COMP4300/6430: Laboratory 1

COMP4300/6430 2011: Laboratory 1

Introduction to the NCI Xe System and MPI
DRAFT

The aim of this lab is get up and running on the NCI Xe system and give you an introduction to MPI.

To do this lab, you need to have obtained a login ID and password by following the instructions on the main lab web page.

The Xe is one of the systems supported by the National Computational Infrastructure program. Staff at Australian Universities are allocated time on this system through a competitive process for use in their research projects. We are extremely fortunate to have been given access to this system for this course. Please use the machine with respect. Note that it is NOT administered by the CS Technical Support Group. There is comprehensive documentation for the NCI Xe system available HERE. You should familiarize yourself with the content. It will be referenced in what follows. Log on to the xe system using your user ID

   ssh xe.nci.org.au -l apr659

Each user has a file space quota. CPU time is also limited collectively over the entire group. This means one user can exhaust all the time of the entire group. Thus please monitor your usage of this machine. Read the pages of the userguide that refer to "Project Accounting", and "Monitoring Resource Usage". On the Xe execute the following commands and determine what they do

nf_limits
quotasu -h
quota -v

Example Programs

A tar file containing all the programs for this lab is available HERE. Save this tar file on your local desktop and then transfer it to the Xe system. Thus from a terminal window on your desktop and in the directory where you have saved the lab1.tar file execute the scp command (replacing apr659 with your login id on the xe system).

  scp lab1.tar apr659@xe.nci.org.au:~

then in a terminal window that is logged on to the Xe untar the file

  tar -xvf lab1.tar

Modules

Before we can compile the above programs we have to set our login environment so that it finds the correct compilers and libraries. The NCI systems achieve this using Linux "modules". Return to the userguide and read the section labelled "Software Environments". Then execute the command

module avail

You can both load and unload a module. For this lab we need to load the "openmpi" module. Do this by executing the command

module load openmpi

`mpiexample1.c`

This program is just to get started. It looks like:

#include  
#include "mpi.h" 
 
int main( argc, argv ) 
int  argc; 
char **argv; 
{ 
    int rank, size; 
    MPI_Init( &argc, &argv ); 
    MPI_Comm_size( MPI_COMM_WORLD, &size ); 
    MPI_Comm_rank( MPI_COMM_WORLD, &rank ); 
    printf( "Hello world from process %d of %d\n", rank, size ); 
    MPI_Finalize(); 
    return 0; 
}

Note there are 3 basic requirements for ALL MPI codes

    #include "mpi.h"
    MPI_Init( &argc, &argv ); 
    MPI_Finalize();

You can find the header file in /apps/openmpi/1.4.3/include/mpi.h. Take a look at it. It provides the definition of MPI_COMM_WORLD ...in a complicated fashion involving another structure that is defined in another routine that forms part of the library (there is no source for this on the xe)....it used to be easier!

MPI_Init and MPI_Finalize should be the first and last executable statements in your code .... basically because it is not clear what happens before or after calls to these functions!! "man MPI_Init" says:

The MPI Standard does not say what a program can do before an MPI_Init or after an MPI_Finalize. In the Open MPI implementation, it should do as little as possible. In particular, avoid anything that changes the external state of the program, such as opening files, reading standard input, or writing to standard output.

If you want to know what an MPI function does you can:

do "man MPI_function" (you need to load the openmpi module first)
Look at the MPI1 standard
Look at the on line MPI1 book
Ask your tutor!

Note that at the moment we are only interested in MPI1.

Compile the code

  make mpiexample1

This will result in

mpicc -c mpiexample1.c    
mpicc -o mpiexample1 mpiexample1.o

mpicc is a wrapper that will end up calling a standard C compiler (in this case gcc). (Do mpicc -v mpiexample1.c to see all the details!). mpicc also ensures that the program links with the mpi library.

Run the code interactively by typing

  
   mpiexample1

You should find the executable runs using just one process. With some MPI implementations the code will fail because you have not defined the number of processes to be used. Using openmpi this is done using the command mpirun.

Try running the code interactively again but this time by typing

  mpirun -np 2 ./mpiexample1

Now try

  
  mpirun -np 6 ./mpiexample1

(Don't set -np to anything over 10).

If you run this program enough times you may see that the order in which the output appears changes. Output to stdout is line buffered, but beyond that can appear in any order.

mpirun has a host of different options. Do "man mpirun" for information. The "-np" refers to the number of processes that you wish to spawn.

So far we have only been running our code on one of the Xe nodes. In total the Xe has 156 nodes. One of these is reserved for interactive logins; the remaining nodes are only available via a batch queuing system. Go back to the userguide and read the section entitled "PBS Batch Use".

Now we will run the same job, but using the PBS batch queuing system. To submit a job to the queuing system we have to write batch script. An example of this is given in file batch_job. Take a look at this. Lines starting with "#PBS" are commands to the queuing system, informing it of how much resources you require and how your job should be executed. We use one of these lines to set the number of processors you want to use. After all this setup information you run the job by issuing the mpirun command, but taking the number of processes from the number of processors allocated by the queuing system.

To submit your job to the queuing system do

qsub batch_job

it will respond with something like

qsub batch_job
303239.xepbs

where 303239.xepbs is the id of the job in the queuing system. To see what is happening on the batch queue do

c43tut@saratoga:~/lab1> qstat
Job id           Name             User             Time Use S Queue
---------------- ---------------- ---------------- -------- - -----
296307.xepbs     hals3ts.ccsdt.j  gxg501           103:38:2 R normal

                    ---lots of jobs---

303237.xepbs     batch_job        apr659                  0 Q express

this gives a long list of jobs. In the above the top job is running as indicated by the R in the S column, while my job is queued as indicated by the Q.

To delete a job from the queue, do

qdel 303237.xepbs

Make sure you are happy with the above since you will need to use the batch system later.

Exercise 1

Modify the code in mpiexample1 to also printout the name of the node each process is executing on. Do this by using the system call

  gethostname(name, sizeof(name));

Run your modified version of mpiexample1 interactively. What nodes of the cluster are being used?
Repeat the above, but now use the batch file. What nodes are now being used?
Modify the batch script so that your MPI code runs on at least two different nodes of the Xe cluster.

Exercise 2

Throughout the course we will be measuring the elapsed time taken to run our parallel jobs. So we start by assessing how good our various timing routines are.

What is the difference between timer overhead and timer resolution?
We can assess the overhead and resolution of a timer by calling it twice in quick succession, printing the difference, and repeating this whole process many times. Why is this? (See lecture 5)
Code that does the above for the gettimeofday system call is provided in walltime.c. Compile and run this, and from the output estimate the overhead and latency of gettimeofday. (If you are not familiar with gettimeofday, do man gettimeofday.)
MPI provides its own timing routine, MPI_Wtime. (Do man MPI_Wtime.) Insert extra code to test the resolution of this routine. What do you estimate the resolution to be?
What does the function MPI_Wtick do? What value does it report?

Exercise 3

In code mpiexample2.c each process allocates an integer buffer of size len (=128integers). Each buffer is initialized to the rank of the process. Process 0 sends its buffer to process 1 and vice versa, i.e. process 0 sends a message of zeros and receives a message of 1s, while process 1 does the opposite.

Compile and run the code interactively using two processes. Verify that it works as you expect.
Now change the code so that len=1024. Attempt to run the code. You should find that it fails to complete. Why? Fix the code so that if complete for any value of len.

Exercise 4

mpiexample3.c is a basic pingpong code. Run the code and make sure it works.

Currently the code only does pingpong between 0 and 1 for a message containing 64 integers and measures the time using MPI_Wtime. Modify the code so that it runs for len=1 to a maximum message size of 4*1024*1024 integers for messages of size 4ⁿ (i.e. 1, 4, 16, 64, 256, 1024 etc). Have the code print out the absolute time and the bandwidth. Are the results what you expected?
What latency did you measure and what peak bandwidth? How does the bandwidth change with message length?
Further modify the code so that it measures the pingpong time between process 0 and all other processes in MPI_COMM_WORLD for messages of 1, 1024 and 1048576 integers.

Run your code on the batch system using 16 CPUs and complete the following table

  -----------------------------------------------------------
    Message   ----time for pingpong between two processes----
  Size(ints)      within_a_node      between_two_nodes
  ------------------------------------------------------------
           1
        1024 
     1048576 
  --------------------------------------------------------

What results did you expect to see? Are the results in line with these expectations? If not why not?

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