Can I run Amber in parallel?

Please note: The FAQ pages at the HPCVL website are continuously being revised. Some pages might pertain to an older configuration of the system. Please let us know if you encounter problems or inaccuracies, and we will correct the entries.

Yes. Amber is inherently parallelized and designed to scale well on a multi-processor machine or a cluster. The underlying parallel system is MPI (Message Passing Interface) which is a commonly available standard that runs on many platforms. Consult our MPI FAQ and follow some of the links in there if you want to have more information about MPI. If you want to use multiple processors for your Amber run, you have to submit the program to a parallel environment. In the case of our main production machines, this environment is called ClusterTools, and the relevant command is mprun:

mprun -np 8 program_name < input_file >output_file

This will run your program on eight processors.

Note that you are only allowed to run Amber this way for small test systems! For any production jobs, you have to submit the task to the GridEngine queuing software (see next section).