The Opal Toolkit is a set of software produced by the National Biomedical Computational Resource (NBCR). This toolkit allows for the computing load for processor intensive scientiﬁc applications to be shifted to a 3rd party and/or generic computing grid. This can be tremendously advantageous in situations where a large amount of computing power is not locally available, but is required, for the task at hand. In particular, many users have discovered that their local computational resources are insufficient for certain types of APBS calculations on large systems or at extremely high accuracy. This client removes this resource limitation by allowing users to run on clusters at NBCR.
Recent developmental versions APBS add optional support for the off-loading of APBS calculations to an Opal service. Currently, the client uses services hosted by the Baker group. Opal support has been integrated into APBS such that the end user will not be able to tell the difference between local and Opal runs of APBS: the APBS Opal client can be invoked in exactly the same way as the main APBS binary with identical output.
The APBS Opal support is in the form of a Python script ApbsClient.py and is installed by default when following the installation procedure outlined elsewhere. The script has been tested on Python 2.5; newer/older versions of Python may or may be functional.
As mentioned above, the basic invocation is the same as the main binary. The only difference is the executable, which is called ApbsClient.py, rather than apbs. This client should be installed by default when APBS is installed. Users can run:
where options are described below and input is an APBS input file. Options available with ApbsClient.py include