| Oracle® Clinical Installation Guide Release 4.6.2 E18817-04 |
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PDF · Mobi · ePub |
| Oracle® Clinical Installation Guide Release 4.6.2 E18817-04 |
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PDF · Mobi · ePub |
This chapter describes how to install Oracle Database 11g Release 2 (11.2.0.2) Patch Set 1 and Oracle Clinical Database Server products on a UNIX computer.
This chapter includes the following topics:
Section 2.2, "Installing Oracle Database 11g Release 2 (11.2.0.2) Patch Set 1"
Section 2.3, "Setting Permissions and Write Access to Oracle-Owned Directories"
Section 2.5, "Installing the Oracle Clinical Database Server"
If you are upgrading to Oracle Clinical 4.6.2, see Chapter 12.
To ensure that your platform meets the minimum requirements for installing Oracle Database 11g Release 2 (11.2.0.2) Patch Set 1 and Oracle Clinical Database Server products, you must perform the following preparatory tasks:
To create the software owner, required groups, and mount points:
Create the software owner and groups:
Create a UNIX user to own the Oracle software. Typically, the user name is oracle.
Create two groups: one is the Oracle Inventory group; the other is the operating system DBA group. Typically, the group names are oinstall and dba, respectively.
Create mount points owned by the oracle user:
Create a software mount point of at least 10 GB.
Create mount points to hold the database files, control files, and log files, respectively.
Test permissions. Ensure that the oracle user can write to the new mount points and all subdirectories.
The performance of Oracle Database 11g Release 2 (11.2.0.2) Patch Set 1 relies on proper tuning of operating system parameters. In addition, if you are creating several Oracle instances, you might have to increase the amount of shared memory and semaphores on the system by setting kernel parameters.
For details, see the "Configure Kernel Parameters" section of the Oracle Database 11g Release 2 Installation Guide for your operating system.
To test that the correct C compiler is installed and that it is accessible:
Log in as the opapps user.
Test for the C compiler type:
ls -l `which cc`
where the ` symbols that wrap the command are single back quotes.
Compare your results to the correct responses listed in Table 2-1.
Test that the make command is accessible:
ls -l `which make`
where the ` symbols that wrap the command are single back quotes.
Compare your results to the correct responses listed in Table 2-2.
Table 2-2 Responses to the 'which make' Command
| Operating System | Response | Symbolically Links To |
|---|---|---|
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Oracle Enterprise Linux x86-64 |
/usr/bin/make |
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Oracle Solaris SPARC |
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HP-UX Itanium |
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If you do not get the correct response, you can either add the path to the cc executable or add the make command to the path in the .cshrc file for the opapps user.
Download and install the latest operating system patches required for Oracle, if necessary. Review the latest platform-specific install bulletins for Oracle Database 11g Release 2 (11.2.0.2) Patch Set 1.
To support Oracle Clinical Database Server, a UNIX computer requires the following version of Oracle Database software:
Oracle Database 11g Release 2 (11.2.0.2) Patch Set 1 Enterprise Edition
However, this requirement might change during the life of this document. Before you begin, check My Oracle Support for the latest requirement.
This section describes the following tasks required to install Oracle Database 11g Release 2 (11.2.0.2) Patch Set 1:
Install Oracle Database 11g Release 2 (11.2.0.2) Patch Set 1
Install Oracle Database 11g Release 2 (11.2.0.2) Patch Set 1 Examples
Install Patch 10213073 to Oracle Database 11g Release 2 (11.2.0.2) Patch Set 1
To install Oracle Database 11g Release 2 (11.2.0.2) Patch Set 1:
Locate the Oracle Database 11g Release 2 (11.2.0.2) Patch Set 1 software for your operating system on the Oracle Clinical and Oracle Thesaurus Management System 4.6.2 operating_system Tech Stack Patches disk in the media pack:
| Operating System | Zip File |
|---|---|
| Oracle Enterprise Linux x86-64 | p10098816_112020_Linux-x86-64_xof7.zip |
| Oracle Solaris SPARC | p10098816_112020_SOLARIS64_xof7.zip |
| HP-UX Itanium | p10098816_112020_HPUX-IA64_xof7.zip |
Follow the instructions in the Oracle Database 11g Release 2 (11.2) Installation Guide for your respective operating system to install Oracle Database 11g Release 2 (11.2.0.2) Patch Set 1.
Choose to install the Enterprise Edition option.
Oracle Database Examples, which is required for Oracle Clinical, includes the following items:
Oracle JDBC Development Drivers
Oracle Database Examples
Oracle Product Demonstrations (optional)
To install Oracle Database Examples:
Navigate to the folder where you extracted the Oracle Database 11g Release 2 (11.2.0.2) Patch Set 1 software.
Change to the examples directory.
Start Oracle Universal Installer from the examples directory and install Oracle Database Examples.
Accept all the default values during the installation.
For more information about installing software and various Oracle product demonstrations from the Oracle Database Examples media, see the Oracle Database Examples Installation Guide.
To install patch 10213073 to the Oracle Database 11g Release 2 (11.2.0.2) Patch Set 1 installation:
Locate the appropriate Oracle Database 11g Release 2 (11.2.0.2) Patch Set 1 patch for your operating system on the Oracle Clinical and Oracle Thesaurus Management System 4.6.2 operating_system Tech Stack Patches disk in the media pack:
| Operating System | Path | Zip File |
|---|---|---|
| Oracle Enterprise Linux x86-64 | /patches | p10213073_112020_Linux-x86-64.zip |
| Oracle Solaris SPARC | /patches | p10213073_112020_SOLARIS64.zip |
| HP-UX Itanium | /patches | p10213073_112020_HPUX-IA64.zip |
Extract the patch zip file to a location that is accessible to the Database Server.
Follow the operating system-specific instructions in the ReadMe file to apply patch 10213073 to the Oracle Database 11g Release 2 (11.2.0.2) Patch Set 1 installation. The ReadMe file is located at the top level of the patch set extraction location.
Every quarter, Oracle provides Critical Patch Updates (CPUs) to address security vulnerabilities, and Patch Set Updates (PSUs) to address proactive, critical fixes and security vulnerabilities.
CPU/PSU 10248523 is current as of this document release and current with the information in the Oracle Health Sciences Applications Critical Patch Update for January 2011 note on My Oracle Support. Be sure to check My Oracle Support for the latest version of CPUs and PSUs, and then apply the latest patch approved for the Oracle Health Sciences applications.
To install CPU/PSU 10248523:
Locate the appropriate Oracle Database 11g Release 2 (11.2.0.2) Patch Set 1 patch for your operating system on the Oracle Clinical and Oracle Thesaurus Management System 4.6.2 operating_system Tech Stack Patches disk in the media pack:
| Operating System | Path | Zip File |
|---|---|---|
| Oracle Enterprise Linux x86-64 | /patches | p10248523_112020_Linux-x86-64.zip |
| Oracle Solaris SPARC | /patches | p10248523_112020_SOLARIS64.zip |
| HP-UX Itanium | /patches | p10248523_112020_HPUX-IA64.zip |
Extract the patch zip file to a location that is accessible to the Database Server.
Follow the operating system-specific instructions in the ReadMe file to apply patch 10248523 to the Oracle Database 11g Release 2 (11.2.0.2) Patch Set 1 installation. The ReadMe file is located at the top level of the patch set extraction location.
After you install Oracle Database 11g Release 2 (11.2.0.2) Patch Set 1 and before you install the Oracle Clinical component, you must:
Note:
You might have to perform these instructions whenever you apply an HSGBU-approved Critical Patch Update, or any Oracle software that uses the Oracle Database 11g Release 2 (11.2.0.2) Patch Set 1 ORACLE_HOME directory.With the Bourne shell, you use the Oracle environment-setting script (oraenv) when granting write access to the ORACLE_HOME directory.
However, the oraenv script gives an error if run by a non-Oracle user. To avoid this error, set the following directory and file permissions:
drwxrwxr-x 18 oracle oinstall 1024 Apr 11 19:11 inventory drwxrwxr-x 3 oracle oinstall 1024 Apr 11 18:29 ContentsXML -rwxrwxrwx 1 oracle oinstall 492 Apr 11 13:15 oraclehomeproperties.xml
Because the Oracle Universal Installer checks if the ORACLE_HOME directory exists and if it has write access, you must change the access settings for this directory before you install the Oracle Clinical component.
To grant write access to the Oracle Database 11g Release 2 (11.2.0.2) Patch Set 1 ORACLE_HOME directory and its contents:
Log in to the server as the oracle user.
Source the Oracle environment-setting script to define ORACLE_HOME:
For C shell, use coraenv.
For Bourne shell, use oraenv.
These shells are located under your Oracle Database 11g Release 2 (11.2.0.2) Patch Set 1 installation.
Note that the oraenv script gives an error if run by a non-Oracle user. To avoid this error, see Section 2.3.1, "Change Permissions for Running oraenv Script" for setup instructions.
Grant group users modification access to all files in the ORACLE_HOME directory:
If you receive any warning messages, you can ignore them.
To set the permissions for the Oracle Inventory (oraInventory) directory:
Log in to the server as the oracle user.
Locate the path for the oraInventory directory. The location is defined in the inventory_loc parameter in the /var/opt/oracle/oraInst.loc file.
For example, suppose you enter:
more /var/opt/oracle/oraInst.loc
The system might return the oraInventory location as:
inventory_loc=/u01/app/oraInventory
Give recursive read and write permission for the oraInventory directory to the group:
chmod -R g+rw /oraInventory_location
For example:
chmod -R g+rw /u01/app/oraInventory
If you receive any warning messages, you can ignore them.
Modify protections on the oraInventory directory to ensure that the group you set up as the oinstall group has write access:
chmod -R g+w oraInventory
Use oinstall instead of dba because the dba group membership gives you access to databases, which is a security issue. The oinstall group gives you access to the Oracle Inventory.
Before you install Oracle Clinical Database Server, you must create the following user groups and accounts:
oclsascr — the group that controls access to the files Oracle Clinical generates for SAS
opapps — the operating system account that owns Oracle Clinical
rxcprod — a special privileged account that runs the Parameterized Submission (PSUB) process
If you integrate the SAS statistics application with Oracle Clinical, define a method to control access to the files Oracle Clinical generates for SAS. Create a user group named oclsascr by adding it to the /etc/group file.
The preferred method for group authentication is that all groups assigned to a user should become the user's default group at login. If this method is acceptable, link the /etc/logingroup file to the /etc/group file.
If the /etc/logingroup file does not exist, create it as a symbolic link to the /etc/group file; changes in the /etc/group file automatically reflect in the /etc/logingroup file.
To create the symbolic link, enter these commands:
% su root# cd /etc# ln -s /etc/group /etc/logingroupIf the /etc/logingroup file already exists with entries, or if it is unacceptable to link it to the /etc/group file, you must change both the contents of /etc/logingroup and /etc/group each time you add a user to the oclsascr group.
You must create the operating system account that owns Oracle Clinical. The user name for the account is opapps, with a home directory named opapps. For example:
/home/opapps
You can choose a different home directory name. The Oracle Clinical documentation uses the variable OPA_HOME to refer to this location on an Oracle Clinical Database Server.
Assign the following attributes to the opapps account:
Make a shell for this user. For example, make the default shell:
/bin/csh
Make the opapps account a member of these two user groups:
oclsascr
The user group that owns the Oracle Inventory. You specified the name of this group during the Oracle Database 11g Release 2 (11.2.0.2) Patch Set 1 installation. Typically, this user group is oinstall.
If you do not know the name of this user group, log in as user oracle and enter the following command:
more /var/opt/oracle/oraInst.loc
The inst_group parameter defines the name of the user group that owns the Oracle Inventory (oraInventory). The inventory_loc parameter defines the path to the oraInventory directory.
Neither the oclsascr group nor the inst_group has to be the primary group for the opapps account.
Oracle Clinical processes most batch requests from clients on the server with the Parameterized Submission (PSUB) process. PSUB runs under a special privileged account named rxcprod, with a default Bourne shell of /bin/sh.
The rxcprod account requires some special privileges so that it can run job requests on behalf of other users who submit jobs with the Secure Shell (ssh) command or schedule jobs with the at command.
This section describes how to install and set up the Oracle Clinical Database Server on one computer. Perform this task once for each Oracle Clinical Database Server computer.
Note:
Read this section completely before you begin. The Installer prompts you for information you should know before you start.The Oracle Universal Installer performs the following operations:
Creates the Oracle Clinical directory structure (see Section 2.5.1 for details)
Installs the Oracle Clinical Database Server application
Builds the executables
Sets permissions on the directories
Creates the environment setup files
Modifies the environment setup files
Creates the directory for storing the SAS files
The Oracle Universal Installer creates the following directory structure for an Oracle Clinical Database Server on UNIX:
OPA_HOME /bin /xmltemp /oc /462 /bin (Symbolic links to the executables) /common (Common files) /dcd (Data Collection Definition) /des (Design) /dm (Data Management) /dx (Data Extract) /glib (Global Library) /install (Install and upgrade scripts) /log (PSUB log files) /lr (Lab Ranges) /patch (Patches to Oracle Clinical) /pd (Procedure Definition) /psub (Parameterized Submission process) /release (Server code release marker) /sec (Security tools) /tools (Miscellaneous tools)
Note that OPA_HOME refers to the root installation directory of the Oracle Health Sciences products, which were formerly known as Oracle Pharmaceutical Applications (OPA). You specify the root installation directory when you install the Oracle Clinical Database Server. Typically, you specify the path to the opapps login directory; for example, /home/opapps.
To transfer the Database Server software from the Oracle Clinical and Oracle Thesaurus Management System 4.6.2 Media Pack:
Locate the appropriate Database Server software for your operating system on the Oracle Clinical and Oracle Thesaurus Management System 4.6.2 operating_system Tech Stack Patches disk in the media pack:
| Operating System | Path | Zip File |
|---|---|---|
| Oracle Enterprise Linux x86-64 | /oc/server_code | server_code_linux-x86-64.zip |
| Oracle Solaris SPARC | /oc/server_code | server_code_sun.zip |
| HP-UX Itanium | /oc/server_code | server_code_hpia.zip |
Extract the appropriate patch zip file to a location that is accessible to the Database Server computer.
To start installing the Database Server software:
Log in to the server computer as the opapps user.
Change the primary group of the opapps account to the group that owns the Oracle Inventory:
newgrp inst_group
where inst_group is the name of the group that owns the Oracle Inventory. You specified the name during the Oracle Database 11g Release 2 (11.2.0.2) Patch Set 1 installation. Typically, this user group is oinstall. (See Section 2.4.2, "Create the opapps Account.")
This temporary change is necessary so that the Installer can update the Oracle Inventory.
Set the X Window display output to the IP address of your local computer. Use the standard format for IP addresses, and add ":0" to the end of the address. For example:
setenv DISPLAY 123.45.67.89:0
Navigate to this location in the folder where you extracted the server code:
server_code_platform\Disk1\install
Change protections on files to 755:
chmod 755 *
Start the Oracle Universal Installer:
./runInstaller
Follow the instructions on the installation screens. For additional information about each screen, see Section 2.5.4, "Attend to the Oracle Clinical Database Server Installation Screens."
The Oracle Universal Installer guides you through the installation and configuration of Oracle Clinical Database Server.
Click Next to continue the installation.
Select Oracle Clinical Server for UNIX 4.6.2.0.XX (where XX is the build number).
Click Next.
Select or enter the ORACLE_HOME location, which is where you installed Oracle Database 11g Release 2 (11.2.0.2) Patch Set 1.
If you select a name, the Installer populates the Path field with the ORACLE_HOME location. You can also browse to the ORACLE_HOME location.
Note that the value you enter here does not indicate the destination of the Oracle Clinical Database Server software that you are currently installing. You define the location of the installation directory in the "Choose Directory OPA Home" screen that follows.
Click Next.
Specify the directory that is the root installation directory of the Oracle Health Sciences products. This directory defines the destination of the Oracle Clinical Database Server software that you are currently installing. Typically, you respond with the path to the opapps login directory. For example:
/home/opapps
The Oracle Clinical documentation uses the variable OPA_HOME to refer to this location. The Oracle Health Sciences products were formerly known as Oracle Pharmaceutical Applications (OPA).
Click Next.
Choose Owner Owner of Oracle Clinical Server Code
Enter the name of the owner of the Oracle Clinical server code. The default value is opapps.
Click Next.
Enter the path to the directory where the oratab file is located. For example, /etc or /var/opt/oracle.
Click Next.
Enter the path to the directory where the tnsnames.ora file is located.
Oracle Enterprise Linux x86-64 — First looks in the /etc directory, and then looks in the $ORACLE_HOME/network/admin directory.
Oracle Solaris SPARC — First looks in the /var/opt/oracle directory, and then looks in the $ORACLE_HOME/network/admin directory.
HP-UX Itanium — First looks in the /etc directory, and then looks in the $ORACLE_HOME/network/admin directory.
Click Next.
Enter the directory where Oracle Clinical generates and saves SAS view files. The Installer creates a sas_view sub-directory within the directory you specify.
The default value is the OPA_HOME directory. For example, /home/opapps.
Click Next.
Review the information on the Confirmation screen before proceeding.
To make changes to your installation settings, click Back. Otherwise, click Next to continue.
Summary Oracle Clinical Server for UNIX 4.6.2.0.XX
Review the information on the Summary screen, which displays the global settings, the space requirements, and the product to install.
To make changes to your installation settings, click Back. Otherwise, click Install to continue.
Oracle Universal Installer copies the files onto the server, links the files, and sets permissions.
To review the progress of the linking phase of the installation:
Open another terminal session as the opapps user.
Enter the following command:
tail -f OPA_HOME/oc/462/relink_rxc.log
In addition, the Install screen displays the location of the log file that records the results of the installation activities for this session. Make note of this information so you can view the log file after the installation.
The End of Installation screen displays the:
Location of the OPA_HOME directory
Name of the code environment
Make note of this information because you need it for several post-installation tasks.
When you have finished reviewing the installation information, click Exit. At the confirmation prompt, click Yes to exit from Oracle Universal Installer.
Tip:
You cannot perform the post-installation tasks (see Section 2.6) from this Installer session. You must close the Installer. However, you can use the same environment. You do not have to restart the Installer until you install the Oracle Clinical database (see Chapter 4).Review the generated installation log files for errors:
installActionstimestamp.log (See Section 1.13, "Reviewing the Installation Log Files" for details.)
OPA_HOME/oc/462/relink_rxc.log
Work with Oracle Support, if necessary, to resolve any errors.
Recall that before you started this installation on UNIX, you changed the primary group of the opapps account to the group that owns the Oracle Inventory (see Section 2.5.3, "Start Installing the Database Server Software"). This temporary change was necessary so that the Installer could update the Oracle Inventory.
To reset the privileges for the opapps account, enter the following command:
newgrp group
where group is the name of your original primary group for the opapps account.
This section describes the following tasks that you perform to complete the installation of Oracle Clinical Database Server on a UNIX computer:
To complete the setup of the opapps account:
Create the log directory for opapps in the following location:
OPA_HOME/log
Define the environment variables for the opapps user:
Open the .cshrc file. This file is located in the home directory after you log in as the opapps user. You can use the following command to view the hidden .cshrc file:
ls -arlt
Add the following lines to the .cshrc file:
set path=( $path ORACLE_HOME/bin ORACLE_HOME/lib )
setenv RXC_LOG OPA_HOME/log
source OPA_HOME/bin/copa_setup_alias
where:
ORACLE_HOME is the directory where you installed Oracle Database 11g Release 2 (11.2.0.2) Patch Set 1.
OPA_HOME is the directory where you installed Oracle Clinical Database Server.
Source the .cshrc file when you finish editing it:
To complete the setup of the rxcprod account:
Open the .profile file for the rxcprod account. This file is located in the home directory after you log in as the rxcprod user. You can use the following command to view the hidden .profile file:
ls -arlt
Add the following path to the .profile file:
PATH=$PATH:OPA_HOME/bin:ORACLE_HOME/bin
where:
OPA_HOME is the directory where you installed Oracle Clinical Database Server.
ORACLE_HOME is the directory where you installed Oracle Database 11g Release 2 (11.2.0.2) Patch Set 1.
On UNIX systems, configurations are defined in the opa_settings file. The Installer creates the opa_settings file in the following directory:
OPA_HOME/bin
In addition, the Installer enters all necessary entries and default values for the Oracle Clinical environment into the opa_settings file.
The db_env_setting records in the opa_settings file define a default value for particular environment variables that are set when the application calls opa_setup. You can override the default values for all databases or for a particular database.
See the Oracle Clinical Administrator's Guide for a list of the environment variables and for information about changing, adding, and verifying values.
Note:
The default settings for all databases or the specific settings, such as NLS_LANG, for a particular database must be correct in the opa_settings file.Examine the db_env_setting records in the opa_settings file and adjust the default values, if necessary. Note the following details:
NLS_LANG determines which language setting Oracle uses when it reads and writes values into the database. The NLS_LANG entry for your Oracle AS10gR2 home and Oracle AS10gR3 home must be consistent with the NLS_LANG entry for the Oracle Database 11g Release 2 (11.2.0.2) Patch Set 1 home and your databases.
For PSUB to work correctly for a UTF8 character set database, the opa_settings file must have the following setting:
db_env_setting:database:NLS_LANG:american_america.utf8
If you do not have a UTF8 character set database, you can use these character sets:
american_america.us7ascii
american_america.we8iso8859p1
Every quarter, Oracle provides Critical Patch Updates (CPUs) to address security vulnerabilities. Install these patches on every computer with an Oracle Home. Check My Oracle Support for information about the latest patch tested with Oracle Health Sciences applications. Article ID 180430.1, Oracle Health Sciences Supported Technology Stacks, lists the latest CPUs supported and contains a link to the separate article about each one.
Note:
Applying the CPU might change permissions on ORACLE_HOME and oraInst.loc. You may have to repeat the instructions in Section 2.3, "Setting Permissions and Write Access to Oracle-Owned Directories."In addition, check My Oracle Support to determine if Oracle has released any new patch sets or any individual patches since the publication of this guide.
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