Important note: If you plan to run on a linux cluster, make SURE you download the cluster binary, or compile from source with the cluster option. If you do not, you will have numerous problems.
EMAN uses a very portable and very coarse-grained type of parallelism. It can function on virtually any multiple processor supercomputer (shared or distributed memory), and can even run on clusters of connected workstations (with certain restrictions). Many of the EMAN command line programs accept the 'proc=' argument. You can discover if an individual command accepts this argument by typing its name followed by 'help', eg 'refine help'. Any command which takes this argument impliments parallelism in the same way (with 2 specific experimental exceptions).
The form for specifying the number of processors to use is [proc=<num>]. That is, 'proc=5' will run the job on 5 processors. Never specify more processors than you have configured. This will cause multiple processes to run on a single processor and slow down the entire job.
Running on SMP computers doesn't require any special configuration. Any command that takes the 'proc=' option (like refine), will automatically run in parallel on these machines. Simply specify the number of processors. Dual/quad processor desktop workstations also fall into this category
If you are running on a distributed supercomputer/cluster with a batch queuing system (OpenPBS or LoadLeveller for example), you may simply be able to run your job through the BQS. You should specify the same number of processors to the EMAN command through proc= as you specify in the batch script. EMAN will automatically interrogate either OpenPBS or LoadLeveller in most cases to get a list of nodes to run on.
If you are running on a set of workstations, or a cluster without a BQS, you will need a configuration file. This may either be called .mparm and be placed in the local directory (where the EMAN commands will be run), or be called $HOME/.eman/mparm, in which case it will apply to any directory not containing a local .mparm file.
The format of this file is quite simple. Each line contains the specification for 1 computer/node. Here is an example for a cluster of 4 computers, 2 single processor and 2 dual processor:
ssh 1 1 node1 / ssh 1 1 node2 / ssh 2 1 node3 / ssh 2 1 node4 /
This file would be placed in $HOME/.eman/mparm. The first column is either 'ssh' or 'rsh' depending on which program is configured for logging in from one machine to another. Note that for this to work, the individual machines MUST be configured to allow the same user to log in from one machine to another with NO password entry. Read the man pages for 'ssh' or 'rsh' to learn how to do this. You can test to see if this is configured properly by setting up the configuration file then typing 'runpar test'. This will run a simple command on each processor. If it fails, an error message should be reported. If you see a 'password:' prompt, then the machines are not configured properly. On some machines it may be necessary to configure ssh-agent.
The second column is the number of processors on that particular node. The third column is always 1. The fourth column is the network name of the computer. The fifth column is not used in the '$HOME/.eman/mparm' file, but IS used if the file is placed in the run directory.
To use EMAN on clusters of computers, the directory where processing is being done should be cross-mounted on all of the computers being used. EMAN 1.7+ no longer cares about this requirement in most cases, but it is still a good idea to follow this proceedure. On some machines, the directories aren't mounted in the same place. In most workstation setups, the 5th column will be the same on all lines, but if your local configuration has the directory mounted in different places on different machines, you can use this column to specify the path to the run directory on each node.
One other note. It is not possible to run a single job across mixed platforms. If you have 2 SGIs and 2 PC's, you cannot run a single job on all 4 machines.
Current distributions of linux have some known problems with their NFS implementations. Specifically, if two nodes append to the same file within a few seconds of each other, the file will be corrupted. Lacking a better solution, the rather extreme measure of writing a custom fileserver for EMAN was undertaken. When the cluster version of EMAN is run, virtually all file I/O operations are passed through a single-threaded fileserver running within runpar on the host machine. Not only does this avoid NFS bugs, but it seems to run faster than NFS. This feature is disabled in the single processor and shared memory binary versions EMAN.