| Oracle® Clinical Installation Guide Release 4.6 Part Number A83779-08 |
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| Oracle® Clinical Installation Guide Release 4.6 Part Number A83779-08 |
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View PDF |
This chapter describes how to set up a new Oracle Clinical Database Server on a UNIX computer.
Installing an Oracle Clinical Database Server on a UNIX computer requires you to complete the following tasks:
Section 2.2, "Granting Write Access to Oracle-Owned Directories"
Section 2.6, "Installing the Oracle Clinical 4.6 Database Server"
If you are installing the Oracle Clinical Database Server on a Windows computer, see Chapter 3 for installation instructions.
If you are upgrading to Oracle Clinical 4.6, see Chapter 9.
To support Oracle Clinical Database Server, a UNIX computer requires the following version of Oracle Database software:
Oracle Database 11gRelease 11.1.0.6.0 plus Patch Set 1 (11.1.0.7.0), plus individual patchesEnterprise 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:
Section 2.1.1, "Install Oracle Database 11g Release 11.1.0.6.0"
Section 2.1.2, "Install Oracle Database Examples 11g Release 1"
Section 2.1.4, "Apply Oracle Database 11g Standalone Patches"
To install Oracle Database 11g Release 11.1.0.6.0:
Locate the Oracle Database 11g software for your operating system on the media pack:
| Operating System | Disk | Software |
|---|---|---|
| Oracle Enterprise Linux | V14216-01 | Oracle Database 11g Release 1 (11.1.0.6.0) |
| Oracle Solaris | V14414-01 | Oracle Database 11g Release 1 (11.1.0.6.0) |
| HP-UX Itanium | V14232-01 | Oracle Database 11g Release 1 (11.1.0.6.0) |
Follow the included instructions for installing Oracle Database 11g.
Choose to install the Enterprise Edition option.
Oracle Database Examples, which is required for Oracle Clinical 4.6, includes the following items:
Oracle JDBC Development Drivers
Oracle Database Examples
Oracle Product Demonstrations (optional)
Note:
You do not need to install any of the sample schemas. They are not required for either Oracle Clinical or Thesaurus Management System. You can add them later if you change your mind.To install Oracle Database Examples:
Locate the appropriate Database Examples zip file for your operating system on the media pack:
| Operating System | Disk | Path | Zip File |
|---|---|---|---|
| Oracle Enterprise Linux | V22167-01 | /patches | linux.x64_11gR1_examples.zip |
| Oracle Solaris | V18332-01 | /patches | solaris.sparc64_11gR1_examples.zip |
| HP-UX Itanium | V18332-01 | /patches | hpia64_11gR1_examples.zip |
Install the software according to the Oracle Database Examples Installation Guide, which is included on the media pack.
Accept all the default values during the installation.
To apply Patch Set 1 (Patch Set 11.1.0.7.0) to the Oracle Database 11g installation:
Locate the appropriate Oracle Database 11g Patch Set 1 software for your operating system on the media pack:
| Operating System | Disk | Path | Zip Files |
|---|---|---|---|
| Oracle Enterprise Linux | V22167-01 | /patches | p6890831_111070_Linux-x86-64.zip |
| Oracle Solaris | V18476-01 | /patches | p6890831_111070_SOLARIS64.zip |
| HP-UX Itanium | V18476-01 | /patches | p6890831_111070_HPUX-IA64_1of2.zip
p6890831_111070_HPUX-IA64_2of2.zip |
Extract the patch zip file(s) to a location that is accessible to the Database Server.
Follow the operating system-specific instructions in the ReadMe file to apply Patch Set 1 to the Oracle Database 11g installation. The ReadMe file is located at the top level of the patch set extraction location.
After you apply Patch Set 1 to upgrade your Oracle Database 11g installation to Release 11.1.0.7.0, you must apply several Oracle Database 11g standalone patches.
To apply the standalone patches:
Locate the appropriate Oracle Database 11g standalone patches for your operating system on the media pack:
| Operating System | Disk | Path | Zip Files |
|---|---|---|---|
| Oracle Enterprise Linux | V22167-01 | /patches | p7327166_111070_Linux-x86-64.zip
p8307947_111070_Linux-x86-64.zip p8348464_111070_Linux-x86-64.zip |
| Oracle Solaris | V18332-01 | /patches | p7327166_11107_Solaris-64.zip
p8307947_11107_Solaris-64.zip p8348464_11107_Solaris-64.zip |
| HP-UX Itanium | V18332-01 | /patches | p7327166_111070_HPUX-IA64.zip
p8307947_111070_HPUX-IA64.zip p8348464_111070_HPUX-IA64.zip |
Extract the appropriate patch zip files to a location that is accessible to the Database Server.
Follow the operating system-specific instructions in the ReadMe file to apply the standalone patches to the Oracle Database 11g installation. The ReadMe file is located at the top level of the patch set extraction location.
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. You must grant write access to the Oracle Database 11g ORACLE_HOME directory.
Note:
You might have to perform these instructions whenever you apply an HSGBU-approved CPU Security Update, or any Oracle software that uses the Oracle Database 11g ORACLE_HOME directory.To grant write access to the ORACLE_HOME directory and its contents:
Log in to the server as 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 installation.
Grant group users modification access to all files in the ORACLE_HOME directory:
If you receive any warning messages, you can ignore them.
Give recursive read and write permission to the oraInventory directory:
Locate the path for the oraInventory directory. The location is the value of the inventory_loc setting 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/oracle/oraInventory
Give recursive read and write permission for the oraInventory directory to the group:
chmod -R g+rw /path_location_oraInventory
For example:
chmod -R g+rw /u01/app/oracle/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.
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 Jul 29 19:11 inventory drwxrwxr-x 3 oracle oinstall 1024 Jul 29 18:29 ContentsXML -rwxrwxrwx 1 oracle oinstall 492 Sep 11 13:15 oraclehomeproperties.xml
In an Oracle Solaris environment, when you use the Bourne shell (sh) to run the oraenv script, the script may fail with the following error:
Test: Argument Expected
To work around this known issue:
Navigate to the following directory:
$ORACLE_HOME/bin/oraenv
Open the oraenv script file and locate the following text string:
-e $ORABASE_EXEC
Change the -e to -f:
-f $ORABASE_EXEC
Perform the tasks in this section logged on to the server as root.
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/logingroup
If 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.
Create the operating system account to own 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 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 rsh (remsh for HP-UX Itanium) command and the at command.
To use the rsh (remsh for HP-UX Itanium) command to submit jobs on behalf of another user, the rxcprod user must be present in the /etc/hosts.equiv file. Modify the existing file or create a new file, and then add this line:
official_host_name rxcprod
where official_host_name is the official name of the computer on which you are installing Oracle Clinical.
You must use the official name — not an alias — for the computer. The official name is the first listing after the IP address in the /etc/hosts file.
On some platforms and configurations, the /etc/hosts.equiv entry does not work because of security differences. For example, the /etc/hosts.equiv entry does not work on HP-UX Itanium 11.11 when YP or DNS are not used. The workaround involves creating a file named .rhosts. This user-specific file must reside in the login directory of each user who runs PSUB jobs. The .rhosts file should be owned by that user. (You can use the chown command to set the owner.) Create or modify the .rhosts file so that it contains the same entry as you would place in the /etc/hosts.equiv file.
To use the at command to submit jobs on behalf of another user, the rxcprod user must be present in the at.allow file.
To edit the at.allow file:
Change to the appropriate directory location depending on your operating system and open the file:
| Oracle Enterprise Linux: | /etc/at.allow |
| Oracle Solaris: | /usr/lib/cron/at.allow |
| HP-UX Itanium: | /usr/lib/cron/at.allow |
Add the following line to the at.allow file:
rxcprod
You might have to edit the /etc/group.
The performance of Oracle Database 11g 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 on this topic, see the "Configure Kernel Parameters" section of the Oracle Database 11g 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 |
|---|---|---|
|
Oracle Enterprise Linux |
/usr/bin/make |
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Oracle Solaris |
|
|
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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.
This section describes how to install and set up the Oracle Clinical 4.6 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 2.6.1 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 Installer creates the following directory structure:
OPA_HOME /bin /xmltemp /oc /46 /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 4.6 and Oracle Thesaurus Management System 4.6.1 Media Pack:
Locate the appropriate Database Server software for your operating system on the media pack:
| Operating System | Disk | Path | Zip File |
|---|---|---|---|
| Oracle Enterprise Linux | V22167-01 | /oc/server_code | server_code_linux-x86-64.zip |
| Oracle Solaris | V17174-01 | /oc/server_code | server_code_sun.zip |
| HP-UX Itanium | V17174-01 | /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 installation. Typically, this user group is oinstall. (See Section 2.3.2.)
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 Universal Installer:
./runInstaller
The Installer acts in two phases. In the first phase, the Installer collects information about your system. During this phase, you can move backward and forward through the screens, revising your entries. During the second phase, the Installer runs the scripts to set up the Oracle Clinical 4.6 software according to the information you provided in the first phase. Attend to the Installer's screens as described below.
Click Next to continue the installation. Alternatively, you can click Installed Products to review a list of installed Oracle products.
Select OC Server for UNIX 4.6.0.0.XX (where XX is the build number). Click Next.
Select or enter the ORACLE_HOME location, which is where you installed Oracle Database 11g.
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. 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. Click Next.
Enter the path to the directory where the tnsnames.ora file is located.
Oracle Enterprise Linux — First looks in the /etc directory, and then looks in the $ORACLE_HOME/network/admin directory.
Oracle Solaris — 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.
Specify the location to store SAS files. The default value is the OPA_HOME directory. Click Next.
Review the destination settings before proceeding. To make changes to the settings, click Back. Otherwise, click Next to continue.
This screen lists the target directories. Note that the Installer only displays ORACLE_HOME in the Destination field. It might differ from your actual directory path.
Click Install.
The Installer copies the files onto the server, and then links the files.
To watch the progress of the link, open another terminal session as opapps and then enter the following command:
tail -f OPA_HOME/oc/46/relink_rxc.log
In addition, the Install screen displays the location of the InstallActiontimestamp.log file, which records the results of the installation activities. Note the location of this log file so that you can review it when the installation finishes.
This screen displays the location of the OPA_HOME and OPA_HOME/bin directories, and the name of the code environment. Make note of this information because you need it for several post-installation tasks.
To finish the installation:
Click Exit.
Click Yes to exit the Installer.
Tip:
You cannot perform the post-installation tasks (see Section 2.7) 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:
InstallActiontimestamp.log
OPA_HOME/oc/46/relink_rxc.log
Work with Oracle Support, if necessary, to resolve any errors.
Recall that before you started this installation, you changed the primary group of the opapps account to the group that owns the Oracle Inventory (see Section 2.6.3). 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 tasks 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:
Add the following lines to the 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
OPA_HOME is the directory where you installed Oracle Clinical
Source the .cshrc file when you finish editing it:
On UNIX systems, configurations are defined in the opa_settings file. The Installer creates the opa_settings file in the following directory:
opapps/bin
In addition, the Installer enters all necessary entries and default values for the Oracle Clinical 4.6 environment into this 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 on changing, adding, and verifying values.
Note:
The default settings for all databases or the specific settings for a particular database, such as NLS_LANG, 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 must be consistent with the NLS_LANG entry for the Oracle Database 11g 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
Note:
Do not create new databases with the default character set (AL32UTF8) by the Assistant.Oracle publishes a CPU Security Update patch quarterly. Apply the latest CPU Security Update patch approved for the Oracle Health Sciences applications to this computer. Check My Oracle Support to determine the latest version.
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.
Note:
Applying the CPU Security Update might change permissions on ORACLE_HOME and oraInst.loc. You may have to repeat the instructions in Section 2.2, "Granting Write Access to Oracle-Owned Directories."
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