Re: [kepler-users] Kepler Manual

Dear Barasa, We have some good introductory tutorials in our Getting Started Guide. In addition, the Users Guide is a useful reference. Both of these are available from within Kepler's Help menu, and can also be downloaded in several language translations here:

Re: [kepler-users] Composite actor

Hi Vicki, A copy of your workflow, or a reduced version that illustrates the problem, would be helpful. The attached example workflow has three composites that simply delay for 2 seconds, and firing occurs for all three. How does your workflow differ from this? Matt On Fri, Dec 27, 2013 at

Re: [kepler-users] Saving a class in Kepler

Hi Kenneth -- Sure enough, you are right, it seems that saving a class does not work in Kepler due to a bug. Once you have created a class in a workflow, you should be able to right click on it and select 'Save Archive (KAR)...', which allows you to save in a kar file of your choice in your 'My

Re: [kepler-users] Size Limitation of ArrayTokens?

I also took a look, and tried a larger array -- the attached workflow processes 30K integers through an array and back out again, and works fine. So there isn't an inherent limit at 20K elements. So I'm not quite sure what's happening with yours, but maybe this will help to debug. Matt On

Re: [kepler-users] R actor problem

Hi Claas, So I looked at your workflow and executed it, after getting the EML paths properly configured for my system. The workflow ran as expected, and produced the path to the data fram on output Display2. This is as expected. I then added to the workflow by adding another RExpression actor,

Re: [kepler-users] Confluence Module in kepler

Hi, I don't see a confluence module for Kepler in our system. Could you clarify where you found out about this module, or what it's functionality covers? In any case, for modules that don't ship with Kepler 2.3, you should be able to install their associate suite from the Module Manager, which

Re: [kepler-users] Kepler -nogui execution without X11GraphicsEnvironment

Albert -- Did you try running the command line shell with the -nogui and -runwf arguments? Something like: kepler.sh -nogui -runkar /home/mbj/myworkflow.kar The location of kepler.sh will vary by platform, but if you get it on your path, then you should be good to go. More details are here:

Re: [kepler-users] Kepler 2.3 and MATLAB

Wade -- Matlab is a bit trickier than R because the linkage to Kepler uses JNI via a shared library (dll on Windows) for matlab, whereas we use a shell invocation for R. So, for it to work, both the class path has to be right and the dll has to match the OS and architecture. I don't have Windows

Re: [kepler-users] Add new actor to my local Kepler library

If all you are trying to accomplish is to get several actors that you developed to work together, then putting them in the same suite is one solution. An alternate solution is to make your suite that you are running depend on the other modules that contain actors that you need. For example, if

Re: [kepler-users] How to get the System execution Time for workflows

Luis -- If you install the optional Reporting suite, it includes a Workflow Run Manager which provides a listing of all of your workflow runs, and includes the execution time for each run along with a lot of other useful information, as well as the ability to archive runs, return to earlier runs,

Re: [kepler-users] (no subject)

The mailing list archives can be searched here; http://www.mail-archive.com/kepler-users@kepler-project.org/ http://www.mail-archive.com/kepler-dev@kepler-project.org/ Regarding your R errors -- are you sure R is on your path and executing? Can you execute any of the R demos that ship with

Re: [kepler-users] Perl actor for Kepler 2.3

Josep, If you already created the actor for Kepler 1.0, then for the most part it will be able to work in 2.0 with some repackaging and minor redesign. The actor API is still basically the same, but the way we package actors in KARs and modules has changed. A perl actor would be generally

Re: [kepler-users] Metadata repository for Kepler.

binab...@umail.iu.edu wrote: Thanks for the very detailed response Matt, really appreciate it. I will dig in further and post again if I encounter questions. Thanks again!! On Tue, Dec 6, 2011 at 4:32 PM, Matt Jones jo...@nceas.ucsb.edu wrote: Hi Bina --- The answer differs for metadata

Re: [kepler-users] Metadata repository for Kepler.

Hi Bina --- The answer differs for metadata for data and metadata about processes. For data, Kepler can utilize metadata from a wide variety of repositories via the 'EcoGrid' SOAP web service interfaces, but mostly it uses the Metacat repository run as part of the KNB network for now. That is

Re: [kepler-users] IPAW 2012 CFP

this year -- great stuff is afoot in the provenance world. More details: http://ipaw2012.bren.ucsb.edu/**index.php/Call_for_**Participationhttp://ipaw2012.bren.ucsb.edu/index.php/Call_for_Participation Matt Jones NCEAS, UC Santa Barbara ___ Kepler

Re: [kepler-users] Web Service Selection with Kepler

Anne -- I thought your papers and approach were great when they originally came out. Did the actors that you created end up in a released module in Kepler? And if not, would you be willing to create such a module for a future release? Matt On Wed, Nov 30, 2011 at 2:17 PM, Ngu, Anne Hee Hiong

Re: [kepler-users] is Kepler development linked to NCEAS funding?

Hi David -- Kepler is not directly funded by NCEAS, except that NCEAS contributes in-kind support to helping to maintain the project. We've traditionally supported Kepler on a variety of extramural grants, some of which are to NCEAS (e.g., SEEK, REAP, SanParks), and others of which are to other

Re: [kepler-users] Are there any graphical INPUT actors in the community?

I believe that the folks at SDSC created the BrowserUI actor for just this purpose -- you write an HTML page containing the input questions you want, configure the BrowserUI to display it at the right point in the workflow, and then gather the output from the configured ports. Ilkay probably has

Re: [kepler-users] Question on output port from File Copier actor...

Marc -- I tried this and it worked for me -- see attached Kepler workflow. I did discover that one of the displays would not show if the file being copied already exists in the destination directory -- it seems in that case that it fails silently, which is arguably a bug. In the future, could

Re: [kepler-users] Kepler DOM timeout

This is a known bug, reported here: http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5098 Kepler should not need connectivity, and it should be using a locally-cached version of the MOML DTD. For some reason TBD the code that loads the DTD as a local resource is not being called or finding the

Re: [kepler-users] Kepler DOM timeout

bug 5098. On Mon, Apr 11, 2011 at 10:51 AM, Matt Jones jo...@nceas.ucsb.edu wrote: This is a known bug, reported here: http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5098 Kepler should not need connectivity, and it should be using a locally-cached version of the MOML DTD. For some reason

[kepler-users] Kepler Memory Usage

Yes -- you can set the max heap size by giving -Xmx4096m as an argument to the java command that you use to start kepler. Set whatever maximum heap size you need, but also note that this may limit some memory-intensive actors from working properly. I presume that you are using a shell script to

[kepler-users] Run kepler in command line

at 12:43 PM, Matt Jones mbjones.89 at gmail.com wrote: Hi Fatemeh, Kepler 1.0.0 is obsolete, and has been deprecated for a long time. You should upgrade to kepler 2 (currently 2.1, but soon to be 2.2). Nevertheless, I got an old version of kepler 1.0.0 up and running on windows XP, and here's

[kepler-users] Is Kepler OEM-Ready

Dear Madhavi, That is a fascinating, and very pointed, question. As an open source project, and as a software system that explicitly has built an infrastructure to allow 3rd parties to build their own modules, Kepler is nicely situated for 3rd parties to build high quality extensions that work

[kepler-users] NGS Specific

Madhavi, Some Kepler users have definitely used Kepler at scales like this -- Norbert's work on plasma fusion simulations that generate 800GB of data in a 30 hour simulation run under Kepler control comes to mind. However, the performance at large scale like this will entirely depend on the

[kepler-users] R installation for Kepler 1.0.0 on Windows (bis)

Hi John, I think you missed option 4: - The list is filled with busy people and it slipped through the cracks. Sorry. But, to the point of your questions: 1) When we first shipped Kepler 1.0.0, there were two windows installers: one with R included, and one without to keep the download sizes

[kepler-users] set parameter from outside

Yes, use a PortParameter instead, and it can be set on an incoming channel, which overrides the parameter setting. Matt On Thu, Dec 2, 2010 at 10:04 AM, lgomes at inf.puc-rio.br wrote: Hi, suppose I have an actor which has a parameter and I want that another actor sets its value, is it

[kepler-users] how to open a workflow from the command line

David -- When you are executing from a KAR file, you need to use the '-runkar' option, rather than the '-runwf' option. Try: $ /usr/local/Kepler-2.0/kepler.sh -runkar /home/dlebauer/pecan/kepler/pecan.kar I'm not sure about the other errors about directories not existing -- someone else will

[kepler-users] Cannot run suite 'kepler-2.0.0', error is: java.lang.ClassNotFoundException: org.kepler.Kepler

Thanks, Thomas, for the feedback. I'll ask David to take a look at the issue you report and see if there's an improvement to the build that is needed. Regards, Matt On Fri, Aug 13, 2010 at 5:40 AM, Tomasz ?ok tzok at man.poznan.pl wrote: Hi again, I have just fixed this issue. Previously I

[kepler-users] rename actor in kar file

Chris, I replicated these bugs, and so I have filed defect reports that we will work on for a future release. I will have to ask the development team to assess the difficulty in fixing these. The new bugs are: For the comma in the filename issue:

[kepler-users] Kepler 2.0, intermodular libraries conflict

check functionality of different Kepler actors, etc.? Second, I'll try to use separate class loader for my module. I've already found the docs about it. Thank you for answers, Tomek Matt Jones jones at nceas.ucsb.edu: I think it would be a good idea to upgrade these jar files to more

[kepler-users] Kepler 2.0, intermodular libraries conflict

I think it would be a good idea to upgrade these jar files to more recent releases, assuming that testing shows no adverse effects on the modules that depend on them. As these are in very low-level modules, there may be many different modules that depend on them, so we would need to test several

[kepler-users] kepler's semantic type checking of connected ports

Yes, I see I can replicate this on my machine, and it happens even if they are the same type, or the input type is a subclass of the output type. I filed a bug report (http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5136). Thanks for pointing it out. Matt On Mon, Aug 9, 2010 at 3:30 PM,

[kepler-users] where is the reporting suite

Dear Ming, We have not yet released the reporting suite -- but we are in the fina testing stages to do so. We expect to release it very soon, and when we do you will see the reporting suite in the module manager and will be able to activate it. We'll plan on sending an announcement when the

[kepler-users] Fwd: WANDS'10 call for participation

if you're interested. Cheers, Matt -- Forwarded message -- Date: Wed, May 12, 2010 at 1:33 AM Subject: WANDS'10 call for participation -- please help distribute To: Matt Jones jones at nceas.ucsb.edu *** WANDS: The 1st International Workshop on Workflow Approaches to New Data-centric

[kepler-users] Status of Kepler-2.0?

Hi Tom, Kepler 2.0.0 is being prepared for release, and is going through testing. For that purpose, we are developing a series of release candidates. These will not be supported after 2.0.0 comes out, but any issues you find with them would be valuable to report to kepler-dev to improve the

[kepler-users] Query with the Expression actor

Harini, The expression actor simply evaluates the expression, and places the result on the output port. So, if you have two ports (a1, a2) and the incoming value to a1 is 3 and incoming value of a2 is 5, then the expression 'a1' will output 3 on the output port, and the expression 'a1 + a2' will

[kepler-users] Greetings/newbie questions about Kepler

Edward and Christopher covered most of the differences between Kepler and Ptolemy, especially with respect to the 1.0 release. The current development version of Kepler that is leading to our 2.0 release includes a number of additional major differences, some of which include: 1) Module-based

[kepler-users] [kepler-dev] SRB account needed ?

I've learned that SDSC seems to be migrating away from the SRB and instead setting up a new iRODS service. Certainly that may affect the accounts that people use, and it may also have implications for whether the SRB actors continue to function properly -- I'm not sure if the iRODS server uses

[kepler-users] Where to go with the problems of internationalization or how create account into forum?

In addition to what Chad said, a group in Japan worked on internationalizing Kepler for scientists in Japan (contact Akiko Ogawa on this list). They might be interested in contributing to improvements that allow for general internationalization. They also found it was useful to translate the

[kepler-users] Problem with not all data going through a workflow

Hi Barbara, You need the DDF director for your Boolean switch actors to work, so stick with that. Looking at your workflow, I think you need to remove the DDF director from the inner Check Range subworkflow. This allows the outer workflow to control the execution with its DDF director. When I

[kepler-users] multiport as output

Hi Ufuk, There is an example in the R chapter of the User Guide (available from the Help menu in Kepler 1.0.0, or from the kepler-docs subversion repository). See page 348, section 11.4.1.1.5 (Example Five: Using Ports Configured as Multiports ). Its not clear from your description exactly

[kepler-users] writing a custom director

I also believe that Ilkay Altintas and Daniel Crawl have implemented a 'smart-rerun' feature for at lease some specific scenarios (e.g, specific restrictions on actors maintaining state) that allows workflows to be rerun from provenance, or to pick up an aborted workflow partway through a run.

[kepler-users] XSLT Actor xml input

Dan Crawl seems to have checked in some fixes to the Kepler XSLT actor that allow it to accept XMLToken as input and no longer writes the temp files to disk. Does this meet your needs, Chris? For now you can only access these changes from the development build, but it will be released with the

[kepler-users] Anyone doing GIS workflows?

Hi Chris, We've done a few wfs that used GIS operations, mainly for processing tasters before data analysis. We created a few utility actors for GIS. One wraps The GDAL library and enables reprojection, clipping, and image format conversions. There is another actor to handle various

[kepler-users] kepler in web mode

Years ago we (Ilkay) worked on a web start version of kepler that we tried for a while. It was fairly difficult to set up and maintain, especially because of a variety of jar signing issues, and we didn't see many benefits of that approach over a plain installer. So we never formally pursued it,

[kepler-users] Kepler help

Hi Michael, The MatlabExpression actor calls the local shared library for Matlab, which it needs to be able to find. If you read the actor documentation in the Actor Reference Manual (or from the Help menu in Kepler), it describes how to set the appropriate environment variables before running

[kepler-users] What kind of actor is it?

Jose, That is the Expression actor. You can find it by searching for Expression, and you can enter any expression that fits the expression language. There is a detailed description in section 8.1 of the Kepler user manual starting on page 238. There is also a more detailed treatment of the

[kepler-users] Newbie question

Dear Jos?, There are many other good workflow systems in existence, but I'd have to agree with you that Kepler sounds like a good fit. Taverna is a good system, but is heavily centered on executing web services. We've done a lot of work in Kepler to create various versions of a command line

[kepler-users] Extracting XML Attributes

As an alternative, if compiling the source isn't something you want to undertake, maybe Dan could package up a KAR file for you to import into your installed version of Kepler. Dan, do you think this would be feasible? Matt On Wed, Oct 15, 2008 at 8:59 AM, Daniel Crawl crawl at sdsc.edu wrote:

[kepler-users] kepler-1.0.0beta1 released

project, and others. Matt Jones, on behalf of the Kepler project members -- ~ Matt Jones jones at nceas.ucsb.edu National Center for Ecological Analysis and Synthesis (NCEAS) UC Santa Barbara http://www.nceas.ucsb.edu/ecoinformatics

[kepler-users] Kepler, adding composite actors?

Lots of us would like to have this working, and it is right on the top of the list for some of the SEEK developers. But it is complicated and we are rearchitecting the system to support archive file formats that should make it far easier for us to add in new actors or workflows that are both