Monday, December 08, 2008

E-Science Demos

We'll be demonstrating OGCE workflow management tools and XMC-Cat (a new cataloging service) at E-Science Conference on Wednesday night.



Friday, December 05, 2008

EScience Tutorial Agenda

This is Sunday, Dec 7 from 8:00 to 5:00 PM (US Eastern Standard Time). You can also view remotely the live broadcast. For instructions, see An archived broadcast will be available from the same URL.

Presentation material is available from

Talks will be given by Marlon Pierce, Suresh Marru, and very special guest star Stephen Simms.
  • Introduction and attendee feedback
  • (Talk) Gateways overview (Marlon)
  • (Talk) TeraGrid: Resources Overview and Getting Started (Simms)
  • (Talk/Demo) LEAD portal and workflow (Suresh)
  • (Demo/Talk) GridChem workflows (Suresh)
  • (Demo/HO) OGCE and TGUP Portals (Marlon)
  • (Demo/HO) OGCE hands on and simple workflows with XBaya (Marlon, Suresh)
  • (Talk/HO) Building OGCE portal and services (Marlon)
  • (Talk/Demo/HO) Building GTLAB gadgets (Marlon)
  • (Optional Talk) Web 2.0 for science gateways (Marlon)
  • (Optional HO) Building the portal, GTLAB, and services
  • (Optional HO) Using various portals (OGCE, TeraGrid User Portal, LEAD)
  • (Optional HO) Workflows in depth

Thursday, December 04, 2008

Javadocs for OGCE Components

If you want to make Javadocs for OGCE components (the portal, GTLAB, Axis services, etc), use the command

mvn javadoc:javadoc -f path/to/component/pom.xml

For example, the GTLAB javadoc can be made with the command

mvn javadoc:javadoc -f jsf_standalone/pom.xml

The docs will be located in jsf_standalone/target/site. Load with your browser.

Wednesday, December 03, 2008

OGCE Swarm Service Talk at E-Science

Sangmi Pallickara will present the Swarm Job Submission Service at Friday, Dec 12 at the E-Science conference:

This talk will be web-cast. See for details.

E-Science Gateways Tutorial Web Cast

Our OGCE and Gateways tutorial at E-Science is Sunday, December 7 from 8:00 am to 5:00 pm. See The entire conference (including our tutorial) is being web-cast; see for more information.

We will post a more detailed agenda on this blog.

Friday, November 14, 2008

SC08 Demo Time Correction

The IU booth demo is 1:00-3:00 on Wednesday, November 19th. These are roughly 2 30 minute demos at 1:00 and 2:00, with 30 minute breaks.

OGCE Portal 2.4 Posted

Version 2.4 is ready. This features the File Manager applet from the TeraGrid User Portal, as well as numerous bug fixes and miscellaneous enhancements. See for more details.

Tagged SC08 releases of OGCE Axis Services and GTLAB are also available.

Wednesday, November 12, 2008

OGCE Web Site and Download Reorganization

The OGCE Web Site is being revised to better reflect the reorganization of our downloadable components. Here are the major download suites:
  • The OGCE portlet-based Grid portal: this download combines Tomcat, Gridsphere portlet container, and many OGCE portlets developed with OGCE libraries.
  • The OGCE Axis Web Services Suite: this includes several OGCE services (currently GPIR, the Resource Prediction Service, and the Resource Discovery Service) combined into an integrated, one-step build.
  • The OGCE Workflow Suite: this suite contains workflow composer and engine (XBaya), the GFAC application factory, XRegistry, and related components.
  • GTLAB: This is a collection of Java Server Faces tags and supporting code for building Grid portlets and gadgets. The current version supports simple tag pipelining (so you can associate multiple tasks with a single HTML button click). Tags are no longer limited to Grid clients--any thing can be used.
  • OGCE Gadget Container: this is a preview of our work to build an Open Social and iGoogle-compatible container. We view this as the successor to the portlet standard we have used in the past.
See the web site for more information.

Tuesday, November 11, 2008

SC08 Demos: 1:00-3:00

OGCE team will be giving demos in the Indiana University booth at SC08 on Tuesday from 1:00 pm to 3:00 pm. Demos will include
  • OGCE workflow tools
  • JavaScript Grid clients
  • Tag libraries for building iGoogle style Grid gadgets.
  • Gateway information services
  • Application portals using Pylons
  • Demo portals for the life sciences
Please feel free to come by the IU booth for informal demos.

Updated GCE08 Schedule

The GCE08 Workshop presentation schedule at Supercomputing 2008 in Austin has been updated:

Monday, November 03, 2008

Tentative GCE08 Schedule Available

A draft GCE08 Workshop presentation schedule at Supercomputing 2008 in Austin is now available:

The program will be updated as we confirm speakers' travel schedules, but the program is set. Slides and papers will be made available from this URL as they become available.

Tuesday, October 07, 2008

The Dreaded "GRAM Job submission failed: The job manager failed to open stderr" Error

The COG will produce the following infamous error

GRAM Job submission failed: The job manager failed to open stderr

if you don't have values in $HOME/.globus/ set correctly. The "ip" parameter must be set to the real hostname or static IP address of your portal server. That is, it should be something like


You can edit this file by hand, but note it will be overwritten if your rebuild the portal. You should make sure that the <portal.server.ip> value in ogce-portal-only/pom.xml is set correctly.

Monday, September 22, 2008

Nightly Build Update

The "portal only" release was upgraded to Tomcat 5.5.27, but the build and test scripts on the NMI testbed were still set to use the older Tomcat 5.5.12. This has been corrected.

For more info on the nightly build, see

Nightly Builds OK

There is a bug in the NMI nightly build scripts that prevents Tomcat from starting. This causes the build to report a failure, but the compilation steps complete successfully.

Friday, September 12, 2008

Tagged Update to GTLAB

Numerous improvements and bug fixes to the GTLAB tag libraries have been tagged as "GTLAB-2008". These supersede the TG08 tagged version. To get the updates, use

svn checkout

Major changes include
  • Bug the prevented task inter-dependencies from working correctly has been fixed.
  • Each GTLAB tag can now be associated with its own resource property file. Previously all tags used the same property file.

Tagged Preview of OGCE portal 2.4

The OGCE "portal only" release has been tagged as a preview. This version includes numerous bug fixes and updates. To get it, use

svn checkout

Most updates are courtesy of Lukas Hoffman.


* Edited files: portlets/gp-common/src/main/webapp/css/fileBrowser.css
* This isn't really a portlet, it just contains files that are used by the GridPort portlets

Interactive Job Submission / jobsubmit-portlet

* Edited files: portlets/jobsubmit-portlet/src/main/webapp/templates/xportlets-jobsubmit.vm
* Added *'s for certain fields in the job submission form & a note saying those fields were required.
* Added a way to link to standard output and standard error files
* Added help instructions in "?" viewing window
* If user left stdout/stderr field blank, job output is displayed in portlet when job completes. see 'lukas code' where stdout is mentioned in and xportlets-jobsubmit.vm
* If user enters path from root to stdout/stderr, there's a link to download the file. This is glitchy though, it only works if filetransfer portlet is connected to correct host, and it doesn't work for relative paths.

File Manager/file-manager and Comprehensive File Management/comp-file-management

* Edited files: portlets/comp-file-management/src/main/webapp/jsp/fileBrowser.jsp
portlets/gp-common/src/main/webapp/jsp/fileBrowser.jsp - identical to fileBrowser.jsp above
* Added an image href to the file/directory listing
* Files are now sortable by name, filetype, and size. Default is sort by filetype. User can click on a heading to select a sort.
If user clicks on a heading twice in a row, the sort is in reverse order.
* Refresh button went to home directory, now it's refresh current directory.
* Fixed something in but I forgot what the problem was.
destListing.setRemoteHost(destResources[0]); //lukas code, previous array size = 1 --> this portlet crashes.
//don't know why this fix works, but it works...

File Transfer Portlet / GridFTP Portlet / filetransfer (Deprecated)

Edited files: portlets/filetransfer/src/main/webapp/gridftp-browser.vm
* is all my own code, so the directory contains a javadoc html page for this class
* fixed bug where file download & file transfer don't work if filenames contain spaces.
* fixed bug where clicking on a link twice really fast made portlet crash
* fixed two or three "annoying but not fatal" bugs that I don't remember now, although I probably wrote that it was a fix in the source code comments
* Added a "Type" (Filetype field) so the file list matches the information that any Windows directory listing gives you
* Made the "Date Modified" dates look better
* Files/Directories are now sortable by Name, Size, Type, and Date Modified. They stay sorted that way until the user clicks on a heading.
* Sorting is in reverse order when user clicks a heading twice.
* Made icons and file/directory names clickable, for easier access with the mouse. Before, the link to download a file was on one side & the
file name was on the other, which is annoying for the user. Now the user can click directly on the file name or icon to download it, or
directory name/icon to go there.
* Moved things around to make portlet look better. Mostly, moved all buttons and links toward the top and put file listing under them.
* User can now
make a new directory
rename a file/directory
delete 1 or more files at a time
delete a directory
go to any directory in 1 step by typing in the full path name, or path name relative to current directory, or ".." to go up a directory
(typing "dir1/dir2/dir3" and pressing submit is faster than clicking 3 links)
* Added error messages when the commands above fail & display to the user.
* Added help instructions in "?" viewing window
* Luke Hammill fixed problem where if you accidentally transfer a file to itself (same action as: mv fileA fileA) file gets deleted. (fix not in version i sent you)
* back.gif button can now go to '/', which it couldn't before.
* 'Home' link now always goes to directory that showed up when the host was first loaded, which it didn't before.
* You can delete several files at a time using checkboxes.

Wednesday, September 10, 2008

GCE08 Submission Deadline Extension

The deadline for submitting papers to GCE 08 has been extended to September 22. See for more information.

Monday, September 08, 2008

Condor Installation Example

The following is an example installation for Condor 6.8.8. This is required to use the Condor and Condor-G portlets. Additional configuration is required to enable Birdbath and Condor-G, so see the portlet notes at

Note also that this version of Condor will not work on newer RHEL and Fedora releases, so you will need to get the library. Do the following as root:

[shell> yum install

Now do the following in the condor-6.8.8 release directory.

[shell> condor_install

Press enter to begin Condor installation

STEP 1: What type of Condor installation do you want?

Would you like to do a full installation of Condor? [yes]

Press enter to continue.

STEP 2: How many machines are you setting up for Condor?

Are you planning to setup Condor on multiple machines? [yes] no

Press enter to continue.

STEP 3: Install the Condor "release directory", which holds
various binaries, libraries, scripts and files used by Condor.

It looks like you've installed a Condor release directory in:
Do you want to use this release directory? [yes] no

Have you installed a release directory already? [no] no

Where would you like to install the Condor release directory?
That directory doesn't exist, should I create it now? [yes]
Installing a release directory into /home/mpierce/condor ...

[------------------------------Stuff deleted------------------------------]


Using /home/mpierce/condor as the Condor release directory.

Press enter to continue.

STEP 4: How and where should Condor send email if things go wrong?

If something goes wrong with Condor, who should get email about it?

What is the full path to a mail program that understands "-s" means
you want to specify a subject? [/bin/mail]

Using /bin/mail to send email to

Press enter to continue.

STEP 5: Filesystem and UID domains.

To correctly run all jobs in your pool, including ones that aren't relinked
for Condor, you must tell Condor if you have a shared filesystem, and if
so, what machines share it.

Please read the "Configuring Condor" section of the Administrator's manual
(in particular, the section "Shared Filesystem Config File Entries")
for a complete explaination of these (and other, related) settings.

Do all of the machines in your pool from your domain ("")
share a common filesystem? [no]

Configuring each machine to be in its own filesystem domain.

Do all of the users across all the machines in your domain have a unique
UID (in other words, do they all share a common passwd file)? [no]

Configuring each machine to be in its own uid domain.

Press enter to continue.

STEP 6: Java Universe support in Condor.

Enable Java Universe support? [yes] no
OK, Java Universe will be left unconfigured.

Press enter to continue.

STEP 7: Where should public programs be installed?

The Condor binaries and scripts are already installed in:
If you want, I can create some soft links from a directory that is already
in the default PATH to point to these binaries, so that Condor users do not
have to change their PATH. Alternatively, I can leave them where they are
and Condor users will have to add /home/mpierce/condor/bin
to their PATH or explicitly use a full pathname to access the Condor tools.

Shall I create links in some other directory? [yes] no

Press enter to continue.

STEP 8: What machine will be your central manager?

What is the full hostname of the central manager?

Your central manager will be on the local machine.

Press enter to continue.

STEP 9: Where will the "local directory" go?

Condor will need to create a few directories for its own use

You have a "condor" user on this machine. Do you want to put all the
Condor directories in /home/condor? [yes] no

Do you want to put all the Condor directories in
/home/mpierce/condor/home? [yes]

Creating all necessary Condor directories ... done.

Press enter to continue.

STEP 10: Where will the local (machine-specific) config files go?

Condor allows you to have a machine-specific config file that overrides
settings in the global config file.

You must specify a machine-specific config file.

Should I put a "condor_config.local" file in /home/mpierce/condor/home?
Creating config files in "/home/mpierce/condor/home" ... done.

Configuring global condor config file ... done.
Created /home/mpierce/condor/etc/condor_config.

Press enter to continue.

Setting up as your central manager

What name would you like to use for this pool? This should be a
short description (20 characters or so) that describes your site.
For example, the name for the UW-Madison Computer Science Condor
Pool is: "UW-Madison CS". This value is stored in your central
manager's local config file as "COLLECTOR_NAME", if you decide to
change it later. (This shouldn't include any " marks).

Setting up central manager config file /home/mpierce/condor/home/condor_config.local ... done.

Press enter to continue.

STEP 11: How do you want Condor to find its config file?

Condor searches a few locations to find it main config file. The first place
is the envionment variable CONDOR_CONFIG. The second place it searches is
/etc/condor/condor_config, and the third place is ~condor/condor_config.
/home/condor/condor_config exists.
Renaming to: /home/condor/condor_config.old.

Should I put in a soft link from /home/condor/condor_config to
/home/mpierce/condor/etc/condor_config [yes]

Press enter to continue.

Condor has been fully installed on this machine.

/home/mpierce/condor/sbin contains various administrative tools.
If you are going to administer Condor, you should probably place that
directory in your PATH.

To start Condor on any machine, just execute:

Since this is your central manager, you should start Condor here first.

Press enter to continue.

You should probably setup your machines to start Condor automatically at
boot time. If your machine uses System-V style init scripts, look in
for a script that you can use to start and stop Condor.

Please read the "Condor is installed... now what?" section of the INSTALL
file for things you should do before and after starting the Condor daemons.
In particular, you might want to set up host/ip access security. See the
Adminstrator's Manual for details.

Friday, August 15, 2008

Using OGCE portlets in Gridshere 3.1 (preliminary)

We had a request to get OGCE portlets running in Gridsphere 3.1. Below is the way to do this manually. We'll try to make an automated version of this with Maven next.

0. Shutdown tomcat.

1. In the ogce-portal-only directory, run the command mvn clean install -f global-config/pom.xml

2. Remove our versions of hibernate, hsqldb, and ehcache (probably these crept in from GS 2.1--I don't think we need them). Specifically,

rm global-config/common/target/cog-common-1.0/lib/hibernate2-OGCE.jar

rm global-config/common/target/cog-common-1.0/lib/hsqldb-1.7.1.jar

rm global-config/common/target/cog-common-1.0/lib/ehcache-0.9.jar

3. Copy the remaining jars into your Tomcat's shared/lib. Something like
cp global-config/common/target/cog-common-1.0/lib/* /Users/mpierce/GridSphere31/apache-tomcat-5.5.20/shared/lib/

4. Copy the OGCE portlet as is from the ogce-portal-only dir. That is, from ogce-portal-only, run "mvn clean install -f portlets/proxymanager-portlet" and then
cp -r portal_deploy/apache-tomcat-5.5.12/webapps/proxymanager-portlet/ /Users/mpierce/GridSphere31/apache-tomcat-5.5.20/webapps/proxymanager-portlet

5. Create empty files named after the portlets for Gridsphere. This used to be done in $CATALINA_HOME/webapps/gridsphere/WEB-INF/CustomPortal/portlets

Now these apparently go in $HOME/.gridsphere, so do this:

touch ~/.gridsphere/portlets/proxymanager-portlet.2

6. Edit the proxymanager's web.xml file to use the correct namespace for the PortletServlet (i.e., remove the "gridlab" section from the full name):


7. In proxymanager-portlet/WEB-INF/lib, delete gridsphere-ui-tags-2.1.jar

8. Start tomcat and add the portlet using the Gridsphere Layout Manager.

Tuesday, August 05, 2008

GCE08 Workshop at Supercomputing 2008

We are hosting GCE08, the fourth workshop in this series. Papers on portals, gateways, and other scientific user environments are welcome. For more information, see

Thursday, July 10, 2008

New GPIR Service URL for GPIR Portlet

The old TeraGrid GPIR service is being retired and replaced. To point to the new server, edit GPIR's portlet.xml file and replace


To rebuild this portlet, use the command "mvn clean install -f portlets/gpir-portlet/pom.xml" from the "ogce-portal-only" directory.

Monday, July 07, 2008

Correction to OGCE 2.3 tar download

The default value for the property <project.home> in ogce-portal-only/pom.xml was incorrectly set. While this can be edited manually, it prevents the portal from building out of the box if one follows the documentation.

Also, the obsolete filetransfer module, which causes the errors described at on some machines, has been removed.

These have been corrected in the download link at The version number has been incremented to 2.3.1 to reflect this minor update.

Saturday, June 07, 2008

GTLAB TG08 Tutorial Release

The TG08 tutorial release of GTLAB is now available from

GTLAB provides Java Server Faces components and backing beans that simplify the process of Grid Web application development. You can use GTLAB to develop standalone Web applications, portlets, and Google Gadgets.

Friday, June 06, 2008

OGCE Portal Release 2.3 Available

OGCE portal release 2.3 is available from This release features major revisions to the XBaya workflow composer as well as minor bug fixes to GPIR and the build system.

The XBaya updates are part of the comprehensive enhancements to the OGCE workflow tools,

Tuesday, June 03, 2008

TG08 Gateways Summary

Courtesy of Nancy Wilkins-Diehr:

For those attending TeraGrid 08, June 9-13 in Las Vegas we have a
terrific representation of Science Gateways at the conference.

Gateway-related topics are featured in:
14 papers
7 demonstrations
5 posters
5 birds-of-a-feather sessions
3 student competition entries
2 tutorials
1 vis gallery entry
And a face-to-face gateway meeting in a pear tree on Thursday June 12,

Full information on the conference can be found at and a listing of gateway-specific
activities at

Thank you to the many of you on this list who are contributing to making
the conference a success. I hope to see many of you in Las Vegas next

Monday, June 02, 2008

TeraGrid 08 OGCE Tutorial Outline

Tutorial is Monday, June 9. We will make slides and material available for download.

8:30-9:30: Intro, building and using the portal, writing simple grid portlets (Marlon Pierce)

9:30-10:00: Workflow suite part 1 (Suresh Marru, Gopi Kandaswamy)

10:00-10:30: break

10:30-11:15: Worflow suite part 2 (Suresh, Gopi)

11:15-11:45: Web 2.0 for gateways (Gregor von Laszewski)

11:45-12:00: Teragrid gateway authorization requirements and GridShib (Tom Scavo)

Tuesday, April 29, 2008

OGCE Tutorial at TeraGrid 2008

We will give a 1/2 day tutorial on June 9th at TeraGrid 2008 in Las Vegas. For more information, see

Topics will include building and using the basic portal, using GTLAB to make Grid Web clients, using the OGCE workflow suite of tools to wrap science applications, and Web 2.0 activities for science gateways.

Monday, April 21, 2008

GPIR Service Download Available

An updated version of the Grid Portal Information Repository (GPIR) Web Service is available for download. This is a standalone repackaging of the GPIR Web Service in older OGCE portal releases.

The GPIR service powers the GPIR portlet in the main portal download. Get the GPIR service if you want to provide your own status information server for your grid.

Monday, March 24, 2008

Mac OSX Maven Build Errors

We have reports of the following build error on Macs:

[INFO] ------------------------------------------------------------------------
[INFO] ------------------------------------------------------------------------
[INFO] Error building POM (may not be this project's POM).

Project ID: org.apache.maven:maven-parent:pom:5

Reason: Cannot find parent: org.apache:apache for project: org.apache.maven:maven-parent:pom:5 for project org.apache.maven:maven-parent:pom:5


Workaround: Download and install the Maven third party jars as described in the "Download" section.

The error does not appear in the Mac nightly build dashboard, so we are trying to discover the cause.

Tuesday, February 26, 2008

Example OGCE Portal

A running, persistent version of the portal software is available from

To log in, you can use the account guest/guest123. If you have a TeraGrid account and credentials in the TeraGrid MyProxy server, you can try out the user interfaces.

To get a personal account or to use this portal with other Grid deployments, contact us for assistance.

Bug Fix in GPIR Portlet

There is a minor bug fix in the GPIR portlet. Clicking machine name links in the portal served from Linux hosts produced an error because of a missing XML parsing library. The fix is available in SVN.

To update existing portals (versions 2.2.0 and 2.2.1), simply replace ogce-portal-only/portlets/gpir-portlet/pom.xml with the update from

Monday, January 28, 2008

Spurious Tomcat Startup Errors

When starting the portal server for the first time, you will notice several errors (see below for a sample) if you are using our script. These are the standard errors produced by Tomcat's if no server is running and can be ignored.

Our script first calls Tomcat's before calling We do this to prevent accidentally starting two servers that try to use the same ports. This can be a little tricky to clean up (Tomcat's may not work and you may have to use the kill command).

-bash-3.00$ ./
# Starting up Portal Tomcat... #
Using CATALINA_BASE: /usr/local/dev/maytal/ogce-portal-only/portal_deploy/apache-tomcat-5.5.12
Using CATALINA_HOME: /usr/local/dev/maytal/ogce-portal-only/portal_deploy/apache-tomcat-5.5.12
Using CATALINA_TMPDIR: /usr/local/dev/maytal/ogce-portal-only/portal_deploy/apache-tomcat-5.5.12/temp
Using JRE_HOME: /usr/local/dev/maytal/jdk1.5.0_14
Jan 28, 2008 12:48:29 PM org.apache.catalina.startup.Catalina stopServer
SEVERE: Catalina.stop: Connection refused
at Method)
at org.apache.catalina.startup.Catalina.stopServer(
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(
at sun.reflect.DelegatingMethodAccessorImpl.invoke(
at java.lang.reflect.Method.invoke(
at org.apache.catalina.startup.Bootstrap.stopServer(
at org.apache.catalina.startup.Bootstrap.main(
viUsing CATALINA_BASE: /usr/local/dev/maytal/ogce-portal-only/portal_deploy/apache-tomcat-5.5.12
Using CATALINA_HOME: /usr/local/dev/maytal/ogce-portal-only/portal_deploy/apache-tomcat-5.5.12
Using CATALINA_TMPDIR: /usr/local/dev/maytal/ogce-portal-only/portal_deploy/apache-tomcat-5.5.12/temp
Using JRE_HOME: /usr/local/dev/maytal/jdk1.5.0_14