2
Cerius
Installation and Administration
Guide
Release 4.5
July 2000
9685 Scranton Road
San Diego, CA 92121-3752
858/458-9990 Fax: 858/458-0136
Copyright*
This document is copyright © 2000, Molecular Simulations Inc. ("MSI"), a subsidiary of Pharmacopeia, Inc. All rights reserved.
This documentation is the copyrighted work of MSI. This documentation and the software
described therein are furnished under a License/Purchase Agreement between your organization and MSI and may be used only in accordance with the terms of such agreement. Any
other unauthorized use, reproduction or distribution, including posting the documentation
on an external computer network, is expressly prohibited.
Restrictions on Government Use
This is a "commercial" product. Use, release, duplication, or disclosure by the United States
Government agencies is subject to restrictions set forth in DFARS 252.227-7013 or FAR 52.22719, as applicable, and any successor rules and regulations.
Trademark Acknowledgments
Catalyst, Cerius2, CHARMm, Discover, Insight II, QUANTA, AtlasBase, Biosym, GeneAtlas,
Materials Studio, MSI logo, SeqFold, Target Explorer, WebLab, ViewerPro, and ViewerLite
are registered trademarks or trademarks of Molecular Simulations Inc. All other trademarks
are the property of their respective holders.
Publication Acknowledgment and References
To print photographs or files of computational results (figures and/or data) obtained using
Molecular Simulations software, acknowledge the source in an appropriate format. For
example:
"Computational results obtained using software programs from Molecular Simulations
Inc. Dynamics calculations performed with the Discover program using the CFF91 forcefield, ab initio calculations performed with the DMol program, and graphical displays
generated with the Cerius2 molecular modeling system."
To reference a Molecular Simulations Inc. publication in another publication, Molecular Simulations Inc. is the author and the publisher. For example:
Molecular Simulations Inc., Cerius2 Modeling Environment, Release 4.5, San Diego: Molecular Simulations Inc., 2000.
Request for Permission to Reprint
MSI may grant permission to republish or reprint its copyrighted materials. Requests should
be submitted to MSI Scientific Support, either through electronic mail to support@msi.com,
or in writing to:
*U.S.
version of Copyright Page
MSI Scientific Support
9685 Scranton Road
San Diego, CA 92121-3752
Please include an acknowledgement "Reprinted with permission from Molecular Simulations Inc., Document name, Month Year, Molecular Simulations Inc., San Diego." For example:
Reprinted with permission from Molecular Simulations Inc., Insight II User Guide,
March 2000, Molecular Simulations Inc.: San Diego.
Contents
How to Use This Book
vii
Who should use this book . . . . . . . . . . . . . . . . . . . . . . . . . . vii
How to find information . . . . . . . . . . . . . . . . . . . . . . . . . . . vii
Typographical conventions . . . . . . . . . . . . . . . . . . . . . . . . .viii
1. Before You Install
1
Selecting an installation procedure . . . . . . . . . . . . . . . . . . . .1
For either installation procedure . . . . . . . . . . . . . . . . . . . . . .1
Hardware and operating system requirements . . . . . . .2
Platform support . . . . . . . . . . . . . . . . . . . . . . . . . . .2
Root password requirement . . . . . . . . . . . . . . . . . . . . . .3
Where to install . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .3
2. Standard Installation
5
Sequence of events . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5
Standard installation step by step . . . . . . . . . . . . . . . . . . . . .5
Load the distribution medium . . . . . . . . . . . . . . . . . . . .5
Extract the software . . . . . . . . . . . . . . . . . . . . . . . . . . . .6
Run the install script . . . . . . . . . . . . . . . . . . . . . . . . . . . .7
Enabling the license manager. . . . . . . . . . . . . . . . . .9
Installing a license after software installation . . . . . . . . . . .10
Verify the license installation. . . . . . . . . . . . . . . . . . . . . . . .10
Using the MSI License Pack for license administration. . . .11
Connecting past MSI releases . . . . . . . . . . . . . . . . . . . . . . .11
3. Manual Installation
13
Sequence of events . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .13
Manual installation step by step . . . . . . . . . . . . . . . . . . . . .13
Create an msi user account . . . . . . . . . . . . . . . . . . . . . .14
Create an installation directory. . . . . . . . . . . . . . . . . . .15
Log in as msi . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .15
Load the distribution medium . . . . . . . . . . . . . . . . . . .15
Configure site-specific files . . . . . . . . . . . . . . . . . . . . . .15
Installation and Administration Guide/July 2000 v
.
Modify the hosts.equiv file. . . . . . . . . . . . . . . . . . . . . . 17
Install a license file . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
Enable the license manager (floating/token licenses only)
19
Verify the license installation . . . . . . . . . . . . . . . . . . . . . . . 22
4. After Installation
23
Testing the installation . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
Setting up workstation accounts. . . . . . . . . . . . . . . . . . . . . 23
Special case setup using SGI LG1 graphics . . . . . . . . . 24
SGI workstation setup . . . . . . . . . . . . . . . . . . . . . . . . . 24
Setting up remote display systems . . . . . . . . . . . . . . . . . . . 25
APPENDIXES
A. The applcomm.db File Format
31
File contents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
Records describing machines . . . . . . . . . . . . . . . . . . . . . . . 32
Records describing supported network protocols . . . . . . . 33
Records describing supported applications . . . . . . . . . . . . 33
Example applcomm.db file entries . . . . . . . . . . . . . . . . . . . 34
B. MSI Sales and Support
37
How to Contact Us . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
North America. . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
Europe . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
Asia/Pacific . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
Japan . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
Internet . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
vi
Installation and Administration Guide/July 2000
How to Use This Book
Who should use this book
This book is for licensees of Release 4.5 of Cerius2™.
To install Cerius2 you should be familiar with basic UNIX
commands and shell environment variables. The examples in this
book presume that the C-shell is in use.
If you are installing into a networked environment, the network
should be installed, tested, and running before you install this
software. Complex installations with multiple license servers may
require additional experience with TCP/IP utilities and NFS™.
How to find information
If you want to know about...
Read...
Installation requirements and criteria for Chapter 1, Before You Install
selecting standard or manual
installation procedures
The installation procedure for the
majority of customers
Chapter 2, Standard Installation
Installation and Administration Guide/July 2000
vii
. How to Use This Book
If you want to know about...
Read...
The installation procedure for
experienced system administrators
Chapter 3, Manual Installation
Setup and configuration of user
accounts
Chapter 4, After Installation
Additional topics
Appendix A, "Creating UNIX User Accounts"
Appendix B, "License Administration Issues"
Appendix A, "The applcomm.db File Format"
Typographical conventions
Unless otherwise noted in the text, this book uses the typographical
conventions described below:
◆ Words in italic represent variables. For example:
Change to the ~msi/product directory.
In this example, the name of the directory in which you
installed the software product replaces the value
product.
◆ Examples of installation scripts and the contents of files
are represented in a Typewriter font. For example, the
following illustrates a dialog you might have with the
install script:
Do you wish to continue with the installation? y
◆ Terms introduced for the first time and words you type
are presented in boldface type. For example:
A group is a collection of user-related rows and columns.
viii
Installation and Administration Guide/July 2000
1
Before You Install
Selecting an installation procedure
This book describes the complete installation procedure twice, from
two points of view. You can choose to follow either the standard
installation, or the manual installation procedures.
Standard installation
The majority of readers should follow the standard installation
procedure described in Chapter 2. The standard installation makes
use of installation scripts to automate the editing of setup files.
Manual installation
Follow the manual installation procedure described in Chapter 3
only if you have extensive experience with UNIX system
administration tasks. The manual installation is appropriate for
readers who are:
◆ Accomplished system administrators who prefer to
directly edit setup files without the assistance of
installation scripts
◆ Wary of automated installation scripts, and want to
learn more about the scripts before running them
For either installation procedure
Read the rest of this chapter regardless of the installation procedure
you select.
Installation and Administration Guide/July 2000 1
1. Before You Install
Hardware and operating system requirements
Platform support
Cerius2 4.5 is supported under the SGI IRIX 6.5.4 release or higher.
Acceptance testing has been performed on all IRIX maintenance
releases through 6.5.7. If you need to upgrade your system please
visit the following site at SGI:
http://support.sgi.com/colls/patches/tools/relstream/
index.html
MSI does not support versions of IRIX earlier than 6.5.4. Only
limited testing has been done on IRIX 6.2 systems. If you have
upgraded your IRIX 6.2 system with the SGI patches supplied by
MSI and are successfully running Cerius2 4.0 then there is a
possibility the Cerius2 4.5 will run under that configuration.
However, MSI is not supporting this type of installation.
RAM and swap space
requirements
MSI recommends that each workstation hosting Cerius2 should be
configured with a minimum of 128 MB of memory plus 120 MB of
swap space.
To run certain memory-intensive modules such as calculating
energy minimizations on very large molecules, you may need to
add more swap space or more RAM or both.
Disk space
requirements
The files installed from the Cerius2 distribution medium require the
following amounts of disk space:
◆ 740 MB for Silicon Graphics workstations
◆ 25 MB for the Software Developers Kit
◆ 30 MB for the MSI License Pack (if not already installed)
Additional SGI
system requirements
The default 14 point lucida font for the Cerius2 user interface is not
installed on SGI systems by default. To get this font, you should
install:
x_eoe.sw.Xoptfonts
2
Installation and Administration Guide/July 2000
For either installation procedure
If this component is not installed on your system, Cerius2 uses an
alternate font.
Root password requirement
In order to install this software, you must have the root password
for the workstations that will host Cerius2 and for your license
servers. Your alternative is to have someone who knows the root
passwords assist you with the installation. The root password is
required to accomplish the following tasks:
◆ Creating the msi login account
◆ Installing the license management files into the /etc
directory (lmup -b does this automatically)
◆ Modifying the system start-up files to include license
manager information (lmup -b does this automatically)
Note
Although you should know the root password for the above
reasons, we recommend that you do NOT run installation scripts
as root!
Where to install
The software is loaded into the home directory of a UNIX login
account named msi.
Note
If you already have a login account named msi, which was not
created for the purposes of storing Molecular Simulations
product releases, then you can use another name. If you do so,
whenever this book refers to ~msi (the home directory of the msi
account), you need to substitute the home directory of the
account you created to store Molecular Simulations products.
Installation and Administration Guide/July 2000 3
1. Before You Install
4
Installation and Administration Guide/July 2000
2
Standard Installation
For a discussion of the choice between the standard and manual
installation procedures, see “Before You Install” on page 1.
Sequence of events
The standard installation of this software product follows this
sequence of events:
1. Create a directory to contain the product
2. Extract the product’s files from the release medium to
the installation directory
3. Run the install script
After installing this software, perform the post-installation
instructions described in Chapter 4, “After Installation” on page 23.
Standard installation step by step
The following sections describe each step in the standard
installation procedure.
Load the distribution medium
Insert your Cerius2 CD-ROM disc into the CD-ROM drive.
Installation and Administration Guide/July 2000 5
2. Standard Installation
Extract the software
Follow these steps to extract the product files from the mounted
CD-ROM disk:
1. Change to the directory on which you mounted the CDROM disk. For example:
>
cd /CDROM
2. Get a directory listing and look for the name
INSTALL.EXE.
>
ls
On most systems, the filenames in the listing are shown
in uppercase letters, but on some systems the filenames
are converted to lowercase letters.
3. Run the INSTALL.EXE script, using the uppercase or
lowercase version of the name as determined in the
previous step.
>
./INSTALL.EXE
NOTE: We recommend you do not run INSTALL.EXE as
root.
4. The INSTALL.EXE script displays a list of the Molecular
Simulations software products on the CD-ROM disk,
then checks for the existence of an msi user account. If
found, the script prompts for permission to use the msi
user's home directory. Respond y to use the
recommended directory structure. In this case, the
INSTALL.EXE script creates a product subdirectory in
the home directory of the msi account. Respond n to
specify a different directory.
5. The product list re-displays. Enter the Product_ID
displayed in the first column of the list that corresponds
to the product you wish to install. Enter one Product_ID
only, exactly as shown in the list.
6. If you told the INSTALL.EXE script in step 4 not to use
the msi home directory, the script prompts for the path
6
Installation and Administration Guide/July 2000
Standard installation step by step
name of an alternative directory in which to extract the
product's files. Enter the full pathname of the alternative
installation directory. If you plan to use the software
over the network, be sure to enter a fully qualified
network path. The script creates a product subdirectory
in the directory you specify.
7. Your ~msi directory is searched for an installed License
Pack1 directory (~msi/License_Pack). If none is found
then you are prompted to either install the License_
Pack, or to enter the path to a previously installed
License_Pack. By default the License Pack is installed in
the ~msi directory, although you can specify an
alternative directory. If you already have a License Pack
installed, that version is verified to make sure it is the
same or newer than the version shipped with this
release, and is updated if necessary.
8. When the installation directory is determined, and the
License Pack location is defined or created and installed,
the INSTALL.EXE script extracts the files for the
product you specified. This may take as much as several
hours, depending on product size, machine speed, and
network traffic.
9. When all files are extracted, the INSTALL.EXE script redisplays the product list. If you have another Molecular
Simulations product to install, enter its Product_ID as
shown in the first column of the product list. If not, type
exit.
This completes the file extraction stage of the installation.
Run the install script
What you will need
◆ A valid license file. If a new license was emailed to you,
1The
MSI License Pack is required for this release. A License Pack is a centralized location for all license
management tools and the license file to support multiple MSI releases.
Installation and Administration Guide/July 2000 7
2. Standard Installation
be sure to have that license saved to a file to install
during installation.If you are a maintenance customer
and you maintenance is current, you may use your
existing license file. You may also continue with the
installation if you have a non-expired demo password.
Running the script
Run install as follows:
>
cd ~msi/cerius2_2.0/install
>
./install
The install script prompts for confirmation to continue.
Specifying the startup script path name
In the next step, the install script displays the full path name of the
directory in which you installed the software. This path name will
be written into the program’s start-up script, so be sure it is correct.
If your network uses automounted NFS drives, you may want to
delete the initial /tmp_mnt portion of the path name, or if the path
is not the full network path then you will want to modify it to be
sure all users can access the files.
Setting the License
Pack path
The install script displays the default path for the License Pack to
be used with this MSI release. If it is incorrect, follow the prompts
to enter the correct path to the License Pack.
File Configuration
Next, a list of files is displayed. These files are automatically
configured with the location of this installation and the License
Pack, as necessary. To modify this configuration later you may
execute the config_files script at any time.
Setting the OracleRead path
Next, the install script asks if you want to set the path to the OracleRead interface. You can use a default path determined by the
$ORACLE_HOME environment variable or select another one.
Using Daylight
software
In the next step, you are asked if you have a Daylight installation
which you plan to use. If this is the case, you can use a default path
determined by the $DY_ROOT environment variable or select
another one.
Next, locate a Daylight license. This is usually defined by the $DY_
LICENSEDATA environment variable. However, you can change
this by entering another location.
8
Installation and Administration Guide/July 2000
Standard installation step by step
Selecting a default
menu deck
The install script next prompts you to select a default menu deck
configuration. Cerius2 displays a deck of menu cards, with each
card representing an application module. The set of application
modules shown in the menu deck can be organized from a
materials science or life science point of view. This option only
selects the initial default menu deck configuration. You can easily
customize your own menu deck at any time to add or remove
menu cards, as discussed in “Customizing Cerius2” in Chapter 8,
“Visualizer Utilities,” of the Cerius2 Modeling Environment
documentation.
In response to this prompt, type 1, 2, or 3, as follows:
◆ Type 1 to specify a default menu deck with a materials
science point of view
◆ Type 2 to specify a default menu deck showing the
application modules appropriate for the Drug
Discovery Workbench option
◆ Type 3 to specify a default menu deck showing all
standard Cerius2 application modules
Installing a license file
Next, the install script looks for a license named msilicense.dat in
the License Pack. Then:
◆ If the msilicense.dat file is found in the License Pack,
the script prompts for whether you wish to continue
with license installation.
◆ If the msilicense.dat file is not found in the License
Pack, then follow the online instructions. You will be
able to install alicense, or continue withour installation.
Enabling the license manager
If you decide to install a new license, or to use a previously
installed license, you are prompted to start the license manager for
the currently installed license, if the license type requires it (that is,
for a floating or token license). If you know the daemon is already
running for this license, then you can answer no to the prompts.
However, if you would like to start or restart the license daemons,
then answer the questions accordingly.
Installation and Administration Guide/July 2000 9
2. Standard Installation
Once a license is installed, you are prompted to enable the license
manager on the machine on which you are running the install
program. If you answer yes to these prompts and have root
permissions, the license daemons are set up to automatically restart
at boot time as well as brought up to use with this new installation.
Installing a license after software installation
If you choose not to install a license during the installation then you
should execute the following commands, from the install directory,
to do so:
>
source ~msi/License_Pack/msi_lic_cshrc
>
get_license
>
reset_lic_env
>
lmup (floating/token licenses only)
>
license_verifier
Verify the license installation
Once the Cerius2 files are installed, and the license manager
daemon is running, you can verify the license installation by
performing the following commands:
>
source ~msi/License_Pack/msi_lic_cshrc
>
license_verifier
>
lmstat -a
(if using a token or floating license)
To test the installation and set up and configure user accounts, turn
now to Chapter 4, “After Installation” on page 23.
10
Installation and Administration Guide/July 2000
Using the MSI License Pack for license administration
Using the MSI License Pack for license
administration
To have automatic access to the License Pack tools (e.g., license_
verifier, lmup -b, lmstat, etc.), enter:
>
source ~msi/License_Pack/msi_lic_cshrc
We recommend that your license administrator either place the
above line in their .cshrc file, or create an alias:
>
alias set_msi_lic ‘source \
~msi/License_Pack/msi_lic_cshrc’
to set the license environment automatically or as needed.
Following are instructions describing how to make sure all your
MSI releases use the same License Pack. Please refer to the separate
MSI License Guide for details.
Connecting past MSI releases
Using the MSI License Pack you can now manage all of your MSI
releases using a single set of license management tools and a single
license file. Releases shipped with the MSI License Pack are already
set up to use the licenses within the License Pack. OlderMSI
releases need to be modified to use this same license file. For
detailed instructions on how to connect past releases with the MSI
License Pack see the separate MSI License Guide.
These releases automatically install and use the MSI License Pack:
Catalyst 4.5
Cerius2 3.9, 4.0, 4.2MS, 4.5LS
CNX 2000
Insight II 98.0, 2000
QUANTA 98,
SDK 4.0
XPLOR 98.1
Installation and Administration Guide/July 2000 11
2. Standard Installation
12
Installation and Administration Guide/July 2000
3
Manual Installation
This chapter is a description of the manual installation procedure
for experienced UNIX system administrators who prefer to edit
start-up files directly rather than rely on installation scripts.
Note
The majority of readers should follow the standard installation
procedure, skipping this chapter entirely. For a discussion of the
choice between installation procedures, see “Before You Install”
on page 1.
Sequence of events
The manual installation of Cerius2 follows this sequence of events:
1. Create the msi user account
2. Create the directory ~msi/product_name
3. Log in as the user msi
4. Load the release medium into the installation directory
5. Configure certain site-specific files
6. Modify the hosts.equiv file.
7. Install a license file, if necessary
8. Enable the license manager
Manual installation step by step
The following sections describe each step in the manual installation
procedure.
Installation and Administration Guide/July 2000 13
3. Manual Installation
Create an msi user account
What to do
1. Create a UNIX user group named msi:
msi:*:800:
2. Create a UNIX user account named msi:
msi::800:800:MSI Products Owner:/home/msi:/bin/csh
3. Give the msi account a password.
Discussion
In order to maintain a reasonable level of organization on your
system, we recommend that you install all Molecular Simulations
products into the home directory of a user named msi. This account
will only be used to hold and install products, and not for day-today use of a product.
If you prefer to use a name other than msi for this holding account,
you will not have any problems. Simply substitute your account
name for msi when reading this guide.
As is true with all user accounts, it is best to put the msi home
directory on a file system that will not be overwritten during
operating system upgrades (that is, not directly on /usr).
Place the msi home directory on a file system with sufficient space
to hold all your Molecular Simulations products. Of course, if you
run out of room on the file system that contains the msi home
directory, you can always load a new product on another file
system, and use a symbolic link to make it appear as though that
product is loaded in ~msi.
The msi user must exist on all machines from which you plan to
run the program. If you’re not using Network Information Services
(formerly known as Yellow Pages), you must create an msi
account on each machine that will host an msi product.
The msi account must have a password to use any of the installation
scripts.
14
Installation and Administration Guide/July 2000
Manual installation step by step
Create an installation directory
What to do
4. The script which unloads the software creates the
subdirectory named cerius2_2.0 in the home directory of
the msi user. If you wish to install the software
elsewhere, create that directory now.
Discussion
Using a separate directory for each product release enables you to
install other Molecular Simulations products, including future
releases of this product, without disturbing the present release.
Log in as msi
What to do
5. Log in (or su - msi) as msi.
Discussion
This ensures that the files loaded from the media are owned by msi.
Load the distribution medium
What to do
6. Mount the CD-ROM disc on a directory named
/CDROM, and change to this directory.
7. Run INSTALL.EXE from the CD-ROM disc.
Configure site-specific files
What to do
8. Identify the site-specific files that must be edited. These
files are listed in the product.config file. Make a backup
copy of each, then make the required edits.
Discussion
You must modify all site-specific files after the Cerius2 media is
loaded. The following is an example of the modifications needed
for this script:
~msi/cerius2_2.0/bin/cerius2
Search for the string %MSIInstallRoot% and substitute the fully
qualified absolute path name of the installation directory. For
example, if the home directory of the msi account is /home/msi,
Installation and Administration Guide/July 2000 15
3. Manual Installation
the lines of the script cerius2 that specify C2DIR should be changed
to read as follows:
[ -z "$C2DIR" ] && C2DIR=/home/msi/cerius2_2.0
c2dir=/home/msi/cerius2_2.0
Similarly, search for the string %MSILicense_Pack_Dir% and
replace it with the fully qualified path name of the installation
directory.
Further, if you want to set the path to the Oracle-Read interface,
search for the line:
C2_ORACLE_HOME=%ORACLE_HOME%
and replace %ORACLE_HOME% with an appropriate path name.
Your first choice might be a default path determined by the
$ORACLE_HOME environment variable.
In the next step, you set a path to a Daylight installation if you have
one and plan to use it. Search for the line:
C2_DY_ROOT=%DY_ROOT%
and replace %DY_ROOT% with an appropriate path name. You can
use a default path determined by the $DY_ROOT environment
variable or select another one.
In order to locate a Daylight license, search for the line:
C2_DY_LICENSEDATA=%DY_LICENSEDATA%
and replace %DY_LICENSEDATA% with a path pointed to by the
$DY_LICENSEDATA environment variable, or enter another
location.
Next, search for the string %MSIInstallDex%. Substitute either
materials, ddw, or user to determine the default menu deck
configuration for Cerius2:
C2_DEX=materials Specifies a materials science menu deck
C2_DEX=ddw
Specifies a Drug Discovery Workbench
menu deck
C2_DEX=user
Specifies the default Cerius2 menu deck
16
Installation and Administration Guide/July 2000
Manual installation step by step
For further information on menu deck configuration, see “Run the
install script” on page 7.
Molecular Simulations provides a script to automate updating this
file. Change to the ~msi/cerius2_2.0/install directory and run the
script config_files:
>
cd ~msi/cerius2_2.0/install
>
./config_files
Other site-specific files are supposed to be edited similarly. For the
list of files to configure, see the contents of the file product.config in
the install directory. If you have additional questions, contact MSI
Scientific Support.
Modify the hosts.equiv file
What to do
Discussion
9.
Edit your /etc/hosts.equiv or NIS-controlled
hosts.equiv file, as appropriate for your network. Make
sure that both localhost and the hostname of the Cerius2
host are recognized as trusted hosts.
In order to start remote applications, the program needs to be able
to execute a remote shell (rsh) on the machine where the remote
application will run. This is done even if the application is going to
run only on the local machine.
In order for this to work, the /etc/hosts.equiv file must contain two
entries: one for localhost, and one for the name of the remote
system.
If you are running NIS, and you either:
◆ store your hosts.equiv file in an NIS-controlled master
file, or
◆ use netgroups in your hosts.equiv file
then you must modify either the netgroup file, or the hosts.equiv
file so that both localhost and the name of the system are
Installation and Administration Guide/July 2000 17
3. Manual Installation
recognized as trusted hosts. This will allow remote shells to be
initiated without a password.
If you are not managing your hosts.equiv file through NIS, then
you need to modify the product host’s /etc/hosts.equiv file. You
can do this manually, or you can use the update_hosts_equiv script
in the install directory, as follows:
>
cd ~msi/cerius2_2.0/install
>
./update_hosts_equiv -u
Install a license file
Note that if you are a maintenance customer and have an up-to-date
license already installed in the License Pack you are using for this
software, you may skip this section.
What to do
Discussion
10. Set up the license administration environment and
install a license. If you have received a license file from
Molecular Simulations by e-mail, edit and save the email in a file and run get_license to install it.
>
source ~msi/License_Pack/msi_lic_cshrc
>
cd ~msi/cerius2_2.0/install
>
get_license
A license file is the input to the license management software used
by Molecular Simulations products. The format is too complex to
edit by hand. An error in this file may cause the product to fail its
license management check at run time.
For this reason it is highly recommended that you use an e-mailed
copy of your license file. If you must enter a license by hand (e.g.,
you do not have e-mail and were faxed a license) extreme care must
be taken to enter the data exactly.
If using an e-mailed
license file
18
If your license file is delivered by Internet e-mail, save the e-mail
message as a file. Be sure to remove all e-mail header and trailer
Installation and Administration Guide/July 2000
Manual installation step by step
information from the file. The first line of your msilicense.dat file
should begin:
SERVER ... or INCREMENT ...
The last line of your file should begin:
#L_INFO...
To install the license file use the install_license command:
>
install_license <license file>
You may list multiple licenses separated by spaces, in which case
the files are automatically merged (if necessary), filtered to attempt
to fix any corruption which may have occurred during email
transmission, and installed as msilicense.dat in the License Pack
licenses directory.
The license_verifier program tells you if there are any lines with
problems. You are instructed to run this when you test the
installation.
For more complete details on license installation refer to the MSI
License Guide.
Enable the license manager (floating/token licenses
only)
What to do
11. Create links for the license management daemons (msid
and lmgrd) and the license file (msilicense.dat) from the
directory to the /etc directory of the license server.
12. Edit the license server’s start-up files to launch the
license daemons at system boot time.
13. Remove old license daemons and startup files from the
/etc directory.
14. Either reboot the license server or start the license
management daemons manually.
Installation and Administration Guide/July 2000 19
3. Manual Installation
Discussion
Molecular Simulations provides the script lmup -b to automate
these steps. This script creates the necessary links to the /etc
directory, edits the startup files, then starts the license management
daemons. Root access is required to run this script with the -b
option; you are prompted for the root password at the appropriate
time.
To use the script, type these commands while logged into the host
that will act as license server:
>
source ~msi/License_Pack/msi_lic_cshrc
>
lmup -b
If you used the lmup -b command, your installation is now
complete. For final instructions, turn to “Verify the license
installation” on page 22.
Install/enable
without the script
Use the following instructions if you prefer to perform these steps
without running the supplied script.
Installing and enabling the license manager involves linking certain
files from the License_Pack directory to the /etc directory. If you
prefer to use a directory other than /etc, please refer to the separate
MSI License Guide.
Which license server?
The following steps should be performed while logged in to your
license server.
If your license type is node-locked (for a single workstation), your
Cerius2 host does not require license daemon support. Make sure
your license is in the ~msi/License_Pack/licenses or the $MSI_
LIC_PACK_DIR/licenses directory and named msilicense.dat. You
can then skip to the next section, “Verify the license installation” on
page 22.
If your license type is float or token, your Cerius2 host and your
license server may be different computers. If so, be sure to copy the
license files and edit the start-up scripts while logged in to the host
on the SERVER line of your license. Make sure the path on the
DAEMON line is ~msi/License_Pack/<platform>/exe/msid
20
Installation and Administration Guide/July 2000
Manual installation step by step
Note
Link license files
Edit startup files
While this release if for SGI machines only, the License Pack can
be installed on other platforms.
For all supported host architectures using float or token licenses,
the following files must be linked to the /etc directory of your
license server:
>
ln -sf ~msi/License_Pack/<platform>/exe/lmgrd \
/etc/lmgrd
>
ln -sf ~msi/License_Pack/licenses/msilicense.dat \
/etc/msilicense.dat
>
ln -sf ~msi/License_Pack/logs/msilicense_<port>.log \
/etc/msilicense_<port>.log
The next steps vary for each host architecture:
◆ For Silicon Graphics workstations, use these commands:
>
sed -e "s@%LOCKMSI%@lockmsi@g; \
s@%LICENSE%@msilicense.dat@g; \
s@%LOGFILE%@msilicense_<port>.log@g; \
s@%NON_ROOT_USER%@<msi or other user name>@g"
~msi/License_Pack/bin/msi_lmboot > /tmp/msi_lmboot
>
cp /tmp/msi_lmboot /etc/init.d/msi_lmboot
>
ln -sf /etc/init.d/msi_lmboot /etc/rc2.d/S99msi_lmboot
>
ln -sf /etc/init.d/msi_lmboot /etc/rc0.d/K10msi_lmboot
Remove old start-up files manually or by running:
>
Important
Start the license
manager daemon
~msi/License_Pack/bin/rm_old_msilm sgi
Due to possible security problems the license manager
daemons must be run as a non-privileged (non-root) user.
Once the above files have been copied and edited, you can start the
license manager daemon with these commands:
>
/etc/lmgrd -c /etc/msilicense.dat \
>>/etc/msilicense_<port>.log
Installation and Administration Guide/July 2000 21
3. Manual Installation
Again, instead of performing all steps manually, we highly
recommend that you run lmup -b as described on page 20.
Verify the license installation
Once the product files are installed, and the license manager
daemon is running, you can verify the license installation by
performing the following commands:
>
source ~msi/License_Pack/msi_lic_cshrc
>
license_verifier
>
lmstat -a
(if using a token or floating license)
To test the installation and set up and configure user accounts, turn
now to Chapter 4, “After Installation” on page 23. Also refer to the
Standard Installation section, “Using the MSI License Pack for
license administration” on page 11, for details on how to make sure
all your MSI releases use the same License Pack. For more complete
license management information refer to the separate MSI License
Guide.
22
Installation and Administration Guide/July 2000
4
After Installation
This chapter shows how to set up and configure user accounts for
Cerius2.
Testing the installation
To start the program, type the following line at the shell prompt:
alias cerius2 ~msi/cerius2_2.0/bin/cerius2
Now you have an alias named cerius2. To run a one-time test of the
installation, type the alias name as the command to run the
program:
cerius2
Setting up workstation accounts
There are two ways to set up the user accounts of each user
authorized to run Cerius2:
◆ Add the Cerius2 bin directory to the search path
◆ Set up aliases for the executable files
To add bin to the search path, add the following line to the bottom
of each Cerius2 user’s .cshrc file:
set path = ( $path ~msi/cerius2_2.0/bin )
Installation and Administration Guide/July 2000 23
4. After Installation
As an alternative, you can create aliases for the executable files in
the bin directory. To do so, edit the .cshrc file of each qualified
Cerius2 user, adding a line like the following:
alias cerius2 ~msi/cerius2_2.0/bin/cerius2
Add an alias for each executable provided with Cerius2 in the bin
directory. For example, the following example sets up an alias for
the pf command:
alias pf ~msi/cerius2_2.0/bin/pf
After the next login, the user can type this command to invoke
Cerius2:
cerius2
Special case setup using SGI LG1 graphics
For each Cerius2 user working on a Silicon Graphics workstation
with an 8-bit graphics board (an LG1 board), add the following line
to their .cshrc file:
setenv NMR8BIT
SGI workstation setup
Window manager
required settings
Cerius2 requires certain window manager settings. Add the
following lines to the .Xdefaults file in each Cerius2 user’s home
directory:
4Dwm*clientAutoPlace: false
4Dwm*positionIsFrame: false
These settings enable Cerius2 to manage its windows correctly
when starting up. If you must manually place the Cerius2
windows, you do not have these settings in your .Xdefaults file.
GL vs. OpenGL
Graphics mode
24
The Cerius2 image uses GL, OpenGL, or X graphics. GL provides
the best performance on older SGI hardware such as XZ or Extreme
and must be used with 8-bit graphics hardware such as 8-bit Indy.
Installation and Administration Guide/July 2000
Setting up remote display systems
OpenGL mode is faster on newer hardware such as Impact, O2, and
Octane. The Cerius2 startup script selects the most appropriate
mode based on the local hardware. You can override this by using
one of the environment variables shown below. If you use a remote
display, especially one that is 8-bit, you may need to override the
automatic local mode selection and force an alternate mode.
setenv FORCEOPENGL 1
setenv FORCEGL 1
setenv FORCEX11 1
Be sure to use only one of the above environment variables or the
results become unpredictable.
Setting up remote display systems
Like most products designed to run in an X Window System
environment, Cerius2 can execute on one machine and display on
another. This section discusses the requirements and conditions for
remote display of Cerius2.
Licensing issues
The Cerius2 license management system enables you to execute one
instance of the core Cerius2 Visualizer module for each license you
purchase. The method of display is not metered in any manner; the
license manager only counts the number of concurrent executions
of the Cerius2 Visualizer on your Cerius2 host computer.
This licensing system provides you with the flexibility to organize
the use of Cerius2 as best fits your needs. Even a single workstation
(node-locked) license of Cerius2 can be displayed on a remote
machine, as long as it’s the only instance of Cerius2 executing on
that workstation.
Remote display on a
UNIX workstation
If the displaying computer is a UNIX workstation, you need only
set the X Window System environment on that computer as
described in the previous sections. You can then run xhost and set
your DISPLAY environment variable in the usual way. See your
Installation and Administration Guide/July 2000 25
4. After Installation
displaying system’s documentation or your network administrator
for instructions on running X Window System programs remotely.
Remote display on a
Macintosh or PC
If the displaying computer is an Apple Macintosh or an IBMcompatible PC running the Microsoft Windows™ operating
system, the computer must meet these requirements:
◆ The computer must run network software compliant
with the TCP/IP protocols. The network interface card
should be installed and cabled, and the network
software should be installed, tested, and running before
attempting to run Cerius2 remotely.
◆ You must use an X server software product from a thirdparty vendor. Some vendors supply X server products
and TCP/IP-compliant network software in the same
package. Some X server products presume the presence
of an installed and tested TCP/IP network.
◆ The computer’s display system must support a
minimum of 256 simultaneous colors. Even if your X
server software supports monochrome or 16-color
displays, Cerius2 requires 256 colors or more.
◆ The computer’s display system must support a
minimum display size of 1024x768 pixels. Larger
display sizes are strongly recommended for effective
use of Cerius2. Note that this requirement rules out the
use of smaller Macintosh monitors with a resolution of
640x400 pixels.
◆ The computer must have enough memory to run the X
server software with acceptable performance. The
memory requirement for X server software differs with
each product, but you should consider eight megabytes
of memory a minimum for displaying Cerius2 on either
Macintosh or Microsoft Windows platforms.
Molecular Simulations has performed limited testing on two X
server products:
◆ For the Macintosh: MacX™ by Apple Computer, Inc.
MacX requires Apple’s MacTCP network software.
◆ For Microsoft Windows: eXceed™ 6.0, by Hummingbird
26
Installation and Administration Guide/July 2000
Setting up remote display systems
Communications, Ltd.
This list of tested X server products does not constitute an
endorsement or recommendation by Molecular Simulations. You
should be able to set up other X server products by following the
guidelines in the following sections.
Mouse button
mappings
Setting up X server
products
Each X server product has its own way to map the three mouse
buttons of a UNIX workstation to the single button of a Macintosh
mouse or to the two buttons of a PC mouse. Because Cerius2 makes
extensive use of all three mouse buttons, be sure to learn how your
X server product emulates a three-button mouse.
The following paragraphs discuss each setup requirement
generically, then show the steps you must take to implement the
requirement in the tested X server products. Your X server software
may use different terminology and different methods to
accomplish the same task.
These are the tasks you must perform to set up your X server to
display Cerius2:
1. Set your X server for single window or rooted window
mode covering the full screen.
2. Place certain settings in the .Xdefaults file in your home
directory on your Cerius2 host. Load those settings with
the command xrdb.
3. Run a Motif-compliant window manager on the host
computer.
Single window mode
X server products generally enable you to select one of two display
modes:
◆ In multiple window mode, the X server software acts as
the window manager for all X client windows. X client
sessions appear alongside sessions of the native
operating system.
◆ In single window or rooted window mode, the X server
software presents a single large window in which all X
client windows are displayed.
Installation and Administration Guide/July 2000 27
4. After Installation
Cerius2 displays multiple windows and must control the placement
and size of each of them. You must set your X server to display a
single window in which all X clients run.
◆ The MacX software refers to single window mode as
Rooted mode. You specify Rooted mode using the
Display Preferences dialog box invoked from the Edit
menu. Use the Color Root Preferences item at the end of
the Edit menu to specify the size of the root window, in
pixels, as the maximum resolution of your display
system.
◆ The eXceed software uses the term single window mode
and refers to the opposite setting as multiple window
mode. Multiple window mode is the eXceed default; to
display Cerius2, select Tools/Configuration/Window
Mode. In the resulting dialog box, select Single Window
from the Window Mode listbox.
X fonts
If your Xserver software has 75dpi and 100dpi fonts, Molecular
Simulations recommends that you install both sets for best results:
Xdefaults settings
In the .Xdefaults file (or its equivalent) in your home directory on
your UNIX host, make sure these settings are in place:
mwm*interactivePlacement: false
mwm*clientAutoPlace: false
On SGI workstations, substitute 4Dwm for mwm in these lines.
Load your Xdefault settings into the workspace of the current X
session by typing (for C-shell users):
xrdb -l ~/.Xdefaults
You can run this command at the same time you start an X server
session, as shown below.
Motif-compliant
window manager
28
When you operate in single window mode, you must designate a
window manager on the host computer to control the various X
Installation and Administration Guide/July 2000
Setting up remote display systems
client windows. Cerius2 requires a Motif-compliant window
manager. You should run 4Dwm, which is Motif-compliant.
Starting an X server
session
You can set up an icon or client script to automate some of the
above steps. You can start your remote X Window session with
your host-based window manager in place the way it would be if
you logged in to that workstation’s console.
The following is one example of setting up such a script using the
conventions of the eXceed software on the Windows 95 platform.
1. To set up a client script when using the eXceed software,
select Tools/Client Starter from the eXceed menu once
you’ve started the Xserver.
2. In the resulting dialog box, select the Start Method as
REXEC(TCP/IP), and the Program Type as X Window,
then fill in your User ID, Host Name, and (optionally)
your Password. For the command, type this line:
>
xterm -display <IP_address or hostname>:0
You can save the file using File/Save_As for later quick
access. Click on Run! to launch the command, and enter
your password if necessary.
3. Once the xterm comes up on your display, start the
window manager with:
>
4Dwm &
4. Use the same steps in this remote session to start Cerius2
as you would at the console of the host workstation.
Installation and Administration Guide/July 2000 29
4. After Installation
30
Installation and Administration Guide/July 2000
A
The applcomm.db File Format
A Molecular Simulations application running on one host can
invoke and run Molecular Simulations applications resident on
other hosts. For this to happen, the invoking application must
know the machine on which each peer application is available, the
name of the executable file on that machine, and the operating
system and networking protocols in use by that machine.
Molecular Simulations applications store this information in a
human-readable file similar in concept to the UNIX file /etc/
services, which lists network services and the ports on which they
are available. This application communications database file is
named applcomm.db.
Under normal circumstances, applcomm.db is edited automatically
during installation of the invoking Molecular Simulations
application and does not need to be altered. This appendix
documents the file’s format for those cases when you need to
augment the information in this file.
File contents
The applcomm.db file contains records describing machines in the
network, possible communication protocols, and applications that
can be run on those machines.
Three different types of records can appear in this file. The symbol
in the first position of each line is a control character and must be
one of the following:
# - Comments
M - Records describing machines in the network
P - Records describing communication protocols
Installation and Administration Guide/July 2000 31
A. The applcomm.db File Format
A -
Records describing applications
The following points apply to record lines in general:
◆ Empty records (containing only spaces and/or tabs) are
legal and are treated as comments
◆ All other records are ignored, but a warning message is
displayed with the contents of the ignored record
◆ Fields in the records are separated by spaces and/or
tabs
Records describing machines
The following points apply to record lines that describe machines
on your network:
◆ Machines can be (but need not be) grouped in classes.
There is no special meaning in the class name, with the
exceptions of MVS and manual.
◆ One machine may belong to more than one class.
◆ Classes (and machines) can also be grouped. However,
looping is forbidden: if class A belongs to class B, class B
may not belong to class A.
◆ Grouping in classes helps the coding of A-records.
◆ If a machine is not defined in any M-records, it gets
assigned the class default.
The format of an M-record is as follows:
M
class
machine1
[machine2 ...]
where:
class
Name of the class, which can be any arbitrary
name.
machine
Name of a remote machine or a machine class.
Examples:
# SGI
32
Installation and Administration Guide/July 2000
Records describing supported network protocols
M
M
M
M
M
slow
medium
fast
Indigo
sgi
beauty bohr clover dirac watson
bam-bam buster dino gomez ram
altoid newton null
ram buster dino null
slow medium fast Indigo
# Other machines
M rios
hanz franz hogan
M hp720 avoid devoid
# all of them
M unix sgi rios hp720
Records describing supported network
protocols
The format of a P-record is as follows:
P
protocol
machine1 [machine2 ...]
where:
protocol
Either unix or tcp
machine
Either the actual host name or a class name as
defined in an M-record
If a machine is not defined in any P-records, UNIX protocol is
accepted for a local UNIX machine, and tcp otherwise.
Examples:
P unix
P tcp
unix
unix eagle.tc.cornell.edu rain.cray.com
Records describing supported applications
The format of an A-record is as follows:
Installation and Administration Guide/July 2000 33
A. The applcomm.db File Format
A
A
machine application executable [argument [...]]
class
application executable [argument [...]]
where:
machine
Actual host name on which application is available
class
A machine class, defined by an M-record
application
The application name (charmm, xplor, and so on)
executable
The command that should be executed on the
machine to run the application (If this command
does not exist in the user’s default path, the full
path name must be given in the A-record.)
argument
Any argument that must be passed to the
application
An A-record is necessary for every application that you want to
start by using the Molecular Simulations remote job module.
Examples:
A remote_unix
rjrd
/home/msi/quanta/exec/rjrd
A remote_unix
xplor /home/msi/xplor/xplor.bat
Example applcomm.db file entries
The following applcomm.db extract contains example entries for
quantum applications.
#
#
#
#
A
A
A
A
#
34
These lines specify the locations of the ADF
files. You may need to alter the specifications
if you want to run ADF on a machine on which you do
not have Cerius2 licensed.
SGI adf c2_install_dir/exec/adf.exe
SGI ADFBIN c2_install_dir/adf/bin
SGI ADFUTILITIES c2_install_dir/adf/bin
SGI ADFRESOURCES c2_install_dir/Cerius2-Resources/ADF/atomicdata
The following line specifies the location of the main
Installation and Administration Guide/July 2000
Example applcomm.db file entries
#
#
#
A
#
#
#
#
A
#
#
#
A
A
#
#
#
#
A
A
#
#
A
#
#
#
A
#
#
#
#
A
Gaussian 92 directories. Replace the path name with that
for your own installation. If you don't have Gaussian
92, omit this line.
SGI g92root /usr/mydir/gaussian92
The following line specifies the location of the main
Gaussian 94 directories. Replace the path name with that
for your own installation. If you don't have Gaussian
94, omit this line.
SGI g94root /usr/mydir/gaussian94
The following lines specify an alternative location for the
Gaussian 92 and Gaussian 94 scratch directories. If this
line is omitted, the current working directory is used.
SGI g92scratch /usr/disk2/gaussian.scratch
SGI g94scratch /usr/disk2/gaussian.scratch
The following two lines are standard. Only change them
if you have a non-standard installation, or if you
want to run mopac on a machine on which you do not
have Cerius2 installed.
SGI mopacdir c2_install_dir/mopac
SGI mopac6exe c2_install_dir/mopac/mopac6.exe
The following line specifies the location of the MOPAC7
executable. If you don't have MOPAC7, omit this line.
SGI mopac7exe /usr/mydir/mopac7/mopac7_sgrw/mopac.exe
The following line specifies the location of the MOPAC93
executable. Replace the path name with that of your own
installation. If you don't have MOPAC93, omit this line.
SGI mopac93exe /usr/mydir/mopac93/m93_src/mopac93.exe
The following line specifies the location of the
DMol3 executable. Only change it if you have a
non-standard installation, or if you want to run DMol3
on a machine on which you do not have Cerius2 installed.
SGI dmol3exe c2_install_dir/exec/dmol3
Installation and Administration Guide/July 2000 35
A. The applcomm.db File Format
36
Installation and Administration Guide/July 2000
B
MSI Sales and Support
How to Contact Us
North America
In the United States, Mexico, and Canada, you can reach us in the
following ways:
1. Email us at support@msi.com
2. Telephone at 1-858-799-5509 from 6:00 am until 6:00 pm
Pacific Time, business days. In the U.S. and Canada, call
toll free, 1-800-756-4674.
3. FAX at 1-858-458-0431.
Europe
In Europe you can contact us in the following ways:
1. Email us at support@msi-eu.com
2. Telephone at (44) 845-741-3375 from 9:00 am to 5:00 pm
UK time, business days. (Note that calls are charged at a
local rate in most European countries.)
3. Fax at (44) 1223-413-301.
Asia/Pacific
Throughout the Asia/Pacific region you can reach us in the
following ways:
1. Email us at support@msi.com
Installation and Administration Guide/July 2000 37
B. MSI Sales and Support
Your request will be redirected to the most appropriate MSI
support office.
Japan
In Japan you can contact us in the following ways:
1. Email us at support@cubs.bio.rsi.co.jp
2. Telephone at (81) 03-3206-3575.
3. FAX at (81) 03-3206-3580 or (81) 03-3206-3577.
We will do our best to resolve your problem within 24 hours. Of
course, some questions and problems will take longer, but we will
keep in communication with you until the problem is resolved.
Internet
For additional help please look at the MSI World Wide Web
Support page:
http://www.msi.com/support/support.html
38
Installation and Administration Guide/July 2000
Index
A
applcomm.db
example 34
applcomm.db file format 31
C
cut-and-paste 3
D
default menu deck 9
disk space requirements 2
E
eXceed 26
F
license file, creating 18
license file, e-mailed 18
license manager 9, 19
M
machine records, applcomm.db 32
Macintosh 26
MacTCP 26
MacX 26
manual installation 1, 13
minimum display size 26
motif-compliant window manager 28
mouse button mappings 27
msilicense.dat 9
multiple window mode 27
N
NIS 17
node-locked license 20
float license 20
R
G
GL vs. OpenGL 24
H
hosts.equiv 17
I
install script 7
installation directory 15
L
LG1 graphics 24
RAM and swap space requirements 2
remote display on a Macintosh or PC 26
remote display on a UNIX workstation 25
remote display systems 25
requirements, hardware and operating system
2
root password requirement 3
rooted window 27
S
scientific support
email address 37
FAX 37
international 37
phone number 37
Installation and Administration Guide/July 2000 39
.
selecting an installation procedure 1
set up and configure user accounts 23
SGI system requirements, additional 2
single window mode 27
site-specific files, configuring 15
standard installation 1
startup files, editing 21
start-up script 8
supported applications 33
supported network protocols 33
T
TCP/IP protocols 26
testing the installation 23
token license 20
V
verify the license installation 10
W
window manager settings 24
Windows 26
World Wide Web 38
X
X fonts 28
X server products 26
Xdefaults, SGI 24
xterm 29
40
Installation and Administration Guide/July 2000
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