GROMACS 5.0.x CUDA/GPU Detection Failure With Ubuntu 14.04 nVidia 331.113 Update – Fix With An apt-get

If not for the near-20x speedup I’ve achieved running GROMACS on an nVidia GTX 770 Classified over an Intel i7 Extreme 6-core, nVidia in Ubuntu would almost be more trouble than its worth. The initial installation of the nVidia drivers from the nVidia website works, then the first time Ubuntu auto-updates the drivers to the latest-and-greatest, you’re never entirely sure what the next boot is going to look like – usually a black screen at best. And, if you found this page while looking for a solution to the nVidia driver update black/blank screen, my solution (which has worked without issue to date) is to ditch lightdm and use the GNOME Display Manager (gdm) instead (this apparently appears to be a theme with Ubuntu 14.04 installs on SSD drives as well).

sudo apt-get install gdm

Now, with that settled, the latest update (331.113) broke my GROMACS GPU install (performed using the steps outlined at: GROMACS 5.0.1, nVidia CUDA Toolkit, And FFTW3 Under Ubuntu 14.04 LTS (64-bit); The Virtues Of VirtualBox). The error for my system looks as follows:

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“OrtVc1 failed #1.” Workaround In Gaussian09; Warning About (Pre-)Resonance Raman Spectra In GaussView 4/5

And Happy New Year.

Two issues (one easily addressable, one only by external workaround) related to the prediction of Raman intensities in Gaussian09 – for which there’s next-to-nothing online to address either of them (likely because they don’t come up that often).

OrtVc1 failed #1.

In simulating the Raman spectra of very long (> C60) polyenes as a continuance of work related to the infinite polyacetylene case (see this post for details: Bond Alternation In Infinite Periodic Polyacetylene: Dynamical Treatment Of The Anharmonic Potential), I reached a length and basis set for which Gaussian provides the following output and error:

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The EMSL Basis Set Exchange 6-31G, 6-31G(d), And 6-31G(d,p) Gaussian-Type Basis Set For CRYSTAL88/92/95/98/03/06/09/14/etc. – Conversion, Validation With Gaussian09, And Discussion

Jump to the basis sets and downloadable files here: files, 6-31G, 6-31Gd, 6-31Gdp.

If you use these results: Please drop me a line (damian@somewhereville.com), just to keep track of where this does some good. That said, you should most certainly cite the EMSL and Basis Set references at the bottom of this page.

It’s a fair bet that Sir John Pople would be the world’s most cited researcher by leaps and bounds if people properly cited their use of the basis sets he helped develop.

The full 6-31G, 6-31G(d), and 6-31G(d,p) series (yes, adding 6-31G(d) is a bit of a cheat in this list) from the EMSL Basis Set Exchange is presented here in the interest of giving the general CRYSTALXX (that’s CRYSTAL88, CRYSTAL92, CRYSTAL95, CRYSTAL98, CRYSTAL03, CRYSTAL06, CRYSTAL09, now CRYSTAL14 – providing the names here for those who might be searching by version) user a “standard set” of basis sets that are, for the most part, the same sets one does / could employ in other quantum chemistry codes (with my specific interest being the use and comparison of Gaussian and GAMESS-US in their “molecular” (non-solid-state) implementations). Members of the CRYSTAL developer team provide a number of basis sets for use with the software. While this is good, I will admit that I cannot explain why the developers chose not to include three of the four most famous basis sets in all of (all of) computational chemistry – 3-21G (upcoming), 6-31G(d,p) (presented here), and 6-311G(d,p) (also upcoming).

Continue reading “The EMSL Basis Set Exchange 6-31G, 6-31G(d), And 6-31G(d,p) Gaussian-Type Basis Set For CRYSTAL88/92/95/98/03/06/09/14/etc. – Conversion, Validation With Gaussian09, And Discussion”

Afrika Bambaataa Via DJ Shadow And Cut Chemist, Westcott Theater, 10 November 2014 – Photo Gallery On LiveHighFive.com And Flickr

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A bit of a diversion from the usual posting faire, I had the privilege of catching the Syracuse stop of DJ Shadow and Cut Chemist’s Renegades of Rhythm tour from the other side of the security gate (for the first 10 minutes, anyway, then a bunch from the back). 80% performance and 20% history lesson, the set featured selections from Afrika Bambaataa’s own vinyl collection (current in the process of digitization at Cornell Library, where hip hop’s Amen Ra currently graces the campus as a Visiting Scholar).

The extra-special access provided through arrangement between the performers and Gregory Allis of, among other things, Live High Five. From Greg’s post of the event at livehighfive.com:

DJ Shadow and Cut Chemist brought their touring ethnomusicology lesson to a respectable and excited crowd on a cold Tuesday in Syracuse, NY a few weeks back. After catching the show in Austin during the tour’s first leg, it was pretty much mandatory to follow up with a second helping of tunes cultivated from Afrika Bambaataa’s personal stash. It isn’t often that the longtime friends pair up and bring their skills on the road, but it’s always a spectacle when they do!

A few things need to be said: 1) Hip Hop = DJ’s, MC’s, Breakdancing, and Graffiti, 2) DJ Shadow and Cut Chemist incorporated all those elements into the performance and tour, 3) Afrika Bambaataa deserves every ounce of recognition he has coming to him, and 4) the beginning of Boogie Down Production’s “South Bronx” is one of the hardest things on Earth.

For the full set, off to flickr -> flickr.com/photos/somewhereville/sets/72157649174784268/

Different X-Axis Values, But The Same X-Axis Units – Getting Excel 2013 (OSX-Specific) To Produce Multiple Scatter Plots On The Same Graph

Posting a workaround to re-introduce a feature for Excel 2013 that I think was removed for some reason and for which information on Excel 2013 (OSX-specific) is impossible to find through google searches. It is my hope that newer versions of Excel don’t have this thoroughly annoying problem (and if there’s an obvious way I don’t know about to make this happen in a single shot, feel free to drop a line).

If you found this page via google, I’m going to assume you were searching for something like the following questions (which I’m including below so that search engines find similar questions):

How do I add:
– data with two different X-axes to a single plot in Excel?
– multiple plots to the same graph in Excel with different X-values but the same X-axis units?
– a second dataset to a plot in Excel with new X-axis values?
– a new dataset with different abscissa values in Excel?
– a secondary X-axis to plot new data on the same graph in Excel?

My Scenario – Overlaying Two Spectra On The Same Graph

This issue came up for me when trying to generate some simple spectral overlays in Excel. The problem proceeds as follows:

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“Stu’s Last Lesson” – Sky & Telescope’s Focal Point For December, 2014

As posted on the CNY Observers website (direct link).

Greetings fellow astrophiles,

2014oct23_stuDr. Stuart Forster (a.k.a. STU – full caps) was one of the THE fixtures in the CNY amateur astronomy scene and his name still comes up regularly, often as part of some pearl of wisdom being imparted to new observers and seasoned members alike (I’ll leave you to read the top of the Stuventory page for more info about STU and to check out links to some of his images on the Syracuse Astronomical Society website). The trials and tribulations of Ryan Goodson and myself to handle the massive equipment collection we’ve come to refer to as the “Stuventory” is olde hat to local observers who’ve kept track of the process from a far. The sorting, documenting, and distribution of the Stuventory has taught us both about how very unique the hobby of amateur astronomy can be when you step beyond the 1×7 mm binoculars in your head and effort the collection of more and more photons.

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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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For The Windows-Specific: Sed For Windows And A .bat File To Get Gaussian09 Files Working With aClimax

Provided you’ve installed Sed For Windows and know its proper path, the .bat file below should make all the modifications you need to your Gaussian09 .out files (in differently-named files at that) to get them properly loading in aClimax (see the previous post for all the details). A few simple steps:

1. Download and install Sed for Windows. Currently available at: gnuwin32.sourceforge.net/packages/sed.htm

2. Find its location on your machine. Under XP (where I’m using aClimax), this should be C:\Program Files\GnuWin32\bin

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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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Remembering The Godfather Of Solar Astronomy, Robert “Barlow Bob” Godfrey

As appeared on the CNY Observers & Observing website on 20 June 2014:

The field of amateur astronomy hosts many different personalities. Some love to know anything and everything about astronomy equipment. Some prefer the study of astronomy through the ages. Some enjoy the banter around a large scope with others at midnight. Some enjoy the quiet solitude of a small dome or open field. Still others enjoy setting their equipment up in the middle of the chaos of a large group of people to show them the sights. Some take their love of outreach well past the observing field, taking it upon themselves to educate others by taking what they know (or don’t yet know) and making it accessible to the larger audience of amateurs and non-observers alike.

Amateur astronomy has seen a few key players pass this year, starting with John Dobson this past January and the noted comet hunter Bill Bradfield just a week ago. Both are noteworthy in their passing in that, amongst a large, large number of astro-hobbyists, their names are held in higher esteem because of their unique contributions to amateur astronomy. In the case of Bill Bradfield, he singly was responsible for finding 18 comets that bear his name, making him responsible for helping map part of the contents of our own Solar System from his home in Australia (reportedly taking 3500 hours to do so). In the case of John Dobson, he not only synthesized many great ideas in scope building with his own to produce the class of telescope that bears his name, but he also made it part of his life’s work to bring the distant heavens to anyone and everyone through his founding of what we call today “sidewalk astronomy.”

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