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Re: [ice-users] Using Nek5000 in ICE

Ram,


Good questions. Robert will work through these issues with you. Robert, please create bugs for 2a, 2b and 3.


As for 1, the file will appear in the Resources View, but the contents of the file will appear in the Output tab. In fact, when you open the output tab, it will highlight the resources view so that you can select the file you want to view. Greg, Alex and I have been talking about remodeling this, so please let us know if you have thoughts.


If you manually use visnek, then it won't show up in ICE's list. ICE only shows the files that it is tracking from its runs. However, it should still show up in your Eclipse project (itemDB or something else), which you can view in the Project Explorer/Resources Perspective (different than the Resources View). The solution to this it to add visnek as a step in the Nek5000 workflow item, (the JobLauncher in org.eclipse.ice.nek5000/src).


Jay


Jay Jay Billings
Oak Ridge National Laboratory
Twitter Handle: @jayjaybillings
From: ice-users-bounces@xxxxxxxxxxx <ice-users-bounces@xxxxxxxxxxx> on behalf of K. N. Ramachandran <knram06@xxxxxxxxx>
Sent: Thursday, August 11, 2016 6:00 PM
To: Ice user discussions
Subject: Re: [ice-users] Using Nek5000 in ICE
 
Hello Jay, Robert,

I have been able to build ICE (using ICE) only for Linux x86-64 using the Build instructions, so that worked as expected, thank you.

I am continuing to check the Nek5000 integration in ICE and just had some questions:

1) Based on https://wiki.eclipse.org/Using_Nek5000_with_ICE in the section on Viewing Results, it says that the Nek5000 Standard Output resource files should be visible in the Output Files and Data tab (of the Nek5000 Model Launcher).

I currently see these files as part of the Resources tab instead which is not part of the Output files tab. So this is more of a cosmetic issue I guess.

2) Using the visnek utility (needs tcsh), I have been able to generate a conj_ht.nek5000 VisIt file. However

a) This file does not appear in the Resources tab.

b) How would I launch VisIt using this file in ICE? I have already added VisIt connection information using the steps at https://wiki.eclipse.org/ICE_Embedded_Visualizations . I am able to process the conj_ht.nek5000 file in standalone VisIt and I am not sure how to do this in ICE.

3) I have an up to date version of the ICE source code (the next branch). I had built this using ICE, but the resulting executable could not process the Nek5000 input file, i.e. I got the java NullPointer exception, I had first reported. 

Should I be using a different branch? I worked around this by using the ICE package you had prepared earlier with the changes to support Nek5000.

Hope this helps. Please let me know if you might need more information.

Thanks.

On Mon, Aug 8, 2016 at 10:23 AM, Jay Jay Billings <jayjaybillings@xxxxxxxxx> wrote:
Ram,

You're welcome. Here's a link to our developer documentation: http://wiki.eclipse.org/ICE_Developer_Documentation

There are build instructions there, but they are old and for use if you are not using ICE to develop ICE. If you are using ICE, just go to the "Developer" menu in the menu bar, then look for the ICE submenu to clone ICE and build it.

Jay

On Mon, Aug 8, 2016 at 10:00 AM, K. N. Ramachandran <knram06@xxxxxxxxx> wrote:
Hello Jay,

Thanks for this and the update on fixing the REST interface. I will look further into the wiki for the build instructions.

On Fri, Aug 5, 2016 at 6:07 PM, Jay Jay Billings <jayjaybillings@xxxxxxxxx> wrote:

Ram,

Sounds like it is time for you to join the ice-dev list and check out our wiki's developer section! :-)

We can definitely set you up to do local builds. Checkout The org.eclipse.ice.parent/pom.xml file to eliminate the other architectures. Builds instructions are on the wiki. Robert will double check them next week.

Jay

On Aug 5, 2016 6:02 PM, "K. N. Ramachandran" <knram06@xxxxxxxxx> wrote:
Hi Robert,

Thank you for resolving those issues. I took the latest build and that solves problems 1 and 2 like you said and problem 4 was resolved by building nek5000 separately in the examples folder. I was able to successfully run the conj_ht problem through ICE. I will keep using this current approach and if I have ideas to improve the process, I will let you know. 

Also, I was thinking that since I am able to build ICE in ICE, I can just pull in your changes (in a different branch) and rebuild my local version. This way, you won't have to repackage the build after making relevant changes. Does this sound alright?

If so, I might need a bit of help in tweaking the build so that it produces binaries only for Linux. Right now, it produces binaries for extra OSes (like Win and Mac) and this costs some build time. I am also not clear where to change the settings for this and so might need some pointers there too.

Thank you.


On Fri, Aug 5, 2016 at 1:43 PM, Smith, Robert W. <smithrw@xxxxxxxx> wrote:

Hello Ram,


Thank you for testing this out for me. You found a very embarrassing mistake I'd made. I hadn't actually merged the branch I'd been doing the more recent Nek5000 fixes in with the next branch, so the version you downloaded was out of date. However, now the versions on the site really are up to date, which should fix problems 1 and 2. 


For problem 4, we expect the nek5000 executable to be built inside the folder containing the data files for the problem. I've added a section on building nek to the tutorial https://wiki.eclipse.org/Using_Nek5000_with_ICE​, though if you have any suggestions for improvements to the process they would be more than welcome.


I'll look into improvements for problems 3 and 5.


Thanks for the help with testing!


Robert

From: ice-users-bounces@xxxxxxxxxxx <ice-users-bounces@xxxxxxxxxxx> on behalf of K. N. Ramachandran <knram06@xxxxxxxxx>
Sent: Friday, August 05, 2016 11:58 AM
To: Ice user discussions
Subject: Re: [ice-users] Using Nek5000 in ICE
 
Hello Robert,

No problem at all, regarding the delay. Thank you for notifying on the build. I was able to test it out and the initial import seems to mostly work. I did notice that:

1) The logical values like IFFLOW are not being imported, i.e. if the value is True, the checkbox is not ticked. This seems to affect the OUTPUT field values too.

2) I enforce the Logical values and when I write out the new .rea file, I see values of 'yes' in place of 'T' for the Logical values. I haven't been able to run the example, but I think it would fail since Nek5000 may not interpret 'yes' properly?

3) This is more of a cosmetic issue. I create a Nek5000 Launcher and the Execution Path in the 'Hosts' section, already has a default path that seems to be an artifact. Would it be better to just leave it blank?

4) When I setup everything and click 'Go!', I get a runtime error that './nek5000' does not exist. From what I understand by going through the Nek5000 manual, we need to do a makenek first which generates the nek5000 executable. This is then used by the 'nek' script/executable.

5) Another cosmetic issue. Repeated instances of launching the job, causes more stderr and stdout files to accumulate in the 'Files' dialog box under 'Resources'.

I understand each set of them correspond to a particular job instance but currently, they are all listed flatly. Perhaps listing each set of files under an icelaunch id might help?

Hope this helps. Please let me know whenever you want this to be re-tested.


On Fri, Aug 5, 2016 at 9:29 AM, Smith, Robert W. <smithrw@xxxxxxxx> wrote:

Ram,


As of this morning, the new executables at http://download.eclipse.org/ice/builds/next/​ should now have the fix ready. Sorry for the delay, but there were problems with application signing for the build server yesterday afternoon. Please try them out and let me know if you're still having trouble with the Nek5000 functionality.


Robert

From: ice-users-bounces@xxxxxxxxxxx <ice-users-bounces@xxxxxxxxxxx> on behalf of K. N. Ramachandran <knram06@xxxxxxxxx>
Sent: Thursday, August 04, 2016 3:07 PM

To: Ice user discussions
Subject: Re: [ice-users] Using Nek5000 in ICE
 
Hi Jay, Robert,

No problem at all. Just wanted to check and I will test it out and let you know whenever it is ready.

Thank You.

On Thu, Aug 4, 2016 at 3:05 PM, Billings, Jay Jay <billingsjj@xxxxxxxx> wrote:

Ram,


​And if you wouldn't mind, it would be awesome if you could test this when Robert finishes it up.


I have to apologize: Our Nek5000 plugin was very out of date!


Jay


Jay Jay Billings
Oak Ridge National Laboratory
Twitter Handle: @jayjaybillings
From: ice-users-bounces@xxxxxxxxxxx <ice-users-bounces@xxxxxxxxxxx> on behalf of Smith, Robert W. <smithrw@xxxxxxxx>
Sent: Thursday, August 04, 2016 3:00 PM
To: Ice user discussions
Subject: [EXTERNAL] Re: [ice-users] Using Nek5000 in ICE
 

Hello Ram,


I've been working on the Nek5000 functionality this week, and I should have a working build in the unstable branch by the end of the day, along with more detailed instructions for the tutorial on the wiki.


Robert

From: ice-users-bounces@xxxxxxxxxxx <ice-users-bounces@xxxxxxxxxxx> on behalf of K. N. Ramachandran <knram06@xxxxxxxxx>
Sent: Thursday, August 04, 2016 2:24 PM
To: Ice user discussions
Subject: Re: [ice-users] Using Nek5000 in ICE
 
Hi Jay, Robert,

If you need to test or improve the Nek5000 integration with ICE, I can help with that as well. Feel free to let me know.

Also, I guess the unstable branch is still broken?

Thank You.

On Mon, Aug 1, 2016 at 10:54 PM, Jay Jay Billings <jayjaybillings@xxxxxxxxx> wrote:
Ram,

The unstable branch is still broken. Robert's fix didn't work. We'll let you know as soon as we get it fixed.

Jay

On Mon, Aug 1, 2016 at 5:45 PM, K. N. Ramachandran <knram06@xxxxxxxxx> wrote:
Hi Robert Smith,

Thanks a lot for the response. I will try the unstable build later and will let you know in case I couldn't finish the tutorial. I understand that Nek5000 might still return an error message in that case.

Thanks.

On Mon, Aug 1, 2016 at 4:53 PM, Smith, Robert W. <smithrw@xxxxxxxx> wrote:

Hello Ram,


The tutorial you were following was out of date. You were correct about the placement of the *.rea file, which should go in your ~/itemDB/Nek5000_Model_Builder folder instead. I've updated the tutorial to reflect this. 


I've also pushed a bug fix to the unstable version that should allow you to finish the tutorial. However, it seems that the Nek5000 code has gone through some major changes since the last time we'd worked with it in ICE, so the end result from Nek5000 will just be an error message. I'm continuing to work on it, and hopefully will have it working again soon.


Regards,

Robert Smith

From: ice-users-bounces@xxxxxxxxxxx <ice-users-bounces@xxxxxxxxxxx> on behalf of K. N. Ramachandran <knram06@xxxxxxxxx>
Sent: Monday, August 01, 2016 10:51 AM
To: Ice user discussions
Subject: [ice-users] Using Nek5000 in ICE
 
Hello all,

I am currently trying to setup Nek5000 in Eclipse ICE, by following the instructions at


and I am facing a few issues here.

1) The link instructs to create the Nek5000 Model Builder folder at

/home/{user}/ICEFiles/default

and place the *.rea file in it, but that does not seem to have an effect.

Instead, when I add the Nek5000 Model Builder Item (using the Item Viewer), I see the Nek5000 folder created in ~/ICE/workspace/itemDB/Nek5000_Model_Builder instead.

2) If I copy a *.rea file to the itemDB/Nek5000_Model_Builder folder, then I get a NullPointerException when trying to create the Model Builder item. The error log for this is attached here (error_on_copy.log).

If I remove out the Nek5000 folder and restart ICE, I can add the Model Builder item again, with no Exceptions being thrown. Of course, there is no *.rea file here and nothing gets imported.

Installation Details:
I had last installed Eclipse ICE on 29th July using the Install_ICE.py script from http://eclipseice.ornl.gov/downloads/ice/ and using stable install.

When I click on Help --> About ICE, I still get

Version: master
Build id: 20160419

Does that mean this is the 19th April build?


Thanking You,
K.N.Ramachandran
(Ram)

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Jay Jay Billings
Oak Ridge National Laboratory
Twitter Handle: @jayjaybillings

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K.N.Ramachandran

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K.N.Ramachandran

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K.N.Ramachandran

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K.N.Ramachandran

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To change your delivery options, retrieve your password, or unsubscribe from this list, visit
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_______________________________________________
ice-users mailing list
ice-users@xxxxxxxxxxx
To change your delivery options, retrieve your password, or unsubscribe from this list, visit
https://dev.eclipse.org/mailman/listinfo/ice-users




--
K.N.Ramachandran

_______________________________________________
ice-users mailing list
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To change your delivery options, retrieve your password, or unsubscribe from this list, visit
https://dev.eclipse.org/mailman/listinfo/ice-users




--
Jay Jay Billings
Oak Ridge National Laboratory
Twitter Handle: @jayjaybillings

_______________________________________________
ice-users mailing list
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To change your delivery options, retrieve your password, or unsubscribe from this list, visit
https://dev.eclipse.org/mailman/listinfo/ice-users




--
K.N.Ramachandran

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