This project has received funding from the European Union’s Horizon 2020
research and innovation programme under grant agreement n° 654237
Lesson 6: Portlet for job submission
Mario Torrisi – University of Catania - Italy ([email protected])
Sci-GaIA Winter School
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Outline
MyJob portleto G&C Engine monitoring module
o UsersTracking database
Portlet Templateo Get portlet code
o Build and deploy
o Job submission and log inspection
Portlet codeo Code structure
o Java Classes
o processInputFile() method
o submitjob() method
o Customization script
MyJobs Portlet
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MyJobs portlet
Is a core component of the Catania Science Gateway
Framework
Allows users to manage their jobs on DCIs
o Check jobs status
o Retrieve output when jobs complete their execution
MyJobs.war
Interacts with the Grid & Cloud
Engine Monitoring module
You can simply download and
deploy MyJobs portlet into your
Science Gateway
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MyJobs Portlet
Download
o http://grid.ct.infn.it/csgf/binaries/MyJobs.war
Deploy
o cp /path/to/MyJobs.war /path/to/plugin-sdk/dist
o Check server.log file, you should see MyJobs was successfully deployed
Add MyJobs to page
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MyJobs Portlet
Active Job
List
Done Job
List
Job status
Job Label
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User Tracking Database
Each user action which involves the distributed
infrastructure will be tracked by the UsersTracking
Database
Download sql script from here to create the Users Tracking
Database schema
The G&C Engine uses the GridOperations table to
register applications and services accessing the distributed
infrastructure
mysql> describe GridOperations;+-------------+--------------+------+-----+---------+----------------+| Field | Type | Null | Key | Default | Extra |+-------------+--------------+------+-----+---------+----------------+| id | int(11) | NO | PRI | NULL | auto_increment || portal | varchar(120) | NO | | NULL | || description | varchar(200) | NO | | NULL | |+-------------+--------------+------+-----+---------+----------------+3 rows in set (0.00 sec)
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GridOperations table
How to get GridOperations values
o id – application identifier
o portal – portal name, see picture below to get the right value
o description – human readable application label
Application registration in the GridOperations table is
mandatory for the MyJobs portlet
+-------------+| Field |+-------------+| id || portal || description |+-------------+
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MyJobs Portlet
In order to MyJobs Portlet (and all the other applications)
works properly you need to create a JDBC Connection
Pool and JDBC Resources in the application server, used
by the G&C Engine to communicate with the Users
Tracking Database.o JDBC Connection Pool is a group of reusable connections for a particular
database1
o JDBC resource (data source) provides applications with a means of
connecting to a database.[ … ] A JDBC resource is identified by its Java
Naming and Directory Interface (JNDI) name1
1 https://docs.oracle.com/cd/E26576_01/doc.312/e24928/jdbc.htm#GSADG00576
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Application server
JDBC Connection Pool/Resource
G&C Engine
JNDI Resource
Users Tracking
Database
JDBC Driver
Connection Pool
connection
connection
connection
connection
lookup
SQL connection
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JDBC Connection Pool/Resource
To create JDBC Connection Pool and JDBC Resource you
can
1. Edit the domain.xml file
/path/to/liferay-bundle/glassfish-3.1.2/…/config/domain.xml
Look for <resources> tag
Add an new connection pool using the properties highlighted in next
slide, pay attention to set the right address of DB container
• Tip check the docker inspect command
Add two jdbc resources using the properties highlighted in next slide
Look for <servers> tag
Add two jndi resources as shown in the next slide to allow lookup
Save and close file
Restart domain
2. Configure them through the Glassfish Web Admin interface
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Here what you should have in your domain.xml file
JDBC Connection Pool
<resources>
...
<jdbc-connection-pool driver-classname="" datasource-
classname="com.mysql.jdbc.jdbc2.optional.MysqlConnectionPoolDataSource" res-
type="javax.sql.ConnectionPoolDataSource" description="" name="UsertrackingPool">
<property name="User" value="tracking_user"></property>
<property name="Url"
value="jdbc:mysql:// :3306/userstracking"></property>
<property name="Password" value="usertracking"></property>
</jdbc-connection-pool>
<jdbc-resource pool-name="UsertrackingPool" description="" jndi-
name="jdbc/UserTrackingPool"></jdbc-resource>
<jdbc-resource pool-name="UsertrackingPool" description="" jndi-
name="jdbc/gehibernatepool"></jdbc-resource>
...
<resources/>
<servers>
<server name=”server” config-ref="server-config">
<resource-ref ref="jdbc/UserTrackingPool"></resource-ref>
<resource-ref ref="jdbc/gehibernatepool"></resource-ref>
...
<servers/>
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JDBC Connection Pool
1
2
3
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JDBC Resource
1
2
3
Template Portlet
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Template Portlet
The Template Portlet is a complete example of portlet able
to submit a sequential Job into a distributed environment.
Its Java code extends the Liferay MVCPortlet class and
uses JSP pages to generate the input GUI
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Template Portlet(Features)
It provides a full example of:
o Defining distributed infrastructure settings where the application will run
o Managing input elements from web forms as application input
o Managing upload file requests
o Managing portlet configuration to handle distributed infrastructure settings
o Viewing/Managing the ‘pilot_script’ that contains the batch instructions that will be executed on the remote.
It is a multi-infrastructure multi-middleware portlet to execute the same application on several infrastructures and middleware (currently supports: gLite-based Grids, HPC Clusters, Cloud resources)
It can be used as starting point to develop your own applications
o A customization script is provided in order make its reuse easy
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Template Portlet(Build & Deploy)
Clone the source repository
o cd /path/to/plugin-sdk/portlet
o git clone https://github.com/sci-gaia/template-portlet.git
o cd template-portlet
o ant deploy
Add to page
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Template Portlet(Usage)
template-portlet
o Performs the hostname command on DCIs
You can consider it like ‘HelloWorld’ while approaching new
programming languages
o It accepts:
An input file in order to show how to manage file as input of a real
application
A job label string in order to organize users interactions in the MyJobs
portlet (Optional)
o It has two buttons:
Submit: to submit job
Cancel: to reset form fields
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Template Portlet(Job submission)
Now you are …
… almost ready to submit jobs
A few mandatory steps are missing
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Template Portlet(Configuration)
Tip: insert the right values in GridOperations table
Add
infrastructure
Manage
infrastructure
View / Edit
pilot_script
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Template Portlet(Configuration – Infrastructure Management)
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Before testing the job execution
Install Grid CA certificates, follow instruction for your system from here
Download the tar at this link2 and extract it in the /etc/grid-security/ folder of your liferay container. It contains a directory for each trusted VO. Inside each VO directory two types of files can be found:o An LSC file contains a description of the certificate chain of the certificate used
by a VOMS server to sign VOMS attributes.
o An X509 certificates used by a VOMS server to sign attributes
Open the VPN or be sure the eTokenserver allows incoming connections on port 8082 form your portal IP address
Check the eTokenserver service is reachableo Connect to http://etokenserver2.ct.infn.it:8082/eTokenServer/
o From the interface generate the robot proxy request
o Execute curl or wget on the generated request
2 http://italiangrid.github.io/voms/documentation/voms-clients-guide/3.0.3/
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Template Portlet(Job submission)
Select a file
(optional)
Specify a label
(optional)
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Job Execution(Log inspection)
Liferay server.log file reports:
o A full dump of the portlet preference values
o The GridEngine Initialization
o The Robot proxy retrieval
[mi_hostname_portlet:108] dump:Infrastructure #1
enableInfrastructure : 'yes'nameInfrastructure : 'EUMEDGRID-Support infrastructure'acronymInfrastructure: 'EUMEDGRID'
INFO JSagaJobSubmission - Getting adaptor name...JSagaJobSubmission - Using adaptor: wms
INFO RobotProxy - proxyPath=/tmp/7f7e1e98-0fd1-4ebb-a1ae-0627efddf600INFO RobotProxy - get proxy: http://etokenserver.ct.infn.it:8082/eTokenServer/eToken/332576f78a4fe70a52048043e90cd11f?voms=gridit:gridit&proxy-renewal=true
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Job Execution(Log inspection)
The JSAGA job submission string
The input sandbox file transfers
The job id and the job status thread execution
INFO JSagaJobSubmission - jobSandbox:/opt/liferay-portal-6.1.1-ce-ga2/glassfish-3.1.2/domains/domain1/autodeploy/mi-hostname-portlet/WEB-INF/job/pilot_script.sh>pilot_script.sh,/tmp/20130717133558_test_input_file.txt>20130717133558_test_input_file.txt,/tmp//jobOutput/multiinfrastructuredemojobdescription1_1/<hostname-Output.txt,/tmp//jobOutput/multiinfrastructuredemojobdescription1_1/<hostname-Error.txt
Connecting to Gsiftp service at: wms014.cnaf.infn.it:2811...
JSagaJobSubmission - Job Submitted: [wms://wms014.cnaf.infn.it:7443/glite_wms_wmproxy_server]-[https://wms014.cnaf.infn.it:9000/kznSb62LcqCW0fXTiTfr7Q]UsersTrackingDBInterface - UpdateJobsStatusAsync running in Thread : Thread[pool-103-thread-1,5,grizzly-kernel]
Portlet Code
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Portlet code(Code structure)
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AppInfrastructureInfo.javao This class extends InfratructureInfo G&C Engine class to provide
some other useful methods
AppInput.java
o This class is meant to collect all application GUI inputs and must be dynamically instantiated inside the action method as soon as the user press the ‘Submit’ button
AppPreferences.java
o Class that contains all portlet’s preferences values
ConfigurationActionImpl.java
o This class implements ConfigurationAction Liferay interface
o Manage the code for portlet configuration
TemplatePortlet.java
o We will see this class more in depth later …
Portlet code(Java Classes)
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Portlet code(Java Classes)
Constats.java
o This class is meant to collect application constants
Utils.java
o This class is used to manage useful methods that interact with:
Application preferences
file2String(), string2File() methods
G&C Engine infrastructure parameters conversion
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Portlet code(TemplatePortlet.java)
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ThemeDisplay themeDisplay = (ThemeDisplay) actionRequest
.getAttribute(WebKeys.THEME_DISPLAY);
User user = themeDisplay.getUser();
String username = user.getScreenName();
appInput.setUsername(username);
Gets AppPreferences and AppInfrastructureInfo from portlet
preferences
Gets username using Liferay API
Action method
@ProcessAction(name = "submit")
public void submit(ActionRequest actionRequest,
ActionResponse actionResponse) throws IOException, PortletException {
AppInput appInput = new AppInput();
PortletPreferences preferences = actionRequest.getPreferences();
String JSONAppPrefs = GetterUtil.getString(preferences.getValue(
Constants.APP_PREFERENCES, null));
AppPreferences appPrefs = Utils.getAppPreferences(JSONAppPrefs);
String JSONAppInfras = GetterUtil.getString(preferences.getValue(
Constants.APP_INFRASTRUCTURE_INFO_PREFERENCES, null));
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Action method
UploadPortletRequest uploadRequest = PortalUtil
.getUploadPortletRequest(actionRequest);
File uploadedFile = processInputFile(uploadRequest, username,
timestamp, appInput);
List<AppInfrastructureInfo> enabledInfras = Utils
.getEnabledInfrastructureInfo(JSONAppInfras);
if (enabledInfras.size() > 0) {
InfrastructureInfo infrastructureInfo[] = Utils
.convertAppInfrastructureInfo(enabledInfras);
submitJob(appPrefs, appInput, infrastructureInfo);
Extracts UploadRequest from ActionRequest, calls processInputfile()
method and then submitJob()
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private File processInputFile(UploadPortletRequest uploadRequest,
String username, String timestamp, AppInput appInput)
throws IOException {
File file = null;
String fileInputName = "fileupload";
String sourceFileName = uploadRequest.getFileName(fileInputName);
if (Validator.isNotNull(sourceFileName)) {
_log.debug("Uploading file: " + sourceFileName + " ...");
String fileName = FileUtil.stripExtension(sourceFileName);
_log.debug(fileName);
appInput.setInputFileName(fileName);
String extension = FileUtil.getExtension(sourceFileName);
_log.debug(extension);
// Get the uploaded file as a file.
File uploadedFile = uploadRequest.getFile(fileInputName, true);
File folder = new File(Constants.ROOT_FOLDER_NAME);
// This is our final file path.
file = new File(folder.getAbsolutePath() + Constants.FILE_SEPARATOR
+ username + "_" + timestamp + "_" + fileName
+ ((!extension.isEmpty()) ? "." + extension : ""));
FileUtil.move(uploadedFile, file);
}
return file;
}
processInputFile()
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Initializes variable for JobSubmssion
private void submitJob(AppPreferences preferences, AppInput appInput,
InfrastructureInfo[] enabledInfrastructures) {
// Job details
String executable = "/bin/sh";
String arguments = FileUtil.getShortFileName(pilotScript) + " "
+ appInput.getInputFileName();
String outputPath = "/tmp/";
String outputFile = "hostname-Output.txt";
String errorFile = "hostname-Error.txt";
String appFile = "hostname-Files.tar.gz";
// InputSandbox (string with comma separated list of file names)
String inputSandbox = pilotScript + "," + appInput.getInputSandbox();
// OutputSandbox (string with comma separated list of file names)
String outputSandbox = appFile;
...
submitJob()
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submitJob()
// Prepare the GridEngine job description
GEJobDescription jobDesc = new GEJobDescription();
jobDesc.setExecutable(executable);
jobDesc.setArguments(arguments);
jobDesc.setOutputPath(outputPath);
jobDesc.setOutput(outputFile);
jobDesc.setError(errorFile);
jobDesc.setOutputFiles(outputSandbox);
jobDesc.setInputFiles(inputSandbox);
// GridEngine' MultiInfrastructure job submission object
MultiInfrastructureJobSubmission miJobSubmission = null
...
// Ready now to submit the Job
miJobSubmission.submitJobAsync(appInput.getUsername(), portalIPAddress,
applicationId, appInput.getJobLabel());
Creates GEJobDescription object
Actual job submission
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Customization script
customize.sh
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References
Template portlet source code repository
o https://github.com/sci-gaia/template-portlet
Discussion Forum
o http://discourse.sci-gaia.eu/
EGI IGTF Release
o https://wiki.egi.eu/wiki/EGI_IGTF_Release
VOMS Clients guide
o http://italiangrid.github.io/voms/documentation/voms-clients-
guide/3.0.3/
