GUI-based Installation

  1. Select Installation Type
  2. Enter Oracle Information
  3. Install Cartridge
  4. Grant Permissions
  5. Configure FastROCS Server
  6. Configure RMI Server
  7. Load Test Data and Build Index

A graphical user interface is provided to facilitate installation. The cartridge may be installed on a single server, or distributed across multiple servers with the Oracle and RMI servers on different machines. Oracle components must be installed on the Oracle server, but no such restriction exists for RMI servers.

The following information is necessary for successful installation

  1. Oracle SID. This is the unique per-machine identifier of an Oracle database and is used by JDBC drivers to connect to Oracle.
  2. Oracle database name (as defined in TNS_NAMES.ORA). This is the database name that SQL*Plus uses to connect to Oracle. The Oracle SID and database name are normally the same, athough the Oracle database name may contain an additional domain name. The SID can be no longer than 8 characters (an Oracle database gorgonzola.cheese.com would be truncated to an SID of gorgonzo).
  3. Password for the Oracle SYS account.
  4. A list of existing users to whom cartridge access shall be granted.
  5. The maximum amount of RAM to allow the RMI server (60 Mb/100K molecules) and whether or not to cache molecules in memory.
  6. Location of the OpenEye license file.
  7. Locations of the FastROCS and OMEGA executables, if shape indexes are to be built.

Prior to installing remote RMI servers, the following tasks must be completed:

  1. The Oracle components must be installed on the Oracle server.
  2. The jdbc6.jar file needs to be copied to the lib directory of the unpacked cartridge distribution from which the RMI server will be installed. This file is located in the $ORACLE_HOME/jdbc/lib in any Oracle installation.

The installer logs messages in the directory log/install/<install date>. If installation fails, the install logs may help diagnose the problem.

To run the installer navigate to the bin subdirectory of the OpenEye cartridge distribution and run install.bat (Windows) or install.sh (Linux). The installer will not work properly if started from a working directory other than bin subdirectory. On Windows, the install.bat script should be run as Administrator. Installation of the cartridge service may fail if the installation is not performed from the Administrator account.

Select Installation Type

On the first screen select the type of installation to be performed. When installing on the Oracle server, it is standard to install both the Oracle components and RMI server. The Install RMI server only option should be used for a FastROCS server that is physically separate from the Oracle server.

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Enter Oracle Information

On the second screen enter the Oracle database information, and the location of the OpenEye Toolkit location and Cartridge license file.

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Install Cartridge

The tablespaces that the Cartridge user and tester will use may be selected on the next screen. Note that the installer does not create new tablespaces. Custom tablespaces for these users must be created beforehand. A shared password will need to specified for these users. Previous installations of Oracle components will have to be removed before proceeding. The name ‘localhost’ can be used as the RMI hostname for most installations where the RMI server is being installed on the same machine as the Oracle server. A particular hostname may need to be specified for servers that contain multiple network interface cards.

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Grant Permissions

On the next screen, select from the list of existing users that will be granted access to the cartridge functionality. After cartridge installation, the SQL script DIR/sql/grant.sql may be used to grant permissions to additonal users. The test user ARNACHM1_TEST us automatically granted permission to use the cartridge. Note that Oracle comes with a large number of built-in users.

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Configure FastROCS Server

If FastROCS domain indexes are to be used in conjunction with the cartridge, the ‘Configure FastROCS’ checkbox will enable configuration of the RMI server to interoperate with FastROCS. Note that this configuration should only be done on the FastROCS server. If the Oracle and FastROCS servers are on separate machines, install the cartridge on the Oracle server first, and then install an RMI server on the FastROCS server.

Specify the full path to the OMEGA binary. OMEGA is used to generate conformers when building or rebuilding indexes on SMILES or MOL file columns. The maximum number of parallel OMEGA processes to be used in building indexes may be specified with a slider that reflects the number of processes and cores on the FastROCS server. Next, the full path to the FastROCS installation directory must be provided, and the port number on which the RMI server will communicate with the FastROCS server. Note that the RMI server will spawn its own instance of the FastROCS server, so the port number should be chosen to avoid ports used by non-cartridge instances of the FastROCS server.

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Configure RMI Server

For the penultimate step select the number of RMI task threads (or the maximum number of concurrent requests the RMI server can service); the maximum memory usage for the Java RMI process; whether to enable the cache of OpenEye molecules and (if more than one processing core is present) whether to enable a dedicated thread pool for structure index creation. These settings are described in configuring the RMI server. Once this screen is completed the RMI server will be started and the connection between the test user and data cartridge validated. The server configuration is stored in a file called ‘server.properties’ in the bin subdirectory. Messages from the cartridge are logged in the file log/rmi/rmi_server.log (relative to the cartridge root). On a Windows machine Apache Procrun is used to install the RMI server as a Windows service (see http://commons.apache.org/daemon/procrun.html). The service can be edited and controlled from a GUI started using the batch file monitorService.bat created in the bin subdirectory. If running the RMI server as a process instead of a service is preferred, a batch file runServer.bat is created in the bin subdirectory of the cartridge installation, and may be started manually. Linux installations include a shell script that may be used to start the RMI server process manually. The aforementioned runServer.sh script is located in the bin subdirectory of the cartridge installation.

After cartridge installation, the RMI server may be altered to manually load the indexes and cache on startup. Whenever the configuration file is edited, the Java RMI process must be restarted.

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Load Test Data and Build Index

In this optional step, the test data may be loaded into the cartridge tester’s (ARNACHM1_TEST) schema. This loads 260K structure from the NCI open database into a table called nci_open. After loading the test data, a structure domain index may be built for the table. Once the structures are loaded and the index built, example commands may be run from SQL*Plus while connected as ARNACHM1_TEST user. Once this step is complete, a final screen shows a summary of the install.

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