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Grafic++ Install with Environment Modules

Grafic++ MPI/C++ code to generate initial conditions for cosmological simulations using multiscale gaussian random fields, based on Edmund Bertschinger's GRAFIC-2 package. Provides a replacement for both grafic1 and grafic2.

Download from sourceforge http://sourceforge.net/projects/grafic/

Extract in a sensible place, change to that directory


cd /usr/local/src/GRAFIC
wget
tar xvf grafic++-1.1.3.tar.gz

Load requisite modules and export FFTW variables (as they won't be found). Seriously, it will drive you nuts if you don't do this.

Espresso Installation with Environment Modules

Espresso (Extensible Simulation Package for Research on Soft matter) is a "highly versatile software package for performing and analyzing scientific Molecular Dynamics many-particle simulations of coarse-grained atomistic or bead-spring models as they are used in soft-matter research in physics, chemistry and molecular biology."

Download the tarball and extract in a sensible place.


mkdir /usr/local/src/ESPRESSO
cd /usr/local/src/ESPRESSO
wget http://download.savannah.gnu.org/releases/espressomd/espresso-3.1.0.tar.gz

Software Freedom Day, 2012

SFD Melbourne 2012

Software Freedom Day: Saturday September 15

Linux Users of Victoria and Free Software Melbourne is hosting Software Freedom Day in Melbourne!

President's and Secretary's Combined Report to the Linux Users of Victoria, Inc, Annual General Meeting, 2012

To begin with it is necessary to say that circumstances has meant that this will be a report that combines the duties of President and Secretary, a matter that will be discussed further. Overall however, looking back over the past year, it can said that this has been another successful for Linux Users of Victoria. Starting from September last year, we hosted a very successful Software Freedom Day, which was extremely well-attended by relevant members of the community, providing an excellent opportunity for networking and planning.

OpenMPI 1.6.1 with PGI compilers installation issue

When installing the latest version of Open MPI (Version 1.6.1) with PGI compilers (specifically 12.5), the installation fails.

The following configure option are set:


CC=pgcc CXX=pgcpp F77=pgf77 FC=pgf90 ./configure --prefix=/usr/local/${BASE}-pgi --with-openib --with-tm=/usr/local/torque/latest --enable-static --enable-share

For Torque "latest" in this context is only 2.4.17, however that shouldn't be the issue. The make fails as follows:


make[6]: Leaving directory `/usr/local/src/OPENMPI/openmpi-1.6.1/ompi/contrib/vt/vt/tools/vtunify'

Dunlop Armour Review - Big W Purchase

Following attempted postings at:
http://www.bigw.com.au/sports-leisure/bikes-accessories/bikes/mountain-b...

I ride approximately 20km per day, to and from work. About half this distance is hills and bends (following a river) and about half is inner urban and mostly flat.

For the past six months I have struggled daily with this bike.

To change gears without the derailleur slipping the upper gears have to turned in the opposite direction to the lower gears. This is not documented in the user and maintenance manual.

Ticker Tape News for Drupal 7

The "marquee" element was originally designed by Microsoft for early versions of Internet Explorer. Rather like Netscape's "blink" element, it is usually thoroughly unloved by web developers, for being proprietory, non-standard, causing usability problems, and is distracting to other content. It is considered deprecated by the W3C and not advised for use in any HTML documents.

MATLAB X-Forwarding, Command Line, and PBS Scripts

Recently it has been noticed that MATLAB bench suite fails when forwarding (by "fails" I mean the applications dies horribly) OpenGL commands. This is not a problem unique to MATLAB, but rather to a range of applications, however there is a simple workaround. My experience is that this a fairly recent problem too, so I shake my fist in futility at certain video card manufacturers who harming scientific research, dammit.

Events and Registration in Drupal 7

One of the more interesting experiences with Drupal version upgrades is the discovery that your favourite third party module is no longer available, or is not ready yet for a production service. This is particularly the case when you're not the person managing the upgrade process. Or better still, you are managing it now, because the first attempt wasn't managed, as such.

OpenFOAM Cluster install with GCC and OpenMPI

OpenFOAM (Open Field Operationa and Manipulation) is a computational fluid dynamics toolbox which simulates "anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics, electromagnetics and the pricing of financial options." All this and free and open source as well.

Note that this installation instructions are substantially different to the version 1.5 install instructions.

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