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 … Continue reading “More On The Virtues Of VirtualBox – ACID Under Ubuntu 14.04 (By Way Of OpenSuse 11.2)”

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 … Continue reading “OrthoDB 1.6 Installation On Ubuntu 14.04 (And Related) – Build Errors And The Simple Fixes”

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 … Continue reading “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)”

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

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

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

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

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 … Continue reading “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)”

Brief Update: Amber 11 And AmberTools 1.5 In Ubuntu 12.04 LTS

This post is a brief update to a much longer and more involved discussion of Amber 11 and AmberTools installation in Ubuntu 10.04 LTS (Lucid Lynx) (as the changes are minor and the parallelization setup remains largely the same). You can find this more involved discussion at www.somewhereville.com/?p=1422. Long/Short – the installation under Ubuntu 12.04 … Continue reading “Brief Update: Amber 11 And AmberTools 1.5 In Ubuntu 12.04 LTS”

Abinit 6.8.1 In Parallel With OpenMPI 1.4.1 In Ubuntu 10.04.2 LTS (And Related)

It has been a banner week for Ubuntu installations. The installation of Abinit 5.6.5 with OpenMPI 1.3.1 (previously reported at www.somewhereville.com/?p=384) wasn’t bad, but several games had to be played (at the time) to make everything compile and run correctly. I’m pleased to report that Abinit 6.8.1 and OpenMPI 1.4.1 seem to play better together, … Continue reading “Abinit 6.8.1 In Parallel With OpenMPI 1.4.1 In Ubuntu 10.04.2 LTS (And Related)”