Frequently Asked Questions

General Questions

Installing Pipeline

Pipeline Web Start

Accessing the Pipeline Server

Using Pipeline

General Questions

What is Pipeline?

The LONI Pipeline is a distributed system for constructing, validating, executing and disseminating scientific workflows on grid computing architectures.

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How Pipeline is different from other workflow processing environments ?

A major difference between this and other workflow processing environments is that the LONI Pipeline does not require new tools and services to include, or be built against, the core Pipeline libraries. The Pipeline environment references all data, services and tools as external objects. This allows the Pipeline to run as a light-weight middleware, but at the same time, restricts the scope of its applications. For example, the Pipeline does not provide a set of internal core libraries, filters and processes for rudimentary image processing (e.g., image addition).

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Who Uses Pipeline?

A distributed client-server and platform-agnostic computational infrastructure has been provided to the institutions featured here.

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What are the requirements of LONI Pipeline?

The Pipeline requires Oracle Java 6 (JRE 1.6) or higher to run. To find out which Java version you have: in Windows, click Start-> Run… and type cmd and hit OK, then type java -version; in Linux/UNIX/Mac, under terminal, type java -version. Please note, other varieties of Java (which is not Java HotSpot distributed by Oracle) is not tested and LONI Pipeline may not work properly.

If you are using Mac OS X v10.7.5 (Lion) and above and are downloading the LONI Pipeline installer for the first time, you may not be able to launch the installer because of a new feature called Gatekeeper. Please go to System Preferences… > Security & Privacy > General tab and select Anywhere (You can change it back after installation is complete).

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What license is the LONI Pipeline released under?

Pipeline is released under the LONI license.

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Who funded development of the LONI Pipeline?

A list of funding agencies can be found here.

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How I acknowledge my use of the Pipeline in my paper/publication?

Please refer to Acknowledgments and Credits page.

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Is it necessary to write shell script wrappers for executable programs in order to describe these executables as Pipeline modules?

The pipeline environment does not require any modifications, rebuilds, redeployments of existent tools which provide a well-defined command-line executable invocation syntax. However, sometimes it may be helpful or necessary to wrap executable tools via external shell scripts (e.g., tcsh, csh, bash, etc.) Examples of these situations include:
* instances of command-line executable tools that have a well-defined invocation syntax, however, output implicit number, types and formats of results/data that can not be inferred a priori e.g. VolumeMultipleRegression tool.
* tools that require customized environmental variable settings, system controls or job-submission parameter settings (e.g., SPM, FSL/FEAT, etc.)

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May I package my workflows as part of a tool and distribute to others?

Once a workflow has been constructed, it can be saved as a .pipe file, which can be sent to collaborators. If specific servers are being accessed, privileges must exist for the user to connect to the server.

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May I use the Pipeline client to execute workflows on my own computer?

Yes, in describing a module definition, simply specify the path of the executable to point to a local copy.

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Do you have training sessions? If yes, how can I participate?

We organize several training events throughout the year, registration requirements and location for each event is different, please see the Pipeline Training Page for upcoming events and their details.

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Installing Pipeline

I get “LONI Pipeline is damaged and can’t be opened. You should move it to the Trash.” or “LONI Pipeline can’t be opened because it is from an unidentified developer” messages when trying to install on Mac OSX, how can I fix this?

It is likely that your OS X’s GateKeeper prevents you from running LONI Pipeline. Open System Preferences and click on “Security & Privacy” icon. Unlock the lock in case it is locked and select “Anywhere” option. Now try to open LONI Pipeline package again and installation should work. After the Pipeline installation is done, you can change the Gatekeeper option to previously selected value. For more information, please refer to Apple’s documentation.

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Pipeline Web Start

I get “pipeline.jnlp can’t be opened because it is from an unidentified developer.” message when trying to run Pipeline Web Start on Mac OSX, how can I fix this?

It is likely that your OS X’s GateKeeper prevents you from running LONI Pipeline. Open System Preferences and click on “Security & Privacy” icon. Unlock the lock in case it is locked and select “Anywhere” option. Now try to open LONI Pipeline package again and installation should work. After the Pipeline installation is done, you can change the Gatekeeper option to previously selected value. For more information, please refer to Apple’s documentation.

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Accessing Pipeline Server

How can I get access to the LONI Pipeline server?

It is a two-step process. First, if you don’t have a LONI account, fill out the LONI account application, which lets you download LONI software (including the LONI Pipeline), and post on the LONI forums. Second, if you need to connect to LONI Pipeline crainum server, you need to fill out the application form here. Note that you need to login with your LONI account in the first step. If you have any questions regarding account application, email us at pipeline@loni.usc.edu.

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Why I can’t connect to Pipeline server from my computer?

LONI Pipeline server moved from UCLA to USC. Your old credential will not work with our new server. You need to re-apply for an account at USC. Please go to LONI Pipeline Account Application page to apply.

It is recommended that you have the latest version of the client when you connect to our server. You can download the client here.

Pipeline uses port 8001 to communicate with the server. If you are getting Server Not Found problem but you are sure that the server you’re connecting to is up and running then it is probably your firewall or something else blocking your connection. Please make sure the port 8001 is bypassed by your firewall. If you are in a local network, please check with your system administrator to make sure there is nothing blocking the port 8001 on your end.

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I have a LONI Pipeline account (from UCLA), why I can’t connect to LONI Pipeline server at USC (cranium.loni.usc.edu)?

LONI Pipeline server moved from UCLA to USC. Your old credential will not work with our new server. You need to re-apply for an account at USC. Please go to LONI Pipeline Account Application page to apply.

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I am getting “Server not found”, “Authentication rejected”, or “Authentication failed” error messages, what can I do?

If you are getting “Server not found” message, it’s most likely caused by invalid hostname or firewall settings. LONI Pipeline server moved from UCLA to USC, to find out the new hostname, you can download the latest version of the client. Pipeline uses port 8001 to communicate with the server, so please make sure the port 8001 is open on your computer.

If you are getting “Authentication rejected”, or “Authentication failed” message, it indicates your credential is invalid. If you are connecting to our USC server, you can go to http://password.loni.usc.edu to verify/change your password, or email us pipeline@loni.usc.edu with your registered email and we’ll reset your password (we will never ask for your password).

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What happens if I get an ‘Incompatible Versions’ error when I try to connect to a Pipeline server?

Your version of the client is out of sync with the version the server is running. Download the latest version of the client and try connecting again. If you still receive the error message and you’re sure you have the latest version of the client, the server is probably running an older version of the Pipeline. In this case, contact the server administrator and ask them to update to the latest version of the Pipeline server.

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How can I change my LONI Pipeline account’s password?

You can go to http://password.loni.usc.edu to do so.

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Using Pipeline

How do I disseminate my new computations tool and a corresponding Pipeline wrapper to the community?

Once you have constructed a new module definition, you may submit it for addition to the LONI pipeline server by emailing it to pipeline@loni.usc.edu for approval and distribution through the LONI server.

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If my executable has a GUI, how can I view it locally while the process is running remotely through a Pipeline server?

There are several steps that need to be carried out in order to accomplish this. In particular, you need to run an X server on your local machine, write a wrapper script to properly set up the DISPLAY environmental variable prior to running the executable, and specify that the job should be submitted to a node with external network access. The details can be found in the User Guide Advanced Topics.

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How can I provide feedback, make feature requests, or obtain help with the software?

If you want to make feature requests or need some technical help with the software that is not addressed in the user guide or server setup guide, you can check out our forums. You can do keyword search, and if you could not find answer, you can post your questions there. We will get back to you as quickly as we can.

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I think I’ve found a bug! How can I tell you guys?

You can file a bug report through the Pipeline client. Select Help -> Report a Bug from the top menu bar. If desired, fill out the optional fields for name, email and server username. You can also attach the workflow being processed and enter in any details about the bug.

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