Lev Lafayette

Underworld is a "3D-parallel geodynamic modelling framework capable of deriving viscous / viscoplastic thermal, chemical and thermochemical models consistent with tectonic processes, such as mantle convection and lithospheric deformation over long time scales.... Underworld utilises a Lagrangian particle-in-cell finite element scheme (the prototype of which is the Ellipsis code), and is visualised using gLucifer."

Also available at the Access Grid website.

Purpose of the Document

The Access Grid is a software suite that provides video, audio and file collaboration, built on well-known streaming audio (Robust Audio Tool, or RAT) and Vic (Video Conferencing tool). This document seeks to help network administrators implement Access Grid with respect to local security policies and firewalls.

This is the procedure for compiling OpenMPI with Portland group versions of C, C++ and Fortran. Part of the continuing adventure of installing Underworld on Wexstan.

First, collect the necessary modules: module load pgi/7.2, Download and extract (tar xvf openmpi-1.3.2.tar.gz) openmpi in the appropriate place (/usr/local/src/OPENMPI).

What do you do when you receive a "bad superblock" error on a USB or other Flash drive? Well, firstly you kick yourself for not backing up important data on said drive for the past nine days; you're old enough to know better than that. Secondly, you kick yourself for using that piece of rubbish called the FAT32 filesystem which was default for Windows 95, but is what every USB drive ships with because it's the last file format released by Microsoft that actually communicates with other operating systems, despite the fact that it's as buggy as hell and is prone to disaster.

From their website.

VAMP/VASP [Vienna Ab-initio Simulation Package] is a package for performing ab-initio quantum-mechanical molecular dynamics (MD) using pseudopotentials and a plane wave basis set. The approach implemented in VAMP/VASP is based on a finite-temperature local-density approximation (with the free energy as variational quantity) and an exact evaluation of the instantaneous electronic ground state at each MD-step using efficient matrix diagonalization schemes and an efficient Pulay mixing. These techniques avoid all problems occurring in the original Car-Parrinello method which is based on the simultaneous integration of electronic and ionic equations of motion. The interaction between ions and electrons is described using ultrasoft Vanderbilt pseudopotentials (US-PP) or the projector augmented wave method (PAW). Both techniques allow a considerable reduction of the necessary number of plane-waves per atom for transition metals and first row elements. Forces and stress can be easily calculated with VAMP/VASP and used to relax atoms into their instantaneous groundstate.

Or, in other words...

Further adventures in attempting to install Underworld 1.2 on Wexstan.

Previous instruction for installing Mesa largely work, but with the following exceptions.

Use a new directory name and run the configuration as modified...


mkdir -p /usr/local/mesa/7.4
./configure --prefix=/usr/local/mesa/7.4-gcc


... and discover a new and interesting failure.


checking for LIBDRM... configure: error: Package requirements (libdrm >= 2.4.3) were not met:

Wextan is a 64 bit Opteron Linux Cluster with 32 Opteron 246 CPUS with 64 Gb Ram and 0.5 Terabytes of Hard Disk Storage running Fedora Core 5. A user wants to install Underworld v1.2 on this machine.

Mesa (why does their website use frames?) is an open source 3D graphics library based on the OGL specification. It's been around since 1993 and is still in regular development, making it quite popular for scientific applications.

NAMD is a parallel molecular dynamics code for large biomolecular systems. Version 2.7b1 has some advantages over 2.6 and an extensive user's guide.

Download the tarball (registration required), put it somewhere sensible (e.g., /usr/local/src/NAMD) and unpack (tar xvf NAMD_2.7b1_Source.tar.gz) and enter that directory.