LAMMPS Optimized for Intel on Quad Socket Xeon

LAMMPS is a molecular dynamics program capable of running very large (billions of atom) dynamics simulations. It is modular with many contributed packages to add extra potential energy functions, atom types etc.. There was recently added a package, USER-INTEL, that adds some nice code optimizations for Intel Xeon hardware. We grabbed the latest source code and did a build with this new code and fired it up on our quad Xeon test system and got very good performance.

Changing Priorities

I’d never used a Dremel before.

But I’d have to learn if I wanted a PC that stood out from all the nondescript beige boxes my friends owned. So I spent the afternoon tracing the pattern on side panel of my Lian-Li aluminum case using a stencil I’d found online. Had YouTube been around at the time, I would have searched to find a Dremel tutorial but it would be few more years before it existed.

OpenFOAM performance on Quad socket Xeon and Opteron

OpenFOAM is a collection of programs and libraries for computational fluid dynamics, CFD, and general dynamical modelling with many solver types. It can give linear scaling and excellent parallel performance on Quad socket many-core systems. Read on to see performance on a 40-core Xeon and 48-core Opteron system.

Why quad Xeon? 95% of peak LINPACK on 40 cores!

I’ve been doing application performance testing on our quad socket systems and I am especially liking the quad Xeon box on our test bench. I realized that I haven’t published any LINPACK performance numbers for this system (that’s my favorite benchmark). I’ll show the results for the Intel optimized multi-threaded binary that is included with Intel MKL and do a compile from source using OpenMPI. It turns out that both openMP threads and MPI processes give outstanding, near theoretical peak performance. Building from source hopefully shows that it’s not just Intel “magic” that leads to this performance … although I guess it really is.

Summer Newsletter

To the best of my knowledge, it’s been at least six years since we’ve written about life behind-the-scenes here at Puget Systems. So we’re going to kick off a whole new generation of newsletters – focused more on the people and less the technology – as we dive into this summer season of 2014. I hope you enjoy this little glimpse of what working at Puget Systems is really like, day to day.