Parallel Mesh Causing Error

The graphical user interface of Elmer
willsprocket
Posts: 33
Joined: 18 Jun 2022, 05:32
Antispam: Yes

Parallel Mesh Causing Error

Post by willsprocket »

Hello,

I've just started using ElmerGUI on Windows10. When I attempt to use parallel solving in ElmerGUI the results can't be viewed and it generates the error "Unable to start EmlerGrid for mesh unification". The VTK files are generated and I can view them using ParaView if I load them directly (not by initiating from ElmerGUI). No errors occur when I use a single thread/mesh.

Any assistance would be greatly appreciated.

Will

1st Year Engineering Student
Rich_B
Posts: 421
Joined: 24 Aug 2009, 20:18

Re: Parallel Mesh Causing Error

Post by Rich_B »

Hello,

The typical setup includes setting 'Post File' to 'case.vtu' in the Model -> Setup menu, which will generate VTU files, instead of VTK.

It will be helpful if you could post a small example of your issue, by attaching a zip archive of your ElmerGui project folder.

Thanks, Rich.
Rich_B
Posts: 421
Joined: 24 Aug 2009, 20:18

Re: Parallel Mesh Causing Error

Post by Rich_B »

Hello,

Also, take a look through this forum thread:

viewtopic.php?t=7556

Rich.
willsprocket
Posts: 33
Joined: 18 Jun 2022, 05:32
Antispam: Yes

Re: Parallel Mesh Causing Error

Post by willsprocket »

I incorrectly remembered the file extension, it does generate VTU files. One for each mesh partition and one that references all of them (with an extension of pvtu).

When I try to view the results inside the ElmerGUI is when I get the error. The result can be loaded manually in ParaView and the result looks valid.

I've attached a test case that generates the error, but I had to omit the mesh because of the attachment size limit of 1MB.

Thank you for the help,

Will
Attachments
case.zip
(9.08 KiB) Downloaded 78 times
willsprocket
Posts: 33
Joined: 18 Jun 2022, 05:32
Antispam: Yes

Re: Parallel Mesh Causing Error

Post by willsprocket »

Update:

If I switch to case.ep and edit the merge command to

Code: Select all

ElmerGrid 15 3 %ep -partjoin %n
as shown in the manual (Ch 7), I'm able to view the result in ElmerGUI.

It would be nice to know what I'm doing wrong with the default settings (case.vtu and " echo 'No need to merge VTU files!' ")

Thanks, Will
Rich_B
Posts: 421
Joined: 24 Aug 2009, 20:18

Re: Parallel Mesh Causing Error

Post by Rich_B »

Hello,

The ElmerGUI manual, ch 7, shows how to setup a parallel run. This particular chapter is a bit older. There's a newer set of instructions in GetStartedElmer.pdf, chapter 8. Please run through your example again with the newer instructions, and let us know what happens.

Also in GetStartedElmer, there is a chapter 'Elmerfem Wiki', that contains an example of Electromigration. Take a look, it might be useful for you.

Lastly, if you could create a new mesh that is simpler and coarser, and will compress to be under 1 MB, you may be able to post a full working example.

Thanks, Rich.
Rich_B
Posts: 421
Joined: 24 Aug 2009, 20:18

Re: Parallel Mesh Causing Error

Post by Rich_B »

Hello,

There is also an ElmerGUI tutorial, Electro-kinetics, that may be of interest to you.

Rich.
Rich_B
Posts: 421
Joined: 24 Aug 2009, 20:18

Re: Parallel Mesh Causing Error

Post by Rich_B »

Hello,

So I tried running the attached project in parallel, and there is something wrong. This case used to work, about a year ago.

Here's the first error, from elmersolverlog.txt:
job aborted:
[ranks] message

[0] process exited without calling finalize

[1-3] terminated

---- error analysis -----

[0] on DESKTOP-D6N8F4T
ElmerSolver_mpi.exe ended prematurely and may have crashed. exit code 3

---- error analysis -----


Program received signal SIGSEGV: Segmentation fault - invalid memory reference.
A working project folder is attached.

Rich.
Rich_B
Posts: 421
Joined: 24 Aug 2009, 20:18

Re: Parallel Mesh Causing Error

Post by Rich_B »

Hello,

To be sure we had an up to date project, I recreated the elmergui project from scratch, using the tutorial instructions step by step. Then using the default parallel settings, just click on the box for 'use parallel solver' and change the number of processors to 4.

This time the project ran a little further, creating a single merged .vtu file, which loads fine in Paraview. We still have a seg fault, and trying to start ElmerVTK complains about unable to start Elmergrid for mesh unification.

The ElmerGUI console output is stored in elmerguioutput.txt, and the solver log is stored in elmersolverlog.txt.

Rich.
Attachments
FlowStepGUI-parallel-new.zip
(785.98 KiB) Downloaded 83 times
Rich_B
Posts: 421
Joined: 24 Aug 2009, 20:18

Re: Parallel Mesh Causing Error

Post by Rich_B »

Hello,

One more iteration, this time a plain command line approach. I used the case.sif created by ElmerGUI and a batch file to call elmergrid and elmersolver.
job aborted:
[ranks] message

[0] process exited without calling finalize

[1-3] terminated

---- error analysis -----

[0] on DESKTOP-D6N8F4T
ElmerSolver_mpi ended prematurely and may have crashed. exit code 3
The runnable project is attached.

Rich.

Edit: If the line 'Post File = case.vtu' is commented out, the solution runs to completion without any error message.
Attachments
parallel-cli.zip
(480.08 KiB) Downloaded 80 times
Post Reply