Workstation networks require two files, the namd2 executable and the conv-host program. The conv-host program starts namd2 on the desired hosts, and handles console I/O for the node programs.
To specify what machines namd2 will run on, the user creates a file called "nodelist". Below is an example nodelist file:
group main host brutus host romeo
The "group main" line defines the default machine list. Hosts brutus and romeo are the two machines on which to run the simulation. Note that conv-host may run on one of those machines, or conv-host may run on a third machine.
The "rsh" command ("remsh" on HPUX) is used to start namd2 on each node specified in the nodelist file. If NAMD fails without printing any output, check to make sure that "rsh" works on your machine, by seeing if "rsh hostname ls" works for each host in the nodelist. If you want or need to use "ssh" instead, then add "setenv CONV_RSH ssh" to your login or batch script and try "ssh hostname ls" to each host first to ensure that the machine is in your .ssh/known_hosts file.
Some automounters use a temporary mount directory which is prepended to the path returned by the pwd command. To run on multiple machines you must place a "pathfix" line in your nodelist file before any "host" lines. For example:
group main pathfix /tmp_mnt host alpha1 host alpha2
A number of parameters may be passed to conv-host. The most important is the "+pX" option, where X specifies the number of processors. If X is less than the number of hosts in the nodelist, machines are selected from top to bottom. If X is greater than the number of hosts, conv-host will start multiple processes on the machines, starting from the top. To run multiple processes on members of a SMP workstation cluster, you may either just use the +p option to go through the list the right number of times, or list each machine several times, once for each processor. The default is +p1.
You may specify the nodelist file with the "++nodelist" option and the group (which defaults to "main") with the "++nodegroup" option. If you do not use "++nodelist" conv-host will first look for "nodelist" in your current directory and then ".nodelist" in your home directory.
If you always want to run on the machine you are logged in to you may use "localhost" in place of the hostname in your nodelist file, but only if there are no other machines. You will not need "pathfix". For example, ".nodelist" in your home directory could read:
group main host localhost
Once the nodelist file is set up, and you have your configuration file prepared (alanin.conf, in this example), run NAMD as follows:
conv-host +pX namd2 alanin.conf
Intel and Alpha processors produce binary files (restart and DCD files) which must be "byte-swapped" to be read on other platforms. The flipbinpdb and flipdcd programs will perform this conversion. NAMD and VMD now handle this conversion automatically for most files.