| Oracle® Clinical Installation Guide Release 5.1 E53553-02 |
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PDF · Mobi · ePub |
| Oracle® Clinical Installation Guide Release 5.1 E53553-02 |
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PDF · Mobi · ePub |
This chapter describes how to install Oracle Database and the Oracle Clinical database server on a UNIX computer.
This chapter includes:
If you are upgrading Oracle Clinical, see Chapter 11. If you are using Oracle Real Application Clusters (RAC), see Section 1.4, "Supported Configurations with Oracle Data Guard and RAC".
For database tier system requirements, see the 12.1.0.1 Oracle Database Installation Guide for your operating system at http://docs.oracle.com/cd/E16655_01/nav/portal_11.htm.
Critical Patch Updates See Section 1.9, "Applying Oracle Critical Patch Updates."
Oracle Database 12.1.0.1 includes many new features including multitenancy, which allows you to create one or more pluggable databases (PDBs) contained in a single root or container database (CDB). You can install Oracle Clinicalon either a pluggable database or a non-CDB database (as in 11g). For more information on multitenancy, see http://docs.oracle.com/database/121/CNCPT/cdbovrvw.htm.
Oracle recommends learning about these new features in Oracle White Paper Plug into the Cloud with Oracle Database 12c at http://www.oracle.com/technetwork/database/plug-into-cloud-wp-12c-1896100.pdf and, for more details, the Oracle® Database New Features Guide 12c Release 1 (12.1) at http://docs.oracle.com/database/121/NEWFT/toc.htm.
Oracle Clinical 5.1 is supported with an Oracle Real Applications Cluster (RAC) distributed database installation on UNIX. Oracle recommends:
Configuring a Maximum Availability Architecture (MAA) in which you use Oracle RAC for both your primary and standby database, synchronized using Oracle Data Guard.
Using the Single Client Access Name (SCAN) option. This RAC feature provides a single name for clients to access Oracle databases running in a cluster. The benefit is that the client's connect information does not need to change if you add or remove nodes in the cluster. Having a single name to access the cluster allows clients to use the EZConnect client and the simple JDBC thin URL to access any database running in the cluster, independent of which server(s) in the cluster the database is active. SCAN provides load balancing and failover for client connections to the database. The SCAN works as a cluster alias for databases in the cluster.
SCAN is configured during the installation of Oracle Grid Infrastructure that is distributed with Oracle Database. Oracle Grid Infrastructure is a single Oracle Home that contains Oracle Clusterware and Oracle Automatic Storage Management (ASM). You must install Oracle Grid Infrastructure first in order to use Oracle RAC.
Oracle Data Guard is included in Oracle Database Enterprise Edition.
See Section 1.4, "Supported Configurations with Oracle Data Guard and RAC".
For more information see:
Oracle® Database 2 Day + Real Application Clusters Guide both at http://docs.oracle.com/cd/E16655_01/nav/portal_16.htm
Grid Infrastructure Single Client Access Name (SCAN) Explained (My Oracle Support Article ID 887522.1). See "Finding Information on My Oracle Support."
Oracle Data Guard and other high availability documentation at http://docs.oracle.com/cd/E16655_01/nav/portal_14.htm
To ensure that your platform meets the minimum requirements for installing Oracle Database 12c Release 1 (12.1.0.1) and Oracle Clinical database server, you must perform the following preparatory tasks:
If you are using Real Application Clusters (RAC) you need to perform these tasks on every machine.
For more information, see "Creating Required Operating System Group and User" in the Oracle Database 12.1.0.1 Installation Guide for your operating system. For example, the link for Oracle Solaris is: http://docs.oracle.com/database/121/SXCQI/toc.htm#BGBEAGAJ
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. These instructions refer to the user name as oracle.
Create two groups: one is the Oracle Inventory group; the other is the operating system DBA group. These instructions refer to the group names as 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.
Ensure that the oinstall group can write to the new mount points and all subdirectories.
Before you install Oracle Clinical database server, create the following user group and account:
oclsascr — The group that controls access to the files Oracle Clinical generates for SAS
opapps — The operating system account that owns Oracle Clinical and that runs the Parameterized Submission (PSUB) process.
The oclsascr user group controls access to the files Oracle Clinical generates on the database server for SAS, including data extract files, which contain patient data.
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. This account also has the privileges to run parameterized submission (PSUB) jobs. The user name for the account is opapps, with a home directory named opapps. For example:
/home/opapps
Oracle Clinical documentation uses the variable OPA_HOME to refer to this location on an Oracle Clinical database server.
Do the following:
Make a shell for this user. For example, make the default shell:
/bin/csh
Make the opapps account a member of these user groups:
oclsascr
oinstall
dba
Neither oclsascr nor oinstall group needs to be the primary group for the opapps account.
The opapps account also runs the PSUB service RXCPSDPS and the PSUB Launcher PSLAUNCH.
The performance of Oracle Database 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 section on configuring kernel parameters in the of the Oracle Database 12c Installation Guide for your operating system available here: http://docs.oracle.com/database/121/nav/portal_11.htm
To test that the correct C compiler is installed and that it is accessible:
Log in to the database server 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.
Note:
The symbolic link may vary depending on where the C Compiler is installed.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 Linux x86-64 |
/usr/bin/make |
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Oracle Solaris SPARC |
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HP Itanium 11.31 |
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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; see Section 2.2.2.2, "Create the opapps Account".
Download and install the latest operating system patches required for Oracle, if necessary. Review the latest platform-specific install bulletins for Oracle Database 12c Release 1 (12.1.0.1).
This section includes:
To install Oracle Database 12c Release 1 (12.1.0.1):
Locate the Oracle Database software in the staging area on the database server where you downloaded it; see Section 1.5, "Downloading and Extracting the Software."
Start the Installer:
./runInstaller
Or, if the database server has multiple Oracle Homes, then enter:
./runInstaller -invPtrLoc ORACLE_HOME/oraInst.loc
For example:
./runInstaller -invPtrLoc /u01/app/oracle/product/121010_qa/oraInst.loc
Install Oracle Database 12c Release 1 (12.1.0.1). For instructions see the readme file and the section "Running Oracle Universal Installer" in the appropriate installation guide for your operating system at http://docs.oracle.com/database/121/nav/portal_11.htm.
Choose to install the Enterprise Edition.
Oracle Database Examples includes the following items:
Oracle JDBC Development Drivers (required)
Oracle Database Examples (required)
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 Oracle Thesaurus Management System. You can add them later if you change your mind.To install Oracle Database Examples:
Extract the zip file containing Oracle Database Examples in the examples directory.
Start Oracle Universal Installer from the examples directory.
./runInstaller
Or, if the database server has multiple Oracle Homes, then enter:
./runInstaller -invPtrLoc ORACLE_HOME/oraInst.loc
For example:
./runInstaller -invPtrLoc /u01/app/oracle/product/121010_qa/oraInst.loc
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 at http://docs.oracle.com/database/121/nav/portal_11.htm.
After you install Oracle Database and before you install the Oracle Clinical component, you must:
Note:
You might have to perform these steps whenever you apply an HSGBU-approved Critical Patch Update, or any Oracle software that uses the Oracle Database 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 Clinical 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 Oracle Clinical.
To grant write access to the ORACLE_HOME directory and its contents:
Log in to the server as the oracle user.
Find 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 12c Release 1 (12.1.0.1) installation.
Note that the oraenv script gives an error if run by a non-Oracle user. To avoid this error, see Section 2.4.1, "Change Permissions for Running oraenv Script".
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.
This section describes how to install and set up the Oracle Clinical database server.
The Installer performs the following operations:
Creates the Oracle Clinical directory structure (see Section 2.5.6, "Oracle Clinical Database Server Directory Structure for UNIX" for details)
Installs the Oracle Clinical database server
Builds the executables
Sets permissions on the directories
Creates the environment setup files
Modifies the environment setup files
Creates the Oracle Wallet to store credentials for OCPSUB and RXC_DISC_REP
Creates the directory for storing the SAS files
You must have the following information ready to enter in the Installer screens:
Home Details: The ORACLE_HOME location, which is where you installed Oracle Database 12c Release 1 (12.1.0.1); for example:
root:app/oracle/product/12101/dbhome
If you are installing in a RAC installation, the names of all RAC nodes where the same product(s) should be installed.
OPA Home: the directory where Oracle Clinical will be installed; Oracle recommends:
/home/opapps
Owner of Oracle Clinical Server Code must be opapps
Location for files oratab, tnsnames; for example:
/etc
$ORACLE_HOME/network/admin
RXC_SAS_VIEW: the directory where Oracle Clinical will generate SAS views; Oracle recommends:
/home/opapps/sas_view
Oracle Wallet location and password. The Installer uses these to create the database Wallet in the location you specify. The database Wallet stores the password for two accounts:
The OCPSUB proxy account, which is used for database access for parameterized submission (PSUB) jobs. If your installation includes multiple databases using either replication or RAC, each database needs an OCPSUB account and its credentials are created in this Wallet on the database server during Oracle Clinical database installation.
The RXC_DISC_REP account. If you use disconnected replication you must insert credentials for this account manually. See Section 4.4.3, "Set Up Disconnected Replication (Optional)."
Note:
If you have already created a Wallet through a previous installation of Oracle Clinical 5.0 or higher, you can continue using it instead of creating a new one by entering the location and password for the existing Wallet.To start installing the database server software:
Log in to the database server as the opapps user.
Change the primary group of the opapps account to the group that owns the Oracle Inventory:
Note:
Make a note of the current group so that you can set it back after the installation.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 installation. Typically, this user group is oinstall. (See Section 2.2.2.2, "Create the opapps Account.")
This temporary change is necessary so that the Installer can update the Oracle Home.
Set the X Window display output to the IP address of your local computer. Use the standard format for IP addresses.
For example:
setenv DISPLAY 123.45.67.89
Locate the Oracle Clinical software in the directory in the staging area on the database server where you downloaded it; see Section 1.5, "Downloading and Extracting the Software."
Open the ldflags file at root: app/oracle/product/12.1.0.1/lib and add the following flag:
-lnnz12
To start the Installer:
Log in to the server computer using the opapps account.
In the staging area, locate the directory where you downloaded Oracle Clinical (see Section 1.5, "Downloading and Extracting the Software") and extract the .zip file if you have not already done so.
Navigate to this location:
server_code_platform\Disk1\install
Change protections on all files to 755:
chmod 755 *
Run one of the following commands, depending on whether or nor you are using Oracle Real Application Cluster (RAC):
For a non-RAC installation:
./runInstaller
Or, if the database server has multiple Oracle Homes, then enter:
./runInstaller -invPtrLoc ORACLE_HOME/oraInst.loc
For example:
./runInstaller -invPtrLoc /u01/app/oracle/product/121010_qa/oraInst.loc
For a RAC installation:
./runInstaller -local
Or, if the database server has multiple Oracle Homes, then enter:
./runInstaller -local -invPtrLoc ORACLE_HOME/oraInst.loc
For example:
./runInstaller -invPtrLoc /u01/app/oracle/product/121010_qa/oraInst.loc
This ensures that the installation is performed only on the local node.
Note:
See "Using the Silent Installer" for instructions for running the Installer as a file with pre-entered parameter values.Note:
Although there is a button for deinstalling products on the Welcome screen, Oracle does not support using the Installer to deinstall Oracle Clinical or Oracle Clinical Remote Data Capture (RDC) Onsite.In the Select a Product to Install page, select Oracle Clinical Server for UNIX 5.1.0.0.x.
Follow the instructions on the installation screens, providing the information you assembled in Section 2.5.1, "Gather Required Information".
You can review the progress of the installation:
Open another terminal session as the opapps user.
To review the relinking progress, run the following:
tail -f $OPA_HOME/oc/51/relink_rxc.log
Open the InstallActionstimestamp.log in the oraInventory/logs directory.
At the end of the installation, the installer screen displays the:
Location of the OPA_HOME directory
Name of the code environment
Make note of this information. You need it for several post-installation tasks.
Review the generated installation log files for errors:
$ORACLE_BASE/oraInventory/logs/installActions.log
The current log file is installActions.log. All previous log generations have a timestamp appended to the name.
OPA_HOME/oc/51/relink_rxc.log—information on the relinking activities
OPA_HOME/oc/51/config_wallet_timestamp.log—information on Oracle Wallet configuration
OPA_HOME/oc/51/config_wallet_err_timestamp.log—this file is created only if there are errors in the Oracle Wallet configuration
Work with Oracle Support, if necessary, to resolve any errors.
The Installer creates the following directory structure for an Oracle Clinical database server on UNIX:
OPA_HOME /bin /xmltemp /oc /51 /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 Oracle Health Sciences products that 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.
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 2.5.2, "Prepare to Install the Oracle Clinical 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 12c Release 1 (12.1.0.1).
OPA_HOME is the directory where you installed Oracle Clinical database server.
Source the .cshrc file when you finish editing it:
On UNIX systems, configurations are defined in the opa_settings file, which the Installer creates in the following directory:
OPA_HOME/bin
The Installer enters all necessary entries and default values for the Oracle Clinical environment into the opa_settings file.
See the Oracle Clinical Administrator's Guide for a list of the environment variables and for information about changing, adding, and verifying values.
Review the opa_settings file and adjust the default values, if necessary. Note:
The db_env_setting records in opa_settings 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 Section 1.8, "Choosing a Character Set" for important information.
NLS_DATE_FORMAT must be set to DD-MON-RRRR. It is possible to override this setting for display in RDC Onsite, the Patient Data Report, and Oracle Clinical data entry, but the value in opa_settings must be DD-MON-RRRR.
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