Using mpiBLAST

 Using mpiBLAST

This is part one of a two-part tutorial on  mpiBLAST. The full tutorial includes

• Installing mpiBLAST
• Using mpiBLAST

Organization and Setup

Before downloading a bunch of databases to use with mpiblast, it'd be a good idea to make a decision about where the databases are going to be kept. Each user will need to have a profile for it in their home directory telling mpiblast where to find the databases and also where to find work space. These need to be available to all of the worker nodes, so putting the files on an  NFS mount would be a good idea.

Optional components are often kept under /opt. My NFS mount is at /shared, so I'll be putting all of my databases into /shared/opt/mpiblast.

This directory needs to be writable by users so that they can format the databases to be run over different numbers of processes. There are a few different ways to do this. The directory could be set to be world-writeable, so that anyone can write to the directory. This is done with chmod a+w. Another way would be to change the permissions to be group-writeable (chmod g+w), create a new group (addgroup mpigroup), add all the mpiblast users to that group, and change the owner of the directory to that group (chown mpigroup:mpigroup). The second method is more secure, but may take more work to setup the new group and then add the users to the group using  LDAP.

As a third option, you could let users download their own database files and set mpiblast to point within the users' home directories using the .ncbirc fi