ALMOND 3.3 is distributed in CD-ROM format or as a compressed tar file downloadable from the download page of the Molecular Discovery WEB site. The CD is recorded using iso9660 format with Rock Ridge and Joliet extensions and is readable in UNIX workstations (including Linux and SGI) and in any PC running Windows. The tar files must be decompressed before use using the commands:
gunzip filename.tgz
tar xvf filename.tar
The procedure for installing ALMOND is very simple:
- If you plan to install ALMOND in a computer where no previous version is present go to the Install section.
- If the version of ALMOND running in your system is older than version 3.3.0 go to the Install section.
- If ALMOND is installed in your computer but the license has expired please, do not reinstall the product. Contact Molecular Discovery in order to obtain a new license key.
ALMOND can be installed on a NFS server and exported, in such a way that different hosts can share this resource and execute ALMOND on the local CPU. If you plan to share the ALMOND install directory between different host please read the section Installing ALMOND on a NFS server before starting.
STEP 1.
If you downloaded ALMOND from Internet or your computer has got a local CD-ROM you can execute the installation program directly from the CD-ROM. Proceed to STEP 2.
If you have no CD-ROM directly attached to your computer you will need to transfer the CD-ROM contents to a temporary directory in a local filesystem. The distribution CD-ROM is readable in most computers running UNIX or Windows. The contents can be transferred using FTP, rcp etc...
If you transfer the CD-ROM contents, make sure that the capitalization of the files was preserved. If you use FTP please make sure to transfer all the files as binary data.
STEP 2.
Gain super-user privileges. This is not strictly required and is necessary only to write some icons in the directory /usr/lib/images. In any case you must have read and execute permissions for the source directory and writing and execute permissions for the destination directory.
Change to the directory containing the distribution. This can be the temporary directory where you have decompressed the tar file, the mount point of your local CD-ROM or any directory where you have transferred the contents of the CD-ROM. For example:
cd /CDROM
Start the ALMOND installation tool
./ainstall
Platform currently supported by ALMOND are SGI IRIX version 6.5 and PC with Intel processors running Linux version 2.4 (distribution RedHat version 7.1 and higher). In order to check the version of your operating system you can type:
uname -r
Type the name of the directory Destination, the directory where the ALMOND programs will be installed. This should be the name of a new, non-existing directory. Do not create this directory before running ainstall. Be aware that you must have permission to create such directory.
Press the Install button.
The program will copy all the required files to the installation directory and prepare the ALMOND binary file. Exit from the program pressing the Exit button.
The IRIX version of ALMOND 3.3 uses two SGI libraries that might be not present in your system. The installation program will search in the local disk and would present a warning message if it does not succeed on finding them. If you get this warning message you can still proceed with the installation, but we recommend you to install the required libraries before using ALMOND. Please read the section Installing required libraries for detailed instructions.
The graphical libraries required by the Linux version of ALMOND 3.3 are automatically copied into the directory Destination without checking the library already installed in the system.
A copy of the output produced by the program is dumped to a file called INSTALLATION.LOG or, if you are installing directly from the CD-ROM, to the window where you started ainstall.
STEP 3
The installation program creates a file named almond.csh that should be aliased before the program can run. If you wish to make ALMOND generally available we suggest to add the following like to the /etc/cshrc file (you will need administrator privileges to do this):
alias almond /usr/local/almond/almond.csh
where we assume that the installation directory for ALMOND is /usr/local/almond
If you have no administrative privileges in your computer you can obtain the same results adding such a line to the file .cshrc present in your home directory.
The file almond.csh set up the access to the required libraries before starting the program. Please note that in previous installations the file almond.csh was sourced, please remove old source lines in order to avoid potential conflicts. Additionally, the file contains some configuration options that can be changed for special purposes. System administrators are encouraged to edit and customize this file to better adapt the program to the system environment. Please consult the section Editing the almond.csh file
STEP 4
If you added the above mentioned line to your configurations file you will need to open a new window. In this window type:
almond
ALMOND will show a message like this:
No suitable license line was found for this host.
Please send the following line to Molecular Discovery.
willy 1542612352 L ALMN_32 09-Sep-2005 yDffg67QsttTyyyaB key
License requests should be submitted online to our
web site: http://www.moldiscovery.com
Please copy this line verbatim and submit a license request to Molecular Discovery using the license manager included in the Molecular Discovery WEB site
License lines returned by Molecular Discovery should be copied verbatim into the file license, present in the ALMOND install directory. Until this file does not contain a suitable license line, ALMOND will keep showing the above information or an error message and will not start.
Installing required libraries.
IRIX
Some ALMOND 3.3.0 plots of the IRIX version make use of SGI's Inventor library. If it is not installed on your system, the installation or updating tool will show a warning message in the screen. If you see such a message during the install please proceed with the installation. Once it is finish you must install the required library.
The Inventor Execution Only Environment libraries (inventor_eoe.sw) are distributed in any release of IRIX 6.x. Find in the IRIX distribution CD-ROM's the product "Inventor Execution Only Environment", using the Software Installation Tool. If you are installing ALMOND in a system running IRIX 6.5, press the Customize Installation button, open the product folder and make sure that the sub-product "Inventor n32 Run-time" is selected for installation.
Linux
The graphical libraries required by the Linux version of ALMOND 3.3 are automatically copied into the sub directory lib of the directory Destination without checking the library already installed in the system. ALMOND has been tested on Linux RedHat version 7.1 and higher with full installation. The correct working of ALMOND on uncomplete installation of redHat 7.1 and higher is not guaranteed, as well as the working on other Linux distributions.
Installing ALMOND on a NFS server.
Start installing ALMOND in the server using the steps 1 and 2 of the general procedure described above. This can be done locally on the server or from any workstation sharing a exported server directory. In any case, make sure that you have writing permissions on the installation directory during the install. For regular ALMOND use, the installation directory can be mounted "read-only".
For example, lets imagine that ALMOND is installed in the server bigboss, in the directory /usr/programs/almond. This directory is exported to the workstations willy and billy which mount this directory read-only as /nfs/almond.
In each workstation the following tasks should be done:
1. Alias the file almond.csh adding the following line to the local /etc/cshrc file of every workstation
alias almond /nfs/almond/almond.csh.
2. Review the file almond.csh and make sure that the settings are suitable for the workstations. Edit and change as required (refer to the following section for a description of the almond.csh file).
3. Make sure that every workstation contains the required Inventor library.
4. Start ALMOND in every workstation. Collect the lines produced in a single block of text:
willy 1542612352 03 09-Sep-2001 1734912222 KEY 1172848414
billy 1521566712 03 09-Sep-2001 1734912222 KEY 1234671178
Send the line produced by every workstation to Molecular Discovery, as described above. They will send back similar lines containing the license keys. Copy verbatim these lines to the file license, present in the ALMOND install directory. Until this file does not contain a suitable license line for a certain host, ALMOND will keep showing the above information or an error message and will not start.
A different line is required for every workstations or system running ALMOND. If the server itself is not used to run ALMOND, no license line is required for this host.
The file almond.csh sets some environment variables required for ALMOND normal operation. In a simple local install, the installation program automatically creates a suitable file and no user intervention is required. However, in complex site installations or after changes in the directories, etc.. the file can require some editing.
The file almond.csh basically serves to set some environment variables and to run the program. These environment variables are:
ALMOND_DIR
Defines the complete path to the installation directory. It should be changed when this directory is moved elsewhere or in NFS installs, when the path is different from the point of view of the workstations.
ALMOND_MODEL_LIBRARY
Defines the complete path to the directory where the library models are stored. By default, this variable is set pointing to a pre-defined subdirectory of the installation directory. Either the system administrator or the users can set this variable pointing to a different directory to suit their own needs.
IRIX
LD_LIBRARYN32_PATH
This variable points to the place where suitable dynamic object libraries are placed, usually the lib subdirectory hanging from the installation directory. This variable is overridden to ensure that the suitable library at linked at run time
Linux
LD_LIBRARY_PATH
This variable points to the place where suitable dynamic object libraries are placed, usually the lib subdirectory hanging from the installation directory. This variable is overridden to ensure that the suitable library at linked at run time
Customizing ALMOND look.
On IRIX platforms, ALMOND 3.3.0 uses SGI schemes in order to have a consistent look and feel with other SGI applications. In addition, the aspect of the program can be changed using the schemes browser (schemebr) provided with the IRIX operative system. If the icons were not installed due to insufficient writing permission, it's still possible to install them copying the icons present in the CD-ROM (directory /icons) to the the directory .icons of every user.
On Linux platforms, the default scheme has been hard coded and there is no ALMOND icon for the moment
On both platforms, the color of the background and the foreground of the main window can be also changed including in root directory a resource file called Almond. The directory gifts present in the distribution directory contains an example that can be used as a template.