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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OrthoDB 1.6 Installation On Ubuntu 14.04 (And Related) – Build Errors And The Simple Fixes

UPDATE: 20 May 2016 – With thanks to OrthoDB’s very own Fredrik Tegenfeldt, here’s a more distro-complete fix for the Makefile.rules file.

# BRH flags
ifeq ($(USE_BRH),1)
BRH_DIR        = $(BASE_DIR)
CPPFLAGS    += -I$(BRH_DIR)/src
ifeq ($(WITH_RPATH),1)
LDFLAGS        += -L$(LIB_DIR) -Wl,-rpath,$(LIB_INSTDIR)
else
LDFLAGS        += -L$(LIB_DIR)
endif
LDLIBS        += -lbrh
endif

ifeq ($(USE_BOOST_THREAD),1)
CPPFLAGS    += -pthread -DHAS_BOOST_THREADS
LDFLAGS        += -pthread
LDLIBS      += -L$(DIR_BOOST_LIB) -lboost_system -L$(DIR_BOOST_THREAD) -l$(LIB_BOOST_THREAD) -lpthread
endif

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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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)

Update: 17 May 2016 – Doesn’t happen often and is always nice to see. Thanks to Lucas Nell (on 26 April – that’s my bad) for taking one additional step out of the whole process with the script below. Simply replace “[put-your-password-here]” with your actual password (and no brackets), same the below as some_name.script (or whatever), chmod +x some_name.script to make it official, and you’re good to go to make the additional mod.

sudo -s

cd /etc/NetworkManager/system-connections

export pwd="\n[vpn-secrets]\npassword=[put-your-password-here]"

for f in PIA*
do
  sed -i 's/password-flags=1/password-flags=0/g' "${f}"
  echo -e "${pwd}" >> "${f}"
done

exit

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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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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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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Generating Molecular Orbitals (And Visualizing Assorted Properties) With The Gaussian09 cubegen Utility

To begin, this post owes its existence to the efforts of Dr. Douglas Fox at Gaussian, Inc., who provided me with an alternative explanation of how the cubegen utility works. After much wailing and gnashing of teeth, I intend on taking Dr. Fox’s advice and asking Gaussian Support for assistance earlier in my endeavors. What follows below, I hope, will save you some significant frustration (and, given how little there is online that really describes the extra workings of cubegen in a clear and example’ed way, it is my expectation that this page appeared early in your search list).

What I wanted out of cubegen that I couldn’t figure out how to get:

The situation was simple. I wanted my molecule centered and bound within an arbitrarily-sized box (X,Z,Y) for making images and doing additional post-processing. Specifically, I wanted to be able to take many different molecules (from hydrogen gas to big biomolecules) defined within the same-sized box for layering and presentation (different boxes for each, but all the same size).

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Compiling And Running GAMESS-US (1 May 2013(R1)) On 64-bit Ubuntu 12.X/13.X In SMP Mode

Author’s Note 1: It is my standard policy to put too much info into guides so that those who are searching for specific problems they come across will find the offending text in their searches. With luck, your “build error” search sent you here.

Author’s Note 2: It’s not as bad as it looks (I’ve included lots of output and error messages for easy searching)!

Author’s Note 3: I won’t be much help for you in diagnosing your errors, but am happy to tweak the text below if something is unclear.

Conventions: I include both the commands you type in your Terminal and some of the output from these commands, the output being where most of the errors appear that I work on in the discussion.

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CudaMiner Installation In Ubuntu 12.04 LTS Using CUDA Toolkit 5.5 And “Additional NVIDIA Drivers”

Author’s Note 1: It is my standard policy to put too much info into guides so that those who are searching for specific problems they come across will find the offending text in their searches. With luck, your “build error” search sent you here.

Author’s Note 2: It’s not as bad as it looks (I’ve included lots of output and error messages for easy searching)!

Author’s Note 3: I won’t be much help for you in diagnosing your errors, but am happy to tweak the text below if something is unclear.

Conventions: I include both the commands you type in your Terminal and some of the output from these commands, the output being where most of the errors appear that I work on in the discussion.

Input is formatted as below:

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Compiling LAMMPS (3Apr13, But Likely Others) In Ubuntu 10.04 Part 1. Using MPICH2 And FFTW2 (And Ubuntu Notes On Installing Intel Fortran And C++ Composers XE for Linux)

I’ll qualify this post by saying that (1) I have given up on Ubuntu 11.x and 12.x because they are consistently unstable on my hardware (so, if you have issues running this installation on those versions, I may not be of much help (although I suspect things should work)), (2) I am starting this install from a fresh 32-bit Desktop Ubuntu 10.04 install (so do not know if there are any issues with other software one might have installed on a Linux box if a problem comes up), and (3) the procedure comes out of the current lack of an Ubuntu binary currently listed as available (as of 6 April 2013) from the LAMMPS website (lammps.sandia.gov/download.html#ubuntu). If (3) changes and is available in an MPI form, what’s below will hopefully be unnecessary.

Building Trouble And Solutions

My initial “just unzip, untar, and make linux” attempt on a fresh 10.04 install produced the following error (which I’m reproducing in the expectation that you found this page by typing one of the errors below into a search engine, so you’ll find the error and the solutions). NOTE: I build all my programs in /opt for organizational purposes (so replace accordingly):

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