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PBS Access Web 2018.1

Administrator's Guide

PBS Access Web 2018.1 Administrator's Guide

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Updated: March 29, 2018.

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Contents

1 What's New.................................................................................................................... 4

2 Get Started..................................................................................................................... 5

2.1 System Requirements for PBS Access............................................................................ 72.2 System Requirements for Interactive Application Components........................................... 92.3 Supported Product Configurations................................................................................ 102.4 Document Conventions...............................................................................................112.5 Prerequisites for Installing PBS Access......................................................................... 122.6 Prerequisites for Installing Interactive Application Components........................................ 13

3 Installing PBS Access and Interactive Application Component....................... 15

3.1 Installing PBS Access................................................................................................. 163.2 Installing Interactive Application Components................................................................17

3.2.1 Installing Interactive Components on the PBS Professional Server......................... 173.2.2 Installing Interactive Components on the PBS MoM............................................. 183.2.3 Installing Interactive Proxy on the PAW Server................................................... 19

4 Configuring PBS Access After Installation........................................................... 20

4.1 Copying Application Definitions and Site Configuration File..............................................214.2 Configuring the PBS Access Service User......................................................................224.3 Configuring the License Server....................................................................................234.4 Onboarding an Application Definition............................................................................244.5 Logging into PBS Access............................................................................................ 264.6 Adding a Service Cluster............................................................................................ 27

5 Changing Port Numbers............................................................................................ 30

5.1 Changing the Gateway Port Number............................................................................ 315.2 Change the PBS Access WebServer Port Number........................................................... 325.3 Change the Postgres Port Number............................................................................... 335.4 Change the Message Broker (ActiveMQ) Port Number.....................................................345.5 Change the Interactive Application Component Proxy Port Number...................................355.6 Change the Interactive Application Component WebServer Port Number............................365.7 Change the Interactive Application Component Job Update Port Number........................... 37

1

6 UnInstalling PBS Access and Interactive Application Component.................. 38

6.1 Uninstalling PBS Access..............................................................................................396.2 Uninstalling Interactive Application Components............................................................ 40

7 PBS Access Service Commands...............................................................................41

8 Managing Service Clusters....................................................................................... 42

8.1 Adding a Service Cluster............................................................................................ 438.2 Editing a Service Cluster............................................................................................ 468.3 Deleting a Service Cluster.......................................................................................... 48

9 Advanced Configurations.......................................................................................... 49

9.1 Configuring the Interactive Application Component........................................................ 509.1.1 Interactive Application Location and Port Configurations....................................... 509.1.2 Verifying the Existence of the Interactive Queue................................................. 509.1.3 Managing Graphical Node Limits....................................................................... 519.1.4 Verifying the Existence of the Interactive Custom Resource.................................. 529.1.5 Interactive Application Definition Configurations.................................................. 53

10 Application Definition.............................................................................................. 54

10.1 Application Definition Components............................................................................. 5510.1.1 Application Input File.....................................................................................5510.1.2 Application Converter File (HPCBP Converter)................................................... 5510.1.3 Application Runtime Scripts............................................................................ 5510.1.4 Site Configuration File....................................................................................56

10.2 Sample Application Definition PBSJobApp....................................................................5710.3 Administration of Application Definition.......................................................................5810.4 Adding a New Application Definitions..........................................................................5910.5 Application Definition Validation................................................................................. 6010.6 Maintenance of Existing Application Definition..............................................................61

10.6.1 Updating an Application Definition................................................................... 6110.6.2 Removing an Application Definition..................................................................61

10.7 Sitewide Settings..................................................................................................... 6210.7.1 Site Configuration File Content........................................................................6210.7.2 Initial Site Configuration File after Installation of PAS.........................................6210.7.3 Sample of a Site Configuration File................................................................. 6310.7.4 Using Site Configuration Information in an Application Definition..........................6310.7.5 Site Configuration File Backup........................................................................ 6310.7.6 Site Configuration File Validation..................................................................... 64

10.8 Interactive Application Definitions.............................................................................. 65

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10.8.1 Mandatory Interactive Application Definitions Changes....................................... 6510.8.2 Special Interactive Application Arugments........................................................ 6510.8.3 Adding a New Interactive Application...............................................................67

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What's New 11 What's New

Here’s a quick look at the latest features available with PBS Access.

Job Submission EnhancementsSchedule jobs by selecting an input file, by selecting a job profile or while monitoring jobs.

Refining Job MonitoringUse a filter to refine your job monitoring criteria to view all jobs or subsets of jobs.

Flexible Customization of Job Listing DisplayAdd or remove job attributes in the job monitoring display, adjust the column size, and sort the list.

Job Custom ActionExecute a custom action while a job is in a particular state.

Improved Job ManagementMove a job to a different queue, terminate a job, remove unwanted jobs, resubmit and download jobs.

Profile ManagementCreate and manage profiles so that you can submit multiple jobs to the same application with the samearguments, thereby streamlining job submission.

Folder and File ManagementPerform folder and file operations like creating a folder, uploading job input files, viewing and workingon files, and viewing image files.

Remote SessionsActivate a remote session by submitting interactive jobs. You have install the interactive applicationalong with PBS Access to work on the remote sessions.

Get Started 22 Get Started

Use PBS Access to submit jobs to a Workload Manager.

This chapter covers the following:

• 2.1 System Requirements for PBS Access (p. 7)

• 2.2 System Requirements for Interactive Application Components (p. 9)

• 2.3 Supported Product Configurations (p. 10)

• 2.4 Document Conventions (p. 11)

• 2.5 Prerequisites for Installing PBS Access (p. 12)

• 2.6 Prerequisites for Installing Interactive Application Components (p. 13)

Companies who have invested in high-performance computing (HPC) resources -- like clusters,supercomputers and cloud environments -- need these resources operating reliably around the clock.And just as importantly, the systems need to be easy to use, manage, and scale while still being cost-effective.

Altair’s PBS Access™ addresses these challenges with the most comprehensive suite of integrated HPCSystems available from a single vendor. PBS Access simplifies and streamlines the management of HPCresources with powerful policy-based job scheduling, user-friendly web portals for job submission andmonitoring.

PBS Access understands your applications and how they work. It automatically fills in key inputparameters, like the number of processors and amount of memory required. PBS Access stagesinput data sets and automatically returns output files when your job completes. Your productivityimproves since there are no complicated commands to learn. With minimal configuration, PBS Accessautomates the job submission process, allowing users to spend more time creating better models andsimulations. You no longer need to write, modify or maintain dozens of scripts for your applications andthe platforms you use.

PBS Access is a platform for collaboration and remote visualization of applications and data. It enableshigh performance remote display of applications over the networks using a web browser.

PBS Access provides features to access, process and visualize CAE results from anywhere, withoutinstalling any post-processing desktop applications through the user friendly web interface. CAEanalysts can monitor simulations in real-time by tracking and visualizing relevant parameters fromsolver log files. Meaningful plots and animations can also be created remotely without downloadinghuge raw results files from compute clusters or remote networks locations. A variety of FEA and MBDsolvers are supported.

PBS Access provides a simple user interface for submitting, monitoring and managing workloadsconnected to a Workload Manager. PBS Access is an ideal solution for customers who:

• want a simple but powerful graphical interface for submitting and monitoring jobs.

• need to browse and modify remote files.

• want to minimize the effort needed to write, modify and test complex application scripts.

PBS Access Web Administrator's Guide2 Get Started p.6

• want to automate job submission tasks to maximize end user productivity while optimizingresource availability.

• require a consistent job submission and monitoring interface.

• would like automated staging of input and output files.

Proprietary Information of Altair Engineering


2.1 System Requirements for PBS AccessSupported platforms and browsers, hardware requirements, and required ports.

Supported PlatformsPBS Access is supported on the following Linux 64-bit platforms:

• Red Hat Enterprise Linux 7.4

• Cent OS 7.4

• SLES 12 SP2

Supported BrowsersPBS Access is supported on the following browsers:

Windows

• Firefox latest ESR (Only Extended Support Release is supported. Please refer to https://www.mozilla.org/en-US/firefox/organizations/)

• Google Chrome latest

• Microsoft Edge (limited testing)

• Safari (limited testing)

Linux

• Not supported at this time.

OSX

• Firefox latest ESR (Only Extended Support Release is supported. Please refer to https://www.mozilla.org/en-US/firefox/organizations/)

• Google Chrome latest

• Safari Latest

Hardware RequirementsPBS Access requires a minimum hardware configuration:

Hardware Minimum Requirement Recommended

CPU 2 CPU cores with a minimum speedof 2.5 GHz

4 CPU cores with a minimum speedof 2.5 GHz

Memory (Physical) 2 GB 8 GB

Disk Space 4 GB 10 GB



Ports Used by PBS AccessThe PBS Access installer does not have any auto-port detection logic in place, so these ports must befree for PBS Access to be installed successfully.

Table 1: Ports Used by PBS Access

Port Service Using the Port

4443 Gateway

4543 Web Server

4643 Postgres Database

4743 Message Broker (ActiveMQ)

4822 Interactive Application Component Proxy

4843 Interactive Application Component Webserver

4909 Interactive Application Component Job Update

Note: You can change port numbers used by PBS Access.

Note: Result Visualization Services (RVS) component is not part of PBS Access Web 2018.1release. This will be supported in future releases. Please contact support-pmteam for anyupdates on this.



2.2 System Requirements for InteractiveApplication ComponentsHardware and system requirements necessary for running an interactive application.

Graphics• Only NVIDIA and [AMD] ATI cards are supported.

• Install the 3D adapter drivers provided by the manufacturer.

• Full 3D acceleration or Pixel Buffer support should be enabled by the Linux drivers.

GPU Cores and MemorySpecific to the interactive applications being run.

CPU Cores and Physical MemorySpecific to the interactive applications being run.

Other• For running interactive sessions, X Server and application on local display must be configured and

working.

• X Server must be configured to export True Color (24 bit or 32 bit) visuals.

• Use Virtual Private Networking or secured channels for communication between clients andinteractive server if encryption is required.

• The PBS Professional execution host must be able to access and run the applications availablethrough PBS Access



2.3 Supported Product ConfigurationsSupported product configurations for using PBS Access.

PBS Access PAS PBS Professional Hyperworks

2018.1 2018.1 13.1.3

14.2.3

14.0

2017.2

Tip: HyperWorks is required to plot and visualize CAE results.



2.4 Document ConventionsCommon typographical conventions for PBS Access technical publications.

PBS Access Home (PA_HOME)The PBS Access home directory which contains configuration and logging files. Default location is/var/spool/PBS_Access/2018.1/home, however this can be overridden during the installation ofPBS Access.

PBS Access Exec (PA_EXEC)The PBS Access execution directory which contains binaries and scripts. Default location is /opt/altair/PBS_Access/2018.1/exec, however this can be overridden during the installation of PBSAccess.

PAS Home (PBSWORKS_HOME)The PAS home directory which contains configuration and logging files. Default location is /var/spool/pbsworks/pas/2018.1/home, however this can be overridden during the installation ofPAS.

PAS Exec (PBSWORKS_EXEC)The PAS execution directory which contains binaries and scripts. Default location is /opt/altair/pbsworks/pas/2018.1/exec, however this can be overridden during the installation of PAS.



2.5 Prerequisites for Installing PBS AccessMandatory requirements for PBS Professional, PAS and a portal service user..

Portal OwnerThe user that owns PBS Access services and the files in PA_HOME and PA_EXEC is by default"pbsworks". After installation, you cannot start PBS Access unless this user exists and has a homedirectory or you can change the owner to an existing user on the system after installation.

PBS ProfessionalEnsure that a supported version of PBS Professional is installed on the HPC cluster.

PASTo take full advantage of all the new features available with PBS Access, the cluster must be updated tothe latest version of PAS. Using an older version of PAS may cause unexpected behavior.



2.6 Prerequisites for Installing InteractiveApplication ComponentsPrerequisites for installing interactive application components.

The following prerequisites have to be met to allow the interactive application to configure ngpus onPBS MOMs (Machine Oriented Miniservers).

Latest PBS Access and PAS Build should have been installed.

PBS Access and PAS should contact through Host Name.

Configuration of PBS ServerPBS Server should have been configured using the PBS Access interactve application installer.

The PBS Access interactive application add-on installer will perform the following:

• Configure PBS and PAS Server

• Install Display Manager Agent

• Unconfigure PBS and PAS Server

• Install Display Proxy

PBS PrivilegesFor the PBS Access interactive application add-on installer to set the custom resource at each executionhost, the root user of all execution hosts must be granted operator access. Prior to starting theInteractive Application Add-on installer, issue the following command to grant this access:qmgr: s s operators+=root@*

If this access is not granted, then you will manually have to set the custom resource by issuing a qmgrset command for each execution host after installation of Interactive Application. For example:set node <node> resources_available.ngpus = 4

After applying such a setting, every user named root from any host on any network will be able tooperate on jobs from other users. To prevent misuse, restrict the above setting to the sub domaincontaining the execution hosts or list them one by one.

After installing interactive application components, you can remove the root user of the PBS MOMs fromthe operators list on the PBS server using the command:qmgr: s s operators-=root@*

Prerequisite Resource Libraries for Interactive ApplicationThe following libraries must be installed before attempting to install interactive application. If they arenot, they can be installed using the appropriate system tools (e.g. RPM, YUM, YAST etc.).



• libc.so.6()(64bit)

• libc.so.6(GLIBC_2.2.5)(64bit)

• libc.so.6(GLIBC_2.3)(64bit)

• libcrypt.so.1()(64bit)

• libdl.so.2()(64bit)

• libdl.so.2(GLIBC_2.2.5)(64bit)

• libGL.so.1()(64bit)

• libGLU.so.1()(64bit)

• libICE.so.6()(64bit)

• libm.so.6()(64bit)

• libm.so.6(GLIBC_2.2.5)(64bit)

• libpam.so.0()(64bit)

• libpthread.so.0()(64bit)

• libpthread.so.0(GLIBC_2.2.5)(64bit)

• libpthread.so.0(GLIBC_2.3.2)(64bit)

• libSM.so.6()(64bit)

• libX11.so.6()(64bit)

• libXaw.so.7()(64bit)

• libXcursor.so.1()(64bit)

• libXext.so.6()(64bit)

• libXmu.so.6()(64bit)

• libXt.so.6()(64bit)

• libXv.so.1()(64bit)

• libz.so.1()(64bit)


Installing PBS Access andInteractive ApplicationComponent 33 Installing PBS Access and Interactive Application Component

Instructions for installing PBS Access so that interactive and non-interactive jobs can be submitted.


• 3.1 Installing PBS Access (p. 16)

• 3.2 Installing Interactive Application Components (p. 17)

PBS Access Web Administrator's Guide3 Installing PBS Access and Interactive Application Component p.16

3.1 Installing PBS AccessInstall PBS Access so that you can submit non-interactive jobs to the Workload Manager.

• Review the system requirements and prerequisites for installation.

• Stop all services by issuing the following command: /etc/init.d/pbsworks-pa stop

• Uninstall previous versions of PBS Access.

• Delete the PBSJobApp application definition that is installed by default during the installation of thePAS.

• The PBS Professional job history must be enabled so that job information is available toPAW. As a PBS Operator or Manager enter the following command: qmgr -c 'set serverjob_history_enable=True'

Installation of PBS Access is very simple and quick. A binary or executable needs to be downloaded orobtained using your usual Altair support channels.

1. As root, install PBS Access using the command:./PBSAccessWeb_<version information>.bin -i console

2. Enter the location where the PBS Access binaries are to be installed.

You may choose to install in the default location.

3. Enter the location where the PBS Access configuration and logs files are to be installed.


4. Review the installation summary and press ENTER.The installation starts. It may take a few minutes for the installation to complete.

Installing Interactive Application Components



3.2 Installing Interactive Application ComponentsInstall components necessary to enable the interactive application capabilities of PBS Access.

Review the system requirements and prerequisites for installation.

A binary that installs the interactive application components needs to be downloaded or obtained usingyour usual Altair support channels.

The installer will need to be run multiple times across several machines and must be performed in thefollowing sequence:

1. Install interactive components on the PBS Professional headnode. This installation will:

• add a custom resource to PBS Professional called "ngpus"

• creates an interactive queue called "iworkq"

• add a new interactive application definition to PAS

• restart PAS and PBS Professional

2. Install interactive components on the PBS MoM.

3. Install proxy software on the machine hosting PBS Access that is necessary for running interacitveapplications.

3.2.1 Installing Interactive Components on the PBSProfessional ServerInstall binaries and configure PBS Professional and the PAS to support interactive applications.


This installation will:

• add a custom resource to PBS Professional called "ngpus"

• add an interactive queue called "iworkq"

• restart PAS

• restart PBS Professional

1. As root, enter the command:./PBSAccess_DMAgent_<version information>.bin -i console

2. PBS Professional is restarted during the installation process, choose whether you want to proceed:

• Choose No to exit and run the installer at a more suitable time.

• Choose Yes to run the installer.

CAUTION: It is advisable that you run the installer when critical jobs are not running.

The installer provides the following four install options.

1. Configure PBS and PAS Server

2. Install Display Manager Agent



3. Unconfigure PBS and PAS Server

4. Install Display Proxy

3. Enter "1" and press ENTER.


Verify if iworkq is created and GPU resource is configured on PBS Professional.

3.2.2 Installing Interactive Components on the PBS MoMInstall binaries and configure the PBS Mom to support interactive applications.


Install necesary components on the PBS MoM to support interactive applications, including TurboVNCand Virtual GL. The installer also configures NGPUs for the execution host.


If you are installing the interactive components on a machine hosting both the PBS ProfessionalServer and the MoM, then the following message is displayed:Manage Instances----------------->1- Install a new instance 2- Modify an existing instance

Enter "1" and press ENTER.











4. Enter the location where the binaries are to be installed.


5. Enter the location where the configuration and logs files are to be installed.


6. Enter the number of GPUs available on the execution host and press ENTER.




Tip: Due to the installation and updating of system software, it is recommended toreboot the system on completing the installation.

8. Once the installation is complete you are asked to reboot the machine.

9. Choose Yes and press ENTER.

Verify that "ngpus" resource has been added to the execution host by executing the command:pbsnodes -av

The new resource should be listed and it should be assigned the value entered for the available numberof GPUs during installation.resources_available.ngpus = 7

3.2.3 Installing Interactive Proxy on the PAW ServerInstall the Guacomole proxy server on the machine hosting PBS Access to support interactiveapplications.



If you are installing the proxy server on a machine hosting either the PBS Professional Server orthe MoM, then the following message is displayed:Manage Instances----------------->1- Install a new instance 2- Modify an existing instance

Enter "1" and press ENTER.







3. Enter the location where the binaries are to be installed.


4. Enter the location where the configuration and logs files are to be installed.


The installation starts. It may take a few minutes for the installation to complete.

Verify that guacd is installed and running by issuing the following command:service guacd status


Configuring PBS Access AfterInstallation 44 Configuring PBS Access After Installation

Mandatory configuration steps that must be completed before PBS Access can be started.


• 4.1 Copying Application Definitions and Site Configuration File (p. 21)

• 4.2 Configuring the PBS Access Service User (p. 22)

• 4.3 Configuring the License Server (p. 23)

• 4.4 Onboarding an Application Definition (p. 24)

• 4.5 Logging into PBS Access (p. 26)

• 4.6 Adding a Service Cluster (p. 27)

Before you start the PBS Access service, you must copy over default application definitions provided byAltair and a corresponding PAS site configuration file. Additionally, a PBS Access service user must beconfigured.

PBS Access Web Administrator's Guide4 Configuring PBS Access After Installation p.21

4.1 Copying Application Definitions and SiteConfiguration FileCopy default application definitions and a PAS site configuration file from the user download area.

Altair provides interactive and non-interactive applications definitions and a corresponding PAS siteconfiguration file (site-config.xml).

Copy those application definitions required for your site.

1. Copy the application definitions from the Altair user download area and place them in thePASrepository.

The PAS repository location is: PBSWORKS_HOME/data/pas/targets/localhost/repository/applications.

2. Copy the site-config.xml file from the Altair user download area to PBSWORKS_HOME/data/pas/targets/localhost/repository.

3. Edit the site-config.xml.

4. For each application, update the value of the XML element <Executable> to the location of theapplication's executable.<Application id="Abaqus"> <ApplicationVersions> <ApplicationVersion> <Option>13.0</Option> <Executable>/opt/scripts/abaqus</Executable> </ApplicationVersion> </ApplicationVersions></Application>

a) Delete any applications in the PBSWORKS_HOME/data/pas/targets/localhost/repository/private/generated/json-applications directory.

5. Restart the PAS server by entering the following command:/etc/init.d/pas restart

The XML application definitions gets converted to JSON application definitions and are storedin PBSWORKS_HOME/data/pas/targets/localhost/repository/private/generated/json-applications.

Note: If you want to make a change to an application definition in the future, thechange must be made to the JSON application definition and not the XML applicationdefinition.



4.2 Configuring the PBS Access Service UserConfigure a user who will own the PBS Access services.

By default, PBS Access assumes that a user called "pbsworks" exists. When PBS Access is started, allservices run under this user and the user owns the files in PA_HOME and PA_EXEC. To start PBS Access,the "pbsworks" user must exist as a local or network user with a /home/pbsworks directory. Alternately,you can configure the service user to be an existing user on the system.

1. Choose one from the following options:

• Create a "pbsworks" user and create a /home/pbsworks directory.

• Edit the /etc/pbsworks-pa.conf file and change the value of PORTAL_NON_ROOT_USER toan existing user on the system.

2. Start the PBS Access server by entering the following command:/etc/init.d/pbsworks-pa start



4.3 Configuring the License ServerConfigure the license servers after PBS Access installation in console mode.

A license server must be configured during the installation of PBS Access, you will be prompted tosupply information about the license server (port and hostname/IP address). You may supply theinformation at this time, or it can be configured with this information post-installation.

Note: You must have administrative privileges to configure the PBS Access license server.

1. Open the file app.properties located at PA_HOME/config/license/.

2. Change the port and hostname of the XML element value of pbsworks.license.server to theport and hostname of the license server in the format [email protected] application namepbsworks.license.application=PBSAccess

#server location for license serverpbsworks.license.server=6200@cntrlicsrv03

3. Restart the PBS Access for these changes to take effect by entering the following command:/etc/init.d/pbsworks-pa restart



4.4 Onboarding an Application DefinitionPort an application definition from a legacy version of PBS Works so that it can be used by PBS Access.

Application definitions must have a PRIMARY_FILE argument defined in the application definition inputfile that represents the primary input file for the solver. If a legacy application definition calls theprimary input file something other than PRIMARY_FILE, then a mapping file must be updated to port theapplication definition. Additionally, if the legacy application definition contains an application argumentthat represents the queue to which the job is submitted, the name of the application argument must beQUEUE. If it is not, the mapping file must be updated.

Note: You can onboard an application definition at any time.

1. Edit the file PA_HOME/config/pas/appmapping/applicationmapping.json.

2. Add the following JSON between the bracket []{ "serverName": "server-1","version": "13.1","applications": [ { "applicationName": "RADIOSS-SMP", "primaryFile": "MASTER_FILE", "queue": "Queues" } ]}

3. Change the value of serverName. The serverName is the name that you provided while adding aservice cluster."serverName": "server-1",

4. Change the value of version."version": "13.1",

5. Change the value of applicationName to the name of the application that you want to port.

Denoted by the XML element <ApplicationName> in the legacy application definition. The legacyXML looks like this:<ApplicationName>Optistruct</ApplicationName>

The JSON should look like this:"applicationName": "Optistruct"

6. Change the value of primaryFile to the name of the application argument that represents theapplication input file for the solver.

Denoted by the XML element <Name> in the legacy application definition. The legacy XML lookslike this:<ArgumentChoice> <ArgumentFileName> <Name>MASTER_FILE</Name> <Description>Select your Optistruct Master file.</Description> <DisplayName>Master File</DisplayName> <InputRequired>true</InputRequired> </ArgumentFileName></ArgumentChoice>

The JSON should look like this:"primaryFile": "MASTER_FILE"

7. Change the value of queue to the name of the application argument that represents the queue towhich the job is submitted.



Denoted by the XML element <Name> in the legacy application definition. The legacy XML lookslike this:<ArgumentChoice> <ArgumentStringEnumerated> <Name>BATCH_QUEUE</Name> <Description>Select the batch queue you would like to submit to.</Description> <DisplayName>Batch Queue</DisplayName> <InputRequired>false</InputRequired> <Option>workq</Option> <Option>testq</Option> <DefaultValue>workq</DefaultValue> </ArgumentStringEnumerated></ArgumentChoice>

The JSON should look like this:"queue": "BATCH_QUEUE"

8. Add additional applications by repeating previous step 5-7 making sure that when you add thenext application to the JSON mapping file you separate the applications using a comma."applications": [ { "applicationName": "PBSJobApp", "primaryFile": "JOB_SCRIPT" }, { "applicationName": "Optistruct", "primaryFile": "MASTER" }]

9. Save the file.

10. Copy your legacy application definitions to the PAS repository.

11. Restart PAS by issuing the command:/etc/init.d/pas restart



4.5 Logging into PBS AccessLog into PBS Access so that you can submit and monitor jobs.

Review the supported browsers before logging into PBS Access.

Before you can submit a job, a service cluster must be added. Only the portal administrator can addservice clusters. The first person to login to PBS Access after installation is considered the portaladministrator.

1. Enter the URL https://<hostname>:4443/pbsworks in the address bar of a supported browser.

where <hostname> is the IP address or hostname of the machine where PBS Access is installed.

The PBS Access login screen is displayed.

Troubleshooting: Contact an Altair Application Engineer if you are unable to accessthe login screen.

2. Enter your username and password.

3. Click Log In.

Add a service cluster.



4.6 Adding a Service ClusterEstablish a connection to an HPC cluster so that you may begin submitting jobs.

Note: Only the portal administrator can configure a service cluster.

Before you can configure a cluster, you must know the hostname of the PAS Server installed on the PBSProfessional headnode and the credentials of an user on the machine hosting the PAS Server.

The first person to login to PBS Access after installation is considered the portal administrator. Theportal administrator is the only user who can add or delete service clusters. A service cluster must beadded before jobs can be submitted to the Workload Manager.

1. Choose one of the following options:

• If no service clusters have been configured, click the Configure one or more services link.

• Click and then click Add.

A list of service clusters that have been previously added is displayed.

Figure 1: Manage Services

2. Click Add located in the upper right-hand of the page.The Add Service Cluster screen is displayed.



Figure 2: Add Service Cluster

3. For Server Name, enter a short name describing the cluster.

4. For URL, enter the URL for connecting to the Workload Manager.

The URL is in the format http:<hostname>:17084/pas, where <hostname> is the hostname ofthe machine where the PAS Server is installed (typically the PBS Professional headnode).

5. For User Name and Password, enter your login credentials. The user name and password mustbe available in PAS.

6. For Root Dir, enter the pathname where user job input and result files are stored.

Ex: /home, /users, /stage

7. Click Add.If the service cluster is added successfully, then a notification is displayed.

Troubleshooting: If the service cluster add fails, contact an Altair ApplicationEngineer.

8. Repeat steps 2 through 6 to add additional service clusters.

9. Click Done.A list service clusters that is added is displayed.

Figure 3: Service Clusters List



The green color next to the service cluster indicates that it is available to use. The red colorindicates that the service cluster is not available. A service cluster may not be available because itis down for maintenance.

Troubleshooting: Contact an Altair Application Engineer if you need assistancecreating a service cluster.


Changing Port Numbers 55 Changing Port Numbers

Change the default port numbers used by PBS Access.


• 5.1 Changing the Gateway Port Number (p. 31)

• 5.2 Change the PBS Access WebServer Port Number (p. 32)

• 5.3 Change the Postgres Port Number (p. 33)

• 5.4 Change the Message Broker (ActiveMQ) Port Number (p. 34)

• 5.5 Change the Interactive Application Component Proxy Port Number (p. 35)

• 5.6 Change the Interactive Application Component WebServer Port Number (p. 36)

• 5.7 Change the Interactive Application Component Job Update Port Number (p. 37)

You must stop PBS Access before changing the port number. For more information about stopping PBSAccess, see PBS Access Service Commands.

PBS Access Web Administrator's Guide5 Changing Port Numbers p.31

5.1 Changing the Gateway Port NumberChange the default gateway port number in PBS Access.


The default location of PBS Access home and exec directories are:

• PA_HOME - /var/spool/PBS_Access/2018.1/home

• PA_EXEC - /opt/altair/PBS_Access/2018.1/exec

The gateway port number has to be updated in nginx.conf and in app.properties

Note: The default gateway port number in this file is 4443.

1. Navigate to PA_HOME/config/api_gateway.

2. Edit the nginx.conf file and update the port number.server { listen 4443; server_name localhost; add_header X-Frame-Options "SAMEORIGIN";

3. Start PBS Access by entering the following command:/etc/init.d/pbsworks-pa start



5.2 Change the PBS Access WebServer Port NumberChange the default PBS Access webserver port number.





The PBS Access webserver port number has to be updated in server.xml, pbsaccess.conf,preferences.conf, storage.conf, dmrest.properties, dmrest.properties.template,app.properties, and in ServiceRegistry.json.

Note: The default interactive application component job update port number in this file is4543.

1. Navigate to PA_HOME/config/pa/tomcat/conf.

2. Edit the server.xml file and update the port number.

Note: Search for Connector port and replace 4543 to your port number.

3. Navigate to PA_HOME/config/api_gateway/default.d.

4. Edit the pbsaccess.conf file and update the port number.proxy_pass https://localhost:4543/pa/$uri;

proxy_pass https://localhost:4543;

5. Edit the preferences.conf file and update the port number.proxy_pass https://localhost:4543/preferences;

6. Edit the storage.conf file and update the port number.proxy_pass https://localhost:4543/storage;

7. Navigate to PA_HOME/config/displaymanager.

8. Edit the dmrest.properties file and update the port number.pbsaccess.storage.service.host=https://localhost:4543/storage

9. Edit the dmrest.properties.template file and update the port number.pbsaccess.storage.service.host=https://localhost:4543/storage

10. Navigate to PA_HOME/config/shared.

11. Edit the app.properties file and update the port number.pbsworks.ams.url = https://localhost:4543/AAService/aaservice/authn/oauth2

12. Edit the ServiceRegistry.json file and update the port number.{"service":[{"name":"ams","host":"localhost","port":"4543","service_name":"AAService","scheme":"https"}]}




5.3 Change the Postgres Port NumberChange the default postgres port number in PBS Access.


CAUTION: Changing the Postgres port number will remove PBS Access database includinglog files. When you run configure-pa-user.sh at the end of this task, it will reconfigurePBS Access.




The postgres database port number has to be updated in configure.sh and in app.properties

Note: The default postgres database port number in this file is 4643.

1. Navigate to PA_EXEC/database/scripts.

2. Edit the configure.sh file and update the port number.PG_PORT=4643;


4. Edit the app.properties file and update the port number.spring.datasource.url=jdbc:postgresql://localhost:4643/pbsworks

5. Navigate to PA_EXEC/init/script

6. Run configure-pa-user.sh as a non-root portal user../configure-pa-user.sh <portal user>



5.4 Change the Message Broker (ActiveMQ) PortNumberChange the default message broker (ActiveMQ) port number in PBS Access.





The message broker (ActiveMQ) port number has to be updated in message-app.properties, env andin activemq.xml.

Note: The default Message Broker (ActiveMQ) port number in this file is 4743.


2. Edit the message-app.properties file and update the port number.pbsworks.messaging.broker.url=tcp://localhost:4743

3. Navigate to PA_EXEC/shared/thirdparty/apache/activemq/bin.

4. Edit the env file and update the port number.ACTIVEMQ_QUEUEMANAGERURL="--amqurl tcp://localhost:4743"

5. Navigate to PA_EXEC/shared/thirdparty/apache/activemq/conf

6. Edit the activemq.xml file and update the port number.<transportConnector name="openwire" uri="tcp://0.0.0.0:4743?maximumConnections=1000&wireFormat.maxFrameSize=104857600>




5.5 Change the Interactive Application ComponentProxy Port NumberChange the default interactive application component proxy (GUACD) port number in PBS Access.





The interactive application component proxy port number has to be updated in guacd.conf,guacamole.properties and in guacamole.properties.template.

Note: The default interactive application component proxy port number in this file is 4822.

1. Navigate to /etc/guacamole/.

2. Edit the guacd.conf file and update the port number.bind_port = 4822


4. Edit the guacamole.properties file and update the port number.guacd-port: 4822

5. Navigate to PA_HOME/config/displaymanager

6. Edit the guacamole.properties.template file and update the port number.guacd-port: 4822


8. Restart Interactive Application Component Proxy (GUACD) by entering the following command:/etc/init.d/guacd restart



5.6 Change the Interactive Application ComponentWebServer Port NumberChange the default interactive application component webserver port number in PBS Access.





The interactive application component webserver port number has to be updated in server.xml,displaymanger.conf, guacamole.properties, and in guacamole.properties.template.


1. Navigate to PA_HOME/config/pa/tomcat/conf.

2. Edit the server.xml file and update the port number.

Note: Search for Connector port and replace 4843 to your port number.

3. Navigate to PA_HOME/config/api_gateway/default.d.

4. Edit the displaymanger.conf file and update the port number.proxy_pass https://localhost:4843/displaymanager;

proxy_pass https://localhost:4843/dm;


6. Edit the guacamole.properties file and update the port number.dm-host: https://localhost:4843/displaymanager


8. Edit the guacamole.properties.template file and update the port number.dm-host: https://localhost:4843/displaymanager




5.7 Change the Interactive Application ComponentJob Update Port NumberChange the default interactive application component job update port number in PBS Access.





The interactive application component job update port number has to be updated indmrest.properties and in dmrest.properties.template.



2. Edit the dmrest.properties file and update the port number.jobsub.monitor.port=4909

3. Navigate to PA_HOME/config/displaymanager

4. Edit the dmrest.properties.template file and update the port number.jobsub.monitor.port=4909



UnInstalling PBS Accessand Interactive ApplicationComponent 66 UnInstalling PBS Access and Interactive Application Component

Instructions for uninstalling previous version of PBS Access and interactive application component.


• 6.1 Uninstalling PBS Access (p. 39)

• 6.2 Uninstalling Interactive Application Components (p. 40)

PBS Access Web Administrator's Guide6 UnInstalling PBS Access and Interactive Application Component p.39

6.1 Uninstalling PBS AccessRemove a previous version of PBS Access.

You must stop PBS Access before uninstalling. For more information about stopping PBS Access, seePBS Access Service Commands.

1. Navigate to the /opt/altair/PBS_Access/2018.1/_PBS_Access_installation directory.

2. Execute the uninstall script by entering the following command:./Change\ PBS_Access\ Installation -i console

The command must contain spaces with escape characters.

3. Follow the instructions provided by the uninstaller.


PBS Access Web Administrator's Guide6 UnInstalling PBS Access and Interactive Application Component p.40

6.2 Uninstalling Interactive ApplicationComponentsUninstall previous version of interactive application components.

You must stop PBS Access before uninstalling. For more information about stopping PBS Access, seePBS Access Service Commands.


1. Navigate to the /opt/altair/pbsworks/2018.1/dmagent/_PBS_Access_installation directory.

2. Execute the uninstall script by entering the following command:./Change\ PBSWorks_DMAgent_2018.1\ Installation -i console

The command must contain spaces with escape characters.

3. Follow the instructions provided by the uninstaller.

Note: This will uninstall Interactive Application Component Agent and Proxy.






The installer provides the following options:





6. Enter "3" and press ENTER.The uninstall will perform the following:

• Deletes the interactive queue

• Unconfigure GPUs as a custom resource

• Uninstall interactive application definition


PBS Access Service Commands 77 PBS Access Service Commands

Commands for starting, stopping, restarting and checking the status of PBS Access.

The below commands should be executed by the portal owner as defined in /etc/pbsworks-pa.conf.

Starting PBS Access/etc/init.d/pbsworks-pa start

Stopping PBS Access/etc/init.d/pbsworks-pa stop

Restarting PBS Access/etc/init.d/pbsworks-pa restart

Determining the Status of PBS Access/etc/init.d/pbsworks-pa status

Managing Service Clusters 88 Managing Service Clusters

Add, Edit, and delete service clusters.


• 8.1 Adding a Service Cluster (p. 43)

• 8.2 Editing a Service Cluster (p. 46)

• 8.3 Deleting a Service Cluster (p. 48)

Only the portal administrator can add, edit, and remove service clusters. Regular users are unable toaccess the Manage Services page.

PBS Access Web Administrator's Guide8 Managing Service Clusters p.43

8.1 Adding a Service ClusterEstablish a connection to an HPC cluster so that you may begin submitting jobs.

Note: Only the portal administrator can configure a service cluster.

Before you can configure a cluster, you must know the hostname of the PAS Server installed on the PBSProfessional headnode and the credentials of an user on the machine hosting the PAS Server.

The first person to login to PBS Access after installation is considered the portal administrator. Theportal administrator is the only user who can add or delete service clusters. A service cluster must beadded before jobs can be submitted to the Workload Manager.

1. Choose one of the following options:

• If no service clusters have been configured, click the Configure one or more services link.

• Click and then click Add.

A list of service clusters that have been previously added is displayed.


2. Click Add located in the upper right-hand of the page.The Add Service Cluster screen is displayed.



Figure 5: Add Service Cluster

3. For Server Name, enter a short name describing the cluster.

4. For URL, enter the URL for connecting to the Workload Manager.

The URL is in the format http:<hostname>:17084/pas, where <hostname> is the hostname ofthe machine where the PAS Server is installed (typically the PBS Professional headnode).

5. For User Name and Password, enter your login credentials. The user name and password mustbe available in PAS.

6. For Root Dir, enter the pathname where user job input and result files are stored.

Ex: /home, /users, /stage

7. Click Add.If the service cluster is added successfully, then a notification is displayed.

Troubleshooting: If the service cluster add fails, contact an Altair ApplicationEngineer.

8. Repeat steps 2 through 6 to add additional service clusters.

9. Click Done.A list service clusters that is added is displayed.

Figure 6: Service Clusters List



The green color next to the service cluster indicates that it is available to use. The red colorindicates that the service cluster is not available. A service cluster may not be available because itis down for maintenance.

Troubleshooting: Contact an Altair Application Engineer if you need assistancecreating a service cluster.



8.2 Editing a Service ClusterUpdate a service cluster password or root directory so that you can continue to submit your jobs.

Note: Only the portal administrator can delete a service cluster.

1. Click .A list of service clusters that have been previously added is displayed.


2. Right-click the cluster that you want to edit.

3. Click Edit from the context menu.

Figure 8: Cluster Edit Option

The Edit Service Cluster screen is displayed.



Figure 9: Edit Service Cluster

4. Update the service cluster information.

5. Click Save.



8.3 Deleting a Service ClusterRemove a service cluster when you no longer want to submit and manage jobs on that cluster.

Note: Only the portal administrator can delete a service cluster.

1. Click .A list of service clusters that have been previously added is displayed.


2. Right-click the cluster that you want to remove.

3. Click Delete from the context menu.

Figure 11: Server Cluster Delete

4. Click Yes.The files and jobs from this cluster will no longer be accessible.


Advanced Configurations 99 Advanced Configurations

Advanced configurations for PBS Access.


• 9.1 Configuring the Interactive Application Component (p. 50)

PBS Access Web Administrator's Guide9 Advanced Configurations p.50

9.1 Configuring the Interactive ApplicationComponentConfigurations when you install interactive application component.

9.1.1 Interactive Application Location and PortConfigurationsConfigure interactive application location and port in PAS.

You can use the information to configure interactive application without reinstalling it. In the PAS, youcan configure the PBS Access location and port in the dmrest.properties file.

The location of dmrest.properties is <PA_HOME>/config/displaymanager/dmrest.properties

The following parameters can be updated in the dmrest.properties:

• jobaction.expiry_time: This parameter defines the sessions timeout. The default value is 30minutes and the session is killed if the user is not accessing the session within this time.

• jobsub.monitor.host: Provide the host system name where interactive application is installed.The configured host name should be accessible from all the compute node. If it is not accessiblethrough hostname, then change the value to host system IP address.

• jobsub.monitor.port: Update the port of the interactive application. All the interactive jobswhich connects to interactive application service with the given jobsub.monitor.host andjobsub.monitor.port information, will provide the updates for job status.

9.1.2 Verifying the Existence of the Interactive QueueVerify that an interactive queue has been configured in PBS Professional.

After running the interactive installer on the PBS Professional headnode, a queue called iworkq shouldexist and it should be configured. An attribute that controls this limit is defined for every Graphical nodeconfigured in the cluster.

The max_queued_res.ngpus provides the available GPU limit for the cluster, resouce_max.ngpusprovides the maximum number of the GPU limit for the node and resouce_min.ngpus provides theminimum number of the GPU limit for the node.

Enter the command:qmgr -c "p q iworkq"

Output similar to the below is displayed.## Create queues and set their attributes.### Create and define queue iworkq#create queue iworkqset queue iworkq queue_type = Executionset queue iworkq Priority = 150set queue iworkq max_queued_res.ngpus = [o:PBS_ALL=5*]



set queue iworkq resources_max.ngpus = 1set queue iworkq resources_min.ngpus = 1set queue iworkq enabled = Trueset queue iworkq started = True

*5 is the GPU count provided during the installation. This is the count of GPUs available on the cluster

Troubleshooting: Contact an Altair Application Engineer if the interactive queue does notexist.

9.1.3 Managing Graphical Node LimitsManage all the node and cluster limits for the GPUs.

The installer configures all the node and cluster limits for the GPUs. Follow the below procedure insituations where these limits might change (e.g. a node going down or being removed, adding newgraphical nodes post install, etc.)

Modify the Cluster GPU LimitManage the cluster limits for the GPUs.

An attribute that controls this limit is defined for the PBS queue (iworkq) that exclusively handlesinteractive job requests for a PBS server.

1. Enter the command:qmgr -c "p q iworkq"

Output similar to the below is displayed.## Create queues and set their attributes.### Create and define queue iworkq#create queue iworkqset queue iworkq queue_type = Executionset queue iworkq Priority = 150set queue iworkq max_queued_res.ngpus = [o:PBS_ALL=5*]set queue iworkq resources_max.ngpus = 1set queue iworkq resources_min.ngpus = 1set queue iworkq enabled = Trueset queue iworkq started = True

Troubleshooting: Contact an Altair Application Engineer if the interactive queue doesnot exist.

The numrical value "5" specified for max_queued_res.ngpus is the available GPU limit for thecluster. This is the cumulative number of all the GPUs available in the cluster managed by the PBSserver.

2. Update the value of max_queued_res.ngpus to accommodate any changes in the limit due toaddition or removal of Graphical nodes or Graphic devices in nodes.



Modify the Node GPU LimitManage the node limits for the GPUs.

An attribute that controls this limit is defined for every Graphical node configured in the cluster.

1. Enter the command:pbsnodes -a

Output similar to the below is displayed.Mom = zeethon.pbsworks.comPort = 15002ntype = PBSstate = freepcpus = 1resources_available.arch = linuxresources_available.host = zeethonresources_available.mem = 3903096kbresources_available.ncpus = 1resources_available.ngpus = 2*resources_available.vnode = zeethonresources_assigned.accelerator_memory = 0kbresources_assigned.mem = 0kbresources_assigned.naccelerators = 0resources_assigned.ncpus = 0resources_assigned.netwins = 0resources_assigned.ngpus = 0resources_assigned.vmem = 0kbresv_enable = Truesharing = default_shared

The numrical value "2" specified for resources_available.ngpus is the available GPU limit for thenode, this is the cumulative number of all the graphical devices available in a particular node.

2. Update the value of resources_available.ngpus to accommodate any changes to the limit due toaddition or removal of Graphical devices to the node.set node v03 resources_available.ngpus = 5

9.1.4 Verifying the Existence of the Interactive CustomResourceVerify that a new resources called ngpus has been added to PBS Professional.

After running the interactive installer on the PBS Professional headnode, a new custom resourcecalled ngpus is added to PBS Professional. This resource is necessary to run interactive jobs. You canverify the existence of this custom resource by viewing the contents of the PBS Professional resourcedefinition file and the scheduler's configuration file.

1. Navigate to the location PBS_HOME/server_priv.

2. Enter the command:grep -A3 "DM STATIC" resourcedef

The resource ngpus should be defined in this file.# *********** BEGINNING OF DM STATIC RESOURCES SECTION.DO NOT EDIT BY HAND ******ngpus type=long flag=nh# *********** END OF DM STATIC RESOURCES SECTION.DO NOT EDIT BY HAND ************sched_config

3. Navigate to the location PBS_HOME/sched_priv.

4. Enter the command:grep ngpus sched_config

The resource ngpus should be displayed in the list of resources defined in this file.



resources: "ncpus, mem, arch, host, vnode, netwins, aoe, ngpus"

Troubleshooting: Contact an Altair Application Engineer if the ncpus resource hasnot been defined in either of these files.

9.1.5 Interactive Application Definition ConfigurationsVerify interactive application definition configuration in PAS.

An application definition will be installed in PBSWORKS_HOME/data/pas/targets/localhost/repository/applications folder and ijob.conf will be updated to point to the interactive applicationserver.


Application Definition 1010 Application Definition

PAS requires a predefined set of instructions, called application definitions, to describe your applicationparameters to users, store their responses, and prepare those responses for job execution via PBSProfessional.


• 10.1 Application Definition Components (p. 55)

• 10.2 Sample Application Definition PBSJobApp (p. 57)

• 10.3 Administration of Application Definition (p. 58)

• 10.4 Adding a New Application Definitions (p. 59)

• 10.5 Application Definition Validation (p. 60)

• 10.6 Maintenance of Existing Application Definition (p. 61)

• 10.7 Sitewide Settings (p. 62)

• 10.8 Interactive Application Definitions (p. 65)

An application definition provides a flexible set of instructions that can be manipulated to allowfor precise control over all aspects of application-specific parameters and job execution. Theseapplication definitions are stored in a central repository and will make PBS Professional aware of eachof them upon server startup. The location of the application directory for a typical installation of PASis:PBSWORKS_HOME/data/pas/targets/localhost/repository/applications.

PBS Access Web Administrator's Guide10 Application Definition p.55

10.1 Application Definition ComponentsOverview of application definition components.

An application definition is comprised of a set of Python scripts and two XML files which could includereferences to site wide configuration settings. A separate application definition with application-specificdetails is required for each application that will be integrated into PAS. Application definitions arecompliant with the Open Grid Forum High Performance Computing Basic Profile (HPCBP), BusinessProcess Execution Language (BPEL), and Job Submission Description Language (JSDL) standards.

For more comprehensive information about application definitions and their associated files see DivingInto Application Definitions.

10.1.1 Application Input File

The application input file is where administrators can define the allowed arguments for a givenapplication. This file is also used by graphical, web-based and even command-line tools to display thesearguments to users for job submission.

The mandatory naming convention for the application input file is app-inp-applicationname.xmlwhere applicationname is whatever name you choose to give your application.

10.1.2 Application Converter File (HPCBP Converter)

The application converter file is where administrators take the values received by the user via theinput file and communicates this information to the PAS and PBS Professional. This file allows the PASadministrator to configure the job submission environment.

The mandatory naming convention for the application converter file is app-conv-applicationname.xmlwhere applicationname is whatever name you decide to give to your application.

10.1.3 Application Runtime Scripts

The application runtime scripts are what really get executed on the execution hosts. The runtimescript, start.py, is what will be executed as the “job script”. This script file is responsible for executingthe application associated with your application definition, using the information entered by the user(defined by the application input file) and converted (via the application converter file). Additionalscripts can also be included that support and enhance the runtime script. Administrators can directlyedit these runtime script(s), taking full advantage of Python to add further inspection and complexity tojob submission and finally execution of the application itself. This adds tremendous flexibility as nearlyinfinite possibilities for job control exist at this phase of job description.



For information about how to use runtime scripts see the tutorials Enhancing your Application withRuntime Scripts, Executing Actions on a Running Job and the Recipes section in Diving Into ApplicationDefinitions.

10.1.4 Site Configuration File

The site configuration file, site-config.xml, is meant to make application definitions more portableby consolidating data that may change from cluster to cluster in a central location. It is whereadministrators can define things like policies, version, and path information for all the availableapplications, billing account information, etc. The data in this file is used by the application input andconverter files.

For information on how to reference the site configuration file in an application definition see thetutorial Maintaining Multiple Versions of an Application, recipes How to Configure & Use Sitewide BillingAccounts, How to Configure & Use Sitewide Policies, and How to Configure & Use Application Policiessection in Diving Into Application Definitions.



10.2 Sample Application Definition PBSJobAppPAS provides a sample application definition, PBSJobApp, which is located in the application definitiondirectory.

PBSJobApp is an example of how an administrator could create an application definition enabling usersto use custom job scripts akin to the more common PBS Professional job script. PBSJobApp allows thesejob scripts to be written in any language by using its runtime script, start.py, to parse the first line(shebang line) to determine the correct interpreter to execute your job script against. PBSJobApp'sversatility allows the following:

• extra arguments to be passed to the job script

• specification of advanced multi-node placement options

• the inclusion of additional files

This application definition in conjunction with the Diving Into Application Definitions documentation willassist administrators to create and deploy application definitions.



10.3 Administration of Application DefinitionThe PAS has a central location for keeping application definitions and will make PBS Professionalaware of each of them upon server startup. The location of the application definition files for a typicalinstallation of PAS is:PBSWORKS_HOME/data/pas/targets/localhost/repository/applications



10.4 Adding a New Application DefinitionsAdding an application definition to the applications directory, followed by a restart of PAS, will exposeyour application definition to the user, as well as notify PBS Professional. Follow these steps to add anapplication definition:

1. Navigate to the applications directory.

2. Create a directory called appname (where appname is the name of the application).

3. Place the application definition input file (app-inp-appname.xml) and the application definitionconverter file (app-conv-appname.xml) in the application directory.

4. Create a subdirectory called runtime and navigate to that subdirectory.

5. Place any runtime scripts into the runtime directory.

6. Restart the PAS Server.The application definitions stored in the application definition repository are converted to JSONand then placed in the directory: PBSWORKS_HOME/data/pas/targets/localhost/repository/private/generated/json-applications



10.5 Application Definition ValidationWhen the PAS Server starts, it performs a validation of the existing application definitions. If applicationdefinitions fail to meet key criteria, they will be moved to an invalid application directory. Thedirectory will be created if it does not exist. The location of this directory for a typical installationof PAS is: PBSWORKS_HOME/data/pas/targets/localhost/repository/private/generated/invalid_applications

In addition, PAS will restore the site configuration file from the last valid backup - site-config.backup.

Error messages will be displayed in the PAS log file indicating why the application definition was invalid.Invalid application definitions can be retrieved from the invalid_applications directory and modifiedto meet the criteria necessary to be considered valid. An invalid application definition will not preventthe PAS Server from starting up.



10.6 Maintenance of Existing Application DefinitionExisting application definitions can be modified or removed. To make PAS aware of the modification orthe removal of an application definition, restart the PAS Server.

10.6.1 Updating an Application DefinitionYou can easily modify an existing application definition using your favorite XML editor.

Follow these steps to modify an application definition:

1. Navigate to the applications directory located at: PBSWORKS_HOME/data/pas/targets/localhost/respository/private/generated/json-applications/

2. Edit and make any modifications necessary to the json application definition files.

3. Restart the PAS Server.

10.6.2 Removing an Application DefinitionRemoving an application definition from PAS is also very simple.

Simply remove the application definition directory from the application and json-applications folder. Youhave to restart PAS to remove your application definition from both PAS and PBS Professional. Followthese steps to remove an application definition:

1. Navigate to the applications directory located at: PBSWORKS_HOME/data/pas/targets/localhost/respository/applications/

2. Remove the application directory and all of its content including the runtime subdirectory andassociated files.

3. Navigate to the json applications directory located at: PBSWORKS_HOME/data/pas/targets/localhost/respository/private/generated/json-applications/

4. Remove the same application directory that you removed in Step 2 and all of its content includingthe runtime subdirectory and associated files.

5. Restart the PAS Server.



10.7 Sitewide Settings

PAS provides a central repository for site specific information such as executable paths, policies, andbilling account information. This information is stored in a site configuration file, site-config.xml. Byputting some site specific application information in the, site-config.xml application definitions canbe made more portable and reusable among different PBS Professional complexes: for example, puttingbinaries locations and version availability information here, makes the rest of the application definitionreusable on a different cluster just by modifying that cluster's site-config.xml. The location of this filefor a typical installation of PAS is: PBSWORKS_HOME/data/pas/targets/localhost/repository

10.7.1 Site Configuration File Content

This file can hold virtually any sort of information, since the information stored in the file canbe referenced by any application definition XML file. Altair has included certain data in the siteconfiguration file for the integration and support of other products from the PBS Professional family. Theexample below shows a sample of the site configuration file with the sections currently used by the PBSProfessional product suite:

• Applications - This section holds application specific information.

• Application versions - For each application, you can insert site supported versions and for eachversion its binary pathname.

• Job projects (billing accounts) - This section is for integrating PAS with other products from Altair.Here you can list a set of strings to be used as “accounting” information to be attached to jobs.

• Policies - Site policies are values that can be used in a site’s application definition XML files and/oras values available in job runtime environment (policies are included as environment variables forthe jobs).

• Application policies - This section is for setting policies that are specific to an application.

10.7.2 Initial Site Configuration File after Installation ofPAS

After installation of PAS the site configuration file will contain references to PBSJobApp, an applicationdefinition that is provided out-of-the-box. Placeholders for billing accounts and policies are provided,but will need to be updated according to your site specifications.<?xml version="1.0" encoding="UTF-8"?><SiteConfiguration xmlns="http://schemas.altair.com/pbs/2007/01/site-config" xmlns:site-config="http://schemas.altair.com/pbs/2007/01/site-config" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://schemas.altair.com/pbs/2007/01/site-config ../schemas/site-config.xsd"> <Applications> <Application id="PBSJobApp"> <ApplicationVersions/> </Application> </Applications> <JobProjects id="BILLING_ACCOUNT"/> <Policies/></SiteConfiguration>



10.7.3 Sample of a Site Configuration File

Here is an example of a site configuration file with modifications for site supported application versions,application policies, billing accounts, and sitewide policies:<?xml version="1.0" encoding="UTF-8"?><SiteConfiguration xmlns="http://schemas.altair.com/pbs/2007/01/site-config" xmlns:site-config="http://schemas.altair.com/pbs/2007/01/site-config" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://schemas.altair.com/pbs/2007/01/site-config ../schemas/site-config.xsd"> <Applications> <Application id="PBSJobApp"> <ApplicationVersions/> <Policies> <Policy> <Option>MAX_CPUS</Option> <Value>4</Value> </Policy> </Policies> </Application> <Application id="Optistruct"> <ApplicationVersions> <ApplicationVersion> <Option>8.0</Option> <Executable>/opt/hyperworks/11.0/altair/scripts/optistruct</Executable> </ApplicationVersion> <ApplicationVersion> <Option>9.0</Option> <Executable>/sw/optistruct9/optistruct</Executable> </ApplicationVersion> </ApplicationVersions> </Application> </Applications> <JobProjects id="BILLING_ACCOUNT"> <Option>Company1</Option> <Option>Company2</Option> </JobProjects> <Policies> <Policy> <Option>MAX_CPUS</Option> <Value>4</Value> </Policy> </Policies></SiteConfiguration>

10.7.4 Using Site Configuration Information in anApplication Definition

For information on how to reference the site configuration file in an application definition see thetutorial Maintaining Multiple Versions of an Application, recipes How to Configure & Use Sitewide BillingAccounts, How to Configure & Use Sitewide Policies, and How to Configure & Use Application Policies inDiving Into Application Definitions.

10.7.5 Site Configuration File Backup

Upon server start-up, PAS will validate the content of the site configuration file and the content ofapplication definitions.

If the content of both the site configuration file and application definitions is valid, the site configurationfile will be backed up to a file called site-config.backup.



If the content of either the site configuration file or any application definition is invalid, the siteconfiguration file will be backed up to a file called site-config.YYYYMMDDMMSS where YYYYMMDDMMSSis the file creation timestamp.

The site configuration file will be restored from the last valid backup, site-config.backup.

Up to five (5) backups will be maintained. All backup files will be maintained in the same directory asthe site configuration file.

.

10.7.6 Site Configuration File Validation

Upon server startup, PAS validates the site configuration file. It is validated against its XML schema. AnXML schema defines the legal building blocks of a particular XML document. An XML schema:

• defines elements that can appear in a document

• defines attributes that can appear in a document

• defines which elements are child elements

• defines the order of child elements

• defines the number of child elements

• defines whether an element is empty or can include text

• defines data types for elements and attributes

• defines default and fixed values for elements and attributes

The validation process also determines if the content of the site configuration file is well-formed (valid).The content is well-formed if the following criteria is met:

• It must have a root element.

• XML elements must have a closing tag.

• XML tags are case sensitive.

• XML elements must be properly nested.

• XML attribute values must be quoted.



10.8 Interactive Application DefinitionsInteractive application definition mandatory and special arguments.

10.8.1 Mandatory Interactive Application DefinitionsChangesXML tags that are required for an interactive application definition.

For an application to be identified as interactive, the corresponding application definition must containthe Interactive element and its value must be set to true in the application input file.<Interactive>true</Interactive>

Additionally, a boolean argument is necessary to run an interactive application which controls how manyGPUs are requested at job submission.<ArgumentChoice> <ArgumentBooleanWithDescription> <Name>GPU</Name> <Description>Is GPU required ?</Description> <DisplayName>GPU(?)</DisplayName> <InputRequired>false</InputRequired> <Value>true</Value> </ArgumentBooleanWithDescription></ArgumentChoice>

The Value element controls the request for GPUs. For 2D applications set it to false and a request forGPUs will not be made for the application. For 3D applications, Value option has to be set to true.

10.8.2 Special Interactive Application ArugmentsArguments that can be added to an interactive application definition.

The following interactive application specific arguments can be added to an application definition to passarguments and environment variables to the application, define a job working directory, create a backupof job input files, and change the viewing mode from Applet to HTML5.

ArgumentsA special string argument having the name DM_APP_ARGS can be added to an application definition sothat arguments can be passed to the application. Multiple arguments can be passed to the applicationby separating them by '/n'.<ArgumentChoice> <ArgumentString> <Name>DM_APP_ARGS</Name> <Description>'\n' separated args</Description> <DisplayName>Arguments</DisplayName> <InputRequired>false</InputRequired> </ArgumentString></ArgumentChoice>



EnvironmentA special string argument having the name DM_APP_ENVS can be added to an application definition sothat environment variables can be passed to the application. Multiple variables can be passed to theapplication by separating them by '\n'.<ArgumentChoice> <ArgumentString> <Name>DM_APP_ENVS</Name> <Description>'\n' separated envs</Description> <DisplayName>Environments</DisplayName> <InputRequired>false</InputRequired> </ArgumentString></ArgumentChoice>

WorkDirectoryA special string argument having the name DM_APP_WDIR can be added to an application definition so ajob working directory is created when the job is submitted.<ArgumentChoice> <ArgumentString> <Name>DM_APP_WDIR</Name> <Description>Working dir</Description> <DisplayName>Workding Dir</DisplayName> <InputRequired>false</InputRequired> </ArgumentString></ArgumentChoice>

Note: The arguments mentioned above are disabled by default. Enable them by setting theInputRequired field to true.

Copy Back FilesA special boolean argument having the name COPY_BACK_FILES can be added to an applicationdefinition so that job input files are copied to the stageout directory.<ArgumentChoice> <ArgumentBooleanWithDescription> <Name>COPY_BACK_FILES</Name> <Description>Should job file(s) be staged out</Description> <DisplayName>Copy back files</DisplayName> <InputRequired>true</InputRequired> <FeatureEnabled>false</FeatureEnabled> <RefreshOnUpdate>true</RefreshOnUpdate> </ArgumentBooleanWithDescription></ArgumentChoice>

Note: The COPY_BACK_FILES arguments is disabled by default. Enable this field by settingthe FeatureEnabled option to true. When FeatureEnabled is set to true, the person who issubmitting the job can choose to stageout job input files or not.

Client View ModeA special enumerated list argument having the name DM_CLIENT_VIEW_MODE can be added to anapplication definition so that the person submitting the job can choose the type of mode to view the jobresults.<ArgumentChoice> <ArgumentStringEnumerated> <Name>DM_CLIENT_VIEW_MODE</Name> <Description>Viewer mode</Description> <DisplayName>Viewer Mode</DisplayName> <InputRequired>false</InputRequired> <Option>Desktop</Option> <Option>HTML5</Option> <Option>Applet</Option> <Value>HTML5</Value>



</ArgumentStringEnumerated></ArgumentChoice>

Note: By default, the HTML5 view mode is enabled.

Mandatory/Optional Application Converter File ChangesIn the app-conv-AppName application definition file, the following section determines which jobs aredisplayed in PBS Access.<jsdl-hpcp:Environment name="DM_JOB">True</jsdl-hpcp:Environment>

If this is set to False, apart from the interactive application jobs, all the other jobs belonging to the userwill be displayed. Ensure that this is set to True.

10.8.3 Adding a New Interactive ApplicationCreate a new interactive application definition by copying a default interactive application definitionsand making application specific changes..

Any time a new application is added to your HPC, a corresponding application definition needs to bewritten. Writing a specific interactive application definition is a bit more complex than writing simpleapplication definitions. We recommend a simple procedure of copying and modifying the GLXSpheresapplication definition which is available after installing the interactive components of PBS Access.

1. Navigate to the PBSWORKS_HOME/data/pas/targets/localhost/repository/applicationsdirectory.

2. Copy the GlxSpheres application definition directory and rename it to the name of the newapplication.If the new application is HyperView, then execute the following command:cp -rp GlxSpheres HyperView

3. Rename the GlxSpheres application definition files to the name of the new application.mv app-actions-GlxSpheres.xml app-actions-HyperView.xmlmv app-conv-GlxSpheres.xml app-conv-HyperView.xmlmv app-inp-GlxSpheres.xml app-inp-HyperView.xml

4. Edit the application input file.

a) Change the value of the <ApplicationId> element to the name of the new application.<ApplicationId>HyperView</ApplicationId>

b) Change the value of the <ApplicationName> element to the new application name.<ApplicationName>HyperView</ApplicationName>

c) Locate the application argument <ArgumentChoice> called VERSION.<ArgumentChoice> <ArgumentStringEnumerated> <Name>VERSION</Name> <Description> Version of the interactive application you selected to start </Description> <DisplayName>Version</DisplayName> <xi:include href="site-config.xml" pointer="xpath1 (//Application[@id='GlxSpheres']/ApplicationVersions//Option)" /> <ArgumentStringEnumerated></ArgumentChoice>

d) Change the attribute @pointer of the <xi:include> element to point to the path of the newapplication:

<xi:include href="site-config.xml" pointer="xpath1 (//Application[@id='HyperView']/ApplicationVersions//Option)" />



5. Edit the application action file.



6. Edit the application converter file.



c) Set the site specific required environment for the application.

You can set the ALTAIR_LICENSE_PATH, NCPUS, ngpus, MEMORY etc according to therequirements for the application.<jsdl-hpcp:Environment name="ALTAIR_LICENSE_PATH">6200@licsrv</jsdlhpcp:Environment>

7. Restart PAS for these changes to take effect.

8. Navigate to the directory PBSWORKS_HOME/data/pas/targets/localhost/repository.

9. Edit the site-config.xml file.

a) Add a new <Application> element that points to the new application executable.<Application id="HyperView"> <ApplicationVersions> <ApplicationVersion> <Option>13.2</Option> <Executable>/altair/hw/13.2/altair/scripts/hv</Executable> </ApplicationVersion> </ApplicationVersions></Application>

Tip: You can also define multiple executable versions for the application.

<Application id="HyperView"> <ApplicationVersions> <ApplicationVersion> <Option>13.1</Option> <Executable>/altair/hw/13.1/altair/scripts/hv</Executable> </ApplicationVersion> <ApplicationVersion> <Option>13.2</Option> <Executable>/altair/hw/13.2/altair/scripts/hv</Executable> </ApplicationVersion> </ApplicationVersions></Application>

Once PAS is restarted, the new application is available in PBS Access.


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