CSCI 3366 (Introduction to Parallel and Distributed Processing), Spring 2001:
Tips for Using MPI on the CS Linux Machines

Overview

You should be able to run MPI programs on any of the CS department's Linux machines, including those in HAS 228 (Janusxx, where xx ranges from 00 through 21), those in HAS 340 (Xenaxx, where xx ranges from 00 through 21), and a new cluster of Linux-only machines (SnowWhite and Dwarfn, where n ranges from 1 through 7). Note that multiboot machines must be running Linux to be usable for this purpose.

Setting up your account

• The MPI-related commands are installed in /usr/local/mpich/bin. You will probably want to add this directory to your path. How to do this depends on which shell your account is set up to use. To find out which shell you are using, type echo $SHELL. The response should be either /bin/bash or /bin/csh.
  • If the response is /bin/bash, edit the file .bash_profile in your home directory. You should see a line that looks like this:

    export USERNAME BASH_ENV PATH

    Just before this line, add a line:

    PATH=$PATH:/usr/local/mpich/bin

  • If the response is /bin/csh, edit the file Local/i386/shell/USER.path in your home directory. You should see a line that looks something like this:

    setenv USERPATH .:$LOCAL/$HOSTTYPE/scripts:....

    Append to the end of this line the characters :/usr/local/mpich/bin. (This is not the standard way of changing one's search path for csh, but it appears to be the only method that works with our local setup.)

  After making either of these changes, log out and log back in again to make the change take effect.

• In order for MPI to start processes on other machines, your account must be set up so that MPI can remotely log into the other machines without prompting for a password. The easiest way to ensure this is by creating a file .rhosts in your home directory containing a list of machine/username combinations from which such logins should be allowed. The file should look something like this with yourname replaced by your username.

  Warning: To avoid a serious security hole, BE SURE that the permissions on this file do not allow others to modify it! (You can use the command chmod go= .rhosts to do this.)

Useful commands

• mpiman: Starts an X-based program that lets you browse man pages for all MPI-related commands and functions. Will not, alas, work if you are remotely logged in via telnet, ssh, or the like.

  An alternative is to read individual man pages with the command

  man -M /usr/local/mpich/man whichpage

  where whichpage is the name of the MPI command or function whose man page you want to read. (Examples are MPI for a general introduction, mpicc for the C compiler, and MPI_Init for the MPI initialization function.)

• mpicc: Compiles C programs using MPI functions.

  Typical usage: mpicc -o foo foo.c

• mpiCC: Compiles C++ programs using MPI functions.

  Typical usage: mpiCC -o bar bar.cpp

• mpif77, mpif90: Compile Fortran 77 and Fortran 90 programs respectively. (Yes, people still write Fortran code.)

• mpirun: Runs an MPI program, starting up a specified number of identical processes.

  Typical usage: mpirun -np 10 foobar (starts 10 processes, each running executable foobar)

  You can specify which machines MPI can use by putting their names in a file and supplying its name via the -machinefile option. So for example you could put a list of allowed machines (the dwarfn machines, e.g.) in file MPIhosts and then say

  mpirun -np 10 -machinefile MPIhosts foobar

  (The file MPIhosts should look something like this.)