource. +3. Then add data storage information in + - Data Movement Interfaces +4. And Save. +5. Similarly you can add multiple storage resources in to your gateway by selecting 'Register' from the left-hand-side menu. +6. To view the added resources navigate to Admin Dashboard --> Storage Resources --> Browse +7. All the resources will be listed. Gateway admin can view, edit, delete them. +NOTE: Currently enabling and disabling storage resources is not an active feature. +<br> +<br> +###<h3 id="StoreResource">Storage Resources</h3> +1. Navigate to Admin Dashboard --> Storage Resources --> Register +2. Add Storage Name, Description and create the resource. +3. Then keep adding information on rest of the tabs appeared. + - Queues + - File Systems (Not required at the moment) + - Job Submission Interfaces + - Data Movement Interfaces +4. And Save. +5. Similarly you can add multiple compute resources in to your gateway by selecting 'Register' from the left-hand-side menu. +6. To view the added compute resources navigate to Admin Dashboard --> Compute Resource --> Browse +7. All the resources will be listed. Gateway admin can view, edit, delete and enable and disable them. +<br> +<br> +###<h3 id="Preference">GatewayPreferences for Resources</h3> +1. Navigate Admin Dashboard --> Gateway Preferences +2. Both compute resource and storage resource specific preferences are defined here. +3. To add compute resource related preferences click "Add a Compute Resource Preferences" and select the resource from the drop-down list. +4. Add/select preferred options and click "Set preferences". Repeat this for all the resources used within the gateway. +<br>Repeat this for every active enabled compute resource in the gateway. +4. For each compute resource, gateway admin need to; + - whether the preferences can be overridden by Airavata - Yes/No + - Resource login name + - Preferred job submission and data movement protocols + - Preferred queue + - Scratch location + - Project allocation number + - Resource specific credential store token +5. For adding storage resource preference click "Add a Storage Resource Preferences", and rest is similar to adding a compute resource preference. +6. For a gateway currently when a storage resource is selected, that resource ID need to be added in to the pga_config.php file in config folder of the hosted gateway. +7. For storage resource preference, gateway admin need to add; + - Login username + - File System Root Location + - Resource Specific Credential Store Token +8. Apart from adding preference the same interface is used to assign a 'Base Credential Store Token". If this is added this is the token used across the gateway for communication with all the compute resources and storage resource. +<br> +<br> +### <h3 id="AppCatalog">Application Catalog</h3> +1. Gateway admin add applications in to the gateway. Adding an application is a 3 step process. +2. Admin need to add application module, interface and deployment information in order to launch specific application jobs on compute resources. +3. What each step means? + - <b class="blue">Application Module</b> + - Navigation: Admin Dashboard --> App Catalog --> Module + - This is the simple introduction of the application; Name, Version and Description. + - Click on 'Create a New Application Module' and provide information. + - Click Create. + - All available modules are also listed; admin has the option of searching for a particular module by providing the name in the search. + - Gateway admin can edit, delete existing modules. + - Deleting a module will be restricted if it has application interfaces and deployments linked. + - <b class="blue">Application interface</b> + - Navigation: Admin Dashboard --> App Catalog --> Interface + - Application interface defines the required inputs, output produced and their characteristics. + - Click on 'Create a New Application Interface' and provide information. + - Click Create. + - All available interfaces are also listed; admin has the option of searching for a particular interface by providing the name in the search. + - Gateway admin can edit, delete existing interfaces. + - Gateway admin cal also clone an existing interface in order to create a new similar interface with slight changes. + - <b class="blue">Application deployment</b> + - Navigation: Admin Dashboard --> App Catalog --> Deployment + - Application deployment describes application deployment details on a specific resource. + - For an application for each resource there is a separate deployment. +<br> +<br> +### <h3 id="Credentials">Credential Store</h3> +1. Navigation: Admin Dashboard --> Credential Store +2. This interface is used to generate SSH key + token pairs. +3. These generated keys can be added in to the authorized key files in each resource for SSH key based communication. +4. When generated key can be either assigned at gateway level; one key + token pair for all the resources OR have separate keys for each resource. +5. SSH keys are used for communication with compute resources and storage resources. + +### <h3 id="Preference">WSO2 IS Configuration</h3> +1. Setting up WSO2 IS for the new gateway. +2. Once PGA is cloned all information related to user identity will be in app/config/pga_config.php. No modifications required for users who are using hosted IS. +3. For user identity management we could either use Airavata WSO2 IS or users own WSO2 IS. +4. Download WSO2 Identity Server 5.0 from http://product-dist.wso2.com/products/identity-server/5.0.0/wso2is-5.0.0.zip +5. Extract the downloaded IS binary archive to a location <IS_HOME>. +6. Set JAVA_HOME variable and add jdk bin directory to the PATH variable. +7. Open <IS_HOME>/repository/conf/carbon.xml and change the following property to false +<HideAdminServiceWSDLs>false</HideAdminServiceWSDLs> +8. Execute the following command to run the server +sh <IS_HOME>/bin/wso2server.sh +You should be able to login to the Identity Server Web App using your browser with url http://localhost:9443/carbon . Default admin credentials are username: admin, password: admin +9. For more information regarding WSO2 Identity Server refer this https://docs.wso2.org/display/IS460/Deploying+in+Production +Gateway admin will be provided with + - Domain URL for the Gateway + - Admin User name + + + + + http://git-wip-us.apache.org/repos/asf/airavata-docs/blob/eed63a29/PGA-Installation.md ---------------------------------------------------------------------- diff --git a/PGA-Installation.md b/PGA-Installation.md new file mode 100644 index 0000000..8776a4c --- /dev/null +++ b/PGA-Installation.md @@ -0,0 +1,198 @@ +# PGA Installation + +[<button type="button" style="color:darkred;text-align:center;font-weight:bold;background-color:Steal;width:200px;border-radius:4px">PGA on MAC OS</button>](#headPGAMAC) +[<button type="button" style="color:darkred;text-align:center;font-weight:bold;background-color:Steal;width:200px;border-radius:4px">PGA on Cent OS</button>](#headPGACENTOS) + +## <a name="head1234"></a>General PGA Prerequisites +1. A Unix or Unix like operating system +2. A web server (e.g apache web server) with PHP 5.4 or higher. Make sure have enabled mod_rewrite module in httpd.conf file and enable PHP SOAP extension +3. Composer +4. MYSQL database (Required if the user is hosting Airavata on his own. To communicate with hosted Airavata this step is not relevant) +5. MCrypt PHP extension +6. Enable OpenSSL PHP extension +7. Follow instructions given in links to install the prerequisites based on the OS ; + - On Ubunutu: http://www.dev-metal.com/install-laravel-4-ubuntu-12-04-lts/ + - On Centos: https://www.digitalocean.com/community/tutorials/how-to-install-laravel-4-on-a-centos-6-vps + - On MAC OS: http://sangatpedas.com/20140219/installing-laravel-osx-mavericks/ +8. Important: Do not need to install Laravel. You can skip the steps given on the links +9. WSO2 IS server + +## <a name="headPGACENTOS"></a>PGA Installation on CentOS 7 +### <a name="head12345"></a>Pre-Installations +1. Install apache +<pre><code>Yum install httpd</code></pre> +2. module_rewrite is auto enabled in apache version in centos7. Its in /etc/httpd/conf.modules.d/00-base.conf file and the line is LoadModule rewrite_module modules/mod_rewrite.so +3. Enable php using <pre><code>yum install php-soap</code></pre> Could be be it is already enabled in CentOS7 +4. Install php using  <pre><code>yum install php</code></pre> +5. install composer +<pre><code>yum install composer</code></pre> +6. Install php-mcrypt <pre><code>yum install php-mcrypt</code></pre> + +### Download and Configure PGA +1. Take the git clone https://github.com/apache/airavata-php-gateway.git +<br> Needs to take the clone in the document root. in centOS7 its var/www/html +2. Change the cloned folder name to your desired folder name(e.g.: php-gateway). This will carry sub folders for the gateway +<pre><code>cp - R airavata-php-gateway /* .</code></pre> +3. In the gateway folder do a <pre><code<composer update</code></pre> +4. Give permission to user data folder +<pre><code>chmod -R 777 /var/www/portals/gateway-user-data/php-gateway</code></pre> +5. Copy pga_config.template and make  pga_config.php +6. In pga_config.php change airavata server, change; + - Airavata Client Configurations + - 'airavata-server' => 'localhostâ, + - 'gateway-id' => 'airavata_test_gateway', + - 'experiment-data-absolute-path' => '/var/www/experimentData',(Here user has to create the experimentData folder in var/www) + - 'gateway-data-store-resource-id' => '' + - Portal Related Configurations + - 'super-admin-portal' => false, (User has one gateway and need to use it to configure the compute resources, storage resources, etc...) + - 'admin-emails' => ['[email protected]'], + - 'portal-email-username' => '[email protected]', + - 'portal-email-password' => '&airavaxxxxxx', + - WSO2 Identity Server Related Configurations + - Add WSO2 IS related details URL, username, password, etc⦠+ +7. Give writing permission chmod -R g+rwx app/storage/ +<br>in the http config file add URL information for the gateway file path (this is in w54 pga server) vi /etc/httpd/conf/httpd.conf +8. Make sure SElinux comparability of airaveata_php_gateway folder. for that give chcon -Rv --type=httpd_sys_content_t airavata-php-gateway/ - this is to make sure this folder is readable by http + +9. ls - lZ shows the SELinux context. after the above chcon command do the same for storage folder as well su -c "chcon -R -h -t httpd_sys_script_rw_t [fullpath]/app/storageâ - this is to make sure the folder is writable + +10. once the URL info added restart the http service +<pre><code>systemctl restart  httpd.service</code></pre> + +11. Configure firewall to allow http and https +<pre><code>firewall-cmd --zone=public --list-services</code></pre> - check existing configurations +<pre><code>firewall-cmd --zone=public --permanent --add-service=http</code></pre> - allow for http +<pre><code>firewall-cmd --zone=public --permanent --add-service=https</code></pre> - allow for https + +<pre><code>firewall-cmd âreload - refresh</code></pre> - to get rules applied. + + + + +## <a name="headPGAMAC"></a>PGA Installation on MAC Yosemite OS +### <a name="head12345"></a>Pre-Installations +1. To install MCrypt for PHP on MAC please follow the steps in http://coolestguidesontheplanet.com/install-mcrypt-php-mac-osx-10-10-yosemite-development-server/. +2. First check wether your MAC has Apache installed. To check availability; +<pre><code>apache ctrl start</code></pre> +3. To stop running Apache use; +<pre><code>apache ctl stop</code></pre> +4. Once above is completed follow the steps given in https://web.archive.org/web/20150507101703/http://sangatpedas.com/20140219/installing-laravel-osx-mavericks for + - Configuring Apache + - Installing Composer (Use sudo commands as and when required for installation) +5. To install Composer use +<pre><code>curl -sS https://getcomposer.org/installer | php</code></pre> +6. Then move Composer using +<pre><code>mv composer.phar /usr/local/bin/composer</code></pre> + +### Download and Configure PGA +1. Go to cd /Library/WebServer/Documents +2. Take a copy from GIT using +<pre><code>git clone https://github.com/apache/airavata-php-gateway.git</code></pre> +3. Navigate to PGA folder +<pre><code>cd /Library/WebServer/Documents/airavata-php-gateway</code></pre> +4. Make sure the storage folder is writable by all users +<pre><code>sudo chmod -R 777 app/storage</code></pre> +5. Move out of app folder and give; +<pre><code>sudo composer update</code></pre> +This will take few minutes +6. You might get an error like this +-------------- +Mcrypt PHP extension required. +Script php artisan clear-compiled handling the post-update-cmd event returned with an error + + + + [RuntimeException] + Error Output: + + +-------------- + +7. install mcrypt installation +http://coolestguidesontheplanet.com/install-mcrypt-php-mac-osx-10-10-yosemite-development-server/ +8. (Optional) Go to [PGA_HOME]/app/config/pga_config.php and change the configuration to match your settings +9. Enable Apache extensions (mod_rewrite module and PHP SOAP extension) +<pre><code>sudo vim /etc/apache2/httpd.conf</code></pre> + uncomment #LoadModule rewrite_module libexec/apache2/mod_rewrite.so + uncomment #LoadModule php5_module libexec/apache2/libphp5.so +10. Now issue composer update command +<pre><code>sudo composer update</code></pre> +11. Restart the web server +<pre><code>sudo apachectl restart</code></pre> + +###Link Airavata and PGA +1. Once the PGA and Airavata are downloaded and locally running; in PGA app/config folder locate the file called pga_config.php.template +2. Copy the located file and name it as pga_config.php +3. In the newly copied file find two configurations for + - Airavata host + - Port +4. Change above configurations + - Airavata host = localhost + - Port = 9930 +5. You are all set to run your own PGA! +6. For steps to register resources, applications, etc⦠use <Link to admin guide> +7. For steps to create projects, experiments and monitor them use <Link to end user guide> +IMPORTANT: In places where the hosted PGA link is used please replace by your locally running PGA URL. + + +## <a name="PGAUbuntuOS"></a>PGA Installation on Ubuntu OS +//http://tecadmin.net/install-java-8-on-centos-rhel-and-fedora/ +### Pre-Installations +1. To install dependencies use commands in https://vpsineu.com/blog/how-to-install-laravel-on-a-centos-7-vps/ +In the command avoid installing mysql and mariaDB +2. Enable the appropriate extensions: navigate to php.ini + <pre><code>sudo vi /etc/php.ini</code></pre> + - Uncomment the following extensions: mcrypt.so, openssl.so, and soap.so. If they do not exists add them as extensions. + <pre><code>extension=mcrypt.so</code></pre> + <pre><code>extension=openssl.so</code></pre> + <pre><code>extension=soap.so</code></pre> + - Locate httpd.conf file + <pre><code>sudo vi /etc/httpd/conf/httpd.conf</code></pre> + - Find 'AllowOverride None' and change to 'AllowOverride All' (Two places to change) + + +### Download and Configure PGA +1. The following guide give a sample installation starting from a fresh Ubunutu 12.04 installation. Similar instructions should be used in other operating systems. +2. Update the ubuntu package manager +<pre><code>sudo apt-get update</pre></code> +<pre><code>sudo apt-get upgrade </pre></code> +3. Install Apache +</pre></code>sudo apt-get install apache2</pre></code> +4. Install PHP 5.4 +<pre><code>sudo apt-get install python-software-properties</pre></code> +<pre><code>sudo add-apt-repository ppa:ondrej/php5-oldstable</pre></code> +<pre><code>sudo apt-get update</pre></code> +<pre><code>sudo apt-cache policy php5</pre></code> +<pre><code>sudo apt-get install php5</pre></code> +4. You can check the installed versions of apache and php using <pre><code>apache2 -v</pre></code> and <pre><code>php -v commands</pre></code> +5. Install the necessary php extensions +<pre><code>sudo apt-get install unzip</pre></code> +<pre><code>sudo apt-get install curl</pre></code> +<pre><code>sudo apt-get install openssl</pre></code> +<pre><code>sudo apt-get install php5-mcrypt</pre></code> +<pre><code>sudo apt-get install php-soap</pre></code> +6. Install Composer System Wide +<pre><code>curl -sS https://getcomposer.org/installer | php</pre></code> +<pre><code>sudo mv composer.phar /usr/local/bin/composer</pre></code> +7. Activate mod_rewrite +<pre><code>sudo a2enmod rewrite</pre></code> +<pre><code>sudo service apache2 restart</pre></code> +8. Open the default vhost config file: + <pre><code>sudo nano /etc/apache2/sites-available/default. </pre></code> +9. Now search for âAllowOverride Noneâ corresponding âDocumentRoot /var/www <Directory /var/www>â +<br>(which should be there TWO times) and change both to âAllowOverride Allâ. Search for these two lines.</br> +10. Exit and save with CTRL+X, Y, ENTER. + +Download PGA from GIT +Download PGA from github to the document root of you web server /var/www. +Use git clone https://github.com/apache/airavata-php-gateway.git or download the zip from the github web page. +Go inside the PGA directory (e.g /var/www/airavata-php-gateway) +Make sure the storage folder is writable +sudo chmod -R 755 app/storage +Go to [PGA_HOME]/app/config/pga_config.php and change the configuration to match your settings + +Now issue composer install command +sudo composer install +Restart the web server +sudo service apache2 restart \ No newline at end of file http://git-wip-us.apache.org/repos/asf/airavata-docs/blob/eed63a29/User-Profiles.md ---------------------------------------------------------------------- diff --git a/User-Profiles.md b/User-Profiles.md new file mode 100644 index 0000000..e4012f8 --- /dev/null +++ b/User-Profiles.md @@ -0,0 +1,43 @@ +# Airavata User Profiles + +### What Are Airavata User Profiles? + +1. When using Airavata as the middleware between your gateway and computational resources first lets identify and understand the user profiles available and their potential. +2. Knowing the profiles and the features of each will assist on shaping your gateway user hierarchy. +3. There are 4 active user profiles in Airavata with different set of features at each level. +4. 'Image - Airavata User Profiles' depicts the features available for each profile. + + +### What each user Profile can do within PGA? + +- Super Admin + - Super admins has access to all the gateways as well as to Airavata and PGA. Currently this role resides with limited members of SGG group at IU. + - Create Gateway and set up identity server for user account management. + - Register Computer resource available to submit jobs through Airavata. + - Add email monitoring accounts detail to Airavata for each gateway. + - Investigate issues with individual experiments from any of the gateways under SciGaP. +<br> +<br> +- Gateway Admin + - Set up gateway preferences for Compute Resources and Storage Resources + - Generate SSH keys and their tokens using Credential Store in Admin Dashboard. + - Add the generated SSH token to Gateway Preferences. + - Add the generated SSH keys to authorized_key files in each resource. + - Can Cancel, clone experiments of a gateway user through Admin dashboard behalf of the user. + - Create Applications and their deployments in to the gateway. +<br><b>NOTE: If user hosts his own gateway; 'Gateway Admin' role will hold features of both Super Admin and Gateway Admin.</b></br><br> + +- Gateway Admin-Read-Only + - Can view everything in Admin Dashboard but cannot Add, Edit or Delete any records from dashboard. + - Can monitor experiments through Experiments Statistics in Admin dashboard. + - Behalf of a gateway user can edit, cancel or clone an experiment. +</br> +<br> +- Gateway User + - Create, launch their own experiments in using available applications and compute resources. + - Monitor progress of experiment execution. + - Group experiments by creating Projects. + - Request new features, applications and report bug, issue using Service Desk + - Password recovery. +</br> + http://git-wip-us.apache.org/repos/asf/airavata-docs/blob/eed63a29/WSO2-IS-Configuration.md ---------------------------------------------------------------------- diff --git a/WSO2-IS-Configuration.md b/WSO2-IS-Configuration.md new file mode 100644 index 0000000..608a493 --- /dev/null +++ b/WSO2-IS-Configuration.md @@ -0,0 +1,38 @@ +## WSO2 IS (Identity Server) + +The steps are for IS configuration when IS is hosted by AIravata team. n this situation you will be a tenant created under Airavata hosted IS. + +### First You Need to; +1. Request from Airavata team for a new Tenant account. For this use +<br><a href="http://airavata.apache.org/community/mailing-lists.html"; target="_blank">Airavata mailing list</a> +OR +<a href="https://www.hipchat.com/gMDHyN1KM"; target="_blank">HipChat</a> +2. As the gateway admin, for the account creation provide; + - First name + - Last name + - Preferred username & password as the admin (This is the username you will use to login to WSO2 IS and gateway as the admin user) + - Email account +3. Once the tenant is created you will receive + - URL for WSO2 IS + - Username and password to login to WSO2 IS +<br> +<br> +### Configuration +1. Login to IS server as the gateway admin; Tenant user. + - Use the URL provided by the Airavata team; <a href="https://idp.scigap.org:9443/carbon/admin/login.jsp"; target="_blank">WSO2 URL for Gateway Admin</a> + - Use the username and password provided by you. (Please change your password in first login) +2. Navigate to Main Tab -->Service Providers --> Add + - Give a service provider name and 'Register' + - Out of the list below expand 'Inbound Authentication Configuration' + - Out of the usb list underneath expand 'OAuth/OpenID Connect Configuration' and click 'Configure' + - You will be navigated to 'Register New Application' UI. +3. To register new application; + - Select OAuth Version = 2.0 + - From Allowed Grant Types select only 'Password' and 'Refresh Toekn' + - Add + +4. Copy the 'OAuth Client Key', 'OAuth Client Secret', Admin username, password and name to pga_config.php. +5. Navigate to Configure â> Claim management â>http://wso2.org/claims. And make "Supported by Default = true" +6. Navigate to Configure --> Users & Roles --> Users. Find the admin user and click 'User Profile'. Add the username at the bottom and update. + +You are all set to start configuring the gateway for job submission. For Gateway Configurations visit <a href="#Gateway-Configuration.md">PGA Configuration</a> http://git-wip-us.apache.org/repos/asf/airavata-docs/blob/eed63a29/airavata-properties.md ---------------------------------------------------------------------- diff --git a/airavata-properties.md b/airavata-properties.md new file mode 100644 index 0000000..76d2d75 --- /dev/null +++ b/airavata-properties.md @@ -0,0 +1,68 @@ +##<h2 id="airavata-properties.md">Airavata Server Properties</h2> +1. API Server Registry Configuration + - Comment out the derby DB properties + - Change MySQL configurations + - registry.jdbc.url=jdbc:mysql://localhost:3306/airavata_expcatalog (replace 'localhost' with correct server name if the DB is in a different server) + - registry.jdbc.user=airavata + - registry.jdbc.password=airavata + - default.registry.gateway=php_reference_gateway (give the gateway name you prefer. Default exists in the file) +2. Application Catalog DB Configuration + - Comment out the derby DB properties + - Change MySQL configurations + - appcatalog.jdbc.url=jdbc:mysql://localhost:3306/airavata_appcatalog + - appcatalog.jdbc.user=airavata + - appcatalog.jdbc.password=airavata +3. Data Catalog DB Configuration + - Comment out the derby DB properties + - Change MySQL configurations + - datacatalog.jdbc.url=jdbc:mysql://localhost:3306/airavata_datacatalog + - datacatalog.jdbc.user=airavata + - datacatalog.jdbc.password=airavata +4. Workflow Catalog DB Configuration + - Comment out the derby DB properties + - Change MySQL configurations + - workflowcatalog.jdbc.url=jdbc:mysql://localhost:3306/airavata_wfcatalog + - workflowcatalog.jdbc.user=airavatadb + - workflowcatalog.jdbc.password=airavatadb +5. Server module Configuration + - Make sure all servers required to start are added as given + - servers=apiserver,orchestrator,gfac,credentialstore +6. API Server SSL Configurations + - Give the correct path for key generation file. This is in the bin directtory and it is shipped defualt with Airavata. + - apiserver.keystore=/home/airavata/LocalAiravata/apache-airavata-server-0.16-SNAPSHOT/bin/airavata.jks +7. Credential Store module Configuration + - Make sure its 'true' in + - start.credential.store=true + - Add the path to SSH key generation file + - E.g.: credential.store.keystore.url=/home/airavata/LocalAiravata/airavata-sym.jks + - Comment out the derby DB properties + - Change MySQL configurations + - credential.store.jdbc.url=jdbc:mysql://localhost:3306/airavata_credentialstore + - credential.store.jdbc.user=airavatadb + - credential.store.jdbc.password=airavatadb + - credential.store.keystore.url=/home/airavata/production-deployment/airavata_sym.jks +8. API Security Configuration + - Make sure + - api.secured=false + - TLS.enabled=false +9. Monitoring Module Configuration + - Add your email address, username and password for email monitoring. This is the email account the job status change emails will be received from compute resources. + email.based.monitor.host=imap.gmail.com + [email protected] + email.based.monitor.password=SamplePassword +10. Zookeeper Server Configuration + - For 'Production' scenario make; + - embedded.zk=false +11. AMQP Notification Configuration + - Users can use RabbitMQ as 'Guest' users. This is the easy method. For this uncomment + - rabbitmq.broker.url=amqp://localhost:5672 + - To use as a 'Production' user + - Navigate to RabbitMQ bin folder. + - Make sure the RabbitMQ server is running. For production use <pre><code>rabbitmq-server -detached</code></pre> to start. + - Create a virtual-host and user with a password. Follow documentation in <a href="http://blog.dtzq.com/2012/06/rabbitmq-users-and-virtual-hosts.html"; target="_blank">RabbitMQ Users & VirtualHost</a> + - To create a user; <pre><code>rabbitmqctl add_user Username Password</code></pre> + - To create a vitrual-host <pre><code>rabbitmqctl add_vhost vhostauthvhost</code></pre> + - Provide permission to created 'Username' to the created vhost <pre><code>rabbitmqctl set_permissions -p messaging airavata ".*" ".*" ".*â</code></pre> + - Uncomment rabbitmq.broker.url=amqp://Username:Password@localhost:5672/Vhost. Add the created username, password and Vhost in the URL. + - If you need to stop RabbitMQ use <pre><code>rabbitmqctl stop</code></pre> + If the RabbitMQ server stopped then the above user creation, vhost cretion and permission granting commmands need to run again after restarting the servers. http://git-wip-us.apache.org/repos/asf/airavata-docs/blob/eed63a29/css/extra.css ---------------------------------------------------------------------- diff --git a/css/extra.css b/css/extra.css new file mode 100644 index 0000000..4e4a405 --- /dev/null +++ b/css/extra.css @@ -0,0 +1,14 @@ +.darkred{ + color: #7f0000; + /*darkred*/ +} + +.lred{ + color: #b20000; + /*lighterred*/ +} + +.blue{ + color: #3333ff; + /*darkblue*/ +} \ No newline at end of file http://git-wip-us.apache.org/repos/asf/airavata-docs/blob/eed63a29/img/MultipleWaystoUseAiravata.png ---------------------------------------------------------------------- diff --git a/img/MultipleWaystoUseAiravata.png b/img/MultipleWaystoUseAiravata.png new file mode 100644 index 0000000..59ffed3 Binary files /dev/null and b/img/MultipleWaystoUseAiravata.png differ http://git-wip-us.apache.org/repos/asf/airavata-docs/blob/eed63a29/img/MultipleWaystoUseAiravata1.png ---------------------------------------------------------------------- diff --git a/img/MultipleWaystoUseAiravata1.png b/img/MultipleWaystoUseAiravata1.png new file mode 100644 index 0000000..38fa949 Binary files /dev/null and b/img/MultipleWaystoUseAiravata1.png differ http://git-wip-us.apache.org/repos/asf/airavata-docs/blob/eed63a29/img/PGAMenu&SubMenu.png ---------------------------------------------------------------------- diff --git a/img/PGAMenu&SubMenu.png b/img/PGAMenu&SubMenu.png new file mode 100644 index 0000000..266602e Binary files /dev/null and b/img/PGAMenu&SubMenu.png differ http://git-wip-us.apache.org/repos/asf/airavata-docs/blob/eed63a29/img/UserProfiles.png ---------------------------------------------------------------------- diff --git a/img/UserProfiles.png b/img/UserProfiles.png new file mode 100644 index 0000000..2a24a48 Binary files /dev/null and b/img/UserProfiles.png differ http://git-wip-us.apache.org/repos/asf/airavata-docs/blob/eed63a29/img/UserProfilesOLD.png ---------------------------------------------------------------------- diff --git a/img/UserProfilesOLD.png b/img/UserProfilesOLD.png new file mode 100644 index 0000000..3685437 Binary files /dev/null and b/img/UserProfilesOLD.png differ http://git-wip-us.apache.org/repos/asf/airavata-docs/blob/eed63a29/mkdocs.yml ---------------------------------------------------------------------- diff --git a/mkdocs.yml b/mkdocs.yml new file mode 100644 index 0000000..7c01758 --- /dev/null +++ b/mkdocs.yml @@ -0,0 +1,23 @@ +site_name: Airavata Documentation +docs_dir: . + +pages: +- Home: 'index.md' +- Installations: + - Airavata: 'Airavata-Installation.md' + - PGA: 'PGA-Installation.md' + - Airavata Property File: 'airavata-properties.md' +- Configuration: + - PGA: 'Gateway-Configurations.md' + - WSO2 IS: 'WSO2-IS-Configuration.md' +- Documentation: + - User Profiles: User-Profiles.md + - Applications: Application-CookBook.md + - Airavata API: AiravataApi.md +- FAQ: FAQ.md +- Contact Us: Contact-Us.md + +theme: readthedocs + +extra_css: + - css/extra.css \ No newline at end of file
