Allinea Software Blog

Sat January 10, 2015 by Mark O'Connor

Faster sequence alignment with Allinea Performance Reports

Recently we've been running bowtie2 on a 16 CPU server with 32 GB RAM. I've tried using the “-p” flag to use more cores but it doesn't seem to make a lot of difference after 8 or so.

Today we're going to do a short performance investigation using the zebrafish genome and example pairs from http://bmi.osu.edu/hpc/software/benchmark/ to check the health of our setup. Should bowtie2 be faster on this relatively powerful server or is this just the way things are?

$ time ../bowtie2 -p16 -x zebrafish -1 ./zebrafish.1M.1.fq -2 ./zebrafish.1M.2.fq -S ./z1.sam
999999 reads; of these:
  999999 (100.00%) were paired; of these:
    464803 (46.48%) aligned concordantly 0...

Tue November 25, 2014 by Mark O'Connor

We’ve been profiling and tuning a lot of real-world HPC codes since the release of Allinea MAP and Allinea Performance Reports and one thing that’s consistently surprised us has been the number of codes that are memory-bound.

Mon November 3, 2014 by Florent Lebeau

OpenFOAM, developed by ESI-OpenCFD is one of the most popular tools for developing CFD (Computational Fluid Dynamics) applications, along with ANSYS Fluent or CD-Adapco Star-CCM+.

Tue September 9, 2014 by Mark O'Connor

This is the third in a three-part series exploring a crazy idea that was born at ISC14 while answering questions about the new energy metrics in Allinea Performance Reports and Allinea MAP – could the information in these reports show us an easy way to increase energy efficiency without having to change the program?

Tue September 2, 2014 by Mark O'Connor

Last week I talked about a crazy idea that was born at ISC14 while answering questions about the new energy metrics in Allinea Performance Reports and Allinea MAP – could the information in these reports show us an easy way to increase energy efficiency without having to change the program

Tue August 26, 2014 by Mark O'Connor

At ISC14 this year I was asked an interesting question while showing off the forthcoming Energy Efficiency metrics in Allinea Performance Reports and Allinea MAP. The question was: what can you do to optimize for energy usage?

Wed July 23, 2014 by Beau Paisley

Allinea DDT and Allinea MAP are excellent tools for finding program flaws and performance issues – they are also very helpful for studying codes and coding techniques. In this article I present a handful of optimization techniques and use Allinea MAP to illustrate their benefits. These tips are focused on scientific programmers who want to adopt best practices and the tips are limited to those that: