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From: Luca C. <lcl...@uc...> - 2008-10-09 18:23:16
|
Reynoldson, Joe wrote: > I am using opal-perl-1.9.2, and I need to specify the number of > processors for a job. I cannot find a method of the JobInputType class > to set number of processors. How can I specify numprocs? > > > > Thanks, > > > > Joe Reynoldson > Dear Joe, we currently do not support that feature in the perl client library. We can add it, it shouldn't be too difficult. Sincerely, Luca |
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From: Luca C. <lcl...@uc...> - 2008-10-09 18:19:36
|
Jennewein, Douglas M wrote: > I need to access our opal services over https, but am unable to do so. > I’ve tried this with the sample java client and the perl client. Here > is the output I get when trying to invoke a service with the generic > service client: > > > > [root@rio opal]# java edu.sdsc.nbcr.opal.GenericServiceClient -l > https://rio.usd.edu/opal/services/GeneSeqer -r getAppMetadata > > > > Reading command line arguments > > Service URL: https://rio.usd.edu/opal/services/GeneSeqer > > Invoking operation: getAppMetadata > > > > HTTPS protocol handler registered > > > > Required property X509_USER_PROXY not set > > > > The sample clients connect fine over http, but http is not available > from the location that needs access to the services – only https is. Is > it possible to configure opal to respond to requests over https? > > > Dear Doug, we support GSI security which is https with also client side authentication. You can find a guide here: http://nbcr.net/software/opal/docs/1.9/security.html Sincerely, Luca |
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From: Jennewein, D. M <Dou...@us...> - 2008-10-09 14:47:33
|
I need to access our opal services over https, but am unable to do so. I've tried this with the sample java client and the perl client. Here is the output I get when trying to invoke a service with the generic service client: [root@rio opal]# java edu.sdsc.nbcr.opal.GenericServiceClient -l https://rio.usd.edu/opal/services/GeneSeqer -r getAppMetadata Reading command line arguments Service URL: https://rio.usd.edu/opal/services/GeneSeqer Invoking operation: getAppMetadata HTTPS protocol handler registered Required property X509_USER_PROXY not set The sample clients connect fine over http, but http is not available from the location that needs access to the services - only https is. Is it possible to configure opal to respond to requests over https? Doug Jennewein Research Analyst Department of Computer Science University of South Dakota Vermillion, SD 57069 (605) 677-5388 (605) 677-6662 (fax) Dou...@us... <mailto:Dou...@us...> |
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From: Reynoldson, J. <Joe...@us...> - 2008-10-09 12:52:34
|
I am using opal-perl-1.9.2, and I need to specify the number of processors for a job. I cannot find a method of the JobInputType class to set number of processors. How can I specify numprocs? Thanks, Joe Reynoldson Computer Science Department The University of South Dakota email: jre...@us... web: http://www.usd.edu/csci |
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From: Doug J. <Dou...@us...> - 2008-09-15 15:47:05
|
Hi, Luca: Thanks for the patch. I'm using rocks 4.3 64 bit. -Doug Luca Clementi wrote: > Jennewein, Douglas M wrote: >> Hi, Luca: >> >> I am using the Opal 1.9.3 Rocks roll, and a patch would be great. >> Thanks! >> >> -Doug >> > > Hi Doug, > we have released Opal 1.9.5 with the cpu input feature. > > Attached there is the patch to from 1.9.3 to 1.9.5, although I think > that this can create some problem. In fact if you have done any > modification to the opal source code it will fail. > > Somewhere next week we will make a new opal roll with this version (I > would wait for that). > What version of Rocks do you have (32 or 64 bits)? > > > Luca > > >> -----Original Message----- >> From: Luca Clementi [mailto:lcl...@uc...] Sent: Wednesday, >> September 10, 2008 1:52 PM >> To: Jennewein, Douglas M >> Cc: opa...@li... >> Subject: Re: [Opaltoolkit-users] Specifying the number of processors >> foraparallel job >> >> Jennewein, Douglas M wrote: >>> Hi, Jane: >>> >>> >>> >>> I looked at the num.procs entry in opal.properties, and determined >> that >>> if I set num.procs but do not pass the "n" parameter to the generic >>> service client I get an error saying that I have not specified the >>> number of processors for a parallel job. Also, if I set num.procs to >> 4 >>> and then launch an opal job with the generic service client passing it >> >>> "n 7" to run on 7 processors I get an error saying there are not >> enough >>> available processors. But if I specify 4 or fewer processors the >>> job runs. This lead me to believe that num.procs is used to specify >>> the total processors available for opal jobs. Is that correct? >>> >>> >>> -Doug >>> >> >> Dear Doug, >> you are right. >> >> num.proc is used to specify the maximum number of proc you want to >> expose with opal, then you have to specify the number of processors >> you actually wanna use when you launch a job. >> >> So for the command line client it is already supported, but not for >> the web interface. >> >> What version are you using? I can patch Opal web interface to support >> that feature and make a new release 1.9.5 in a short time frame (less >> than a week). This was on my TODO list for a long time. >> >> Sincerely, >> Luca >> > -- Doug Jennewein Research Analyst Department of Computer Science University of South Dakota Vermillion, SD 57069 (605) 677-5388 (605) 677-6662 (fax) Dou...@us... |
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From: Luca C. <lcl...@uc...> - 2008-09-13 00:00:34
|
Jennewein, Douglas M wrote: > Hi, Luca: > > I am using the Opal 1.9.3 Rocks roll, and a patch would be great. > Thanks! > > -Doug > Hi Doug, we have released Opal 1.9.5 with the cpu input feature. Attached there is the patch to from 1.9.3 to 1.9.5, although I think that this can create some problem. In fact if you have done any modification to the opal source code it will fail. Somewhere next week we will make a new opal roll with this version (I would wait for that). What version of Rocks do you have (32 or 64 bits)? Luca > -----Original Message----- > From: Luca Clementi [mailto:lcl...@uc...] > Sent: Wednesday, September 10, 2008 1:52 PM > To: Jennewein, Douglas M > Cc: opa...@li... > Subject: Re: [Opaltoolkit-users] Specifying the number of processors > foraparallel job > > Jennewein, Douglas M wrote: >> Hi, Jane: >> >> >> >> I looked at the num.procs entry in opal.properties, and determined > that >> if I set num.procs but do not pass the "n" parameter to the generic >> service client I get an error saying that I have not specified the >> number of processors for a parallel job. Also, if I set num.procs to > 4 >> and then launch an opal job with the generic service client passing it > >> "n 7" to run on 7 processors I get an error saying there are not > enough >> available processors. But if I specify 4 or fewer processors the job >> runs. This lead me to believe that num.procs is used to specify the >> total processors available for opal jobs. Is that correct? >> >> >> >> -Doug >> > > Dear Doug, > you are right. > > num.proc is used to specify the maximum number of proc you want to > expose with opal, then you have to specify the number of processors you > actually wanna use when you launch a job. > > So for the command line client it is already supported, but not for the > web interface. > > What version are you using? I can patch Opal web interface to support > that feature and make a new release 1.9.5 in a short time frame (less > than a week). This was on my TODO list for a long time. > > Sincerely, > Luca > |
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From: Luca C. <lcl...@uc...> - 2008-09-11 21:29:09
|
The new Opal-java-core 1.9.5 is available for download from SourceForge web site. This is a minor release with bug fixes and minor improvements. CHANGELOG: - General - Improved the build script and cleaned up the tar file from some useless files. - Opal Gui - Added the number of CPUs both in the simple and in the complex submission form. Luca |
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From: Jennewein, D. M <Dou...@us...> - 2008-09-10 18:54:37
|
Hi, Luca: I am using the Opal 1.9.3 Rocks roll, and a patch would be great. Thanks! -Doug -----Original Message----- From: Luca Clementi [mailto:lcl...@uc...] Sent: Wednesday, September 10, 2008 1:52 PM To: Jennewein, Douglas M Cc: opa...@li... Subject: Re: [Opaltoolkit-users] Specifying the number of processors foraparallel job Jennewein, Douglas M wrote: > Hi, Jane: > > > > I looked at the num.procs entry in opal.properties, and determined that > if I set num.procs but do not pass the "n" parameter to the generic > service client I get an error saying that I have not specified the > number of processors for a parallel job. Also, if I set num.procs to 4 > and then launch an opal job with the generic service client passing it > "n 7" to run on 7 processors I get an error saying there are not enough > available processors. But if I specify 4 or fewer processors the job > runs. This lead me to believe that num.procs is used to specify the > total processors available for opal jobs. Is that correct? > > > > -Doug > Dear Doug, you are right. num.proc is used to specify the maximum number of proc you want to expose with opal, then you have to specify the number of processors you actually wanna use when you launch a job. So for the command line client it is already supported, but not for the web interface. What version are you using? I can patch Opal web interface to support that feature and make a new release 1.9.5 in a short time frame (less than a week). This was on my TODO list for a long time. Sincerely, Luca |
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From: Luca C. <lcl...@uc...> - 2008-09-10 18:48:03
|
Jennewein, Douglas M wrote: > Hi, Jane: > > > > I looked at the num.procs entry in opal.properties, and determined that > if I set num.procs but do not pass the “n” parameter to the generic > service client I get an error saying that I have not specified the > number of processors for a parallel job. Also, if I set num.procs to 4 > and then launch an opal job with the generic service client passing it > “n 7” to run on 7 processors I get an error saying there are not enough > available processors. But if I specify 4 or fewer processors the job > runs. This lead me to believe that num.procs is used to specify the > total processors available for opal jobs. Is that correct? > > > > -Doug > Dear Doug, you are right. num.proc is used to specify the maximum number of proc you want to expose with opal, then you have to specify the number of processors you actually wanna use when you launch a job. So for the command line client it is already supported, but not for the web interface. What version are you using? I can patch Opal web interface to support that feature and make a new release 1.9.5 in a short time frame (less than a week). This was on my TODO list for a long time. Sincerely, Luca |
|
From: Jennewein, D. M <Dou...@us...> - 2008-09-10 18:21:05
|
Hi, Jane: I looked at the num.procs entry in opal.properties, and determined that if I set num.procs but do not pass the "n" parameter to the generic service client I get an error saying that I have not specified the number of processors for a parallel job. Also, if I set num.procs to 4 and then launch an opal job with the generic service client passing it "n 7" to run on 7 processors I get an error saying there are not enough available processors. But if I specify 4 or fewer processors the job runs. This lead me to believe that num.procs is used to specify the total processors available for opal jobs. Is that correct? -Doug From: Wilfred Li [mailto:wi...@sd...] Sent: Wednesday, September 10, 2008 1:05 PM To: Jennewein, Douglas M; opa...@li... Subject: FW: [Opaltoolkit-users] Specifying the number of processors for aparallel job Hi Douglas, You can specify the number of processors in $OPAL_HOME/etc/opal.properties. Jane From: opa...@li... [mailto:opa...@li...] On Behalf Of Jennewein, Douglas M Sent: Wednesday, September 10, 2008 10:45 AM To: opa...@li... Subject: [Opaltoolkit-users] Specifying the number of processors for aparallel job How can I specify the number of processors to a parallel job when submitting via the advanced submission form? I see that the GenericServiceClient has a "n" parameter that allows this, but I don't see how to do it for web submissions. Doug Jennewein Research Analyst Department of Computer Science University of South Dakota Vermillion, SD 57069 (605) 677-5388 (605) 677-6662 (fax) Dou...@us... |
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From: Wilfred L. <wi...@sd...> - 2008-09-10 18:05:22
|
Hi Douglas, You can specify the number of processors in $OPAL_HOME/etc/opal.properties. Jane From: opa...@li... [mailto:opa...@li...] On Behalf Of Jennewein, Douglas M Sent: Wednesday, September 10, 2008 10:45 AM To: opa...@li... Subject: [Opaltoolkit-users] Specifying the number of processors for aparallel job How can I specify the number of processors to a parallel job when submitting via the advanced submission form? I see that the GenericServiceClient has a "n" parameter that allows this, but I don't see how to do it for web submissions. Doug Jennewein Research Analyst Department of Computer Science University of South Dakota Vermillion, SD 57069 (605) 677-5388 (605) 677-6662 (fax) Dou...@us... |
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From: Jennewein, D. M <Dou...@us...> - 2008-09-10 17:45:08
|
How can I specify the number of processors to a parallel job when submitting via the advanced submission form? I see that the GenericServiceClient has a "n" parameter that allows this, but I don't see how to do it for web submissions. Doug Jennewein Research Analyst Department of Computer Science University of South Dakota Vermillion, SD 57069 (605) 677-5388 (605) 677-6662 (fax) Dou...@us... <mailto:Dou...@us...> |
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From: Luca C. <lcl...@uc...> - 2008-04-29 23:22:52
|
Dear all,
We are pleased to announce the 1.9.4 release of the opal-core-java
package. This release builds on the earlier 1.9.3 version, and adds some
bug fixes and improvements as listed below:
- Opal Dashboard:
- Fixed a bug in the creation of the time series for the charts
- Improved checking for the "Add a File" button in the simple
submission form. Now it checks that the user has actually uploaded
a file.
- The chart now uses integer numbers for the X axis.
- Fixed a bug in the JobStatus page that was not displaying properly
the name of the service
- Opal Services:
- The user can now set the location of the working directory in the
opal.properties if the symbolic links are resolved to different
locations on the head and compute nodes of a cluster
The new release can be downloaded from our website -
http://nbcr.net/software/opal/. As usual, please feel free to use the
Sourceforge Opal Toolkit Tracker
(http://sourceforge.net/tracker/?group_id=211778) to report bugs and
feature requests, and the NBCR Web Services User Forum
(https://nbcr.net/forum/viewforum.php?f=13") for general comments and
feedback.
Sincerely,
Luca
|
|
From: Sriram K. <sr...@sd...> - 2008-04-15 17:53:01
|
Hello Dan, Could you send us some more information about your setup? In particular, what versions of Windows and Java are you using. I suspect you are missing some required jars, and we would like to test this out on a similar system here. Also, did you notice anything untoward in your tomcat logs ($CATALINA_HOME/logs/catalina.out)?The catalina logs can usually be quite helpful in debugging such problems. Thanks for your patience! Sriram ps: Would you mind subscribing to our very low traffic mailing list here: https://lists.sourceforge.net/lists/listinfo/opaltoolkit-users? This discussion can be very helpful to our other users as well. On Apr 15, 2008, at 9:52 AM, <Dan...@sa...> wrote: > Hi Sriram and Luca, > > Thank you very much for your prompt reply. > > I run the opal-1.9.3 Tutorial under Windows and set classpath by > typing “classpath.bat”. The OPAL_HOME is set as an > environment variable by Start → Control Panel → Systems > → Advanced → Environment Variables. Unfortunately, I > get stuck at the last step: > java edu.sdsc.nbcr.opal.GenericServiceClient -l http://localhost:8080/opal/services/BabelServicePort > -a "-ipdb sample.pdb -opdb out.pd > b" -f etc/sample.pdb -r launchJob > > The error message is listed as below. I would be very appreciative > if you could give me some suggestions to solve the problem. > > Best regards, > Dan > > > OUTPUT: > > C:\Tutorial\opal-ws-1.9.3>java > edu.sdsc.nbcr.opal.GenericServiceClient -l http:/ > /localhost:8080/opal/services/BabelServicePort -a "-ipdb sample.pdb - > opdb out.pd > b" -f etc/sample.pdb -r launchJob > > Reading command line arguments > Service URL: http://localhost:8080/opal/services/BabelServicePort > Invoking operation: launchJob > > Command line arguments: -ipdb sample.pdb -opdb out.pdb > Making non-blocking invocation on Opal service - > Exception in thread "main" AxisFault > faultCode: {http://schemas.xmlsoap.org/soap/ > envelope/}Server.userException > faultSubcode: > faultString: java.lang.reflect.InvocationTargetException > faultActor: > faultNode: > faultDetail: > {http://xml.apache.org/axis/}hostname:study-442bb0af9 > > java.lang.reflect.InvocationTargetException > at > org.apache.axis.message.SOAPFaultBuilder.createFault(SOAPFaultBuilder > .java:221) > at > org.apache.axis.message.SOAPFaultBuilder.endElement(SOAPFaultBuilder. > java:128) > at > org.apache.axis.encoding.DeserializationContext.endElement(Deserializ > ationContext.java:1087) > at > org.apache.xerces.parsers.AbstractSAXParser.endElement(Unknown Source > ) > at > org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanEndElement(Unknow > n Source) > at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl > $FragmentContent > Dispatcher.dispatch(Unknown Source) > at > org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Un > known Source) > at > org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source) > at > org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source) > at org.apache.xerces.parsers.XMLParser.parse(Unknown Source) > at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown > Source) > at javax.xml.parsers.SAXParser.parse(Unknown Source) > at > org.apache.axis.encoding.DeserializationContext.parse(Deserialization > Context.java:227) > at org.apache.axis.SOAPPart.getAsSOAPEnvelope(SOAPPart.java: > 696) > at org.apache.axis.Message.getSOAPEnvelope(Message.java:424) > at > org.apache.axis.handlers.soap.MustUnderstandChecker.invoke(MustUnders > tandChecker.java:62) > at org.apache.axis.client.AxisClient.invoke(AxisClient.java: > 206) > at org.apache.axis.client.Call.invokeEngine(Call.java:2765) > at org.apache.axis.client.Call.invoke(Call.java:2748) > at org.apache.axis.client.Call.invoke(Call.java:2424) > at org.apache.axis.client.Call.invoke(Call.java:2347) > at org.apache.axis.client.Call.invoke(Call.java:1804) > at > edu.sdsc.nbcr.opal.AppServicePortTypeSoapBindingStub.launchJob(AppSer > vicePortTypeSoapBindingStub.java:527) > at > edu.sdsc.nbcr.opal.GenericServiceClient.main(GenericServiceClient.jav > a:238) > > C:\Tutorial\opal-ws-1.9.3> |
|
From: Sriram K. <sr...@sd...> - 2008-03-17 20:52:08
|
Hello all, Version 1.9.3 of the Opal Python libraries are now available from our website here: https://sourceforge.net/project/showfiles.php?group_id=211778&package_id=260248 . The key difference from version 1.9.2 is that this release depends on ZSI 2.1_a1, which is not dependent on the outdated PyXML package. Please feel free to use the Sourceforge Opal Toolkit Tracker (http://sourceforge.net/tracker/?group_id=211778 ) to report bugs and feature requests, and the NBCR Web Services User Forum (https://nbcr.net/forum/viewforum.php?f=13") for general comments and feedback. Sincerely, Sriram |
|
From: Sriram K. <sr...@sd...> - 2008-03-01 00:29:13
|
Dear all,
We are pleased to announce the 1.9.3 release of the opal-core-java
package. This version builds on the earlier 1.9.2 version, and adds
key bug fixes and improvements listed as follows:
- Opal Dashboard:
- Fixed a bug in the submission form where input file parameters
were not properly handled on the command line
- Fixed a bug in the automatic interface generation where an
exception was thrown if the number of flags were zero
- Fixed a bug where the usage information wasn't displayed
correctly for the automatically generated interface
- Fixed a locale issue in the formatting of dates used by the
statistics tab of the dashboard
- Opal Services:
- Fixed a bug where the job status was being retrieved
incorrectly during a destroy() operation when a database was being
used to persist
state
- Updated command-line argument validation client to now account
for groups
The new release can be downloaded from our website - http://nbcr.net/
software/opal/. As usual, please feel free to use the Sourceforge
Opal Toolkit Tracker (http://sourceforge.net/tracker/?
group_id=211778) to report bugs and feature requests, and the NBCR
Web Services User Forum (https://nbcr.net/forum/viewforum.php?f=13")
for general comments and feedback.
Sincerely,
Sriram
--
Sriram Krishnan, Ph.D.
http://www.sdsc.edu/~sriram |
|
From: Sriram K. <sr...@sd...> - 2008-02-27 03:35:14
|
Here's the config file - |
|
From: Sriram K. <sr...@sd...> - 2008-02-27 03:34:56
|
Hi,
I think I found a bug in the automatic interface generation. I have
an application that has only untagged params - and no flags or tagged
parameters. If I try to generate an interface from it, the generator
throws an exception - Can not get application configuration file from
remote server. On digging deep, it appears as if it requires the
metadata to contain flags. This is the Tomcat error -
2008-02-26 14:21:27,580 ERROR
edu.sdsc.nbcr.opal.gui.actions.CreateSubmissionFormAction.parseAppMetada
ta(CreateSubmissionFormAction.java:214) - PARSER: Impossible to get
the appMetadata from the Opal server. Error: null
java.lang.NullPointerException
at edu.sdsc.nbcr.opal.gui.common.AppMetadata.getArgFlagId
(AppMetadata.java:196)
at
edu.sdsc.nbcr.opal.gui.actions.CreateSubmissionFormAction.parseGroup
(CreateSubmissionFormAction.java:299)
at
edu.sdsc.nbcr.opal.gui.actions.CreateSubmissionFormAction.parseAppMetada
ta(CreateSubmissionFormAction.java:199)
Sure enough, if I add a dummy flag, it works ok (except of course, if
I click on the flag the application fails because it doesn't expect
the flag). I am attaching the config file for my app - along with
the extra flag. Check it out - you can then get rid of the flags, and
see that it fails.
Also, the generator doesn't do BOOL correctly. It basically creates a
text box, while it should create a drop down list or radio buttons
with true/false. I had to change the BOOL to STRING, and give it a
list of values (true, false) for it to look acceptable.
Sriram
|
|
From: Luca C. <lcl...@uc...> - 2008-02-05 02:04:03
|
Dear all, We are pleased to announce the latest release of the Opal Toolkit - version 1.9.2. This includes the server and client packages for Java, and client packages for Python and Perl. Version 1.9.2 builds upon the earlier 1.9alpha release with bug fixes and improved features. In particular, it provides - * The Opal Dashboard, which is a Web interface that is installed by default with Opal for accessing usage and server statistics * Dynamic Interface Generation, which uses a flexible XML schema for command-line argument specification and automatically generates Web interfaces from it * Improvement of back-end Opal services to support the dashboard and dynamic interface generation For this release, we would also like to announce our the new Opal website: http://nbcr.net/software/opal/, which uses software project management provided by SourceForge.net. All downloads are available from the above website. Web services based on Opal Toolkit version 1.9.2 are currently being used in production on NBCR resources, and are hosted on ws.nbcr.net. Installed services include MEME/MAST, PDB2PQR, AutoDock/AutoGrid, APBS, and Continuity. You can access the Opal Dashboard for ws.nbcr.net at http://ws.nbcr.net:8080/opal/dashboard. From the Dashboard, you can view service statistics, and run jobs using the dynamic interface generation. Please feel free to use the Sourceforge Opal Toolkit Tracker (http://sourceforge.net/tracker/?group_id=211778) to report bugs and feature requests, and the NBCR Web Services User Forum (https://nbcr.net/forum/viewforum.php?f=13") for general comments and feedback. Sincerely, Luca & Sriram |
|
From: Luca C. <lcl...@uc...> - 2007-12-13 03:35:58
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Hi all, We are going to release the opal 1.9 version. I am wondering if you could give a try to the code before we actually release it. To get the code I made a tar.gz on: http://users.sdsc.edu/~clem/opal-core.tar.gz which is what you can get with: svn checkout https://opaltoolkit.svn.sourceforge.net/svnroot/opaltoolkit/opal opal-core The latest documentation can be obtained from the new Web site: http://opaltoolkit.sourceforge.net/ or in the ./docs directory of the tar... Let me know also if you have comment on the web site!! (The Opal GUI documentation is not present yet...) One last thing (actually two ;-)), all the people who are now part of the project should subscribe to the user mailing list (you'll find the link on the web site). The guys who want to commit on the svn should also subscribe to the svnnotification mailing list. clem |
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From: Luca C. <lcl...@uc...> - 2007-12-13 03:13:02
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clem |
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