Monthly Archives: August 2010

Eight Way PMEMD

Since my earlier post about building Amber9 I’ve learned that the Amber code base contains a new development stream and a highly parallel performance oriented development stream. The executables these create are called sander and pmemd respectively. The high performance … Continue reading

Posted in Amber9, Engage VO, High Throughput Parallel Computing (HTPC), multicore, OSG, pmemd, RENCI | Leave a comment

Parallel Amber9

Amber9 is a molecular dynamics software suite with support, via OpenMPI, for parallel execution. This describes the process of compiling and running the serial and parallel versions on the following machine configuration: Operating System: Ubuntu 10.04 8 x Intel(R) Core(TM) … Continue reading

Posted in Amber9, Compute Grids, grid, multicore, OSG | Leave a comment

A Tier-3 Open Science Grid Compute Element

I. RENCI Blueridge as Compute Element RENCI’s new Open Science Grid (OSG) Compute Element (CE) will accept job submissions to be executed on the Blueridge cluster. A CE presents a uniform interface other OSG sites can use to submit jobs. … Continue reading

Posted in Compute Grids, Globus, grid, High Throughput Computing (HTC), OSG, RENCI | Leave a comment