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OpenMPI-PGI on a 64 bit Opteron Fedora Core 5 Cluster

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).

Bad superblock recovery

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.

Installating VASP on 64-bit AMD Opteron Cluster CentOS 5 Linux

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...

Mesa and LIBDRM on a 64 bit Opteron Fedora Core 5 Cluster

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:

PETSc on a 64 bit Opteron Fedora Core 5 Cluster

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.

Installing 32 and 64 -bit Versions of Mesa Graphics Library

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.

Installing NAMD 2.7b1 on a 64-bit AMD Opteron Cluster running CentOS 5 Linux

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.

Harlequin: An Obituary

On Saturday, February 26, 2005, Harelquin the rat died.

He had been in decline for some time, his back legs slowly giving up. On Thursday evening he had stopped eating altogether which caused great concern. However on Friday evening the presentation of some oat and apple baby food was graciously accepted.

Kaben par Andre no Catharina.

Kaben par Andre no Catharina.

Istoria ida iha Tetum, Lingua iha Timor Lorosa'e. Ho inspirisaun ba Connie Willis.

Para Leonardo do Lafayette.

Bom dia hau-nia kolega,

Hau hakarak ko'alia istoria ida kona ba kaben par Andre no Catharina.

Istoria ne iha kona ba mestri bulak no labele sasan,
folia rai ida, lahatene rai, hanoak ahioan ida,
relojiu ahi ida (nebe tenki hadia), be buan ida, no
At-Loron Livre ne. Be ko'alia nada kona ba asu.

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