Moose based app for sintering

[Tesfaye Tadesse]

Dear Sir/Madam,

I was interested in using the moose based app (Crow) for simulating sintering of particles. tried to compile the latest version of source codes from github i.e. https://github.com/SudiptaBiswas/Crow/tree/verified_final_codes

However, i am unable to succeed in compiling the files. below are the kind of errors i am encountering: 

Could you please help me? 

Thanks for your help in advance 

------- 

User/projects/Crow/src/kernels/ACParticleGrowthAniso.C:2:10: fatal error: AnisoGBEnergyUserObject.h: No such file or directory

 #include "AnisoGBEnergyUserObject.h"

User/projects/moose/framework/build.mk:118: recipe for target 'User/projects/Crow/build/unity_src/materials_Unity.x86_64-pc-linux-gnu.opt.lo' failed

make: *** [User/projects/Crow/build/unity_src/materials_Unity.x86_64-pc-linux-gnu.opt.lo] Error 1

In file included from User/projects/Crow/build/unity_src/ics_Unity.C:3:0:

User/projects/Crow/src/ics/BubblesBicrystalIC.C: In member function 'virtual libMesh::Real BubblesBicrystalIC::value(const libMesh::Point&)':

User/projects/Crow/src/ics/BubblesBicrystalIC.C:107:34: error: 'class libMesh::TypeVector<double>' has no member named 'size'; did you mean 'slice'?

     Real dist = (p - bub_center).size();

[Casey Icenhour]

Hello Tesfaye,

Crow utilizes the Marmot application as a submodule, and the first error you see is related to an object only in that code. Unfortunately, this is a controlled application, so you must request access. If you are interested, please go to https://moose.inl.gov/marmot/SitePages/Home.aspx, click on the "Access" link near the top of the page, and fill out the form. A member of the access team will get in touch with you.

As far as the second error goes, "size" was deprecated and replaced with "norm" in libMesh some time ago. If you make that replacement, the error should go away.

Best,

Casey

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[Tesfaye Tadesse]

Hi Casey, 

Thanks a lot for the help. 

requested access to Marmot and will replace 'size' by 'norm'. 

cheers 

-Tesfaye 

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Tesfaye Tadesse Molla

Lecturer, The University of Melbourne

Department of Mechanical Engineering 

Australia
Tel:+61421942550

[Tesfaye Tadesse]

Hi Casey once again, 

Tried to compile by removing the object that has to do with anisotropy features -- i.e. just to avoid the need for access to Marmot object ("AnisoGBEnergyUserObject.h"). 

It seems there are still issues with the "app.mk" file from the moose framework. Below are the latest errors.  Are these also related to access to Marmot ?

Appreciate your help!!

/User/tmolla/projects/moose/framework/app.mk:210: warning: overriding recipe for target '/User/tmolla/projects/moose/modules/phase_field/build/header_symlinks/Revision.h'
/User/tmolla/projects/moose/framework/app.mk:210: warning: ignoring old recipe for target '/User/tmolla/projects/moose/modules/phase_field/build/header_symlinks/Revision.h'
/User/tmolla/projects/moose/framework/app.mk:210: warning: overriding recipe for target '/User/tmolla/projects/Crow/build/header_symlinks/CrowRevision.h'
/User/tmolla/projects/moose/framework/app.mk:210: warning: ignoring old recipe for target '/User/tmolla/projects/Crow/build/header_symlinks/CrowRevision.h'
Checking if header needs updating: /User/tmolla/projects/moose/framework/include/base/MooseRevision.h...
Linking Executable /User/tmolla/projects/Crow/Crow-opt...
/User/tmolla/miniconda3/envs/moose/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /User/tmolla/projects/Crow/lib/libCrow-opt.so:
undefined reference to `InputParameters validParams<LangevinNoise>()'
collect2: error: ld returned 1 exit status
/User/tmolla/projects/moose/framework/app.mk:392: recipe for target '/User/tmolla/projects/Crow/Crow-opt' failed make: *** [/User/tmolla/projects/Crow/Crow-opt] Error 1

[Casey Icenhour]

After removing the references to Marmot objects, I was able to get Crow to build successfully. You might try:

make clobberall

make -j8

In order to clean up stale libraries and rebuild from scratch. Performing "git clean -xfd" signals git to clean up stale files as well, but this will result in the loss of uncommitted changes so make sure you stash or commit anything you don't want to lose!

Note that I have not tried to run the tests for this application, so you may run into other issues related to changes to MOOSE since Crow was last updated (looks like the "verified_final_codes" branch was ~6 months ago). I have CC-ed the developer of Crow on this email thread, so that she can chime in.

There is some ongoing INL work related to sintering modeling with MOOSE that we hope to start publishing in the spring, but I would say that work is not ready for "prime time" yet.

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[SudiptaBiswas]

Tesfaye,

I would recommend you to check out the ‘devel’ branch of ‘Crow’. I made this specifically for interested users. This is a more up to date branch and has examples you can start with. Let me know if you have trouble building/accessing it.

Thanks!

Sudipta 

[Tesfaye Tadesse]

Hi Sudipta and Casey 

Thank you very much for your help!! 

I tried to compile the 'devel' branch of 'Crow' and still have the same issue -- i.e. something that looks to do with the "app.mk" from the moose framework (see errror below).

I also tried the 'make clobberall' command supposedly to bypass any references to Marmot (as per Casey's suggestion) but ended up with the same errors. 

Is there anything that I missed ?

Casey: I look forward to the latest work on modeling of sintering with MOOSE!!

cheers,

----

Linking Library /home/unimelb.edu.au/tmolla/projects/Crow/lib/libCrow-opt.la...
Linking Executable /home/unimelb.edu.au/tmolla/projects/Crow/Crow-opt...
/home/unimelb.edu.au/tmolla/miniconda3/envs/moose/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /home/unimelb.edu.au/tmolla/projects/Crow/lib/libCrow-opt.so: undefined reference to `InputParameters validParams<LangevinNoise>()'

collect2: error: ld returned 1 exit status

/home/unimelb.edu.au/tmolla/projects/moose/framework/app.mk:392: recipe for target '/home/unimelb.edu.au/tmolla/projects/Crow/Crow-opt' failed

make: *** [/home/unimelb.edu.au/tmolla/projects/Crow/Crow-opt] Error 1 

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[SudiptaBiswas]

I was able to build the devel branch as is on my mac. I still updated the syntax of the source code that was giving you the error. Please fetch the latest version of the branch and try rebuilding it again. You might consider cleaning up your directory with 'make clobberall' before rebuilding. You might also need to perform a 'git clean -xfd' to remove any stale libraries if you continue to get linking errors. Make sure you commit your untracked changes before you do git clean.

[Tesfaye Tadesse]

Thank you once again Sudipta!!

Looks like it is working now. will get back to you if i have further questions while using your codes :)

cheers! 

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[Tesfaye Tadesse]

Hi Sudipta once again, 

Just checking: Have you managed to run the tests in the 'devel' branch of 'Crow'? I find both tests fail. In addition, I also tried to run some of your input files but was unable to succeed.

Thanks a lot for your help by the way!! 

-Tesfaye  

On Wed, Sep 16, 2020 at 10:34 AM SudiptaBiswas <sudipt...@gmail.com> wrote:

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[SudiptaBiswas]

You should start here,

https://github.com/SudiptaBiswas/Crow/blob/devel/test/tests/sintering_test1_isomob.i

This works fine. The tests in crow are a bit long, if they are failing timeout ignore that. Try running the files individually. 

[Tesfaye Tadesse]

Got it. Thanks a lot Sudipta!! 

cheers 

-Tesfaye 

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[fatimah Dzr]

Dear Sudipta

Following your solution, I tried cloning to the Crow git and it was done successfully using "devel" branch instead of using my own application. However, every time I tried to compile and create the Crow-opt, this error appears and I don't know how to solve that. I would be grateful if you could help me with this issue.

/home/fatimahdzr/mambaforge3/envs/moose/bin/../lib/gcc/x86_64-conda-linux-gnu/10.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: /mnt/c/moose/projects/gav/lib/libCrow-opt.so: undefined reference to `InputParameters validParams()'

collect2: error: ld returned 1 exit status