O

Allinea Software Blog

Wed July 29, 2015 by Mark O'Connor

Part 1: Optimizing on physical hardware

Introduction

For those who don't know it, Discovar is a life sciences variant caller and small genome assembly code. It turns the output from sequencers into entire genomes given a reference sequence. This is computationally very expensive and I decided to take a look at it under MAP, our OpenMP and MPI profiler.

Compiling and Running Discovar

As with many life sciences codes, downloading, compiling and running the Discovar benchmark was refreshingly straightforward:

    # Build Discovar
    
$ wget ftp://ftp.broadinstitute.org/pub/crd/Discovar/latest_source_code/LATEST_VERSION.tar.gz
$ tar zxf LATEST_VERSION.tar.gz
$ cd discovar-*
$ ./configure...
Wed February 11, 2015

Python is pretty commonplace in scientific computing these days. It is easy to code and powerful - but numerical computation is not a strength that Python has. Its interpreter simply can’t apply the advanced optimizations to your loops and floating point operations that a C++ or Fortran compiler can.

Wed February 4, 2015 by Mark O'Connor
A whirlwind tour of Allinea MAP's new OpenMP profiling capabilities

We're going to see what Allinea MAP 5.0 can do by profiling three versions of a simple PI calculator program with some added I/O for good fun:

A serial version An OpenMP version A mixed OpenMP and MPI version

Let's get started!

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.

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?