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 LTS (Precise Pangolin) is not much different and goes without hitch provided you keep your locations organized. NOTE 1: I’ve not a copy of Amber12, so cannot speak for any changes to its installation procedure. NOTE 2: This install assumes 32-bit only.

Updated Procedure

If you tried installing all of the build software from the 10.04 LTS post, you’ll receive errors like the following (as usual, I include error messages for those who are searching against error messages)…

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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).

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Crystal06 (v.1.0.2) And MPICH-1.2.7p1 In Ubuntu Desktop 8.10 (and 9.04, 64- and 32-bit) Using The Intel Fortran Compiler, Version 1.0

Update 19 May 2009 – This tutorial (and all subsequent modifications) are now on a separate page on this website and will not be modified further in this post.  This page is available HERE.  The forever-name PDF version of the tutorial is available here: crystal06_mpich_ubuntu_cluster.pdf

Pre-19 May 2009 – This document, the end of a very long and involved process, is available as a PDF download (for reading and printing ease) here: crystal06_mpich_ubuntu_cluster_V1.pdf

Introduction

According the Crystal06 manual:

The CRYSTAL package performs ab initio calculations of the ground state energy, energy gradient, electronic wave function and properties of periodic systems. Hartree-Fock or Kohn-Sham Hamiltonians (that adopt an Exchange- Correlation potential following the postulates of Density-Functional theory) can be used. Systems periodic in 0 (molecules, 0D), 1 (polymers, 1D), 2 (slabs, 2D), and 3 dimensions (crystals, 3D) are treated on an equal footing. In each case the fundamental approximation made is the expansion of the single particle wave functions (‘Crystalline Orbital’, CO) as a linear combination of Bloch functions (BF) defined in terms of local functions (hereafter indicated as ‘Atomic Orbitals’, AOs).

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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).

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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).

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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.

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Amber And Ubuntu Part 1. Amber10 (Serial Execution) Installation In Ubuntu 8.10 (Intrepid Ibex)

Posted here is a procedure for building a serial execution (not parallel, that is en route as part of an upcoming post) version of Amber10 under Ubuntu 8.10 (Server or Desktop, makes no difference)…

[15 March 2009: In case you miss it while searching, the MPI build of Amber is provided in a future link.  Check out www.somewhereville.com/?p=437 for installation and commentary.]

Ubuntu continues to be a pleasantly stable and very, very clean Linux distribution (although my last Ubuntu post about a minor glitch was only a few weeks ago).  That said, for the typical research user perhaps not used to dealing with either Linux distributions or code compilation, it may appear to be a little too clean.  In my previous learning endeavors with Fedora and OpenSuse, I often found myself installing the entire DVD for fear of missing an important library or some random program (almost entirely unnecessary after you learn your way around a distribution, but when your hard drives break the 200 GB point, what’s a waste of 5 GB when you don’t have to dig up the DVD again?).  With the standard Ubuntu installation and an internet connection, your only problem becomes determining which programs and libraries are needed to complete a compilation from source.

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Changes To ions.itp Format For AMBER Implementations In GROMACS 3.3.x

No idea how to best propagate a change in a text file (amber_ions.txt) needed for running a force field (ffAMBER) in an open source program (GROMACS), so letting the RSS aggregators do as much of the work as possible.

Alan Wilter S. da Silva, D.Sc., CCPN Research Associate,Department of Biochemistry, University of Cambridge (yes, that one), pointed out a formatting error in the previous version of my ions.itp file (posted on this site as amber_ions.itp, which only identifies it as an AMBER-specific file).

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sed-Based Script For Converting NAMOT And NAMOT2 DNA Output To GROMOS96 Format For GROMACS Topology Generation v1

NOTE: This script works with additions to the ffG53a5/6.rtp (residue topology) files. This information is available at Modifications To The ffG53a6.rtp And ffG53a5.rtp Residue Topology Files Required For Using GROMOS96-NAMOT-GROMACS v1.

The script below is the precursor to the ffAMBER/NAMOT/GROMACS script posted previously. This script takes the output of a NAMOT or NAMOT2 DNA structure generation (.pdb) and does all of the atom label and atom label position conversions, correct 3′and 5′terminal H atom assignments, and makes changes throughout the .pdb file to provide something that should flow seamlessly into the GROMACS pdb2gmx .top generator for the GROMOS96 force field.

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sed-Based Script For Converting NAMOT And NAMOT2 DNA Output To ffAMBER Format For GROMACS Topology Generation v1

In continuing efforts to streamline the simulation of atomistic DNA structures in GROMACS using the ffAMBER force field (the port of AMBER for GROMACS), the following script takes the .pdb output of NAMOT or NAMOT2 and does all of the atom label and atom label position conversions, correct 3′ and 5′ terminal H atom assignments, and random changes throughout the .pdb file to provide something that should flow seamlessly into GROMACS.

“Did you need to post the entire script and not just provide the downloadable text file as a link?” Of course, as I suspect no small number of people looking for how to convert a NAMOT pdb file into ffAMBER-speak will begin by searching based on GROMACS errors, which occur one missing residue label at a time. Hopefully, having the entire script readable by google and yahoo will cause it to pop up high in the search ranking.

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