Installing PETSc and libMesh on CentOS 5
Friday, January 20th, 2012 Posted in Linux, Scientific computing | No Comments »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 ...
Paraview 3.12 on 64-bit CentOS 5.7
Thursday, January 19th, 2012 Posted in Linux, Scientific computing | No Comments »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 ...
Installing Sage 4.7 on CentOS 5
Monday, November 7th, 2011 Posted in Linux, Sage, Scientific computing | No Comments »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 ...
Linux kernel 3.1 config for Gentoo guest on VMWare Fusion
Monday, October 24th, 2011 Posted in Linux, Mac | No Comments »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 ...
How to build ScipPy with Python 2.7.2 on CentOS5
Thursday, August 25th, 2011 Posted in Linux, Python, Scientific computing | 1 Comment »EDIT: added --enable-shared to configure script for building Python, and added /home/yourname/lib to shared library path. This is necessary for building some packages such as pycairo (which you may need to build pygtk and matplotlib). EDIT 2: you should use the ...
Replacing text in place with GNU sed
Monday, April 11th, 2011 Posted in Linux, Software development | No Comments »sed is a stream editor, which means that it accepts a stream of text, processes it, and spits out another stream of text. sed can process files that are too large to load into memory, and it is a completely ...
Building and linking to a shared Fortran library
Monday, October 26th, 2009 Posted in Fortran, Linux, Scientific computing | 1 Comment »I'm using GNU Fortran (gfortran) to build several shared libraries, and then dynamically linking to them from a Fortran program. The process is a little different than what I'm used to for C libraries, so I thought I'd explain it. ...
X.org configuration for a Gentoo guest on VMWare Fusion
Wednesday, October 21st, 2009 Posted in Linux, Mac | No Comments »Here is an xorg.conf for a Gentoo guest running in VMWare Fusion on MacOS 10.6 (Snow Leopard). It's surprisingly simple to set up X when the hardware is fake ;) Gentoo runs great on a Macbook Pro 13". I was ...
Kernel configuration for a Gentoo guest in VMWare Fusion
Friday, October 9th, 2009 Posted in Linux, Mac | 5 Comments »I recently installed Gentoo Linux (amd64) as a guest on my Mac (OS 10.6 Snow Leopard) using VMWare Fusion. I thought I'd post the kernel config that I am using, since I didn't find any out there that I trusted. ...
Profiling memory usage of Python code
Friday, April 17th, 2009 Posted in Linux, Python, Scientific computing, Software development | 2 Comments »In a previous post, I explained how to use the Python profiler. The profile is great for finding out which parts of the code run the slowest, or are called most often. However, the profiler doesn't give any information about ...