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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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).

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Examining The Effects Of Vitamin B12 Conjugation On The Biological Activity Of Insulin: A Molecular Dynamic And In Vivo Oral Uptake Investigation

Published in MedChemComm (direct link: xlink.rsc.org/?doi=C2MD20040F). And Happy Belated New Year. After the methodological work that went into the Molecular Biosystems paper, this was a remarkably simple molecular dynamics study of the changes to vitamin B12 binding in transcobalamin II (TCII) with the B12 conjugated to the first amino acid side chain in the B-Chain of insulin. The structure of the B12-insulin conjugate is shown below in a molecular dynamics snapshot, which reveals that the binding of B12 to its TCII transport protein is negligibly affected.

And apparently the experiments went well, too. Cover hopefully to follow.

Susan Clardy-James, Damian G. Allis, Timothy J. Fairchild and Robert P. Doyle

Abstract: The practical use of the vitamin B12 uptake pathway to orally deliver peptides and proteins is much debated. To understand the full potential of the pathway however, a deeper understanding of the impact B12 conjugation has on peptides and proteins is needed. We previously reported an orally active B12 based insulin conjugate attached at LysB29 with hypoglycaemic properties in STZ diabetic rats. We are exploring an alternative attachment for B12 on insulin in an attempt to determine the effect B12 has on the protein biological activity. We describe herein the synthesis, characterization, and purification of a new B12-insulin conjugate, which is attached between the B12 ribose hydroxyl group and insulin PheB1. The hypoglycemic properties resulting from oral administration (gavage) of such a conjugate in STZ diabetic rats was similar to that noted in a conjugate covalently linked at insulin LysB2911, demonstrating the availability of both position on insulin for B12 attachment. A possible rationale for this result is put forward from MD simulations. We also conclude that there is a dose dependent response that can be observed for B12-insulin conjugates, with doses of conjugate greater than 10-9 M necessary to observe even low levels of glucose drop.

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, this simplified considerably over the previous installation guide by the use of the apt-get version of OpenMPI 1.4.1. A bit of option calling in the configure step is needed (and the errors for not doing it are included below).

0. For the Antsy Copy+Paste Crowd

Commands below.

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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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Running (Only) A Single-Point Energy Calculation In Crystal06/09, Proper Input Format For Long-Range Dispersion Contributions In Crystal09, And Removing The MPICH2 Content From The Output File In Pcrystal

Now enjoying the benefits of dispersion-corrected solid-state density functional theory (and a proper MPICH2 implementation for infrared intensity calculations, although this now a problem for reasons to be addressed in an upcoming post) in Crystal09, three issues in recent calculations caused me to think hard enough about keyword formats and job runs that I have opted to post briefly about what to do in case google and bing are your preferred methods of manual searching.

1. How To Run Only A Single-Point Energy Calculation In Crystal06/Crystal09

This had never come up before and, by the time I needed to find an input file to see what do to, the first google search provided Civalleri’s Total Energy Calculation page that currently has broken links to .zip files. There is quite a bit about the different geometry optimization approaches in the manual, but a search for “single-point” provides no information about what to do for only single-point energy calculations.

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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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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.

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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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