M471 HAMMER USAGE NOTES


(1) Compiling C code: 
Use the wrapper script "mpicc".  This command runs the cc compiler
with the correct include and library paths for MPI and related
libraries. 

% mpicc -o hello hello.c


(2) Compiling Fortran code: 

Use the wrapper script "mpif90".  This command runs the IBM xlf
compiler with the correct include and library paths for MPI and related
libraries. 

% mpif90 -o hello hello.f90


(3) Running MPI code: 

To run on the frontend on 4 processors:

% mpirun -np 4 ./hello 

Note: dont make long running jobs on the frontend, since
this is the machine we all use for editing, compiling 
and debugging when logged in to hammer.  This command will run
4 processes, but since the frontend only has 2 physical processors,
this will not be very efficient for programs that do significant
computation.  It is mostly useful for debugging.  You can see how 
busy the frontend "hammer.hpc.uhnm.edu" machine is by running
% top -o cpu



(4) Running MPI code on the Hammer backend interactively:

Request 2 nodes, 2 cpus per node, interactive, for 900 seconds.
(These nodes will be assigned exclusively to you)

% qsub -I -l nodes=2:ppn=2,walltime=900</tt>
[cd into directory with "hello" command]
% mpirun -machinefile $PBS_NODEFILE -np 4 ./hello

Note: without the "-machinefile $PBS_NODEFILE" option, mpirun will
run all 4 of the "hello" processes on a single node 
(which only has 2 processors).  

To exit an interactive login and return to the Hammer frontend
machine (freeing up the requested nodes for other users),
type "exit"




(5)  To run an MPI code as a batch job, issue the command:</li></h3>

% qsub < batch.job

where batch.job is a script that could look like this:


#!/bin/tcsh -f
#PBS -N yourjobname
#PBS -l nodes=3:ppn=2
#PBS -l walltime=900
cd simple
mpirun  -np 6 -machinefile $PBS_NODEFILE simple





The "yourjobname" is the name you want to assign to your job.
That is the job name that will show up with anyone runs "qstat"
and the output (what you would see on the screen when running
interactively) will be in two files:

   yourjobname.o####
   yourjobname.e####

The output is in the ".o" file, and error messages, if any, are
in the ".e" file.



(6)  Monitoring the status of jobs. 

To see information about running jobs and queues, try:
% qstat

For detailed information about a job in the queing system, type:
% qstat -f ####
where #### is the job number shown by "qstat"

For detailed information about the Math 471 que itself:
% qstat -Q -f ma471


To remove a job from the que: 
% qdel ####
where #### is the job number shown by the qstat command.