Nigel Goddard & Greg Hood
Pittsburgh Supercomputing Center
ngoddard@psc.edu
ghood@psc.edu
NOTE: Before installing this software, please check that you have the latest version by checking the PGENESIS home page: http://www.psc.edu/Packages/PGENESIS We *strongly* advise you to download the latest version if you don't already have it. The following text applies to the old CDROM version of PGENESIS, which has become quite outdated, and may not even run without modification on modern machines and OS versions.
PGENESIS (Parallel GENESIS) can be run on a single workstation; the PVM software system is used to provide the illusion of a parallel computer. It is much easier to run on a network of workstations if they have a shared file system so that any workstation can access any file. If this is not the case, you will need to install PGENESIS independently on each workstation and you will need a copy of the files needed for your simulation (data files, script files, etc), preferably in an identically named directory path.
PGENESIS can be run directly off the CDROM with the command:
/cdrom/pgenesis/bin/pgenesis
You may wish to put /cdrom/pgenesis/bin in your path so that pgenesis is all that is required. For example, cd to /cdrom/pgenesis/Scripts/orient2 and execute pgenesis demo.g. To see the documentation invoke pgenesis -browse. You can cd to your own script directory and run PGENESIS on those scripts. But beware: if you have a customized .simrc in the directory, PGENESIS will ignore it. The simple thing to do is invoke pgenesis without any script, quit at the prompt, then edit the file .psimrc to include whatever customizations you have.
There are several available options, which may be listed by typing pgenesis -help. The most commonly used of these are:
-config <file> - where <file> is a file containing a list of
machines to be used (1 per line)
-nox - run without Xodus
-debug tty - create a window for each pgenesis node
-browse - browse the pgenesis documentation using netscape
Read the Web pages (rooted at /cdrom/pgenesis/Hyperdoc/welcome.html) to take advantage of the new functionality provided by PGENESIS.
PGENESIS can also be installed onto your disk by first installing serial GENESIS (see the regular GENESIS documentation for instructions) and then issuing the command:
/cdrom/Install/PGENESIS_Install install_dir genesis_pathname
where install_dir is the name of the directory in which pgenesis and pvm3 subdirectories will be created, and genesis_pathname is the directory where the serial GENESIS directory is located. For example, "/cdrom/Install/PGENESIS_Install /usr/local /usr/genesis" will make subdirectories /usr/local/pgenesis and /usr/local/pvm3 and reference the serial GENESIS located in /usr/genesis.
Each user should make sure that their PATH is set to include install_dir/pgenesis/bin. If the script files you wish to use are not in your home directory, the examples directory, or the directory you run parallel Genesis in, you will need to add their directory path to the SIMPATH variable in the .simrc file you use. By default this is .psimrc for PGENESIS worker nodes.
Normally the master node sends its output to your screen and the worker nodes send their output to the file /tmp/pvml.???? on the machine they are running on, where ???? is your uid on that machine. Many script bugs can be tracked down by examining those /tmp/pvml.???? files. Note that PVM appends to these files on every run, until PVM is halted and restarted. Also note that if a worker node exits without executing "paroff", some of its output to stdout/stderr which is buffered may not appear in the /tmp/pvml.???? file.
Output from the workers can be redirected to a file by giving the paron command the -output <filename> option. <filename> can be /dev/tty, in which case the worker output appears on your screen mixed with the master's output.
If you are running X-Windows, you can have each worker create its own window and send its output there by using the -debug tty flag when invoking PGENESIS. This requires that your DISPLAY environment variable is set to "hostname:0" when you invoke the pgenesis script.
By default PGENESIS starts the workers using -silent 3 which minimizes the messages printed by the workers (e.g., the banner). To see more worker status messages, give the paron command the -silent 0 option.
Common errors include:
For more information on the finer points of using PVM, refer to the PVM user guide.
NOTE: For instructions on how to run the parallel Genesis beta test see the README.beta file. The file you are now reading tells you how to install parallel Genesis and run it with your scripts.
Libraries are constructed just as for serial GENESIS, each in its own subdirectory in a canonical form. See the GENESIS documentation for descriptions of this form. In this section we describe how to link these libraries with PGENESIS components to create an extended PGENESIS.
Assuming your libraries are subdirectories of a root directory I'll call MYPGEN, these are the steps you follow to create and run extended PGENESIS.