Since the early 1990s the x86 line of CPUs has dominated the computer world. Although it has hardly entered popular consciousness that is all changing. A revolution is afoot, as significant as the change from mainframes to clustered or networked systems some twenty years ago. It is time to welcome our new GPU overlords who, in the November 2010 list of the world's supercomputers, have taken 1st, 3rd and 4th position.
Recently a PEW study surprised many by its announcement that most atheists know more about religion that those of strong belief, despite the fact that a majority consider religion to be "very important" to their lives. In other surprise figures, a sizeable minority of Protestants cannot name the gospels and a similar figure of Catholics are unaware of the sacrament of transubstantiation.
The following is a "sufficiently paranoid" approach to upgrading Drupal core and modules. As always, when one is going down this path the first thing to do is put the site in offline mode from admin/settings/site-maintenance.
Then make a back-up of your site, existing modules and themes, and database.
cp -r drupal-site drupalsite-bak
mysqldump drupal6-site > drupal6-site.sql
Download the core modules, based on the suggested updates from admin/reports/updates. You might even want to turn this into a script;
BEAST (Bayesian Evolutionary Analysis Sampling Trees ) "is a cross-platform program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology".
The GROningen MAchine for Chemical Simulations (GROMACS) is a molecular dynamics simulation package that is very fast and has support for different force fields. It is notable for being used for protein folding at Folding@Home.
The Modules Package is a set of commands and information files that provides a simple command interface for modifying the environment. Each module in The Modules Package is a file containing the information needed to initialize the environment for a particular application (or any environment information). It's awesome, and installation is easy. But there is a bug...
Parallel NETCDF is an implementation of the Network Common Data Form which supports parallel I/O. An excellent summary of the advantages are described by Choudhary, Liao, Gao, and Li.
Installation is fairly trivial. Download the tarball from the site, extract, load some modules, configure for the appropriate site, make and make install, and create modules. For example;
wget http://ftp.mcs.anl.gov/pub/parallel-netcdf/parallel-netcdf-1.2.0.tar.bz2
Valgrind is an instrumentation framework for building dynamic analysis tools. Which is a fancy way of saying that it's a debugging suite that automatically detects many memory management and threading bugs, which is a very good thing. Valgrind can handle dynamically generated code, so long as none of the generated code is later overwritten by other generated code. It can also perform detailed profiling to help speed up your programs. It comes with extensive documentation.
MATLAB is a numerical computing environment allowing matrix manipulation, plotting of functions and data, implementation of algorithms, and high-level programming language. Typically it is run on desktop installs, which is quite problematic if one is doing a large computational problem.
It seemed a trivial request, and once you've realised a couple of minor issues it is; install the NCDF library, a common scientific data format, for R, the well-known statistics software.
There is a usual way to install a package in R. Simply load the program and run the install.packages function; but this didn't quite work.
R
>chooseCRANmirror()
>install.packages(c("ncdf"))
