More On The Virtues Of VirtualBox – ACID 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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OrthoDB 1.6 Installation On Ubuntu 14.04 (And Related) – Build Errors And The Simple Fixes

And Happy New Year,

Yet another random Ubuntu-centric bioinformatics aside in the event others run into the same build issues (with errors included below, as you likely googled those first). For those wondering…

The Hierarchical Catalog of Orthologs v8

Orthology (website, download) is the cornerstone of comparative genomics and gene function prediction. OrthoDB aims to classify protein-coding genes from the increasing number of available sequenced genomes into groups of orthologs descended from a single gene of the last common ancestor (LCA) of each clade of species. Applying this concept to the hierarchy of LCAs along the species phylogeny results in multiple levels of orthology: the more closely-related the species, the more finely-resolved the orthologous relations.

The build here was on a fresh installation of 64-bit Ubuntu 14.04 (Trusty Tahr). All of the errors produced come from running on that clean install, meaning you’ll run into dumb errors (like missing build-essential), didn’t-know-we-needed-that errors (boost), and that’s-probbly-an-Ubuntu-oddity errors (with a modified Makefile.rules file with explicit boost calls linked to below; I suspect the developers are working on a non-Ubuntu distro).

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Some Recent WordPress Theme Hacking Issues (Mass Emails To Non-Existent Domain Name Addresses) And A Couple Of Things To Look For

I’ve spent the past few weeks making several new email client filters each day, with subject lists that look like the following:

Saturday and Sunday Only! Today’s Special Buy of the Day!

One day sale event – today only, [ insert date here ]

[ insert name here ], check out this weeks specials – up to 75% off on selected items

[ Insert name here ], 10% discount for Brand or Generics for purchases placed before [ insert date here ]

We appreciate your past business with us

[ insert name here ], some of your items are back in stock now – complete your order today

[ insert date here ] deals and savings from your supplier

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Private Internet Access, OpenVPN (2.3.2), and Ubuntu 14.04 (.2 LTS) – Yet Another Reported Way To Get Them Working (And The Only One That Works For Me)

If you sign up for an account with Private Internet Access (and this may go for some other VPN providers as well) and follow the only prominent Ubuntu link (12.04) in the Support Section (www.privateinternetaccess.com/pages/client-support/ubuntu-openvpn), you’ll be taken to a reasonably straightforward 9-step process that walks you through the OpenVPN setup – from the install_ubuntu.sh script download to the selection of PIA-points (I just made that up) in your Network Manager GUI (that radial wifi icon or arrows in the upper-right corner).

That is, for Ubuntu 12.04.

The Problem

If you try this in Ubuntu 14.04, everything more-or-less looks and runs the same way. That said, when you try to connect to a PIA-point in the Network Manager, nothing happens. Your wifi radial doesn’t change, flash, or provide any indication that something has gone right or wrong. More importantly (to the lack of feedback, anyway), you are not asked for your PIA password (having put in your username in the install process). This lack of password requesting turns out to be the real kicker (and diagnostic for the fix presented down below).

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Led Astray By (A) Photon – WordPress, Jetpack, and The Perils Of Embedded Clear Sky Charts (And Other)

A re-post from the CNY Observers website (www.cnyo.org).

Greetings fellow astrophiles,

CNYO has been anticipating our first observing session at Beaver Lake for this year, with the first of our two Spring dates (April 23rd) already clouded/snowed out. The forecast for April 30th hadn’t looked too much better based on Monday estimates, leaving us to wonder if attendees would be stuck indoors with a lecture instead of outdoors with the rest of the universe.

I woke up early on the 30th to blue skies and a very bright Sun, certainly already exceeding the expectations of the past few days. But what of the afternoon and evening?

As I am prone to do on the day of an observing session, I headed right for the CNYO Cheat Sheet, where one can find the sky conditions for a large part of Central New York in the form of several Clear Sky Charts (CSCs – and, based on the different cloud cover at different locations, even begin to piece together how the skies at your location may change). The morning’s CSCs are shown in the image below.

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CNYO Observing Log: The Winter Of Lovejoy – Green Lakes, Jamesville Beach, And New Moon Telescopes HQ – January 9 to 14, 2015

A re-post from the CNY Observers website (www.cnyo.org).

2015jan22_stephen_shaner_lovejoy_small

Caption: Comet Lovejoy imaged on January 10th by the ever-impressive CNY astrophotographer Stephen Shaner. From his CNYO Facebook Group post: Last night was the first in over three months it was clear enough to shoot, but it worked out well because Comet Lovejoy is at its peak. Here’s a quick process of about 40 minutes of exposures between 8-9 PM as it crossed the meridian. FOV is roughly three degrees. Distinct pale green coma in the eyepiece but unable to make out a tail or see it naked eye.

The 2015 skies are going to be full of comets. Well, at least six, to be exact, that will be either naked eye- or binocular-visible. That’s still quite a few to those keeping track! The amateur astronomy community has taken heroic efforts to scientifically identify and track new comets in the last, say, 400 years. The rise of, for instance, the Panoramic Survey Telescope & Rapid Response System (or panSTARRS) as a method for finding and tracking both comets and near-earth asteroids (or, lumped together, “objects,” for which you might hear the abbreviation “NEOs”) has greatly increased the number of accounted-for fuzzy objects in our fields of view (and provided us a giant leap in our existential risk assessment infrastructure to boot). Quite simply, we’ve more + better eyes on the skies, meaning we’re bound to continue to find more and more comets and asteroids. You can even subscribe to NASA twitter feeds that announce the passing-by of these hopefully passers-by (see @AsteroidWatch and @NasaNEOCam).

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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/