Catalyst 4.7 Installation Guide
Installation Guide
Release 4.7
March 2002
All updated documentation for the latest release of Catalyst is
available at the Accelrys website documentation library:
9685 Scranton Road
San Diego, CA 92121-3752
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Catalyst, Cerius2, Discover, Insight II, and QUANTA are registered trademarks of Accelrys Inc.
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Mechanics Workbench, WebLab, and the Biosym, MSI, Molecular Simulations and Accelrys
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1. System Requirements
Operating environment . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
Workstation requirements . . . . . . . . . . . . . . . . . . . . . . . 1
Interactive (Client) Platform . . . . . . . . . . . . . . . . . . 1
Server Platform . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
Media for distribution . . . . . . . . . . . . . . . . . . . . . . . 2
Disk space . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
2. Installing Catalyst
Preparing to install the software . . . . . . . . . . . . . . . . . . . . . 3
Installing the software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
Setting up the chemical database server . . . . . . . . . . . . . . . 6
Method 1 (configuration without changing
system files) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Method 2 (changing system files) . . . . . . . . . . . . . . . . . 7
Setting up users and finishing up . . . . . . . . . . . . . . . . . . . . 9
Running Catalyst . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
Starting Catalyst . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
Miscellaneous setup. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
Printing graphics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
Using on-line Help . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
Using HipHop and ConFirm. . . . . . . . . . . . . . . . . . . . 12
3. Instructions for Installing Catalyst
Extracting databases from media . . . . . . . . . . . . . . . . . . . .
Installing licensing information . . . . . . . . . . . . . . . . . . . . .
Installing relational data . . . . . . . . . . . . . . . . . . . . . . . . . .
Configuring the database and finishing up . . . . . . . . . . . .
4. Using Oracle from Catalyst
Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
User authentication . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Environment variables for user and password . . . . . . . . .
Configuring Oracle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Creating table space in Oracle . . . . . . . . . . . . . . . . . . .
Catalyst Installation Guide/March 2002
CATALYST tablespace . . . . . . . . . . . . . . . . . . . . . 20
CATUSER tablespace . . . . . . . . . . . . . . . . . . . . . . 20
Create CATALYST_REGISTER table . . . . . . . . . . 21
Setting up users. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
Modifying Catalyst to use Oracle . . . . . . . . . . . . . . . . . . . . 22
Using relational data with purchased databases . . . . . . . . 23
Troubleshooting Oracle . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
Common errors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
Installation tips . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
Definition of ORACLE_SID . . . . . . . . . . . . . . . . . . . . . 28
Oracle 8.0.5 Support . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
5. Installing the License File
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
The license file. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
Starting the license installation menu . . . . . . . . . . . . . . 31
Search for licenses on media . . . . . . . . . . . . . . . . . . . . . 32
Install emailed license. . . . . . . . . . . . . . . . . . . . . . . . . . 33
Install previously unselected license . . . . . . . . . . . . . . 34
View installed licenses (LM_LICENSE_FILE) . . . . . . . 34
View license verifier results . . . . . . . . . . . . . . . . . . . . . 35
Turn OFF/ON licensing automation . . . . . . . . . . . . . . 35
Frequently asked questions . . . . . . . . . . . . . . . . . . . . . 35
Bring license daemons up (lmup). . . . . . . . . . . . . . . . . 35
View lmstat -a output . . . . . . . . . . . . . . . . . . . . . . . . . . 36
License behavior after installation . . . . . . . . . . . . . . . . . . . 36
Explore unlicensed software programs
on an informal trial basis . . . . . . . . . . . . . . . . . . . . 37
Additional information on license management. . . . . . . . . 38
Catalyst Installation Guide/March 2002
1 System Requirements
Operating environment
Accelrys Catalyst products operate on UNIX platforms and rely on
the C shell being the default shell. In order to run any of Accelrys
Catalyst's products, including all installation and background
jobs, you must use the C shell. Accelrys Catalyst products are not
supported when used from other shells, including the Bourne
shell and the korn shell. If you have questions regarding the shell
you are using, contact your system administrator.
Interactive products are workstation based and operate primarily
within the program Catalyst. This interactive program may invoke
many other programs as background jobs.
The following sections detail the hardware and system software
requirements of our products. When running our products in a
networked environment, you will need to give consideration to
additional system software including NFS, support for rsh and
rcp, etc. The information provided below is intended to provide
only an overview of the major hardware and system software
Workstation requirements
Interactive (Client) Platform
Catalyst operates on Silicon Graphics (SGI) workstations running
IRIX 6.5.10 or higher operating systems. We recommend a minimum of 64 megabytes of RAM and 128 megabytes of physical
swap space. Increasing these resources will often improve the per-
Catalyst Installation Guide/March 2002 1
System Requirements
formance of the software. Catalyst supports all graphics boards
that support Open GL.
Server Platform
The server applications run on Silicon Graphics machines
(described above), Intel compatible 32-bit systems running
RedHat Linux 6.2, or AIX 5.1L.
Media for distribution
This release is shipped on CD-ROMs.
Disk space
Before installing the software, you must verify that there is sufficient room on the installation disk. The exact amount depends on
your configuration, and is reported by the installer program. As a
general guide, the installation may take up to 320 megabytes. Documentation describing the disk space requirements of Catalyst
databases is provided in their distribution.
Catalyst Installation Guide/March 2002
2 Installing Catalyst
Below are instructions for installing Catalyst for general use. The
corresponding HTML files for this document are located at the
Accelrys website.
Preparing to install the software
1. Insert the Catalyst CD in your CD-ROM drive.
In most installations, you can extract the software from the directory
2. Choose a directory where you would like the Catalyst
software to reside. This Guide refers to this directory
throughout these instructions as topdir.
For example, if you installed Catalyst in the directory named
/net/accelrys, use this directory whenever you see the term
If you are using Insight II, please see “Notes for Insight II users”
on page 10 for special instructions.
Excluding the chemical databases (installed separately), the Catalyst
software requires up to 320 megabytes of free disk space. We recommend that you put the installation directory on a network-mounted
file system (NFS). This allows other computers on your network to
access the software.
Catalyst Installation Guide/March 2002 3
Installing Catalyst
3. Create the installation directory and release context
mkdir topdir
mkdir topdir/CAT470
Installing the software
A license must be installed before you can use the Catalyst software. During installation you can choose to install a demo license
or a license that was emailed to you.
1. Contact Accelrys Scientific Support to obtain a license via
email or a demo license password.
For information on how to contact Accelrys, select “How to Contact
Us…” from the Help menu in the Accelrys Installation Utility.
2. Run the Accelrys Installation Utility by typing:
cd topdir/CAT470
The install utility will first ask you if your DISPLAY variable is set
correctly. The display setting shown (usually :0.0) is correct unless
you have remotely logged on to another machine to perform the installation. In that case, you must set the environment variable to the correct value (setenv DISPLAY hostname:0) and rerun the
installation utility.
Second, you are asked to verify that the installation directory is correct. You can answer yes or you can choose a different directory. The
installation utility asks two more questions about the licensing package. After you answer the questions properly, the installation utility
copies several files to the installation directory and launches the
graphical installation interface.
Third, you are asked whether you have the Accelrys License Pack
installed. Follow the online instructions to install or update your
Accelrys License Pack.
Catalyst Installation Guide/March 2002
Installing the software
3. Click “Install Software…”when the Accelrys Installation
Utility dialog box appears.
4. In the next dialog box, select “Install Emailed License” if you
received a license via email OR “Enter Demo Password” if
you do not have an Accelrys license file installed and have
received a demo password.
Follow the instructions on the screen to install your license.
If you already have an Accelrys license installed in the Accelrys
License Pack, you need not install a license during installation of Catalyst. In this case, the Install Emailed License button does not
appear, and Catalyst automatically uses your current license. If you
need to update your license, please refer to Chapter 5 of this guide.
Click Continue if you already have the license installed or prefer to
install it later.
You can install the software before installing a license; however, the
software will not function until a license is installed.
5. If the CD-ROM location is not correctly specified in the
Software Extraction Setup dialog box, click "Set…".
Specify the correct location of the CD-ROM in the "Device
Name" field.
You can ignore references to media other than CD-ROM. The
Catalyst software is delivered only on CD-ROM.
6. Click "Commit".
If you already have other Accelrys products installed in topdir, you
can select a default context by following the online instructions that
Wait while the software is installed and configured.
7. After the software is installed, review the logfiles to see if any
errors were detected.
Catalyst Installation Guide/March 2002 5
Installing Catalyst
Setting up the chemical database server
The next step is to set up the Catalyst chemical database server.
This step only sets up the server; no database is installed during
this step. For instructions on installing databases see Chapter 3.
The Catalyst chemical database server can be set up using two different methods:
1. The first method does not require root privileges to set up, since
no system files are modified. However, the database server
must be started manually every time the system restarts. Use
this method for tentative or temporary installations or if you do
not have root privileges.
2. The second method requires root privileges to set up, since this
method involves modifying system files. With this method, the
server starts automatically every time the system starts. This is
the preferred method for permanent installations of the Catalyst software.
After selecting the server and starting the installation utility,
choose the method that is appropriate for your site.
1. Choose an appropriate computer to run the Catalyst database
The computer should be equipped with at least 64 megabytes of memory. If you have purchased databases from Accelrys, you will also need
additional free disk space mounted locally on this computer. NFS
mounted drives cannot be used to store databases.
Perform the following instructions on the machine you have chosen as
the database server computer.
2. Start the Accelrys Installation Utility by typing:
cd topdir/CAT470
Catalyst Installation Guide/March 2002
Setting up the chemical database server
3. Click "Set Up Chemical Database Server…" in the Accelrys
Installation Utility dialog box.
Depending on your choice of method, follow one of the next two sections.
Method 1 (configuration without changing system files)
Method not requiring root 1. Click "Commit".
A message box appears with the instructions for starting and stopping
the server.
2. Type the following commands at the UNIX prompt to start
the chemical database server:
Make sure that you have a valid license installed before running
the database server.
source topdir/cshrc
setenv CATALYST_OPTIONS $CATALYST_WCONF/catalystd.options
$CATALYST_CONF/catalystd start
If you need to stop the chemical database server, use the command:
$CATALYST_CONF/catalystd stop
3. Go to “Setting up users and finishing up” on page 9 to finish
the installation.
Method 2 (changing system files)
Method that requires root
1. Select "Automatic".
This method creates a shell script containing the commands necessary
to set up the server so that it starts automatically when the system
starts. The setup script does not actually start the server running. It
copies files, creates links, and makes a configuration file. The server is
started the first time with the command given in Step 7 on page 9 or
Catalyst Installation Guide/March 2002 7
Installing Catalyst
by rebooting the system.
2. Specify how you wish to handle the setup script.
Unless you are running the Accelrys Installation Utility as root, you
are only able to save the setup script to a file. The setup script must be
run as root, since it modifies system files.
3. Specify a name for the setup script file.
Usually the default file name is appropriate. You may want to review
this file after it is created to see the exact commands used to set up the
4. Click "Commit".
If you chose to run the setup script immediately, proceed with Step 6;
otherwise, go on to the next step.
5. Run the setup script as root from the command line.
Log in as root and run the setup script by typing:
where setup_script_name is:
or whatever you specified in Step 3.
6. Add a line similar to the following to the "services" file (or to
your yellow pages database):
catD-4.7 9141/tcp
The Catalyst software requires a new service in the /etc/services file of
each computer that will use or host the service. The service name is
You may have to select a different port number if the one above is
already used for some other service.
Catalyst Installation Guide/March 2002
Setting up users and finishing up
If you add the line above to the yellow pages database, then you
do not need to add it to the /etc/services file.
7. Type the following command to start the chemical database
/etc/init.d/catalystd start service_name
Where service_name is catD-4.7 for the Catalyst 4.7 release. If
service_name is omitted, all services specified in the file /etc/config/
catalystd.options are used.
Once started, the server remains running and restarts automatically
when the system restarts.
The command to stop the server is:
/etc/init.d/catalystd stop service_name
Setting up users and finishing up
All users who would like to use the Catalyst software must have a
line added to their .cshrc file.
1. Add the following line to the .cshrc file in each user’s home
source topdir/cshrc
This line sets up the environment for running the Catalyst software.
2. Now source your .cshrc file:
source ~/.cshrc
3. If you have not already started the chemical database server,
start it now.
The command to start the server should be executed on the machine
that hosts the server.
Catalyst Installation Guide/March 2002 9
Installing Catalyst
4. Check the file /usr/tmp/catD-4.7.log to verify that the
chemical database server is running.
Running Catalyst
Notes for Catalyst 4.6 users Files and databases from Catalyst 4.7 are compatible with Catalyst
4.6. A stockroomDB produced by Catalyst 4.6 can be read by Catalyst 4.7. However, a stockroomDB written by Catalyst 4.7 can not
be read by Catalyst 4.6.
Notes for Insight II users
You can run Catalyst and Insight II simultaneously without
switching context. If you are running Insight II, change the setup
for Insight II and Catalyst in your ~/.cshrc file to contain these
set_context your_InsightII_context
setenv CATALYST catalyst_topdir/470
source $CATALYST/wconf/catalyst/catEnvVar.csh
Starting Catalyst
Once you have read all the above information, you are ready to
start Catalyst.
1. Catalyst can now be started using the commands:
cd work_directory
Miscellaneous setup
Printing graphics
Catalyst allows you to make hardcopies of graphics with a PostScript printer. The default print command is lp. If your site uses
lpr for printing, you must modify the $CATALYST_WCONF/
Catalyst Installation Guide/March 2002
Miscellaneous setup
catEnvVar.csh file to set the following environment variable
(please see the comment at the end of the catEnvVar.csh file).
1. Locate the line:
2. Change it to:
That is, remove the #.
Using on-line Help
Catalyst provides extensive online documentation. The documents are in HTML format and are located in the
$CATALYST_HELP directory. The top page is:
By default, Catalyst starts Netscape to display these HTML documents.
1. To access the online help, go to the main Catalyst menu and
select the Help/On Catalyst command.
Catalyst Installation Guide/March 2002
Installing Catalyst
Using HipHop and ConFirm
If you are installing HipHop or ConFirm rather than the full
Catalyst product line, please see the following HTML files for
Catalyst Installation Guide/March 2002
3 Instructions for Installing Catalyst
This section contains instructions for installing the NCI database
for use by Catalyst. Other Catalyst databases can be installed by
similar procedures—be sure to read their README files for additional details. You should install Catalyst before you attempt to
install databases. Specifically, these instructions assume that you
have access to the Catalyst environment variables.
Extracting databases from media
1. Insert the first Catalyst database CD in your CD-ROM drive.
In most installations, you will be able to extract the database information from the directory /CDROM.
Datafiles for some databases require more than one CD-ROM
and may require additional steps.
2. To see a list of files on the CD-ROM type:
You should see a list of database directories and a README file that
describes the installation process.
See the README file for details.
3. Choose a directory where you would like to install the
database files.
This directory should be on a disk attached to the computer that runs
Catalyst Installation Guide/March 2002
Instructions for Installing Catalyst Databases
the Catalyst database server. We will refer to the directory you have
chosen as dbdir for the remainder of these instructions. For example,
you might choose to use the directory /home/NCI to house the NCI
data files. The dbdir directory can also be the same directory in which
you install Catalyst software (i.e., topdir).
4. Use tar to extract the contents of the CD-ROM into dbdir
mkdir dbdir
tar cBf - . | (cd dbdir; tar xvpBf -)
The tar command copies the contents of the CD-ROM into the directory dbdir. This process takes up to 20 min.
5. Please see the README file on the CD-ROM.
Installing licensing information
Databases purchased from Accelrys require a software license
before they can be accessed from inside Catalyst. Contact Accelrys
to obtain an updated license file that contains a token for NCI.
(Please refer to Chapter 5, The license file (page 31) for details.)
Installing relational data
If you have installed a version of Oracle, supported by Catalyst
(see Requirements in Chapter 4, page 17), you can import relational
data associated with NCI and access it using Catalyst. See Chapter
4 for details.
Catalyst Installation Guide/March 2002
Configuring the database and finishing up
Configuring the database and finishing up
Databases are described by a database configuration file. This file
tells Catalyst what computer it should talk to when it wants to
search databases and it tells the database server where to find the
database files.
The sample configuration file for NCI is found in the path dbdir/
470/irix6m3/data/NCI/NCI.bdb.sample. This file must be modified before the database can be used when running Catalyst.
1. Change to the database file directory and make a copy of the
sample configuration file:
Edit the NCI.bdb file
cd dbdir/470/irix6m3/data/NCI/
cp NCI.bdb.sample NCI.bdb
The NCI.bdb file contains five sections: Compounds, 1D Data, 2D
Index, 3D Index, and Dictionary. Each section specifies the host where
the database server is running and the path on that host to the database files.
2. Change the host lines for Compounds, 2D Index, 3D Index,
4D shape index, and Dictionary
Change these so they point to the host where you installed the
Catalyst database server (see Chapter 2 for more details).
3. Change the path lines for those same components
Set the paths to:
For example, assume that you are running the catDisk server on a
machine named sunrise and you have installed the NCI data in the
directory /msi/catalyst on that host. Below is an appropriately modified configuration file for this situation:
Catalyst Installation Guide/March 2002
Instructions for Installing Catalyst Databases
!-------------------------------------------------! Copyright 1991-2000
! All rights reserved
! Biocad database configuration file.
database = NCI
catDB version = 2.1 (177)
id = 9
host = sunrise
path = /msi/catalyst/470/irix6m3/data/NCI/
1D Data:
host = oracle
server = oracle_name
2D Index:
host = sunrise
path = /msi/catalyst/470/irix6m3/data/NCI/
3D Index:
host = sunrise
path = /msi/catalyst/470/irix6m3/data/NCI/
host = sunrise
path = /msi/catalyst/470/irix6m3/data/NCI/
Making the modified file
4. Copy the modified configuration file into the Catalyst
available to Catalyst users
installation tree
cp NCI.bdb $CATALYST_WCONF/databases/NCI.bdb
The NCI database should now be available for use from Catalyst.
Catalyst Installation Guide/March 2002
4 Using Oracle from Catalyst
You can use Oracle to access and manage relational data with
Catalyst release 4.7. Below are instructions for setting up both
Oracle and Catalyst so that they can interoperate. These instructions
assume you are familiar with Oracle and that you have database administrator privileges.
The Catalyst software has been tested with the following versions
of Oracle Server.
Server Platform
IRIX 6.5.10
Windows NT
RedHat Linux 6.2
Server Version(s)
8.0.5, 8.1.7
You may contact Accelrys Scientific Support to obtain an up-todate list of supported server platforms and versions.
Catalyst accesses Oracle by using shared libraries supplied by
Oracle, Accelrys does not distribute these shared objects. If your
Oracle platform is not the same as your Catalyst platform, you
may need to contact your Oracle support provider to obtain the
required client shared libraries. For example, if you only have a
Windows installation of Oracle, you will need the Linux client
shared libraries to run Catalyst with Oracle on Linux, and the 32bit IRIX client shared objects to run catalyst with Oracle on Irix
Catalyst Installation Guide/March 2002
Using Oracle from Catalyst
The following instructions assume that your Oracle Server is
installed and running and that SQL*NET (or Net8 for Oracle8) has
been configured to allow remote clients to access the server. If you
have questions about how to install Oracle or SQL*NET, please
contact your Oracle support provider. The instructions also
assume that you are logged in as the UNIX user "catalyst" with a
corresponding "catalyst" Oracle user authenticated by the OS. If
this is not the case, you may need to replace the connection string
"\/" with what you would usually use; such as:
"user/[email protected]"
User authentication
Catalyst 4.7 provides two methods for authenticating users to the
database: standard user/password authentication, and operating
system (OS) authentication. No extra configuration of the Oracle
Server is necessary to use standard user/password authentication.
OS authentication assumes the user is authentic because they provided a password when they logged into their system account.
With this form of authentication, Catalyst users are not required to
enter a password each time they open a Catalyst database. To set
up this authentication policy, the Oracle instance initialization file
must be modified as shown in the following steps:
1. Edit the instance initialization file to set the following
remote_os_authent = TRUE
os_authent_prefix = ""
You must also make another change so that SQL*NET will allow
Catalyst users to access the database without asking for a password.
2. Change the following parameter in the listener.ora
configuration file:
Catalyst Installation Guide/March 2002
Environment variables for user and password
Environment variables for user and password
Catalyst 4.7 recognizes certain environment variables for specifying the Oracle user name and password. These environment variables are not required, but can be set for convenience.
Environment Variable
The Oracle user. Set to / for OS authenticated
The Oracle password. Set to nothing if OS authenticated. If not empty, this variable is interpreted
as an encrypted password.
Set to supply the Oracle password.
To make Catalyst 4.7 behave identically to Catalyst 3.1 when connecting to Oracle, set the environment variables as follows:
This requires that you set up OS authenticated logins as described
in the previous section. With these settings, Catalyst 4.7 does not
request a password when opening a database.
Configuring Oracle
The Catalyst software assumes that two key tables are available in
the Oracle server. This section outlines how to create and configure
these tables.
We recommend that you create a user named CATALYST, who will
own the Catalyst configuration tables and all databases purchased
from Accelrys.
Catalyst Installation Guide/March 2002
Using Oracle from Catalyst
1. Start the SQL interpreter by entering:
sqlplus \/
SQL> indicates the SQL prompt on your screen.
Creating table space in Oracle
From our Oracle installation experience, we recommend the following. However, these instructions are optional and you may
require a different setup at your site.
We recommend creating two tablespaces using the Oracle system
administration tool (svrmgrl) or SQL*PLUS.
CATALYST tablespace
Based on the size of the commercial databases you purchase from
Accelrys and/or in-house databases that you construct, you may
want to create a large CATALYST tablespace:
2. To create the tablespace using SQL*PLUS, use the following
CREATE TABLESPACE CATALYST DATAFILE '/net/iris150/usr3/catalyst/catora3.dbf'
where /net/iris150/usr3/catalyst/catora3.dbf refers to the file where
the tablespace will reside.
If you prefer to use the DBA Administration Tools, select the Create
Tablespace command and choose the following options:
Size: 400 M
Initial Extent: 10 M
Next Extent: 10 M
CATUSER tablespace
Because the CATALYST tablespace is created with large extents to
accommodate databases such as NCI, the same extent size may not
be efficient for user stockrooms or smaller user-created databases.
We therefore recommend creating a smaller tablespace, CATUS-
Catalyst Installation Guide/March 2002
Configuring Oracle
ERS, and assigning the CATUSER tablespace as default tablespace
for anyone who runs Catalyst.
3. To use SQL*PLUS for creating the tablespace use the
following construct:
CREATE TABLESPACE CATUSERS DATAFILE '/net/iris150/usr3/catalyst/catusr_2.dbf'
where /net/iris150/usr3/catalyst/catusr_2.dbf should be replaced by
the name of the file you will be using for tablespace, and 75M should
be replaced by your expected tablespace size requirement.
If you prefer to use the Oracle Administration Tools, assign the
Catalyst user to CATALYST default tablespace.
The SQL commands given in Steps 4 and 5 are available in the file
You can either follow Steps 4 and 5 below or issue this command in
4. Create the CATALYST_REGISTER table
2 ID number(9) PRIMARY KEY,
3 NAME varchar2(256),
4 USERNAME varchar2(256),
6 ) tablespace CATALYST
5. Create the CATALYST_RESERVE_ID table, making sure that
the reserve id table has one row with the default id of 300, and
make these tables visible to all Catalyst users.
Enter another series of SQL statements:
Catalyst Installation Guide/March 2002
Using Oracle from Catalyst
2 DUMMY number(9) PRIMARY KEY,
3 ID number(9)
4 ) tablespace CATALYST
5 ;
Then use the following SQL statements:
> create public synonym CATALYST_RESERVE_ID for
> create public synonym CATALYST_REGISTER for
> insert into CATALYST_RESERVE_ID (DUMMY, ID) VALUES (1,300);
> grant select, update on CATALYST_RESERVE_ID to PUBLIC ;
> grant all on CATALYST_REGISTER to PUBLIC ;
Setting up users
Each Catalyst user who wants to use Oracle to store relational
information must have an account created inside Oracle. These
users should be given the privileges:
unlimited table space
These privileges can be tuned somewhat if you find that they are
not satisfactory. Contact Oracle customer support for details. See
“User authentication” on page 18 for a discussion of user/password vs. OS authenticated user accounts.
Modifying Catalyst to use Oracle
As distributed, Catalyst 4.7 does not try to communicate with
Oracle. The following instructions enable Catalyst users to use
Oracle to store relational data associated with their Stockroom
Catalyst Installation Guide/March 2002
Using relational data with purchased databases
Oracle requires special
environment variables.
1. Edit the file $CATALYST_WCONF/catEnvVar.csh, following
the instructions at line 100
When you first start Catalyst without any data, a configuration file is
copied from a common area in the catalyst tree to the users' data directory. These files are called $CATALYST_WCONF/Stockroom.bdb
and catDB.bdb.
2. Change the $CATALYST_WCONF/Stockroom.bdb and
catDB.bdb files to contain the correct name of the Oracle
For example, if the Oracle server is named ora3, a proper configuration file template might read:
! ------------------------------------------------! $Header: StockroomDB.bdb.template,v 1.5 1996
01/ 29 21:27:40 shneor Exp $
! Copyright 1992-2000 BioCAD Corporation
! Biocad database configuration file ...
database = StockroomDB
catDB version = 1.2 (2423)
id = -1
1D Data:
host = $host-1d-data
server = ora3
! ------------------------------------------------
In the file above, host refers to the Oracle host machine, and
server refers to the Oracle server.
Using relational data with purchased databases
The commercial databases available from Accelrys also include
relational data associated with each compound in these databases.
These data can be imported into Oracle and manipulated using the
Catalyst interface. This section provides instructions for installing
relational data from these databases into Oracle for use by
Catalyst Installation Guide/March 2002
Using Oracle from Catalyst
1. Go to the database directory
cd dbdir
This directory is the same directory referred to as dbdir in the database installation instructions.
The relational data for a database is located in the subdirectory
470/irix6m3/data/catalyst/dbname or in the directory specified
in the README file on the database installation CD-ROM.
2. Change directories
cd 470/irix6m3/data/catalyst/Sample
3. Use the Oracle import utility “imp” to import the data into
your Oracle server
Before running this program, make sure that you are logged in as user
“catalyst” and that the environment variables $ORACLE_HOME
and $TNS_ADMIN are set to the appropriate values:
imp \/
Oracle prints some version-identification lines to your screen.
4. Now enter the values indicated in bold or accept the defaults,
as indicated, for the following screen prompts:
Import file: expdat.dmp >
Enter insert buffer size (minimum is 4096) 30720>
Accept the Default setting
Now you will see the output line:
Export file created by EXPORT:V08.01.07
Catalyst Installation Guide/March 2002
Using relational data with purchased databases
5. Continue entering values at the screen prompts:
List contents of import file only (yes/no): no >
Ignore create error due to object existence (yes/no):
Import grants (yes/no): yes >
Accept the default
Import table data (yes/no): yes >
Accept the Default
Import entire export file (yes/no): no >
Now you should see the following output:
. importing CATALYST's objects into CATALYST
.. . importing table
.. . importing table
.. . importing table
.. . importing table
.. . importing table
Import terminated successfully without warnings.
6. Add a row to the Catalyst register table in Oracle for this
Start the SQL Plus interpreter:
sqlplus \/
Now enter the SQL statements:
insert into CATALYST_REGISTER (id, name, username, creation)
2 VALUES (202, 'Sample', 'CATALYST', SYSDATE);
7. Now back at the UNIX prompt and in the same directory,
ls -la
Look in the list of files for a configuration file named dbname.bdb
which Catalyst uses to open purchased databases. For example, the
configuration file for the NCI database is NCI.bdb.
8. Edit the dbname.bdb file to remove the “!” in front of the
lines that read as follows:
Catalyst Installation Guide/March 2002
Using Oracle from Catalyst
! 1D Data:
host = none
server = oracle
9. Change the line that reads “server = oracle” to read:
server = oracle-name
where oracle-name is the name of the Oracle server. For example, if
the Oracle server name is ora3, the 1D portion of the configuration file
should be:
1D Data:
host = none
server = ora3
10.Now replace the “none” value above with the name of your
Oracle host
11. Copy the configuration file to the Catalyst tree so that
Catalyst users can find it
cp dbname.bdb $CATALYST_WCONF/databases/dbname.bdb
Troubleshooting Oracle
This section is intended to help you in resolving problems you
may experience with setting up Oracle to work properly with
Catalyst. For more details about Oracle, please consult your Oracle
Versions of Oracle that
work with Catalyst
In version 4.7 of Catalyst the following versions of Oracle have
been tested and are certified to work when properly configured:
♦ Oracle 8.0.5 and 8.1.7 on IRIX
♦ Oracle 8.1.7 on RedHat Linux 6.2
♦ Oracle 8.1.6 on Windows NT
Catalyst Installation Guide/March 2002
Troubleshooting Oracle
Networking tip
The environment variable $TNS_ADMIN should point to the
directory where the tnsname.ora file resides.
Common errors
1. If you get this error message in the Catalyst journal file:
SQL Error: ORA-01562: failed to extend rollback segment (id = 1)
ORA-00604: error occurred at recursive SQL level 1
ORA-01581: attempt to use rollback segment (1) new extent (2) which is being allocated
It means that your rollback segment is full. In this situation you
must either drop and recreate rollback segments or add more
files to the RBS tablespace to create more space.
2. You may get an error while installing the commercial database
using Oracle’s imp utility:
IMP-00017: following statement failed with ORACLE error 1658:
IMP-00003: ORACLE error 1658 encountered
ORA-01658: unable to create INITIAL extent for segment in tablespace CATALYST
. . importing table
14 rows imported
IMP-00017: following statement failed with ORACLE error 1658:
This error results from running out of Catalyst Tablespace in
Oracle. To correct this situation, simply add more data files to the
CATALYST tablespace to create more space.
3. If you get the following error message:
DriverLoader: Failed to load cannot load shared object file: No such file or directory
Failed to load
Error: No suitable driver for URL catocidirect:
Cannot access the database /@ora3.Assertion failure: Could not open database!
This means that Catalyst was unable to locate the Oracle shared
libraries. These shared objects need to be in one of the directories
specified by the LD_LIBRARY_PATH environment variable.
Catalyst will try to add the correct directory based on your
ORACLE_HOME settings (see $CATALYST_WCONF/catEnvVar.csh). If your Oracle shared object libraries are not in a standard
location you will need to add them to your LD_LIBRARY_PATH
with the command:
Catalyst Installation Guide/March 2002
Using Oracle from Catalyst
setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:<full path
of directory containing>
See Step 4 below.
4. Make sure that the part of the LD_LIBRARY_PATH is of the
correct type.
These shared objects must match the platform that you are running catalyst on. A common error is to set ORACLE_HOME to a
single location for both IRIX and Linux installations. This will fail
and may crash while connecting to Oracle, because Catalyst will
try to load the wrong shared objects. You can check this by the following:
[prompt$] echo $LD_LIBRARY_PATH
[prompt$] file /net/catlnx/home/catalyst/CAT470/Linux_2_Intel_32/biosymso/
ELF 32-bit LSB shared object, Intel 80386, version 1, not stripped
[prompt$] file /net/iris58/usr2/oracle/u01/app/oracle/product/8.1.7/lib32/
ELF 32-bit MSB mips-3 shared object, MIPS R3000_BE, version 1, stripped
Note that file reports that these two files are for different platforms. Modify LD_LIBRARY_PATH so that the correct Oracle
libraries are found
Installation tips
If you have set up users to access Oracle with OS authentication,
please make sure that your listener.ora file has the line:
When typing in long SQL statements into SQL Plus, it is convenient to first type the statement(s) into a file using your favorite
text editor. Then use the command:
in SQL*PLUS to execute all the statements in the file.
Definition of ORACLE_SID
1. ORACLE_SID is case sensitive and should ideally be 4 or fewer
characters long (more allowed on some OS).
Catalyst Installation Guide/March 2002
Troubleshooting Oracle
The Oracle 7.3.2 Installation Manual says:
“You can prevent compatibility problems across systems by
observing the following conventions:
♦ Use four or fewer alphanumeric characters.
Do not rely on case-sensitivity to distinguish between SIDs.”
2. In the initora3.ora file—the default init[ORACLE_SID].ora
file—there are several configurable parameters. The default for
these parameters is SMALL, and the parameters for MEDIUM
and LARGE are commented out.
Since our databases are primarily large, read-only databases,
you may want to change these default parameter sizes to
3. Also add the following lines to the initora3.ora file if you are
using OS authentication:
remote_os_authent = TRUE
os_authent_prefix = ""
For changes made to the init[ORACLE_SID].ora file to take
effect, you must shut down and restart the Oracle instance.
Oracle 8.0.5 Support
Catalyst 4.7 uses the CATALYST_RELDB_DRIVERS environment
variable to load appropriate Oracle interface support at run time.
If you have an Oracle 8.0.5 installation on IRIX, you should set this
environment variable as follows to enable Oracle communication:
This environment variable should be set in your ~/.cshrc file or
with the $CATALYST_WCONF/catEnvVar.csh script.
Catalyst Installation Guide/March 2002
Using Oracle from Catalyst
Catalyst Installation Guide/March 2002
5 Installing the License File
This chapter guides you through the installation of one or more
license files to enable Accelrys software on one or more workstations at your site.
The license file
Accelrys products require licenses. If you are a maintenance customer, you should be able to use your existing license, unless you
need to update your maintenance to add new products. If so, you
should contact [email protected] for an updated license. If
you are a new customer a license will be sent via email.
The following instructions apply to users who did not install a
license during software installation and want to install it after the
installation is complete.
Starting the license installation menu
You access the license installation menu by starting the installation
cd $BIOSYM/ (directory containing your catalyst470 installa-
Then click the License Management… button.
Catalyst Installation Guide/March 2002
Installing the License File
Figure 1. License Management menu
The License Management menu (Figure 1) provides you with various tools for installing and managing your Accelrys license(s).
Each option is described in more detail below.
Search for licenses on media
For Catalyst 4.7, this option is not relevant, since your license is
already installed or was received by email.
Catalyst Installation Guide/March 2002
The license file
Install emailed license
If you were recently emailed a license for this release then you can
use the Accelrys Install Utility to install it.
First save the license to a file. Select Install Emailed License from
the License Management Menu. The window shown in Figure 2
Figure 2. Installing an emailed license file
To install a license, save the license in a file. Enter the name and
path of this file in the appropriate window entry space and click
Install License. This copies and renames the file to the
$MSI_LIC_PACK_DIR/licenses directory and changes any necessary DAEMON lines. You can verify that the license has been
Catalyst Installation Guide/March 2002
Installing the License File
installed and is valid for your machine by running the
license_verifier tool from the View pulldown on the Accelrys
Installation Utility or from the License Management menu.
You can also name and place the license file manually, although
this is not normally recommended. If you do want to install it manually, enter:
source top_dir/cshrc
install_license path_to_file
install_license path_to_file1 path_to_file2 …
The install_license program filters the license file in case it became
corrupted during email transmission and properly installs it in the
licenses directory of the Accelrys License Pack.
For more information, please see the Accelrys License Guide.
Install previously unselected license
This option works only if you already have licenses extracted during previous installations and saved in the $MSI_LIC_PACK_
DIR/licenses/backup directory with the extension .970.
Follow the instructions in the License Selection window to complete the installation.
View installed licenses (LM_LICENSE_FILE)
This option allows you to view the licenses that will be set up after
sourcing the /usr/msi/cshrc file. Once you exit the Accelrys
Installation Utility you must source the /usr/msi/cshrc file to set
this variable. If it was previously set and you want to reset it, enter
the command:
Catalyst Installation Guide/March 2002
The license file
View license verifier results
This option displays the results from license_verifier in a scrollable window.
Turn OFF/ON licensing automation
This option allows you to deactivate automated licensing. We recommend that only users familiar with Flexlm licensing software
do this. Normally this is not desired, but in some situations it may
provide the flexibility you need. When you select OFF, a variable
called MSI_LIC_AUTOSEARCH is set to 0 in the $MSI_LIC_
PACK_DIR/config/LIC_CONFIG file, which prevents LM_
LICENSE_FILE from automatically being set when you source the
/usr/msi/cshrc file. This can also be set as an environment variable if desired (see the Accelrys License Guide for details).
Frequently asked questions
We have provided online answers to the most commonly asked
questions concerning licensing.
Bring license daemons up (lmup)
If you have a floating or token license (i.e., your license contains
SERVER and DAEMON lines), you also need to start the license
daemons before running the software. If you are currently running
the Accelrys Installation Utility on the server machine, you can use
this option from the License Management menu to start the daemons. The resulting information is printed in a scrolling window
on the screen. Read all displayed messages carefully. They contain
important information about your floating license and indicate
whether any problems were encountered.
Verify that the license file is working by selecting the View license
verifier results option described on page 35.
Catalyst Installation Guide/March 2002
Installing the License File
You can also perform this action manually by logging onto the
server machine and typing this command (after sourcing
Verify that the license file is working by running license_verifier:
View lmstat -a output
This displays the output from the lmstat command which gives
you status information concerning the licensing daemons. If you
are using a node-locked license you do not need to use the lmup
or lmstat command, since these apply only to floating and token
License behavior after installation
♦ When you run software that has a valid, error-free license file,
a checkout message appears and the software runs normally for
the duration of the session.
♦ If licensing problems are encountered when attempting to run
the software, a message similar to the following appears:
License checkout failed.
: no such feature exists
Searching for valid license.
No working license found: no such feature exists
Error during License Initialization: License_Holder
Problem Code -5: -- Not In License File
An error checking out the License_Holder feature is typically a
problem with setting up the license file environment. These
problems can often be easily isolated and corrected using the
diagnostic tools that we provide, especially the license_
Catalyst Installation Guide/March 2002
License behavior after installation
In addition to the license_verifier, the lmstat diagnostic tool is
very useful in checking whether license daemons are running
when using a floating license. Messages that include the word
“server” in their description are often due to the license daemons not being up.
Please refer Accelrys’s System Guide for more
-----------------------------------Unable to obtain License_Holder Name
This functionality requires a license feature not found
or enabled in your license file. Temporary access is
provided to allow time to explore this software, request
an extended trial with manuals, or to resolve any
problems with license file or installation problems that
block access to this feature. Please contact Accelrys
Scientific Support for assistance.
The license feature name is module; problem code is code
******* Temporary access expires in 30 days *******
Use the License Manager Utility programs (e.g., license_
verifier) described in this License Guide to diagnose common
installation problems.
However, you will be able to use the software for a 30 day grace period
while the licensing problem is addressed. If you have not
addressed this within the 30 day grace period, access to the software is denied until the problem is resolved.
Explore unlicensed software programs on an informal
trial basis
A benefit of our current licensing scheme is that you can explore
Accelrys software for which you are not currently licensed.
♦ When you explore unlicensed software, the following message
Catalyst Installation Guide/March 2002
Installing the License File
This functionality requires a license feature not found
or enabled in your license file. Temporary access is
provided to allow time to explore this software, request
an extended trial with manuals, or to resolve any
problems with license file or installation problems that
block access to this feature. Please contact Accelrys
Scientific Support for assistance.
The license feature name is module; problem code is code
******* Temporary access expires in 30 days *******
We hope you will take advantage of this opportunity. If you are
interested in an in-depth exploration of new software and functionality or manuals for specific software, please contact your local
Customer Support representative to set up a formal trial.
Once the 30 day grace licensing is activated, it cannot be reinstated. If you want to save grace licensing for a later time to
explore other products, you can prevent grace from being
started by setting the environment variable MSI_LIC_NG
before you start your software for the first time. Add the following line in the /usr/msi/cshrc file:
setenv MSI_LIC_NG
When you are ready to explore new products using grace, first
unsetenv this variable. The 30-day grace period starts as soon as
you attempt to check out something for which you are not
Additional information on license management
For complete information on licensing, such as:
♦ Helpful checklists.
♦ Environment variables (including $MSI_LIC_NG, discussed
♦ How to run multiple Accelrys releases using a single license
Please refer to the Accelrys License Guide, which is available in hardcopy and at Accelrys’s website.
Catalyst Installation Guide/March 2002
Accelrys, contacting 4
files listing 13
chemical database server 6
configuration 7
chemical databases 3
ConFirm, installing 12
contacting Accelrys 4
cshrc file, modifying for user setup 9
database 23
configuring 15
extracting 13
license 14
sample configuration file 15
file compatibility 10
HipHop, installing 12
Insight II 10
installation 31
Catalyst 3
databases 13
directory 4
Oracle 28
utility 4
demo 4
installing 4
license management software 38
MSI See Accelrys
NCI database 13
NCI.bdb file 15
Netscape 11
online documentation 11
common errors 27
definition of ORACLE_SID 28
environment variables 23
import utility 24
installation tips 28
server 23, 26
server versions used by Catalyst 17
support for version 8.0.5 on IRIX 29
table space 20
troubleshooting 26
using to access and manage relational data
with Catalyst 17
printing graphics 10
Catalyst Installation Guide/March 2002
register table 21
relational data 14
reserve id table 21
setup script 7
starting Catalyst 10
system requirements 1
topdir 3
troubleshooting Oracle 26
user privileges 22
yellow pages database 9
Catalyst Installation Guide/March 2002
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