Volume 5, Number 2
June 2006

Amber 9 in Redwood

by Taner Pirim

The optimized version of Amber ver.9 is now installed on redwood at /usr/local/appl/amber9 by using Intel Math Kernel Library, MKL, version 8.0 and the Intel 9.0 compilers.. You should set the AMBERHOME environment variable to /usr/local/appl/amber9. The executables are in /usr/local/appl/amber9/exe, and the examples are in /usr/local/appl/amber9/examples. You may browse this directory and copy example files into your own working directory for execution. You should ensure that the $AMBERHOME/exe/ directory is in your PATH environment variable.

We would be interested in hearing how your Amber 9 job performs on redwood. Before the beginning fall semester, MCSR plans to make Amber 9 available on mimosa. The performances of Amber versions 7 and 8 on Redwood and Mimosa had been analyzed for various number of cpus by one of our researchers together with our supercomputer consultant. These benchmark analyses had been posted in the May 2006 release of the Parallel-O-Gram. The next step would be to compare the obtained results with Amber 9 benchmarks. If you would like more information on the previous versions of Amber installed on our systems, please visit our Amber website. For more questions on Amber, please contact us via assist@mcsr.olemiss.edu.