mpiBLAST: Open-Source Parallel BLAST

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Installation Guide

This installation guide is for the mpiBLAST-2.x series which is significantly different from the older mpiBLAST-1.x series. Steps to install mpiBLAST-1.x can be found here.

After installing mpiBLAST-2.0, please refer to the mpiBLAST-2.0 User's Guide for instructions on how to use mpiBLAST-2.0.

Please report all mpiBLAST-2.0 installation troubles to the mailing list

Installation for Unix/Linux/BSD/MacOS X

There are three steps to installing mpiBLAST from source.

  1. Install MPI (if not already installed)
  2. Obtain and Compile the NCBI C++ Toolbox
  3. Obtain and Compile mpiBLAST

Each of these steps are described in more detail below.

1) MPI installation

A successful installation of MPI is required for mpiBLAST to work but mpiBLAST does not require any particular implementation. If your machine(s) does not have an implementation of MPI already installed, there are several popular free implementations of MPI available, such as MPICH2 and Open MPI. However, many Unix/Linux/BSD distributions have an MPI implementation available through a package-managment system (apt-get, yum, yast, etc.), making an installation from source unnecessary.

Help with installing MPI on your machine(s) should be directed to the appropriate MPI implementor and not to mpiBLAST as they will have much greater knowledge about solving your problem.

2) Obtain and Compile the NCBI C++ Toolbox

2.1) Obtain the NCBI C++ Toolbox

2.2) Extract the NCBI C++ Toolbox

tar -xzf ncbi_cxx--Aug_14_2006.tar.gz

2.3) Move into the NCBI C++ Toolbox

cd ncbi_cxx--Aug_14_2006

2.4) Configure the NCBI C++ Toolbox

Needed build Packages: serial, objects, dbapi, algo

Unneeded build Packages: app, gui, connext, ctools

(building with dynamic libraries will decrease file sizes by 100x!)

./configure --with-dll --with-serial --with-objects --with-dbapi --with-algo --without-app --without-gui

A more aggresive configure line

./configure --with-dll --with-serial --with-objects --with-dbapi --with-algo --without-app --without-gui --without-opengl --without-sqlite3 --without-ftds --without-freetype --without-jpeg --without-png --without-tiff

2.4) Build/Compile the NCBI C++ Toolbox (this can take more than 45 minutes!)


3) Obtain and Compile mpiBLAST

3.1) Obtain mpiBLAST-2.0 (available August 1, 2007)

3.2) Move into the mpiBLAST-2.0 directory

cd mpiBLAST-2.0

3.3) Build mpiBLAST-2.0

make builddir=/path/to/ncbi_cxx/<compiler>/build

Installation for Windows

There is no current mpiBLAST-2.0 installation guide for Windows as we do not have hardware to test on. However, if you do install mpiBLAST-2.0 on Windows, please inform us so that we can publish the installation steps here.

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