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Daylight Installation Guide

Daylight Version 4.9
Release Date 08/01/11

Copyright Notice

This document and the programs described herein are Copyright © 1992-2011, Daylight Chemical Information Systems, Inc. Daylight explicitly grants permission to reproduce this document under the condition that it is reproduced in its entirety including this notice, and without alteration. All other rights are reserved.


Table of Contents

1. Basic Daylight Installation

2. Daylight Wrapper Installation

3. Daylight Web Services Installation

4. DayCart Installation

5. FLEXnet Server-Client Installation


1. Basic Daylight Installation

1.1 New Installation - Solaris and Linux

The following set of instructions cover the steps required for a basic installation of toolkit and application software.

1.1.1 Obtain and Install Software

Daylight software is available for download as a platform-specific .tar.gz archive file from the website.

It is possible for any user to own the Daylight files as the Daylight administrator. However, it is highly recommended that one create a user named 'thor' as the owner. Please note that 'root' must NOT own the files as some of the software will not run as 'root'.

Although any directory on a partition with at least 100 MB free space can serve as the install directory, it is recommended that /usr/local/daylight be created for this purpose.

As user 'root': As user 'thor':

1.1.2 Configure System

The following environment variables need to be added to the initialization file (.login, .profile, etc.) for the user 'thor'. Example for csh: Example for sh: Note: For 64-bit machines, $DY_ROOT/bin64 can be added to PATH and $DY_ROOT/lib64 to LD_LIBRARY_PATH. However, please note that most of the software only runs in 32-bit mode. Some 64-bit Linux-based operating systems do not install 32-bit compatibility libraries by default. These will need to be installed in order to run the Daylight software.

Additional users can be added either by including the above environment variables in each user's initialization file or by creating a separate file with the information that can then be sourced from the user's initialization file.

1.1.3 Obtain and Install License

To obtain a license: To install a standard license: See the licensing manual page for more advanced licensing schemes.

1.2 New Installation - Windows

The following instructions cover the steps required for a new toolkit installation. Note: The progob toolkit and program applications like clogp, convert and dayprop are not supported on Windows. See the Release Notes for Windows included with the installation files for information on using the toolkits within the MS Visual Studio environment and with CYGWIN.

1.2.1 Obtain and Load Software

Daylight software is available for download as a self-extracting Windows WinZip file from the website.

To install:

1.2.2 Obtain and Install License

To obtain a license: To install a standard license:

1.3 Update Installation - All Platforms

Once you have downloaded the software for the appropriate platform, follow the steps below to update to a new full version of Daylight software. Please note that you need a valid license with a 'support to' date later than the release date of the software version being installed. If updating using a patch, please see the directions supplied with the patch.

1.4 Optional Configurations - Solaris and Linux

The following sections describe how to configure specific optional features.

1.4.1 DayHTML, DayCGI, and HTTP Webserver

One must configure a webserver in order to run DayCGI/HTTP programs. In addition, this configuration is required if you wish to access the DayHTML documentation (User Manuals, Programmer's Guide, etc.) and the Contributed Code documentation (see New Contributed Code Installation locally from a webserver. The directions below assume that a webserver such as Apache is already installed. For additional DayCGI configuration information, see the DayCGI Manual.

As 'root' add the following, or the appropriate locations if different, to your http configuration file and then restart your server.
To access the DayHTML documents: To configure and test the DayCGI environment:

1.4.2 THOR and Merlin Server

The basic steps required for configuring the THOR-Merlin database system are described below. See the THOR-Merlin Administration Guide for more detailed information.

The following environment variables need to be added to the initialization file (.login, .profile, etc.) for the user 'thor'. Example for csh: Example for sh: Then complete the following steps:

1.4.3 Customize System

Default values for many options such as color and font preference can be changed by editing the appropriate file in either $DY_ROOT/etc/unix or $DY_ROOT/etc/common. See the options manual page for more details.

1.5 Contributed Code - All Platforms

Daylight contributed code, also referred to as 'Contrib', is a collection of freely-distributed open source code. It is a place to find examples on how to use the Daylight Toolkits to accomplish your goals. To encourage contributions to Contrib, we emphasize the "unsupported" aspect of its contents. New users should begin by exploring the directories under $DY_ROOT/contrib. In addition, other Contrib programs not in the Daylight release can be accessed from the Daylight website.


2. Daylight Wrappers

2.1 New Installation - Solaris and Linux

Complete the following steps to setup the Daylight licensed Wrappers: A set of java examples is included in $DY_ROOT/wrappers/java/examples.

2.2 New Installation - Windows

Complete the following steps to setup the Daylight licensed Wrappers: A set of java examples is included in C:\daylight\v\wrappers\java\examples.
  • Add C:\daylight\v\wrappers\java to CLASSPATH.
  • Go to C:\daylight\v\wrappers\java\.
  • Type `javac examples/*.java` .
  • To test type `echo SCOCC | java examples/FmtSmiles` --- the result should be CCOCS

2.3 Update Installation - All Platforms

After updating the Basic Daylight installation as described above, download the new wrapper file and either copy it to $DY_ROOT and unpack it (Solaris and Linux) double-click on the .exe file to unzip and install.

3. Daylight Web Services Installation

3.1 New Installation - Solaris and Linux

The following set of instructions assume that Java JDK 5, Tomcat 5.5 and Axis 1.4 are already installed. Note: Only 32-bit versions of the web services are currently available.

3.1.1 Obtain and Install Software and License

Follow directions above for the New Basic Installation - Solaris and Linux (Section 1.1.1 to Section 1.1.3) to obtain and install the Daylight software and license. Note: The license file must include a program license for each specific web service.

3.1.2 Software Configuration

Complete the following steps to setup the web services. Note: The user must have the appropriate level of priveliges in order to change/add files to the CATALINA_HOME and to start up Tomcat.
  • Copy $DY_ROOT/webservices/dayws.war to $CATALINA_HOME/webapps
  • If necessary, create a setenv.sh file in $CATALINA_HOME/bin
  • Add the following environment variables: DY_HOME, DY_ROOT, LD_LIBRARY_PATH and DY_LICENSEDATA
      Example:
      DY_HOME=/usr/local/daylight; export DY_HOME
      DY_ROOT=$DY_HOME/v; export DY_ROOT
      DY_LICENSEDATA=$DY_HOME/dy_license.dat; export DY_LICENSEDATA
      LD_LIBRARY_PATH=$DY_ROOT/lib/:$LD_LIBRARY_PATH; export LD_LIBRARY_PATH
  • Restart Tomcat
  • Change the location of AXIS_HOME in $DY_ROOT/webservices/wstest/wstest.sh to point to the local axis directory
  • Test the setup by running `$DY_ROOT/webservices/wstest/wstest.sh localhost:port` where port is the port number on which Tomcat is running.

3.2 Update Installation

Follow the directions above (Section 3) to update the basic installation, copy $DY_ROOT/webservices/dayws.war file to $CATALINA_HOME/webapps and restart Tomcat.

4. DayCart Installation

4.1 New Installation - Solaris and Linux

The following set of instructions are an overview of the installation procedures for the DayCart Oracle/PostgreSQL cartridges. The directions below assume that Oracle or PostgreSQL is already installed.

4.1.1 Obtain and Install Software

Follow directions above for Section 1.1.1 of the New Installation to obtain and install the Daylight software.

4.1.2 Obtain License

DayCart is licensed separately so you do not need a standard toolkit/application Daylight license (dy_license.dat) file to use the basic DayCart functions. To obtain a DayCart license follow first set of stepsabovefor Section 1.1.3 of the New Installation. Indicate you want a DayCart license for either Oracle or PostgreSQL. You will be issued a valid license (sql insert statement) by email.

4.1.3 Configuration - Oracle

Complete the following steps to setup the Oracle cartridge. The Oracle server contacts the network listener when it wants to run external procedures like the Daylight cartridge.
  • As user 'thor' locate the directory 'dcischem' within $DY_ROOT.
  • Edit the create.sql script to take out the indicated lines and change the 'c$dcischemlib' path to point to the appropriate cartridge shared object library, e.g., /usr/local/daylight/v/lib/ddlib.so.XX (where XX is the Oracle version).
  • Log-on as an Oracle user with DBA privileges.
  • Create the tablespace 'daylight_ts' with a size of 10M.
  • Create the Oracle user 'c$dcischem' identified by 'secret' with DBA privileges and default 'daylight_ts' tablespace.
  • Run the create.sql script as the 'c$dcischem' user.
  • Check to see if the listener is running and functional (tnsping hostname), if not start it (lsnrctl start) and rerun the tnsping command.
  • Configure the listener by editing the adding the line '(ENVS = "EXTPROC_DLLS=ANY")' after the line '(PROGRAM = extproc)' in the $ORACLE_HOME/network/admin/listener.ora file
  • Stop and restart the listener (lsnrctl stop and lsnrctl start).
  • Install the license by running the license key sql insert statement as the 'c$dcischem' user.
  • See the SQL scripts in the $DY_ROOT/dcischem/TEST subdirectory for a set of verification scripts (run_tests) and examples of use of the cartridge.
  • As an Oracle user with DBA privileges, revoke DBA privileges from user 'c$dcischem' and change the password.
  • To allow users access to the cartridge, grant the 'daycart' role to non-privileged users.

4.1.4 Configuration - PostgreSQL

Complete the following steps to setup the PostgreSQL cartridge:
  • Go to $DY_ROOT/pgcart/. Connect to the PostgreSQL database as the root user (typically postgres) and execute `\i create_pg_schema.sql`.
  • Install the license using the sql statement that was sent to you.
  • Exit the database and locate the default library location by running `pg_config --pkglibdir`. Copy the correct library version of libpgcart.so.XX (where XX is the PostgreSQL version) for your platform from $DY_ROOT/lib/ or $DY_ROOT/lib/ to the PostgreSQL location, simply named libpgcart.so.
  • Log into the database as the root user and run `\i create_pg_functions.sql.

4.1.5 Testing

The following simple queries can be run to test the cartridge:
  • `select getinfo('daycart_version');` with the result of the daylight version installed
  • `select testlicense('daycart');` with the result of '1'
  • `select smi2cansmi('NCC', 0);` with the result of 'CCN'

4.2 New Installation - Windows

The following set of instructions are an overview of the installation procedures for the DayCart Oracle cartridge. The directions below assume that Oracle is already installed and running.

4.2.1 Obtain and Install Software

Follow directions above for the New Basic Installation - Windows (Sections 1.2.1 only) to obtain and install the Daylight software.

4.2.2 Obtain License

DayCart is licensed separately so you do not need a standard toolkit/application Daylight license (dy_license.dat) file to use the basic DayCart functions. To obtain a license follow steps 1 and 2 above for Section 1.2.2 of the New Installation requesting an Oracle cartridge license. You will be issued a valid license (sql insert statement) by email.

4.2.3 Configure System - Oracle

Complete the following steps to setup the Oracle cartridge. The Oracle server contacts the network listener when it wants to run external procedures like the Daylight cartridge.
  • Locate the directory C:\daylight\v\dcischem.
  • Edit the create.sql script to take out the indicated lines and change the 'c$dcischemlib' path to point to the appropriate cartridge shared object library, e.g., C:\daylight\v\bin\ddlib.XX.dll (where XX is the Oracle version).
  • Log-on as an Oracle user with DBA privileges.
  • Create the tablespace 'daylight_ts' with a size of 10M.
  • Create the Oracle user 'c$dcischem' identified by 'secret' with DBA privileges and default 'daylight_ts' tablespace.
  • Run the create.sql script as the 'c$dcischem' user.
  • From a DOS window, check to see if the listener is running and functional (tnsping hostname), if not start it (lsnrctl start) and rerun the tnsping command.
  • Configure the listener by editing the adding the line '(ENVS = "EXTPROC_DLLS=ANY")' after the line '(PROGRAM = extproc)' in the \oracle\product\XX\YY\NETWORK\ADMIN\listener.ora file where XX is the product version and YY is the server
  • Stop and restart the listener (lsnrctl stop and lsnrctl start).
  • Install the license by running the license key sql insert statement as the 'c$dcischem' user.
  • See the SQL scripts in the C:\daylight\v\dcischem\TEST subdirectory for a set of verification scripts and examples of use of the cartridge. The scripts can be run as the c$dcischem user and the results compared with the output in the ref_out files.
  • As an Oracle user with DBA privileges, revoke DBA privileges from user 'c$dcischem' and change the password.
  • To allow users access to the cartridge, grant the 'daycart' role to non-privileged users.

4.2.4 Testing

The following simple queries can be run to test the cartridge:
  • `select getinfo('daycart_version');` with the result of the daylight version installed
  • `select testlicense('daycart');` with the result of '1'
  • `select smi2cansmi('NCC', 0);` with the result of 'CCN'

4.3 Update Oracle Installation - All Platforms

Follow the steps below to update to a new full minor version of DayCart software See the DayCart User Manual for major version upgrades. If updating using a patch, please see the directions supplied with the patch. Please note that you will need a valid DayCart license.
  • Follow directions above for the Update Basic Installation - All Platforms to update the Daylight software.
  • Edit the create.sql script to remove the indicated lines and update the 'c$dcischemlib' path.
  • Run the create.sql script as the 'c$dcischem' user.


5. FLEXnet Installation and Configuration

5.1 New FLEXnet Installation

Daylight supports the following features via Macrovision's FLEXnet Served License Component Model:

  • License file "FEATURE" lines.
  • Floating (non-node-locked) licenses.
All other FLEXnet license features ( including three-server redundancy ) are currently unsupported.

Daylight products available under FLEXnet licensing include the following:

  • Toolkits
  • Programs
  • THOR and Merlin Servers
  • THOR Databases

The following instructions describe a relatively basic installation and assume some familiarity with the FLEXnet software suite. Advanced FLEXnet users are encouraged to consult Macrovision's documentation resources for information about more sophisticated license server configurations. New users will also benefit from consulting Macrovision's background and introductory materials:

5.1.1 Server - Solaris and Linux

  • While Daylight does not require that you download or install the complete Daylight software distribution on the FLEXnet license server, we do recommend that you at least create a Daylight user and group on the FLEXnet license server and set the 'DY_HOME' and 'DY_ROOT' environment variables before proceeding. All Daylight FLEXnet software should be owned by and run as the Daylight user: never as root.
  • Download the appropriate platform-specific FLEXnet software distribution archive .
  • Extract the downloaded .tar.gz archive in $DY_HOME to produce a version-specific 'flexVVV' ( where VVV is the FLEXnet version ) directory (e.g. flex108 ).
  • Obtain a FLEXnet license file from Daylight. Note that the testlicense program is included in both the FLEXnet and standard software distributions.
  • Create the directory $DY_HOME/licenses/flexnet/ and save your license file as $DY_HOME/licenses/flexnet/daylight.lic .
  • Start the FLEXnet License Server Manager (lmgrd) and Vendor Daemon (daylight). The processes can be started manually or automatically at boot time via a startup script. An example rc2.d startup/shutdown file, daylight_flex is included in the etc FLEXnet software distribution subdirectory. To start the daemon manually you may use:
    % cd $DY_HOME/flexVVV
    then
    % ./lmgrd daylight \
    -c "$DY_HOME/licenses/flexnet/daylight.lic"

    Or, if you require a separate daylight daemon log file (e.g. $DY_HOME/logs/flex.log):
    % ./lmgrd daylight \
    -c "$DY_HOME/licenses/flexnet/daylight.lic" \
    -l "$DY_HOME/logs/flex.log"

    To check the license server status:
    % ./lmstat daylight

5.1.2 Client - Solaris, Linux and Windows

  • Perform a basic Daylight software installation on the client machine. Skip the license acquisition and installation steps as you will be using a served floating license file.
  • Client machines must have access to a valid FLEXnet license file and license server to run FLEXenabled software. Any of the following environment variables (or Windows Registry entries) can be used:
    DAYLIGHT_LICENSE_FILE
    LM_LICENSE_FILE

    Daylight recommends setting 'DAYLIGHT_LICENSE_FILE' to the hostname of the license server:
    DAYLIGHT_LICENSE_FILE=@hostname
  • Verify the license availability status:
    % $DY_ROOT/bin/testlicense -v
  • Note that Daylight supports license queueing. If the FLEXnet license server has dispatched the maximum allowable number of licenses for a given FEATURE, it will not be able to issue an additional license for that FEATURE until one of the licenses becomes available. If the environment variable DY_FLEXQUEUE is set to any string, the client will wait till the unavailable license FEATURE is checked back in before proceeding. If DY_FLEXQUEUE is not set, then the client will fail immediately if a license is not available.

5.2 Update FLEXnet Installation

5.2.1 Server - Solaris and Linux

  • Download Daylight's most recent FLEXnet software distribution archive.
  • Extract the archive into a new version-specific FLEXnet directory.
  • Stop the old FLEXnet license server (lmgrd) and Daylight vendor daemon (daylight) then start the new ones. For example, if you want to upgrade a standard 10.8 installation to 10.9, perform the following:
    % cd $DY_HOME/flex108
    % ./lmdown -c $DY_HOME/licenses/flexnet/daylight.lic
    % cd $DY_HOME/flex109
    % ./lmgrd daylight \
    -c "$DY_HOME/licenses/flexnet/daylight.lic" \
    -l "$DY_HOME/logs/flex.log"

    To check the license server status:
    % ./lmstat daylight
    You will also need to update any startup scripts to match the new location.

5.2.2 Client - Solaris, Linux and Windows

  • Simply upgrade the Daylight software on the client machine. Skip the license acquisition and installation steps as you will be using a served floating license file.
  • Environment variables do not need to change.
  • To check the license availability status:
    % $DY_ROOT/bin/testlicense -v
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