More On The Virtues Of VirtualBox – ACID (or AICD) Under Ubuntu 14.04 (By Way Of OpenSuse 11.2)

“Stop that!” – George Carlin

If you’ve obtained source code from an academic lab that was last developed some time ago and you spent a whole day installing libraries and symbolic links and redefining variables in your .bashrc and downgrading libraries and redefining paths and have 20 tabs open in your browser that all go to 20 different obscure error discussions on Stack Overflow and it’s late and you’re tired and you think you might not need the program after all if you do a bunch of other workaround things instead – what’s below is for you.

Academics have been developing small code for (nearly) millions of years to make their lives easier – and we all benefit when that code is made available to others (esp. when it helps in data analysis). When that code is a series of perl or python scripts, there’s generally little reason why you should have any run issues. When they call on external libraries or specific tools, generally that information is available in the README somewhere. Generally speaking, there’s no reason why a code shouldn’t work in a straightforward manner when the developer doesn’t make it known that something else needs be installed to make it work.

So, why doesn’t code A work on your linux box? A few possibilities.

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GROMACS 5.0.1, nVidia CUDA Toolkit, And FFTW3 Under Ubuntu 14.04 LTS (64-bit); The Virtues Of VirtualBox

Summarized below are the catches and fixes from a recent effort to build GROMACS 5.0.1 with FFTW3 (single- and double-precision) and GPU support (so, single-precision). Also, a trick I’ve been doing with great success lately, using a virtual machine to keep my real machine as clean as possible.

0. The Virtues Of VirtualBox

Open source means never having to say you’re sorry.

I’ve made the above proclamation to anyone who’d listen lately who has any interest in using Linux software (because, regardless of what anyone says on the matter, it ain’t there yet as an operating system for general scientific users with general computing know-how). You will very likely find yourself stuck at a configure or make step in one or more prerequisite codes to some final build you’re trying to do, leaving yourself to google error messages to try to come up with some kind of solution. Invariably, you’ll try something that seems to work, only to find it doesn’t, potentially leaving a trail of orphaned files, version-breaking changes, and random downgrading only to find something else stupid (or not) fixed your build problems.

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Stupid-Simple (*nix-Specific) Sed Scripts To Get (All Current) Gaussian09 Output Files Working With aClimax

The following three snippets of Gaussian output are for an optimization and normal mode analysis of simple olde methane (CH4).

...
 ******************************************
 Gaussian 03:  EM64L-G03RevE.01 11-Sep-2007
                31-Aug-2014 
 ******************************************
...
 incident light, reduced masses (AMU), force constants (mDyne/A),
 and normal coordinates:
                     1                      2                      3
                     T                      T                      T
 Frequencies --  1356.0070              1356.0070              1356.0070
 Red. masses --     1.1789                 1.1789                 1.1789
 Frc consts  --     1.2771                 1.2771                 1.2771
 IR Inten    --    14.1122                14.1122                14.1122
 Atom AN      X      Y      Z        X      Y      Z        X      Y      Z
   1   1     0.02  -0.42   0.43    -0.34  -0.13  -0.08    -0.36  -0.23  -0.23
   2   6     0.00   0.08  -0.09     0.00   0.09   0.08     0.12   0.00   0.00
...
 -------------------
 - Thermochemistry -
 -------------------
 Temperature   298.150 Kelvin.  Pressure   1.00000 Atm.
 Atom  1 has atomic number  1 and mass   1.00783
...

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