GROMACS 4.5.5, OpenMPI 1.6, And FFTW 3.3.2 Compilation Under Mountain Lion (OSX 10.8) With XCode (And A Little Help From Homebrew)

Minus a few glitches easily fixed with the right software, this build wasn’t bad at all (and thanks to Adam Lindsay for the title catch).

Now sitting in front of a new Core i7 MacBook Pro, one of the first compilations I wanted to have finished for new projects was GROMACS 4.5.5. As my procedure for compiling GROMACS 3.3.3 had been a highly-traveled page, I wanted to provide a brief summary of my successful 4.5.5 compilation.

A Few Piece Of Info

1. XCode

This used to be disc-download and install, now it’s available as a free download from the App Store (1.57 GB download, so plan to do something else while you wait for the download).

Continue reading “GROMACS 4.5.5, OpenMPI 1.6, And FFTW 3.3.2 Compilation Under Mountain Lion (OSX 10.8) With XCode (And A Little Help From Homebrew)”

Amber 11 And AmberTools 1.5 In Ubuntu 10.04 LTS (And Related, Including A How-To For EOL 8.10)

Having successfully navigated serial and parallel Amber10 installs under Ubuntu 8.10, I am pleased to report that the process for Amber11 with OpenMPI (from apt-get, one doesn’t have to build from scratch) under Ubuntu 10.10 is seemingly much easier (and have it here so I don’t forget). There is a bit of persnicketiness to the order of the serial and parallel installs that must be kept track of (and I’m building in serial-to-parallel order), but the process is otherwise straightforward.

For organizational purposes, I’m building amber11 in my $HOME directory. This removes some of the PATH issues with sudo-ing aspects of the install (and can be moved into another directory after the build is complete).

1. apt-get Installs

The search for dependent programs and libraries is a long and involved one given how many programs I have installed. Therefore, instead of trying to find all of the amber-dependent installs for successful building, I’m simply providing the list of everything I have on the test machine. As hard drives are cheap and Ubuntu will warn of conflicts, I recommend simply installing the below and accepting the 100 Mb hit to NOT have to find the smallest apt-get set (yes, some of these are obviously not needed).

Continue reading “Amber 11 And AmberTools 1.5 In Ubuntu 10.04 LTS (And Related, Including A How-To For EOL 8.10)”

Installing And Mounting Network Drives Using NFS In Ubuntu (And Generally)

This is another piece in an Ubuntu puzzle that, when assembled, will describe how to set up an MPI (message passing interface) computer cluster for running parallel calculations (upcoming).  As a brief explanation of what’s going on, many of the MPI (OpenMPI, MPICH, MPICH2) set-up procedures you may stumble across online describe how to use the network file system (NFS) protocol to set up one directory on a host node (head node/server node/master node/whatever) of your cluster so that, by mounting a directory on a guest node (client node/slave node/whatever) to this network-accessible drive, the head and guest nodes all see the same work directory and executables (both MPI and your program of choice).  There are more clever ways to set the cluster up that will likely run at a slightly faster pace than NFS may allow, but we’ll ignore that at the moment.  The install procedure below is Ubuntu-specific only in the apt-get stage (NFS support is not part of the default installation).  After all of the components are installed (post-apt-get), the setup should be Linux-universal.

LEGEND

Text in black – my ramblings.

Text in bold red – things you will type in the Terminal

Text in green – text you will either see or will type into files (using pico, my preference)

Below is all I need to do in Ubuntu to do what I need it to do.  I’ll be dividing the installation procedure into HOST and GUEST sections for organizational purposes.

Continue reading “Installing And Mounting Network Drives Using NFS In Ubuntu (And Generally)”

Building Parallel Abinit 5.6.x With OpenMPI 1.2.x (And NOT OpenMPI 1.3.x) From Sources In Ubuntu 8.x – iofn1.F90 Problem Solved

This post is an update to my previous post on building Abinit with OpenMPI in Ubuntu, with this post providing a workaround (solution?) to a run-benign but ultimately thoroughly aggravating issue with starting calculations in the abinip parallel build.

The description of the procedure, and the problem in the OpenMPI 1.3.x build, is as taken from the previous page (repeated so that the error makes its way and embeds itself a little deeper into the search engines).

To run parallel Abinit on a multi-processor box (that is, SMP.  The actual multi-node cluster setup is in progress), the command is SUPPOSED to be follows:

mpirun -np N /opt/etsf/abinit/5.6/bin/abinip < input.file >& output

Where N is the number of processors.  For mpirun, you need to specify the full path to the executable (which, for the build above, is as Abinit installs abinip when the build occurs in the /opt directory).  The input.file specification is as per the Abinit users manual so I won’t go into it here. You will also be asked to supply your password because I’ve done nothing to the setup of ssh (you are, in effect, logging into your machine to run the MPI calculation).

Continue reading “Building Parallel Abinit 5.6.x With OpenMPI 1.2.x (And NOT OpenMPI 1.3.x) From Sources In Ubuntu 8.x – iofn1.F90 Problem Solved”

Amber And Ubuntu Part 2. Amber10 (Parallel Execution) Installation In Ubuntu 8.10 (Intrepid Ibex) With OpenMPI 1.3… And Commentary

After considerable trial and building/testing errors, what follows is as simplified a complete installation and (non-X11/QM) testing of Amber10 and OpenMPI 1.3 as I think can be procedure’d in Ubuntu 8.10 (and likely previous and subsequent Ubuntu versions), dealing specifically with assorted issues with root permissions and variable definitions as per the standard procedure for Amber10 installation.

I’ll begin with the short procedure and bare minimum notes, then will address a multitude of specific problems that may (did) arise during all of the build procedures.  The purpose for listing everything, it is hoped, is to make these errors appear in google during searches so that, when you come/came across the errors, your search will have provided some amount of useful feedback (and, for a few of the problems I had with previous builds of other programs, this blog is the ONLY thing that comes up in google).

Continue reading “Amber And Ubuntu Part 2. Amber10 (Parallel Execution) Installation In Ubuntu 8.10 (Intrepid Ibex) With OpenMPI 1.3… And Commentary”

Building Abinit 5.6.5 (And Other Versions) And OpenMPI 1.3 (And Others) From Sources In Ubuntu 8.10 (Intrepid Ibex)

NOTE 25 March 2009: The problem with Open-MPI and Abinit is related to the version of Open-MPI.  1.3.x is used below, while 1.2.x allows you to use the .files for running batch-based Abinit calculations.  See www.somewhereville.com/?p=590 for additional notes.

The purpose of the HPLIP fix reported in a previous post was to install Abinit in Ubuntu via apt-get in order to employ the procedure used by Hooper et al in Chemical Physics Letters to calculate infrared intensities in the low-frequency region for solid-state terahertz (THz) assignments (phew!).  The problem is that the apt-get install of Abinit is an older and serial (non-parallel) version.  Further compounding the problem, the OpenMPI version one can install via apt-get (sudo apt-get install openmpi-bin) does not have F90 (Fortran 90) support, so one cannot simply install OpenMPI, install one of the pre-compiled versions of Abinit, and start using those other processors either on the board or plugged into a gigabit switch.

Continue reading “Building Abinit 5.6.5 (And Other Versions) And OpenMPI 1.3 (And Others) From Sources In Ubuntu 8.10 (Intrepid Ibex)”