Contents

1 About this Document

This document includes basic information about running MPI programs through the Java CoG Kit.

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1.3 Format

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2 Registration

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3 Introduction

The Message Passing Interface (MPI) provides a powerful programming paradigm for high performance computing based on the interchange of messages between processes. An optimized standardized interface is available on almost all high performance computing platforms.

In this guide we will focus on the submission of MPI jobs to a supercomputer or distributed cluster. As an example serves the TeraGrid [1]. However, the examples discussed in this guide are generic enough for you to modify it for your own server environment. We will demonstrate how to submit MPI programs through the Java CoG Kit with the help of the mpirun and the qsub commands. Although we will use the GT2 provider for our submission examples, other providers such as the SSH provider can also be used.

We assume that you have acquired a TeraGrid accounts and that you have a Grid certificate that allows you to submit jobs on the TeraGrid. If you do not know how to do this, please consult with the TeraGrid Web site at http://www.tergrid.org.

4 Example MPI Program

We have chosen an extremely simple test program that prints on each processor the rank and the number of requested processors.

For the rest of this guide, we will assume that you have this program on the TeraGrid under the following directory: $HOME/mpitest/helloworld.c

5 Testing the MPI Program on TeraGrid

It is important to make sure that you can compile the program on a teragrid frontend node, just to verify that your TeraGrid account is properly configured. As an example configuration we will submit it on the TeraGrid frontend node and run it on four backend nodes.

To test and build an executable for the TeraGrid, please login first to the frontend node. In this document we will use the name “laszewski” as a place-holder for your username. Please change the example appropriately.

Place the MPI helloworld.c program in the directory mpitest. This program can now be compiled with the mpicc compiler.

We recommend that you check out if you can run this program on the TeraGrid by simply using the TeraGrid mpirun program. In our example we execute it on four processors.

You should get the following output:

If for some reason this simple test program does not work, your account may not properly configured and you should consult with a TeraGrid systems administrator. However, if your program works, you can proceed to the next examples. The next examples do not require that you are logged into a TeraGrid node. Instead, you can execute them from the clients where you have installed the Java CoG Kit.

6 MPI Job on TeraGrid using mpirun

We assume that you will submit the job to the host tg-grid1.uc.teragrid.org while using the Globus Toolkit version 2 submission (GRAM) service. We will be using the mpirun command that is available in a directory under /soft on the TeraGrid. We will place the output from this program in your home directory on the TeraGrid with the name cog-mpirun.out. We will reuse the helloworld program that you have previously compiled on the TeraGrid as discussed in Section 5.

Before you can submit a job you have to first authenticate your self. Do do so, you create a proxy certificate on the client machine that is used as part of the initialization step.

The command for submitting the job is

The meaning of the flags is as follows:

-s:

The service location of the globus gatekeeper installed on the teragrid. For the ANL/UC sites this is tg-grid1.uc.teragrid.org

-p:

The provider used for this execution. In our example we use GT2 provider

-e:

The executable that is run on the teragrid machine. For our mpi program it is mpirun. Note that we give the complete absolute path of the mpirun program. For the ANL/UC site it is /soft/mpich-gm-1.2.5..10-intel-r2a/bin/mpirun

-args:

The arguments that need to be supplied with the executable. We want to specify that the mpirun should use 4 backend nodes and executes the helloworld program, hence ”-np 4 helloworld”

-stdout:

The remote file that should be used to redirect the standard output. In our example it will be /home/laszewski/cog-mpirun.out on the TeraGrid login node (tg-login.uc.teragrid.org)

The output for this command looks similar to the following. However, the contents maybe slightly different as we have reformatted the output for this guide.

On the TeraGrid, the file cog-mpirun.out will be created with the following contents.

If this program does not work, make sure that you log once more in on the TeraGrid and verify with

if the location of mpirun is properly obtained.

7 MPI Job on TeraGrid using qsub

Previously we showed how to submit an MPI program with the help of mpirun. In certain circumstances you may need more control over the queue parameters or may just submit a non MPI program. In these cases it is useful to use the job submission routine that is part of the batch processing system installed on the machine. At time of writing of this guide, the UC teragrid node used the qsub program from torque. To submit a job through qsub you need to make sure that you create a script that is submitted as part of the submission process. We assume that you have placed the script (qsub-script) in your home directory on the TeraGrid (/home/laszewski/qsub-script).

The meaning of the flags has been explained in the previous section. They just have different values.

The output for this command looks similar to the following. However, the contents maybe slightly different as we have reformatted the output for this guide.

This example assumes you have the script ”qsub-script” on the remote machine. The contents of the file is as follows.

However, in order to make this script work, you must adapt the account information appropriately (we use here TG-ABC).

Once this program is run, the output in form of the standard output and standard error are written into the files “helloworld-pbs.out” and “helloworld-pbs.err”. The contents of the file helloworld-pbs.out will look similar to the one listed below.

For more details on PBS scripts please take a look at the TeraGrid help pages for PBS scripts on: http://www.teragrid.org/userinfo/guide_jobs_pbs.html

8 MPI Job on TeraGrid using MPICH-G2

Kaizar: To be completed
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References

Additional publications about the Java CoG Kit can be found as part of the vita of Gregor von Laszewski http://www-unix.mcs.anl.gov/~laszewsk/vita.pdf. Most documents are avalable online if you follow the links. In future we intend to provide this information without Gregors vita data.

If you need to cite the Java CoG Kit, please use [2].

Appendix

A Java CoG Kit Guides

B Java CoG Kit Guides Under Construction

More guides are under development. The following guides are not yet completed, but are listed here to help us improving these guides. Please, explore them and send us e-mail about improvement suggestions. If you like to contribute a guide yourself, please contact gregor@mcs.anl.gov.

C Available Downloads

First time users of the Java CoG Kit should read the “Guide to Installing the Java CoG Kit” [PDF] [HTML]. We hope that you will find this guide useful to decide which bundles you need. For the more experienced user, we provide the following table.

Binary Distributions

 

• Complete (all providers) [tar.gz][zip]
  Installation Guide [HTML] [PDF]
• Separate providers
  Installation Guide [HTML] [PDF]
  • Main package (includes GT2 providers) [tar.gz][zip]
  • Common GT 3.x.x package [tar.gz][zip] (required for all GT 3.x.x providers)
  • GT 3.0.2 provider [tar.gz][zip]
  • GT 3.2.0 provider [tar.gz][zip]
  • GT 3.2.1 provider [tar.gz][zip]
  • GT 4.0.0 and 4.0.1 provider [tar.gz][zip]
  • Condor provider [tar.gz][zip]
  • SSH provider [tar.gz][zip]
  • WebDAV provider [tar.gz][zip]
  • Local provider [tar.gz][zip]

Source Distributions

 

• Complete source distribution
  Installation Guide [HTML] [PDF]

  Source Distribution [tar.gz][zip]

API Documentation

 

• Complete API [tar.gz][zip]

Module List

 

• Module list [HTML]

CVS

 

• Please consult the Installation Guide [HTML] [PDF]

D Availability of the Document

The newest version of this document can be downloaded by the developers from

1. cvs -d:pserver:anonymous@cvs.cogkit.org:/cvs/cogkit checkout manual/guide

It is not allowed to reproduce this document or the source. This documentation is copyrighted and is not distributed under the CoG Kit license.

E Bugs

This guide is constantly improved and your input is highly appreciated. Please report suggestion, errors, changes, and new sections or chapters through our Bugzilla system at

http://www-unix.globus.org/cog/contact/bugs/

F Administrative Contact

The Java CoG Kit project has been initiated and is managed by Gregor von Laszewski. To contact him, please use the information below.

Index