Installation Instructions for Priism 3.3

1. Create the installation directory

Create a directory (referred to from now on as install_dir) for the installed software:

mkdir install_dir

2. Install the files from the downloaded archive

Uncompress and copy the files from the downloaded archive (replace archive with the full path name of the downloaded file):

cd install_dir
gunzip -c archive | tar -xf -

3. Run post_install.sh

post_install.sh fixes up the paths in the Priism setup files. post_install.sh should be run from the directory in which Priism is installed; i.e. at the command line enter

cd install_dir
./post_install.sh

4. Try it out

After completing the above steps, you should be able to start Priism by entering this at the command line:

source install_dir/Priism_setup.local
Priism

The result should be that a thin dialog with the title "Priism 3.3" and a menu bar should appear in the upper left of the screen. If the dialog does not appear, check that you did run post_install.sh.


5. Customize Priism_setup (optional)

The setup file, Priism_setup, contains settings that should work for most systems. Some settings that you may want to modify or override are discussed below; others are mentioned with comments in Priism_setup.

Location of the shared memory file

The default versions of Priism_setup cause the shared memory file and related temporary files to be put in whatever the environment variable TMPDIR is set to or, if it is not set, /usr/tmp. Because these files may be large (their size is related to the amount of image data loaded into Priism; this can easily be hundreds of megabytes), you will want to override or change the default if this default location does not have much space. To override the default, set the environment variable IVE_SHMDIR to the directory where the files are to be placed. This must be done before Priism is started (it can happen before or after reading Priism_setup). To change the default, alter the logic for how IVE_SHMDIR is set in Priism_setup (in the original versions this happens at lines 179-185 in Priism_setup.

Working set size

There is a limit, the working set size, of how much space the image data and the scaled images derived from that data can take up in the shared memory file. When that limit is exceeded, Priism will start discarding scaled images or moving image data out of the shared memory file and into other temporary files. There is a crude heuristic in Priism_setup which sets the working set based on how much RAM your machine has. This heuristic may not be optimal for your system. For instance, the working set is set at 256 megabytes for systems with more than 320 megabytes of RAM; for systems like that you may want Priism to use more memory so you can load more image data without incurring the performance hit when the working set size is exceeded.

To override the default working set size, set the environment variable IVE_WORKING_SET to the number of megabytes that the working set should be. This must be done be done before Priism is started and after Priism_setup is read since they will reset IVE_WORKING_SET. To change the default, you can alter the heuristic (line 150-160 in the original Priism_setup) and the default of 96 megabytes when the amount of RAM could not be determined (line 119 of the original Priism_setup).

If you change the working set to be something close to or larger than 300 megabytes, you should also change the maximum size of the shared memory file (see below for details).

Maximum size of the shared memory file

The shared memory file has a maximum size that is fixed when the file is created. This maximum size defaults to 300 megabytes. If you increase the working set to something close to or greater than 300 megabytes you should also increase the maximum size. To change the maximum size, set the environment variable IVE_SIZE to the size in megabytes. This must be done before Priism is started. The absolute maximum size is 1000 megabytes for IRIX (at 1050 megabytes, Priism can not start).

Batch queues

Some parts of Priism can submit a script to perform a task offline with the choice to either run it locally or submit it to a batch queue. BatchRegion.html in the HTML directory of the Priism distribution describes the environment variables that control the list of available queues and the mechanism for submitting a job to a queue. Priism_setup contain commented out settings for a particular batch queue setup.


IVE/Priism home page | Download current software | Priism requirements |


modified January 21, 2003

IVE Development Team (ive-web@msg.ucsf.edu)
Macromolecular Structure Group, UCSF (http://msg.ucsf.edu)