GEM - Graphical Explorer of MPI Programs Eclipse Plug-in Update Site

v1.3.0

Welcome to the Gauss Group's GEM Eclipse Update Site at the University of Utah School of Computing.

 

About GEM

GEM is an Eclipse plugin developed to be a graphical front-end for the C/C++ dynamic MPI formal verification tool, In-situ Partial Order (ISP), also developed by the Gauss Group at the Univeristy of Utah.

GEM is designed for Linux and Mac OS/X.

ISP itself is installed separately. The addition of GEM offers a rich graphical front end for ISP, with tools for exploring interleavings and tracking down bugs in MPI programs.

Using ISP, GEM will definitively find MPI bugs in the following classes:

• Deadlocks
• Assertion Violations
• MPI Object Leaks
• MPI Type Mismatches

GEM was originally accepted as a contribution to the Eclipse Parallel Tools Platform (PTP) as of the v3.0 release in December, 2009. GEM is now a part of PTP v4.0, released simultaneously with Eclipse Helios (v3.6) in June, 2010 and also with PTP v5.0 & Eclipse Indigo (v3.7) in June 2011.

Be sure to check out:

• PTP web site.
• PTP 5.0 New & Noteworthy page
• PTP Committers and Contributors

 

New and Noteworthy

GEM v1.3.0 now supports formal verification on remote C/C++ MPI projects.

GEM supports remote C/C++ MPI projects whose connections are through either service provider:

• Remote Tools
• Remote System Explorer

GEM operates and behaves identically with local and remote C/C++ MPI projects (managed-build or makefile). The only limitation is that GEM does not currently support the Happens Before Viewer with remote projects.

 

GEM Publications

• ICPP 2010   —   PSTI Workshop    GEM: Graphical Explorer of MPI Programs
• PLDT 2010   —   AMP Workshop    Seamless Integration of Two Approaches to Dynamic Formal Verification of MPI Programs

 

Conference Presentations

• Super Computing 2009   —   Full day tutorial    "Developing Scientific Applications using Eclipse and the Parallel Tools Platform"
• Super Computing 2010   —   Half day tutorial    "Scalable Dynamic Formal Verification and Correctness Checking of MPI Applications"
• Super Computing 2010   —   Full day tutorial    "Developing Scientific Applications using Eclipse and the Parallel Tools Platform"

 

ISP Overview and Installation

NOTE: It is required for ISP to be installed and working properly before using GEM.

• An overview of ISP (In-situ Partial Order) can be found here.
• The current release of ISP for Linux and Mac OS/X can be downloaded from the ISP release page.
• The ISP user manual is here.

 

Installing an Implementation of MPI

Some implementation of MPI must be installed, MPICH2 or OpenMP both work well. You will also need a process manager for clusters, like mpd installed and running. The ISP plug-in assumes your process manager is already running when it is loaded.

• MPICH2 version 1.0.6p1 (or later)
• Open MPI version 1.2.x and 1.3.x

 

Configuring Eclipse for GEM

GEM v1.3.0 was written for Eclipse 3.7 (Indigo), CDT 8.0 and PTP 5.0. It also works well with:

• Eclipse 3.5 (Galileo) with CDT 7.0 and PTP 4.0
• Eclipse 3.4 (Ganymede) with CDT 6.0 and PTP 3.0

PTP requires a minimum Java execution environment of J2SE-1.5. GEM was compiled against Java 1.5. Our suggestion though, is that you go ahead and make Sun Java 6 the defualt JRE (if it isn't already)

The minimal Java 6 packages you'll need are as follows:

• sun-java6-jre
• sun-java6-jdk

To install the above packages, the following command needs to be executed (Debian based system):

sudo apt-get install sun-java6-jre sun-java6-jdk

Getting the Correct Java Installation

Use the following command to do this:

java -version

This command will print the current active version of java on your system. If there is more than one version of Java installed on your system, use the following command to list them.

update-java-alternatives -l

To change to Sun Java 6, the following command needs to be executed (Debian based system):

sudo update-java-alternatives -s java-6-sun

 

Installing GEM via Eclipse Helios Release Site

As GEM is currently a part of PTP and the Eclipse 3.6 (Helios) aggregation, we recommend installing GEM through the Eclipse Helios releases update mechanism. Be warned though, the latest version of GEM is usually not on the Eclipse update site. For the latest version, see the instructions below for this update site. These steps will be nearly identical with Eclipse Indigo.

If you have an older version of Eclipse, CDT and PTP and just need GEM, you may follow the directions below and utilize this update site to install GEM.

Upgrading Your Eclipse Install

• Upgrade to Eclipse Helios here.

• From the Eclipse help menu, choose Install New Software.
• Click the Available Software Sites link.
• From the Work with drop-down list, select Helios - http://download.eclipse.org/releases/helios

• Next, scroll down to: General Purpose Tools

• Finally, select:
• Parallel Tools Platform (PTP) End-User Runtime
• PTP Graphical Explorer of MPI Programs (GEM)

• Agree to the licensing, etc
• Lastly, agree to restart the workbench

Installing GEM from this Update Site

Follow the steps on the Eclipse Wiki page to install CDT (C/C++ Development Tools) and PTP (Parallel Tools Platform).

More detailed information on the Eclipse CDT is here
More detailed information on the Eclipse PTP is here

• From the Eclipse help menu, choose Install New Software.
• Click the Available Software Sites link.
• Click the Add button.
• Name the site and enter the following URL into the location field.

http://www.cs.utah.edu/formal_verification/GEM/

• On the next dialog, check everything related to GEM.
• Agree to the licensing.
• Lastly, agree to restart the workbench.

 

GEM Documentation and Source Code

• Extensive GEM help documentation is also available here on this site: Help page
• The source code for the GEM Eclipse Plugin is released under the Eclipse Public License and is available here.

Examples Workspace

• 25 working MPI C projects for use with GEM, illustrating common MPI bug classes. workspace-gem.tar.gz

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School of Computing * 50 S. Central Campus Dr. Rm. 3190 * Salt Lake City, UT 84112 * isp-dev@cs.utah.edu
Disclaimer

Last updated on 01/17/11