I recently installed ATLAS on my new workstation and I’ve been wondering what kind of performance gain I would get compared to the reference BLAS. After some searching, I finally found a BLAS benchmarking tool called BLASbench, which is part of the LLCbench suite. This tool has a rather strange build process, so follow the […]
Benchmarking BLAS Part 1: Building BLASbench with gcc Read More »
In a previous post I described how to build an optimized version of NumPy using the Intel compilers and Math Kernel Library (MKL). This post will update those instructions, since it has been a few years and I am now using NumPy 1.6.1, MKL 10.0.1.014 and Red Hat 4.1.1 (kernel 2.6.18-8.el5). First, copy the file
Building NumPy on a 64-bit Red Hat Cluster with Intel MKL Read More »
Our team (Mole Shopper) won Startup Weekend Orlando! It was a great experience, and I highly recommend that anyone who is interested in entrepreneurship attend a Startup Weekend event. An MBA might tell you about how business is supposed to work, but launching a business in 52 hours will show you how business actuallyworks. We owe
We won Startup Weekend Orlando! Read More »
This post will explain the notation used to denote partial derivatives in the output from Sage. It’s confusing at first, but a simple example will make it clear. Here is the input to Sage: var(‘x y’) function(‘test’, x, y) show(test(x, y)) show(diff(test(x, y), x)) show(diff(test(x, y), x, 2)) show(diff(test(x, y), y)) show(diff(test(x, y), y, 2))
Partial derivative notation in Sage Read More »
Microsoft Office tools are not the best choice for scientific publications, but sometimes you have to use them. Some journals actually require Word documents, and many of my collaborators simply don’t do LaTeX. The process outlined below is they best way that I’ve found to make high-quality plots and charts with Microsoft Excel. High-quality graphics
Publication-quality plots with Excel Read More »
Prerequisites: boost-devel, openmpi-devel, valgrind-devel I installed PETSc and libMesh in my user directory, since I have a single-user workstation. Installing PETSc for use with libMesh First, ensure that OpenMPI is installed and the system paths have been configured correctly. You will need to add the directory containing OpenMPI binaries to your $PATH, and the directory
Installing PETSc and libMesh on CentOS 5 Read More »
I finally got around to installing Paraview on my CentOS 5 box. There are no official RPMS for CentOS 5, so I was expecting a painful build process. To my great surprise, I was able to download the Paraview binary for Linux (64-bit) from Kitware, unpack the archive, and run it! As root, I placed
Paraview 3.12 on 64-bit CentOS 5.7 Read More »
I recently upgraded my desktop workstation from an old 32-bit version of Gentoo to 64-bit CentOS 5. I downloaded and installed the latest version of Sage, and the process went smoothly. If you find this post helpful, please check out the Sage Beginner’s Guide at Packt Publishing. Since I don’t use Sage every day, I
Installing Sage 4.7 on CentOS 5 Read More »
The format method for Python strings (introduced in 2.6) is very flexible and powerful. It’s also easy to use, but the documentation is not very clear. It all makes sense with a few examples. I’ll add more as I have time: Formatting Numbers in Python Strings Formatting a floating-point number The result is the following
Python string format examples Read More »
The following kernel configuration was posted by Alessandro Di Marco as a comment on a previous post in which I provided a Linux kernel config for an earlier version of the kernel. In the interest of sharing his contribution, I’m placing it in its own post. I don’t know the author personally and I have
Linux kernel 3.1 config for Gentoo guest on VMWare Fusion Read More »