Pipeline Pilot Server - University of California, Santa …cscenter.pbsci.ucsc.edu:9944/help/docs/pdfs/server_install.pdf · Pipeline Pilot Server Release 8.5 Install Guide ... For

Copyright © 2011 Accelrys Software, Inc.

Pipeline Pilot Server

Release 8.5 Install Guide

May 2011

Contents

Requirements 2 Windows and Linux Hardware 2 Windows Software 2 Linux Software 3 Grid System Support 3 Apache Web Server Support 3 Pipeline Pilot Collections 4

R Software, BioConductor 4 Third-Party Software 4

Included with Pipeline Pilot 4 Included with Java Server Package 4

Discovery Studio Support 4 ODBC Support 5

ODBC Support for Windows 2008 5 Excel Reader (On Server) Support 5

Pre-Install Checklist 6

Server Deployment Scenarios 8 Managing Multiple Installations 8

Side-by-Side Installations 8 Compatibility Across Protocol Databases 8

Sharing an XMLDB with Multiple Servers 8 Support for Server Clustering 9 Support for Distributed Grid Computing 9

Shutting Down Apache 10 Windows Apache Shutdown 10 Linux Apache Shutdown 10

Moving/Migrating an Installation 11

Uninstalling Pipeline Pilot 12 Windows Server Uninstallation 12 Windows-to-Windows Server Relocation 12 Linux Server Uninstallation 12

Installing Pipeline Pilot Server 14 Windows Server Installation 14 Linux Server Installation 15

Running "scirootinstall" on Linux 16 Manually Starting the Linux Server 16 Testing Pipeline Pilot Software on Linux 17

Post-Install Checklist 18

Pipeline Pilot Home Page 20

Quick Install Tips

Accelrys License Files

To install any new Pipeline Pilot software and collections, you need a valid Accelrys license file. If your license is expired, contact Accelrys Customer Support to obtain a renewal. After receiving the updated license, replace the expired file on your server with the new one before installing any new Pipeline Pilot software. Instructions are included with the license file for updating/activating a new license, and for installing newly purchased component collections.

To install Pipeline Pilot on your Windows or Linux server:

■ Shut down Apache. This also shuts down your Pipeline Pilot server.

■ Review the Pre-Install Checklist and perform all recommended pre-installation tasks.

■ Follow the instructions for Installing Pipeline Pilot on your server.

■ Depending on which separately purchased collections you install, you may need to perform additional tasks on your server to ensure these collections run properly. For example, you may need to install third-party software on the server or client. For details, see the Post-Install Checklist.

Additional Information:

■ For information about supported hardware and software, see Requirements.

■ For details about server administration, see the Administration Reference Guide.

■ To install Pipeline Pilot Professional Client, see the Pipeline Pilot Professional Client Install Guide.

■ For details about clustering and grids, see the Clustering Deployment and Support Guide.

https://community.accelrys.com/index.jspa

admin_ref.pdf

client_install.pdf

http://doc.accelrys.com/library/PipelinePilot/doc/clustering.pdf

Pipeline Pilot Server Install Guide 2

Requirements

The Pipeline Pilot platform supports different operating systems. Ensure that your server machine meets all of the recommendations listed below. These recommendations include running the server software, Professional, and Web Port clients, component collections, and associated data, and custom client interfaces.

IMPORTANT! Only install Pipeline Pilot Server behind a firewall. Your license does not permit general access from outside of your organization's network.

Windows and Linux Hardware

Computer ■ Pentium or Xeon class computer, 2.0 GHz (dual core) or 3.0 GHz

CPUs ■ As a guide, one CPU for every two simultaneous users should provide adequate performance

RAM ■ 2-4 GB RAM (3-6 GB may be required for 64-bit Linux), plan on at least 1 GB of RAM per CPU

Disk Space ■ 3-5 GB free disk space for installation

■ 30 GB free disk space for runtime environment, user data files, etc. Disk space depends on the number of installed packages and the data types used with your packages, (e.g., disk space needed to support the Sequence Analysis package depends on the number of sequences and their length, as well as the type of data you need to use with these components.)

Swap Space ■ Swap space is also critical. The available swap file size should be at least 1 to 1.5 times the size of the physical installed RAM, (e.g., a machine with 2 GB of installed RAM should have at least 2 GB of available swap).

Windows Software

Operating Systems

■ Windows Server 2008 SP2

■ Windows Server 2008 R2 (64-bit)

■ Windows Server 2003 SP2 (32-bit)

Web Browsers ■ Internet Explorer 6 (existing Component Collections and applications only), 7, or 8

■ Mozilla Firefox 3.5 or 3.6

System Privileges ■ System Administrator

IMPORTANT! Do not use "scitegic" as a server user name. It is reserved for internal operations.

Tip: For Windows requirements on a client, see the Pipeline Pilot Professional Client Install Guide.

client_install.pdf


Linux Software

Operating Systems

■ Red Hat Enterprise Linux 4 WS or ES (update 5 or later), 32-bit x86. This 32-bit Red Hat configuration is also supported on 64-bit hardware. (Red Hat Enterprise Linux 3 WS is no longer supported.)

■ SuSE 11 64-bit. (On SuSE 10, only the 32-bit version is supported.)

IMPORTANT!

■ The installer fails if it cannot detect the appropriate RPMs.

■ The Next Gen Sequencing collection is only supported on Linux 64-bit machines.

Web Browsers ■ Mozilla Firefox 3.5 or 3.6 to run the Administration Portal on Linux and access the Help Center (online documentation resources).

System Privileges "Root" privileges are required for the following (optional) configurations:

■ To configure user impersonation in the Administration Portal

■ To create a boot script that enables the server to run under a specified user account (so Pipeline Pilot automatically starts when the server is started). The installer creates a boot script that configures the server for automatic startup. If you do not create a boot script, you need to manually start Pipeline Pilot on your server (not recommended).

■ To create a boot script that enables the optional Java Server package components to automatically start.

■ To add a security module that enables Pipeline Pilot to install and run (with SE Linux extensions (Secure Linux) enabled on Red Hat Enterprise Linux 5 or later).

Grid System Support

You can deploy Pipeline Pilot on a grid system. The grid system software that is currently supported includes:

Grid Software ■ Sun Grid Engine (SGE) 6.1

■ PBS Professional 9.2

■ Platform LSF 7.00 Update 3

Notes:

■ Pipeline Pilot should be installed on a Linux machine that can support your distributed grid computing system. There are no additional hardware requirements beyond what is specified for a normal installation.

■ The Administration Portal has settings available for grid engine support, including type, path, and default queue name. The portal also provides a list of queue names for a client to use at run time, but this does not affect the operation of the server in any way. For further details, see the Clustering Deployment and Support Guide.

Apache Web Server Support

To ensure that your clients are able to connect to ports on the Apache web server, you may need to configure your network to permit communication on the ports used by the Pipeline Pilot server.




Pipeline Pilot Collections

Additional component collections that offer more specialized functionality are available as separately purchased collections. These collections are installed at the same time you install Pipeline Pilot on your server. Your Accelrys license file determines which collections to include with your installation product.

You can also install third-party collections obtained through independent software vendors (ISVs) at the same time that you install Pipeline Pilot software. You need to be able to access your ISV source files (on disk). For further information, contact the ISV.

IMPORTANT! Some of the separately purchased collections require third-party software that is not included in your Pipeline Pilot installation. For further information, contact Accelrys Customer Support or see the documentation included with your collections.

R Software, BioConductor

If any of your collections require R Software or BioConductor, an installation guide is available that provides details about how to install and configure these third-party applications. For details, see the R Software Support Guide.

Third-Party Software

Included with Pipeline Pilot

Some third-party software is included with Pipeline Pilot and is copied to your server as part of the installation. The third-party software that is installed on your server includes:

Third-party Software

■ Apache 2.2: Provides client-server connectivity

■ Perl 5.8 from CPAN: Supports components written in Perl

■ Java Runtime Environment: Supports components written in Java and JDK 6.0 to develop custom components in Java

■ DataDirect: Provides connectivity to ODBC-compliant databases such as Oracle, Microsoft SQL Server, MySQL and DB2

Included with Java Server Package

If you install the (optional) Java Server package, the following software is installed on your server:

Third-party Software

■ Apache Tomcat 6.0: Provides client-server connectivity for workflow and portal examples.

■ Apache Derby Database 10.4: Provides persistent storage for web applications and message broker

■ Apache ActiveMQ Message Broker 5.0: Provides a flexible connectivity infrastructure for integrating applications and services

Discovery Studio Support

When installing Discovery Studio and Pipeline Pilot on the same system, it is easier to first install Pipeline Pilot. For further details about how Pipeline Pilot and Discovery Studio work together on the same server, see the online help for Discovery Studio or consult Technical Support. If you run Pipeline Pilot and Discovery Studio on a cluster or grid, information about how to fine-tune the server to improve performance is available in the Clustering Deployment and Support Guide.


http://doc.accelrys.com/library/PipelinePilot/doc/rsoftware_support.pdf

http://doc.accelrys.com/library/PipelinePilot/doc/rsoftware_support.pdf



ODBC Support

If the Integration package is part of your license, ODBC drivers from DataDirect are installed on your server for both Windows and Linux platforms. These drivers support connections to Oracle, Microsoft SQL Server, MySQL, and DB2.

We recommend that you configure an ODBC data source and then test your ODBC connections. For instructions, see the Database Integration Guide. Online help is also available for the DataDirect ODBC drivers included with Pipeline Pilot. From the Pipeline Pilot Server Home Page, select "ODBC Driver Help".

Tips:

■ There is no need to install separate database client software. Although other database drivers may work, the only drivers that were thoroughly tested and confirmed to work properly are the DataDirect drivers.

■ For legal reasons, the drivers that ship with Pipeline Pilot do not support SSL encryption. If you require SSL encryption, contact Accelrys Customer Support.

■ Pipeline Pilot does not provide drivers for querying an MS Access database from Linux. We recommend converting the database format from Access to a format supported by a Pipeline Pilot driver.

ODBC Support for Windows 2008

On Windows 20008, Pipeline Pilot runs as a 64-bit program. 64-bit ODBC drivers are provided with Pipeline Pilot. The default Data Sources (ODBC) tool in the Windows Server 2008 Control Panel/Administrative Tools is designed for these 64-bit database drivers and works correctly.

ODBC driver for Microsoft Access: There is no support for Microsoft Access from 64-bit Windows. For MS Access, use an older version of Windows (e.g. Windows 2003) or convert to a supported database, (e.g. Oracle or Microsoft SQL Server).

Excel Reader (On Server) Support

The Excel Reader (On Server) component is deprecated, but still available because of its lack of portability to Linux, and also because newer versions of the Windows operating systems made it difficult to automate the use of Excel (as this component does) in a service environment. Microsoft does not recommend or support this type of usage. A reference on this subject is the following Microsoft knowledgebase article: “Considerations for server-side Automation of Office” at http://support.microsoft.com/kb/257757.

When used in Windows Server 2008, the Excel Reader component fails when attempting to open the file to read. The simplest workaround to this problem is to use the Excel Reader (Cross platform) component. Alternatively, you can follow the instructions in the Microsoft knowledgebase article “How to configure Office applications to run under a specific user account”. The original is not available, but an archive is currently at http://web.archive.org/web/20050206133802/http://support.microsoft.com/kb/288367. It explains how you might configure Windows to run Excel as a given user, and so fixing its identity when launched under automation. The article includes warnings about the security and stability risks of this approach, but the technique can be used to make the Excel Reader (on Server) functional on Windows Server 2008.

http://doc.accelrys.com/library/PipelinePilot/doc/integration_database.pdf


http://support.microsoft.com/kb/257757

http://web.archive.org/web/20050206133802/http:/support.microsoft.com/kb/288367


Pre-Install Checklist

To ensure that your Pipeline Pilot installation goes smoothly, complete the checklist below. If you have any questions, contact Accelrys Customer Support.

Do this: Details: Done?

1 Obtain required system administrator privileges to install software on your server.

■ Windows: System Administrator

■ Linux: Root

2 Locate your Accelrys license file (*.lic). A valid license file is current (not expired) and accessible during the installation. For each new license file that you obtain, instructions are available that explain how to update and activate the license file.

3 Verify that your server meets the hardware/software requirements.

See Requirements.

4 Check to see if any protocols are currently running on your Pipeline Pilot server.

Active jobs must finish running before installing Pipeline Pilot. Cancel jobs in the Administration Portal (Jobs > Running Jobs).

5 Shut down Apache. Apache cannot be running on the server where you are installing Pipeline Pilot. See Shutting Down Apache.

6 Shut down the Java server. If your server also runs the Java Server package (optional), the Java server cannot be running when you install Pipeline Pilot. Cancel this service in the Administration Portal (Apache > Restart).

7 Close all instances of the Administration Portal and Pipeline Pilot Professional, and Web Port applications.

Shut down all Pipeline Pilot software applications on the server. Close all Pipeline Pilot clients with current connections to the protocol database (XMLDB) on the server you are about to upgrade.

8 Disable all virus scanning software and firewalls on the server.

Some virus scanners and firewall applications can slow down or even corrupt the installation.

9 Verify that you can use Pipeline Pilot’s default port numbers with the Apache web server:

■ 9944 (HTTP)

■ 9943 (HTTPS)

If these port numbers are already in use by another web service, you can manually assign different port numbers for Apache during the Pipeline Pilot installation.

Decide in advance what port numbers to use. You need to refer to these port numbers when accessing the Home Page and server-related applications, so make a note of any custom port numbers you decide to manually assign.

10 Do you need to run the Apache web server under a specific user to extend and control local network resources?

If yes, you need to obtain the specific user account and password.

http://customer.accelrys.com/


Do this: Details: Done?

11 Does your Linux server run Red Hat Enterprise Linux 5 (or later) with SE Linux Extensions enabled?

To install the Pipeline Pilot security module, run the sciseallow script as root.

12 Are you installing Pipeline Pilot on a grid system or cluster?

If yes, configure and test your grid queuing system and ensure that it is fully operational before installing Pipeline Pilot. For details, see the Clustering Deployment and Support Guide.



Server Deployment Scenarios

Managing Multiple Installations

Pipeline Pilot supports side-by-side installations of existing and new products. You can run 8.x and 7.x on the same machine. With side-by-side installations, the installer can copy components and protocols from an existing protocol database (XMLDB) into the new installation. You can also upgrade an existing installation to the latest version.

Side-by-Side Installations

To run different versions side-by-side, each version needs to be installed in a unique path or drive on your server. They cannot all reside in the same directory or subdirectories. You also need to run side-by-side versions of the clients that correspond to each server installation, assuming they are mutually incompatible versions.

On a Windows server, the default path for Pipeline Pilot 8.x is "C:\Program Files\Accelrys\PPS". For 7.5, the path is "C:\Program Files\Accelrys\SES". For 7.0 and earlier versions, the path is "C:\Program Files\SciTegic" (or "SciTegic 7.0" if this location already contains an installation).

Compatibility Across Protocol Databases

The Pipeline Pilot Professional client supports connecting to multiple XMLDBs through the Network tab. Some support is provided for connecting to 7.x servers from 8.x clients. The 8.x client can connect to 8.x, 7.x, or 6.x databases, but can only save files on an 8.x database.

Sharing an XMLDB with Multiple Servers

Pipeline Pilot clients running at multiple sites can access the same protocols and components if they share the same protocol database (XMLDB). To provide this functionality, the computational servers that process protocol jobs at each site need to communicate with one server that operates as the XMLDB for all the other servers. The following figure illustrates a common way to set this up:

Protocol database sharing across an enterprise


Notes:

■ Clients are only aware of the computational server where they run protocols. They have no information about the machine hosting the XMLDB.

■ After installing Pipeline Pilot, you can configure it to use a remote XMLDB by changing a server environment setting called “XMLDB EndPoint” in the Administration Portal (Setup > Server).

■ For more information about reusing an XMLDB, see Moving/Migrating an Installation.

Support for Server Clustering

Clustering is a technique that provides load balancing scalability for jobs by efficiently using available resources over a network. Protocol jobs requested by a client that are connected to a given server are delegated to other computational nodes; the cluster is defined by the set of nodes available for delegation.

Load balancing capabilities are available for Pipeline Pilot server products that run on the Linux platform. A single Pipeline Pilot installation on a shared file system is accessed from multiple server machines. They share the same Pipeline Pilot installation file system and the same component and XMLDB. The only unique aspect to each server node is the specific set of jobs assigned to it for execution.

Support for Distributed Grid Computing

Grid computing is a type of distributed computing in which CPU resources are shared across a computer network, allowing all connected machines to operate as a compute cluster. Pipeline Pilot allows you to take advantage of distributed grid computing technologies such as Sun Grid Engine, PBS Professional, and Platform LSF.

With this technology, a large number of protocol runs can be farmed out to a compute grid, providing efficient use of enterprise compute resources. You can also queue specific long-running protocols, optimizing the turnaround for critical short-running protocols. Overall, this allows a community of Pipeline Pilot users running Pipeline Pilot in a batch fashion to run more protocols with maximum efficiency for each individual job.

Note: For more details, see the Pipeline Pilot Clustering Deployment and Support Guide.



Shutting Down Apache

Before installing a new version of Pipeline Pilot on your server, shut down your Apache web server—this also shuts down Pipeline Pilot server since it runs on Apache. The default port numbers used by Apache are:

■ HTTP: 9944

■ HTTPS: 9943

IMPORTANT! If multiple Pipeline Pilot servers are running simultaneously, multiple Apache services are also running on your server. Be sure to stop all currently running services to completely shut down Apache.

Windows Apache Shutdown

To shut down Apache on a Windows server:

1 Identify what port numbers Apache is currently using on your server. (Make special note if they are different from the default listed above.)

2 From the Windows Control Panel, select Administrative Tools > Services. The Services console opens.

3 In Name, look for your SciTegic/Apache service (for example, "scitegic_apache_7_0_0").

4 If the Status is "Started", right-click and select Stop.

5 Repeat for each instance of SciTegic Apache that is currently running on your server.

6 To ensure that all ports are released, open a command window and run the following:

netstat -a

A list of port numbers currently in use is displayed. This list should not include Apache ports.

Tip: It may take a few minutes for Apache to release the ports. Retype the command to refresh the list.

Linux Apache Shutdown

To shut down Apache on a Linux server:

1 Change directories to your server install directory:

> cd linux_bin

2 Stop the server:

>./stopserver

3 Ensure that the ports are released:

> netstat -lt

A list of port numbers currently in use is displayed. The default Apache port numbers used by Pipeline Pilot should not be listed.

Tips:

■ It may take a few minutes for Apache to release the ports. To refresh the list, retype the command.

■ You can also use the following command to see if Pipeline Pilot is running is to check for running HTTPD processes in the scitegic directory: > ps -ef | grep httpd


Moving/Migrating an Installation

You can move/migrate your server location by uninstalling Pipeline Pilot software and transferring the XMLDB to the new server. After uninstalling, some files remain intact, making it possible for you to relocate existing data to a server re-installation. Specifically, your XMLDB remains intact in the “<install>” folder, so you can easily move/migrate it to a new location.

Default Directory Description Do this:

< install>\xmldb Protocol database storing protocols and components specific to server, including version history and custom protocols. Some files are public (Components and Protocols subfolders); others are owned by specific users (User subfolder).

When moving your server to a new location, copy this directory to the target location, so users can access their protocols, components, and version history.

< install>\xmldb\objects Server startup configuration. This information should only be located where Pipeline Pilot is installed. Contents are configured on your server during installation and must always reside in the default directory.

When moving your server to a new location, use the Administration Portal to customize your server settings on the target server.

< install>\web Custom web applications, web server customizations, job folders.

When moving your server to a new location, you need these files on the target server, so users can continue to run your web applications.

Note: < install> is the name of your Pipeline Pilot installation path, such as “C:\Program Files\Accelrys\PPS”.

Other noteworthy directories include:

Default Directory Description Do this:

< install>\apps\scitegic This directory is removed, but any other non-Accelrys packages in “\apps” are not deleted.

NA

< install>\licensing License-related files. When moving your server to a new location, copy this folder to the target location. During installation, specify the path to your license file to install the appropriate packages.

< install>\public If this directory contains custom user data, including “\public\users”, it is not removed.

NA

< install>\logs Log files. You do not need to copy these files to other servers as new log files are created after installing Pipeline Pilot. Move this folder to preserve the server history, (for usage tracking purposes).

< install>\install Contains installation files.

You do not need to copy these files to other servers.


Uninstalling Pipeline Pilot

IMPORTANT! Before uninstalling Pipeline Pilot from any server, do the following (in order):

1 Shut down Apache.

2 Confirm there are no jobs running on the server. In the Administration Portal, select Jobs > Running Jobs.

3 Back up your XMLDB. Select Resources > Backup.

4 If you customized the location of your XMLDB directory, reconfigure it to the “<install>\xmldb” default location. Select Setup > Folder Locations.

Windows Server Uninstallation

Use “Add/Remove Programs” in the Windows Control Panel to uninstall the server software.

Tip: When you uninstall Pipeline Pilot, your protocol database (XMLDB) remains on your server. You can install a new version of Pipeline Pilot in the same location. You can also migrate your XMLDB to a new server if you plan to reuse it somewhere else.

Windows-to-Windows Server Relocation

To relocate your server on Windows:

1 Transfer the old installation folder to the new location. Copy the folder and its contents to the <install> path at the target location. For example, copy it to “C:\Program Files\Accelrys\PPS”.

2 If you had a custom XMLDB location prior to uninstalling Pipeline Pilot, copy the files from the custom XMLDB location into the new folder (“\xmldb”).

3 Reinstall Pipeline Pilot on your Windows server. You can either install an existing version (the one you just uninstalled) or install an upgrade. Be sure to specify the location where you copied the XMLDB folder on the target.

4 Make sure that any other custom folder locations (Jobs or User Directory) are valid. In the Pipeline Pilot Administration portal, go to Setup > Folder Locations to verify.

5 If the target location is on a different server or port, inform Pipeline Pilot client users, so they can update their active server connections.

Linux Server Uninstallation

1 Stop the server using the stopserver command in the "/opt/Accelrys/installdir/linux_bin" directory.

2 Remove the boot startup and shutdown scripts:

■ rm /etc/rc.d/rc*.d/*ppilotd.<port>

where <port> is the server port number

■ rm /etc/init.d/ppilotd.<port>


3 If you installed on a cluster or a grid, for each node in the cluster:

■ Stop the server (cluster only):

/opt/Accelrys/installdir/linux_bin/stopserver

■ Unmount the exported file system

umount -f /opt/Accelrys

■ Edit /etc/fstab and remove the entry for the exported file system


■ Remove the scitegic mutex directory (cluster only):

rm -rf /var/tmp/scitegic-mutexes-<port>


■ Remove the /etc/pam.d/scitegic file (cluster only):

rm /etc/pam.d/scitegic

■ If you installed the boot scripts:

Remove the startup and shutdown scripts, see step 3 (cluster only).

■ If you installed the SE Linux module, remove it:

/usr/sbin/semodule -r scitegic

■ If you installed the Xvfb init script (grid only), remove it:

rm /etc/rc.d/rc*.d/*scivfb.<port>


rm /etc/init.d/scixvfb.<port>


4 If you installed on a cluster, remove the export entries:

■ Edit /etc/exports and remove the entries for the exported file systems.

5 Remove the scitegic mutex directory:

rm -rf /var/tmp/scitegic-mutexes-<port>


6 Remove the installation:

rm -rf /opt/Accelrys/installdir

7 Remove the user and group entries for the Pipeline Pilot server:

userdel -r <username>

where <username> is the name of the Apache user.

groupdel <groupname>

where <groupname> is the name of the Apache group.

8 Remove the /etc/pam.d/scitegic file:

rm /etc/pam.d/scitegic

9 If you installed the SELinux module, remove it:

/usr/sbin/semodule -r scitegic


Installing Pipeline Pilot Server

You can upgrade an existing installation to the latest version or you can run side-by-side installations of both new and older versions (each version is installed in a unique path or drive). The installer can copy components and protocols from an existing XMLDB to a new installation or they can remain separate.

IMPORTANT! If you are upgrading, decide where you want to keep your existing custom protocols. They will not be deleted, but it’s important to know where your files are located after installing new software.

Windows Server Installation

The default path for installing Pipeline Pilot on Windows is "C:\Program Files\Accelrys\PPS".

To install Pipeline Pilot on a Windows server:

1 From the folder that contains your installation files, run "bin\scitegicsetup.exe". When the Pipeline Pilot installer starts, review the welcome and end user license agreement screens.

2 If prompted, install the required Microsoft runtime libraries (DLLs).

3 Enter the path to your Accelrys license file (*.lic). It determines what software and component collections to install on your server.

Tip: A new protocol database (XMLDB) will be installed (whether it’s a new installation or an upgrade). You have choices for how to use your existing custom protocols with the new XMLDB.

4 Select the older version to upgrade, and then choose how to upgrade your custom protocols:

To do this: Select this upgrade option: Consequences?

Install the new version of Pipeline Pilot on top of the old one (in the same location).

Keep my existing protocols and make them available in the new XMLDB that will replace the old one.

Install to an existing location. Upgrade any existing protocols.

Has no effect on your custom protocols since they are included in the new XMLDB.

Install the new version of Pipeline Pilot in a new location and keep the old version of Pipeline Pilot intact.

Keep my existing protocols in the old installed XMLDB only. Do not copy them to the new installation’s XMLDB.

Install to a new location. Do not upgrade protocols from any existing installations.

You now have two XMLDBs, but your custom protocols are only available in the old XMLDB (not the new one). Note: You can manually import or copy your custom protocols to the new XMLDB.

Install the new version of Pipeline Pilot in a new location and keep the old version of Pipeline Pilot intact.

Keep my existing protocols in the old XMLDB and also copy them to the new XMLDB.

Install to a new location. Copy protocols from selected installation to new location and upgrade them.

You now have two XMLDBs, and your custom protocols are available in both places.

Tip: Use only one XMLDB to save future modifications to your custom protocols.


5 From the list of packages, select the ones to install on your server. (The available packages are determined by your license file. Some optional packages are not installed by default, so be sure to review the list carefully.)

6 If you are upgrading, select a backup option. By default, the installer backs up your XMLDB in “root/public/backups” (in compressed zip format).

7 Verify the HTTP and HTTPS port numbers. The default port numbers are "9944" and "9943". If another service is already using these numbers, you can change the ports used for Pipeline Pilot.

8 By default, the Apache web server runs under your system account. To allow a specific user to run the Apache web server, select Change Apache Account, open the service for your SciTegic/Apache package, and enter the user account and password at the Log On tab.

Notes:

■ If there is a problem during the installation, the last screen of the installer provides an option for viewing your installation log. It provides details about what took place during the installation, to help you pinpoint the nature of the problem. The file is saved in “<install>\logs\install.”

■ After you install Pipeline Pilot on your Windows server, you have the option to install Pipeline Pilot Professional Client on the server. The Pipeline Pilot Server Home Page also has an option for installing Pipeline Pilot (for details, see Post-Install Checklist).

■ Client users can install Pipeline Pilot Professional Client by connecting to the Server Home Page from their web browsers. They can also read the Pipeline Pilot Professional Client Installation Guide to get further details Windows client installation (including system requirements).

Linux Server Installation

IMPORTANT! Ensure that you are a non-root user before you start the installation. Use a newly created account such as "scitegicuser". ("scitegic" is reserved for internal operations, so avoid using this name.)

To install Pipeline Pilot on a Linux server:

1 Change the directory to the location of the installation files; this is the directory that contains the "sciinstall" script.

2 If you are using Red Hat Enterprise Linux 5 or greater, check for the SE Linux extensions. To do this, run the following command:

/usr/sbin/selinuxenabled; echo $?

Tip: If "0" displays when the command is executed, and you did not run the "sciseallow" script as root, do this now.

3 If using impersonation, create an account for this user. The account should use its own group. No regular users should belong to it.

4 Run "sciinstall" as a non-root user.

5 Enter the path to your Accelrys license file. Your license determines what software and component collections to install on the server.

6 Enter the path to your Accelrys license file. Your license determines what software and component collections to install on the server.

7 Enter a target directory for installing the Pipeline Pilot application. For disk space information, see Requirements.

8 Assign the HTTP and HTTPS ports (required by the Apache web server). The default ports are 9944 (HTTP) and 9943 (HTTPS). To assign alternate ports, press N, and then enter the alternate port numbers at the prompt.

client_install.pdf


Tip: The installer checks the ports to ensure that they are available. If it detects a conflict, a warning is displayed and the installation stops. To assign different port numbers, ensure they are available before you re-run the installation program.

9 Select the local directory for lock files. The default directory is "/var/tmp". The lock file directory requires read, write, and execute privileges for all users. For cluster configurations, this directory path must exist on each node's local hard drive.

Notes:

■ It takes a few moments for the installation to finish. When complete, the Apache and Pipeline Pilot servers both start automatically.

■ If you did not create a boot script, you need to manually start the server.

■ On Linux, Pipeline Pilot uses the Pluggable Authentication Modules (PAM) API for authentication and impersonation. PAM provides a centralized mechanism for authenticating all services. If you run the script “scirootinstall”, a default PAM configuration is created in "/etc/pam.d/scitegic". Although the default settings in this configuration file are suitable for most situations, review the file and customize it as necessary. (More information is available in the Administration Reference Guide.)

■ When the SE Linux extensions are enabled, run the "sciseallow" script as root prior to running the installer. This script creates and registers a security module that allows Pipeline Pilot to install and execute. You cannot successfully install Pipeline Pilot if you do not first run this script. An error message is displayed about read-only protected segments when registering the server packages if you do not run it. (Only run "sciseallow" once on a machine.)

Running "scirootinstall" on Linux

Your Pipeline Pilot installation on Linux may also require that you run the script "scirootinstall". For Pipeline Pilot to automatically start when you restart the server and to prepare the server for impersonation, you must run another script called "scirootinstall". You should also run this script if you are installing Pipeline Pilot to work with a grid engine.

Note: Root privileges are required to run the "scirootinstall" script.

To run scirootinstall:

1 As a root user, run another script called "scirootinstall".

2 When prompted, enter the location of the Pipeline Pilot installation, and information about the user who will run the Apache server.

■ To create the boot script, press Y at the boot script prompt.

■ To enable the server to switch impersonation on and off, press Y at the impersonation prompt.

3 Log on as the user who will run the Apache server, and then restart Apache.

Manually Starting the Linux Server

Perform this task only if you did not create a boot script to automatically start Pipeline Pilot when you installed the application (not recommended).

To manually start the server:

1 Change the working directory to program directory of your Pipeline Pilot installation:

> cd <install>/linux_bin

2 Start the server:

> ./startserver

admin_ref.pdf


Testing Pipeline Pilot Software on Linux

The Pipeline Pilot Professional Client software cannot be installed on a Linux server. To verify the server installation you must either connect to the server through a client from a separate Windows machine or use a web browser to access the Pipeline Pilot Server Home Page. The home page may be used to configure the server and run server diagnostics and test protocols.

To access the home page:

Go to "http://servername:9944" where <servername> is the name of your Linux server.

Would you like to: Select this:

Read documentation about using and administrating Pipeline Pilot

Help Center

Install the Pipeline Pilot Professional Client on a Windows computer

Install/Upgrade Client Software

Change server settings or enable impersonation Administration Portal

Run diagnostics or test protocols Server Diagnostic Tests

Launch Web Port Pipeline Pilot Web Port


Post-Install Checklist

After installing Pipeline Pilot on your server, there may be additional configurations required for connectivity and resource access. We recommend you review the information provided below and identify any outstanding tasks you may need to complete.

Note: There are many additional tasks you can perform on the server in addition to the ones listed below. For more detailed information, see the Administration Reference Guide.

Would you like to: Here’s how:

Get more familiar with Pipeline Pilot? Be sure to visit the Pipeline Pilot Home Page and launch the Administration Portal, perform server diagnostic tests, and run example protocols.

From your server’s web browser, go to:

"http://<servername>:9944"

"<servername>" is the name of your Pipeline Pilot server

Learn about managing Pipeline Pilot Server? Review the online documentation, especially the Administration Reference Guide, and get more familiar with the various ways you can configure your Pipeline Pilot server.

From the Pipeline Pilot Home Page, select "Help Center (Administrator Resources) ".

Verify that your collections can properly run? Review the documents included with each separately installed collection to ensure that all requirements are met. In some instances, third-party software may be required on the server or client machines to support a collection. If you have questions, contact Accelrys Customer Support.

From the Pipeline Pilot Home Page, select "Help Center (User Resources) ". A set of documents that explains how to support and use each collection is available on a per-collection basis (organized in alphabetical order).

Share a protocol database across servers? Pipeline Pilot clients running at multiple sites can access the same protocols and components if they share the same XMLDB.

Change the "XMLDB Endpoint" in the Administration Portal so that it points to the server that hosts the protocol database (Setup > Server).

Authenticate users on the server? You can restrict access to the server based on the identity of your network users. Pipeline Pilot supports File, Local, and Domain authentication.

Configure authentication in the Administration Portal (Security > Authentication).

Enable impersonation? Impersonation allows users to access network resources using their network security credentials rather than their server account credentials.

Enable impersonation in the Administration Portal (Security > Authentication).

Restrict publishing rights on the server? All users have read/write access to the shared tabs, allowing all users the rights to “publish”. You can control how users publish protocols on these shared tabs by managing access rights.

Configure access rights in the Administration Portal (Security > Access Rights).

Support Web Port users? Any client user, who needs to run protocols remotely or from a web browser, needs to run Web Port.

A link is available from the Pipeline Pilot Server Home Page for launching Web Port.

admin_ref.pdf

admin_ref.pdf



Would you like to: Here’s how:

Provide database connectivity? ODBC drivers from DataDirect are included with the Integration collection. These drivers support connections to Oracle, Microsoft SQLServer, MySQL, and DB2. A version of the Oracle JDBC driver for connecting to Oracle databases is also available. To use the Integration components with your database, you need to configure data sources on your server.

Read the instructions in the Database Integration Guide for the Integration collection. ODBC Driver Help is also available on the Pipeline Pilot Home Page.

Schedule protocol jobs? You can run Pipeline Pilot protocols outside of the graphical client environment on any computer where Pipeline Pilot is installed with job scheduling.

Install the Integration collection and run command-line program "RunProtocol.exe". Read the Command Line Guide for the Integration collection.

Troubleshoot problems with client-server connectivity? Test your server connections.

Run the server diagnostic tests from the Pipeline Pilot Home Page.

Migrate an existing Pipeline Pilot installation to a new machine? Reuse your protocol database (XMLDB) in the new environment.

Point all clients (Professional and web-based) to the new host, and install the required software on the new host. Update your browser bookmarks to Web Port and any web pages that contain links to protocols. For further details, see Moving/Migrating an Installation.

Upgrade an existing installation? Depending on your installed packages, some additional steps may be necessary to get your server properly configured and running.

Activate any non- Pipeline Pilot packages, such as custom Java components or third-party components, and recompile your client applications that use the Java SDK or .NET SDK with the new versions of "jalpp.jar" or "nalpp.dll".

Upgrade an existing installation and modify the port numbers? Any applications that rely on the new port numbers will need updating.

Update your browser bookmarks to Web Port and any web pages that contain links to protocols.

Deploy Pipeline Pilot on a grid or cluster? Ensure your machines are properly configured to support these features.

Test your grid engine with Pipeline Pilot and ensure that protocols can run on the queues.

Configure the Java Server package that you installed as part of the Pipeline Pilot server installation? Some additional steps may be necessary.

Before you can start the Java Server services, validate the ports that you need to use in the Administration Portal (Apache > Ports). After validation, you can start the Java Server services from the Administration Portal.



http://doc.accelrys.com/library/PipelinePilot/doc/integration_command_line.pdf

http://doc.accelrys.com/library/PipelinePilot/doc/integration_command_line.pdf


Pipeline Pilot Home Page

The Server Home Page is a one-stop place for all things related to Pipeline Pilot applications. It opens in a browser window and provides a way to get assistance and access documentation and programs. From the home page, you can install or upgrade a Pipeline Pilot client, access the Help Center, run the Administration Portal, perform server diagnostic tests, and launch Pipeline Pilot Web Port.

Pipeline Pilot Server Home Page

Documents

Pipeline Pilot Server - University of California, Santa …cscenter.pbsci.ucsc.edu:9944/help/docs/pdfs/server_install.pdf · Pipeline Pilot Server Release 8.5 Install Guide ... For