Linux + LAM MPI + Tree Puzzle
=============================

Shanker Balan
http://shankerbalan.com/

Changelog:

Thu May 22 10:44:08 IST 2003
* Initial commit

###
### Overview
###

The install is straight forward, however users new to the parallel version of
Tree Puzzle might be "puzzled" on how to run the application under LAM for the
first time.

Setup:

1. Install LAM RPM
2. Download and compile tree-puzzle from http://www.tree-puzzle.de
3. Copy the ppuzzle binary to /usr/local

The problem faced by users is that they invoke "ppuzzle" which fails with a
"TREE-PUZZLE needs at least 2 processes for a parallel run"

[raghu@master ~]$ ppuzzle

Halt: TREE-PUZZLE needs at least 2 processes for a parallel run!!!

The parallel version of ppuzzle has to be invoked using "mpirun" like this:

###
### Running ppuzzle under LAM
###

1. Login to master and run "lamboot"

[shanu@master shanu]$ lamboot -v

LAM 6.5.6/MPI 2 C++/ROMIO - University of Notre Dame

Executing hboot on n0 (master - 2 CPUs)...
Executing hboot on n1 (ws1 - 2 CPUs)...
Executing hboot on n2 (ws2 - 2 CPUs)...
Executing hboot on n3 (ws3 - 2 CPUs)...
Executing hboot on n4 (ws4 - 2 CPUs)...
Executing hboot on n5 (ws5 - 2 CPUs)...
Executing hboot on n6 (ws6 - 2 CPUs)...
Executing hboot on n7 (ws7 - 2 CPUs)...
Executing hboot on n8 (ws8 - 2 CPUs)...
Executing hboot on n9 (ws9 - 2 CPUs)...
Executing hboot on n10 (ws10 - 2 CPUs)...
topology done
[shanu@master shanu]$
 
2. Execute "ppuzzle" like this:
          
[shanu@master shanu]$ mpirun -c 2  /usr/local/bin/ppuzzle
          
WELCOME TO TREE-PUZZLE 5.0!
          
Please enter a file name for the sequence data:

3. Stop LAM after the tree-puzzle run

[shanu@master shanu]$ lamhalt -v
LAM 6.5.6/MPI 2 C++/ROMIO - University of Notre Dame

Shutting down LAM
LAM halted
[shanu@master shanu]$

Please refer to the "mpirun" man page for help on running LAM
applications and the usage of the "-c" option.

###
### NOTE
###

I am not a biologist or a Tree-Puzzle user, I just haappened to install it on a
cluster which I help administer for my users. So please dont send me any
tree-puzzle queries, I am as clueless are you are! ;)