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ww3 scotch #849

Merged
merged 42 commits into from
Mar 1, 2023
Merged

ww3 scotch #849

merged 42 commits into from
Mar 1, 2023

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aliabdolali
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Pull Request Summary

Add SCOTCH option for geographical domain decomposition parallelization for unstr WW3.

Description

SCOTCH library has been added as an option for the domain decomposition for unstr WW3.
When PDLIB is used, one dependent switch (METIS or SCOTCH) is required.
GNU and Cmake builds are extended to support PDLIB/SCOTCH and PDLIB/METIS.
The default combination in the existing tests with PDLIB is now with scotch (ww3_tp2.17, ww3_tp2.6 and ww3_tp2.21). One test is added to ww3_tp2.21 to check METIS.

authors: @aliabdolali and @aronroland

Please also include the following information:

  • Add any suggestions for a reviewer @thesser1
  • Mention any labels that should be added: enhancement, new feature
  • Are answer changes expected from this PR? : out_grd change, out_pnt change, restart file change, Regression test

Issue(s) addressed

Commit Message

Add SCOTCH library for geographical domain decomposition

Check list

Testing

  • How were these changes tested?

With intel and gfortran compilers with gnu and cmake build

  • Are the changes covered by regression tests? (If not, why? Do new tests need to be added?)

Add SCOTCH to the default input/switch_PDLIB for ww3_tp2.17, ww3_tp2.6 and ww3_tp2.21.
One test is added to ww3_tp2.21/input/switch_PDLIB_METIS to check PARMETIS.

  • Have the matrix regression tests been run (if yes, please note HPC and compiler)?

HERA with intel compiler and hpc-stack

  • Please indicate the expected changes in the regression test output, (Note the list of known non-identical tests.)

ww3_tp2.17, ww3_tp2.6 and ww3_tp2.21

  • Please provide the summary output of matrix.comp (matrix.Diff.txt, matrixCompFull.txt and matrixCompSummary.txt):

endif()
endif()

if("PDLIB" IN_LIST switches)
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Why not have this in the same "if("PDLIB" IN_LIST switches)" if statement as above?

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Done

@JessicaMeixner-NOAA
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@ukmo-ccbunney @mickaelaccensi @sbrus89 - This PR update requires the SCOTCH library to be built for regression testing, assuming you are running unstructured grid tests, therefore you should probably all review this PR, which would require building SCOTCH. Please let us know if you have any questions, issues or concerns.

@JessicaMeixner-NOAA
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@aliabdolali I believe the automatic checks are failing are due to model/bin/switch_ite_pdlib not having either the METIS or the SCOTCH switch. I believe: switch_ite_pdlib, switch_ugdev2, switch_USACE_1 and switch_USACE_2 should all have SCOTCH added and then maybe @mickaelaccensi can weigh in whether he would like switch_Ifremer2_pdlib to have SCOTCH or METIS.

@aliabdolali
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@aliabdolali I believe the automatic checks are failing are due to model/bin/switch_ite_pdlib not having either the METIS or the SCOTCH switch. I believe: switch_ite_pdlib, switch_ugdev2, switch_USACE_1 and switch_USACE_2 should all have SCOTCH added and then maybe @mickaelaccensi can weigh in whether he would like switch_Ifremer2_pdlib to have SCOTCH or METIS.

Good catch, I was wondering why GitHub actions fail. I added SCOTCH to all with PDLIB. For Ifremer, I added Metis, if Mickael wants, I will change it to SCOTCH.

@aliabdolali
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@aliabdolali I believe the automatic checks are failing are due to model/bin/switch_ite_pdlib not having either the METIS or the SCOTCH switch. I believe: switch_ite_pdlib, switch_ugdev2, switch_USACE_1 and switch_USACE_2 should all have SCOTCH added and then maybe @mickaelaccensi can weigh in whether he would like switch_Ifremer2_pdlib to have SCOTCH or METIS.

Good catch, I was wondering why GitHub actions fail. I added SCOTCH to all with PDLIB. For Ifremer, I added Metis, if Mickael wants, I will change it to SCOTCH.

still failing ... @MatthewMasarik-NOAA any thought?

@JessicaMeixner-NOAA
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Screen Shot 2022-11-09 at 9 28 49 AM
@aliabdolali the checks are having issues with the scotch library it seems

@JessicaMeixner-NOAA
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@aliabdolali
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@aliabdolali maybe this could be of use: https://github.com/NOAA-EMC/WW3/wiki/Code-Management#automatic-tests-update-for-github-action

Awesome, I forgot that I added myself to the wiki. thanks for pointing me to it.

@aliabdolali aliabdolali changed the title Ww3 scotch dev ww3 scotch Nov 9, 2022
@MatthewMasarik-NOAA
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still failing ... @MatthewMasarik-NOAA any thought?

Looks like you guys solved it. I'll check back if these current builds fail

@MatthewMasarik-NOAA
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@aliabdolali looks like the same failure with ite_pdlib. The line that the error points to is 161 in model/src/CMakeLists.txt. This block seems to deal with Parmetis (vs. SCOTCH), so is it not finding the Parmetis library in this case?

It also mentions log file /home/runner/work/WW3/WW3/ww3/build/CMakeFiles/CMakeOutput.log. Anyone know how to access that?

@ukmo-ccbunney
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I will update with results of the regtest run as soon as I have access again...

I've managed to run the ww3_tp2.17/work_b regression test using SCOTCH with our GNU compiler on a Cray EXZ.
All seemed to go well. There are some small differences in the output field compared to the develop (non-scotch) branch, but I take it these are expected?

image

@aliabdolali
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I will update with results of the regtest run as soon as I have access again...

I've managed to run the ww3_tp2.17/work_b regression test using SCOTCH with our GNU compiler on a Cray EXZ.

All seemed to go well. There are some small differences in the output field compared to the develop (non-scotch) branch, but I take it these are expected?

image

Hi @ukmo-ccbunney thanks for checking scotch on your hpc, and yes, since decomposition is different,we expect changes in the results.

@aronroland
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we will sort that out as we check the b4b for the explicit scheme ...

@aronroland aronroland mentioned this pull request Feb 27, 2023
4 tasks
SCOTCH_PATH updates for RDHPCS machines
@JessicaMeixner-NOAA
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@thesser1 @sbrus89 @mickaelaccensi @ukmo-ccbunney we hope we can have official reviews from each of you at some point by 3/1. Please let us know if you've run into issues, have concerns, etc.

@JessicaMeixner-NOAA
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@aliabdolali please merge the develop branch into your branch for this PR to fix the CI issues.

@aliabdolali
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Your fix did not fix the problem for neither of wise nor scotch pr

@JessicaMeixner-NOAA
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Your fix did not fix the problem for neither of wise nor scotch pr

@aliabdolali happy to help look into this, but for this PR I see that the tests are still running and I do not yet see a failure, did I miss something on this PR? I'll check the other PR for a failure next.

@MatthewMasarik-NOAA
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MatthewMasarik-NOAA commented Feb 28, 2023

Hi all, I wanted to point out I've updated the SCOTCH build description on our FAQ to cover how to turn pthreads off in the cmake step. See the bottom of: https://github.com/NOAA-EMC/WW3/wiki/FAQs-page#how-to-install-scotch
fyi, @sbrus89

@aliabdolali
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Hi all, I wanted to point out I've updated the SCOTCH build description on our FAQ to cover how to turn pthreads off in the cmake step. See the bottom of: https://github.com/NOAA-EMC/WW3/wiki/FAQs-page#how-to-install-scotch fyi, @sbrus89

this is great Matt, could you add a minimum GNU version to the wiki, so users know what would be the requirements? I tried version 9.2 the min, but you might know better than me

@MatthewMasarik-NOAA
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Hi @aliabdolali, @JessicaMeixner-NOAA created an issue (https://gitlab.inria.fr/scotch/scotch/-/issues/21) on the SCOTCH gitlab page a few days ago asking about this. We haven't heard any response yet but will be updating here once we do

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I have run regression tests ww3_tp2.17, ww3_tp2.6 and ww3_tp2.21 on our dev HPC machine using GNU gcc/gfortran version 12.1.0.

SCOTCH compiled fine and the regression tests ran ok. There are small differences compared to the develop branch, as expected.

I could not run on our operational HPC as the compiler and Bison versions are too old.

I have not tried with the Cray compiler on our dev HPC yet, only GNU.

@aliabdolali
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Super @ukmo-ccbunney

@MatthewMasarik-NOAA
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I'm completing my review and will post momentarily. @thesser1 if you're available to add your review as well please do

@JessicaMeixner-NOAA
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@mickaelaccensi and @sbrus89 --- I hope you are both still testing this. If you have any issues please let us know. @MatthewMasarik-NOAA and I hope that we will be able to merge this at the end of today. If issues arise we can always come back to address them. @thesser1 -- we should get your approval and will wait for it, so if there are issues we should be aware of or if you have a known timeline for when we should get this review, please let us know.

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Code review

Pass.

Testing

Pass.

I've attached the matrix.comp output for hera and orion (same as posted on erdc/pull/10).

Note: In both the orion and hera output's there were a large number of (0 files differ) which turned out to be detecting linked files from the regtest input/ directory to the work*/ directories. For this reason and the ongoing mod_def issue for unstructured, I added some annotation to the Summary output (for orion. it is the same for the same files on hera).

orion

**********************************************************************                 
********************* non-identical cases ****************************                 
**********************************************************************                 
                                                                                       
1) (0 files differ): due to file (track_i.outer) linked from input/ to work/           
--                                                                                     
mww3_test_02/./work_PR1_c                     (0 files differ)                         
mww3_test_02/./work_PR3_UNO_d_c                     (0 files differ)                   
mww3_test_02/./work_PR3_UNO_b                     (0 files differ)                     
mww3_test_02/./work_PR2_UQ_d                     (0 files differ)                      
mww3_test_02/./work_PR3_UQ_d                     (0 files differ)                      
mww3_test_02/./work_PR2_UQ_a                     (0 files differ)                      
mww3_test_02/./work_PR1_d                     (0 files differ)                         
mww3_test_02/./work_PR2_UQ_c                     (0 files differ)                      
mww3_test_02/./work_PR3_UQ_MPI_c_c                     (0 files differ)                
mww3_test_02/./work_PR2_UNO_MPI_b                     (0 files differ)                 
mww3_test_02/./work_PR2_UQ_MPI_b                     (0 files differ)                  
mww3_test_02/./work_PR1_a                     (0 files differ)                         
mww3_test_02/./work_PR2_UNO_c                     (0 files differ)                     
mww3_test_02/./work_PR3_UNO_a                     (0 files differ)                     
mww3_test_02/./work_PR3_UNO_MPI_a_c                     (0 files differ)               
mww3_test_02/./work_PR1_MPI_c                     (0 files differ)                     
mww3_test_02/./work_PR3_UNO_d                     (0 files differ)                     
mww3_test_02/./work_PR3_UNO_c                     (0 files differ)                     
mww3_test_02/./work_PR3_UQ_a_c                     (0 files differ)                    
mww3_test_02/./work_PR2_UNO_d                     (0 files differ)                     
mww3_test_02/./work_PR2_UNO_MPI_d                     (0 files differ)                 
mww3_test_02/./work_PR3_UQ_c_c                     (0 files differ)                    
mww3_test_02/./work_PR3_UNO_MPI_c                     (0 files differ)                 
mww3_test_02/./work_PR3_UNO_MPI_b                     (0 files differ)                 
mww3_test_02/./work_PR2_UNO_MPI_a                     (0 files differ)                 
mww3_test_02/./work_PR3_UNO_b_c                     (0 files differ)                   
mww3_test_02/./work_PR3_UNO_MPI_d_c                     (0 files differ)               
mww3_test_02/./work_PR3_UQ_d_c                     (0 files differ)                    
mww3_test_02/./work_PR3_UQ_MPI_a_c                     (0 files differ)                
mww3_test_02/./work_PR1_MPI_b                     (0 files differ)                     
mww3_test_02/./work_PR3_UQ_MPI_b                     (0 files differ)                  
mww3_test_02/./work_PR2_UQ_MPI_c                     (0 files differ)                  
mww3_test_02/./work_PR3_UNO_a_c                     (0 files differ)                   
mww3_test_02/./work_PR3_UNO_MPI_b_c                     (0 files differ)               
mww3_test_02/./work_PR1_b                     (0 files differ)                         
mww3_test_02/./work_PR3_UQ_a                     (0 files differ)                      
mww3_test_02/./work_PR3_UNO_c_c                     (0 files differ)                   
mww3_test_02/./work_PR3_UQ_MPI_d_c                     (0 files differ)                
mww3_test_02/./work_PR3_UNO_MPI_d                     (0 files differ)                 
mww3_test_02/./work_PR2_UNO_a                     (0 files differ)                     
mww3_test_02/./work_PR2_UQ_MPI_d                     (0 files differ)                  
mww3_test_02/./work_PR3_UQ_b_c                     (0 files differ)                    
mww3_test_02/./work_PR3_UQ_MPI_b_c                     (0 files differ)                
mww3_test_02/./work_PR2_UQ_MPI_a                     (0 files differ)                  
mww3_test_02/./work_PR2_UNO_b                     (0 files differ)                     
mww3_test_02/./work_PR3_UNO_MPI_c_c                     (0 files differ)               
mww3_test_02/./work_PR2_UNO_MPI_c                     (0 files differ)                 
mww3_test_02/./work_PR3_UQ_MPI_c                     (0 files differ)                  
mww3_test_02/./work_PR3_UQ_MPI_d                     (0 files differ)                  
mww3_test_02/./work_PR3_UQ_b                     (0 files differ)                      
mww3_test_02/./work_PR3_UNO_MPI_a                     (0 files differ)                 
mww3_test_02/./work_PR1_MPI_d                     (0 files differ)                     
mww3_test_02/./work_PR2_UQ_b                     (0 files differ)                      
mww3_test_02/./work_PR1_MPI_a                     (0 files differ)                     
mww3_test_02/./work_PR3_UQ_MPI_a                     (0 files differ)                  
mww3_test_02/./work_PR3_UQ_c                     (0 files differ)                      
--                                                                                     
                                                                                       
-- 2) usual non-b4b                                                                    
mww3_test_03/./work_PR3_UQ_MPI_d2                     (16 files differ)                
mww3_test_03/./work_PR3_UNO_MPI_e                     (1 files differ)                 
mww3_test_03/./work_PR3_UQ_MPI_d2_c                     (15 files differ)              
mww3_test_03/./work_PR2_UQ_MPI_d2                     (15 files differ)                
mww3_test_03/./work_PR3_UNO_MPI_d2                     (12 files differ)               
mww3_test_03/./work_PR2_UNO_MPI_d2                     (17 files differ)               
mww3_test_03/./work_PR2_UNO_MPI_e                     (1 files differ)                 
mww3_test_03/./work_PR1_MPI_d2                     (11 files differ)                   
mww3_test_03/./work_PR3_UNO_MPI_d2_c                     (16 files differ)             
mww3_test_03/./work_PR3_UQ_MPI_e                     (1 files differ)                  
mww3_test_03/./work_PR3_UQ_MPI_e_c                     (1 files differ)                
ww3_tp2.10/./work_MPI_OMPH                     (7 files differ)                        
ww3_tp2.16/./work_MPI_OMPH                     (4 files differ)                        
ww3_ufs1.3/./work_a                     (3 files differ)                               
--                                                                                     
                                                                                       
3) (0 files differ): due to file (anl.grbtxt) linked from input/ to work/              
--                                                                                     
ww3_ta1/./work_UPD2_U_cap                     (0 files differ)                         
ww3_ta1/./work_UPD6_O                     (0 files differ)                             
ww3_ta1/./work_UPD0F_U                     (0 files differ)                            
ww3_ta1/./work_UPD5_U                     (0 files differ)                             
ww3_ta1/./work_UPD2_U                     (0 files differ)                             
ww3_ta1/./work_UPD2_O                     (0 files differ)                             
ww3_ta1/./work_UPD3_U_cap                     (0 files differ)                         
ww3_ta1/./work_UPD3_U                     (0 files differ)                             
ww3_ta1/./work_UPD0F_O                     (0 files differ)                            
ww3_ta1/./work_UPD6_U_cap                     (0 files differ)                         
ww3_ta1/./work_UPD6_U                     (0 files differ)                             
ww3_ta1/./work_UPD5_O                     (0 files differ)                             
ww3_ta1/./work_UPD5_U_cap                     (0 files differ)                         
ww3_ta1/./work_UPD3_O                     (0 files differ)                             
--                                                                                     
                                                                                       
4) (1 file differ): due to 'APPLE partioning' string in file OUTPUT_TOY.txt            
--                                                                                     
ww3_tp2.14/./work_OASACM6                     (1 files differ)                         
--                                                                                     
                                                                                       
5) (1 file differ): due to unstructured mod_def's                                      
--                                                                                     
ww3_tp2.17/./work_mc1                     (1 files differ)                             
ww3_tp2.17/./work_ma                     (1 files differ)                              
ww3_tp2.17/./work_mc                     (1 files differ)                              
ww3_tp2.17/./work_mb                     (1 files differ)                              
ww3_tp2.17/./work_b                     (1 files differ)                               
ww3_tp2.17/./work_c                     (1 files differ)                               
ww3_tp2.17/./work_a                     (1 files differ)                               
ww3_tp2.17/./work_ma1                     (1 files differ)                             
ww3_tp2.6/./work_ST4                     (1 files differ)                              
ww3_tp2.6/./work_pdlib                     (1 files differ)                            
ww3_tp2.6/./work_ST0                     (1 files differ)                              
ww3_ts4/./work_ug_MPI                     (1 files differ)                             
--                                                                                                                                                             
**********************************************************************                 
************************ identical cases *****************************                 
********************************************************************** 

hera

**********************************************************************       
********************* non-identical cases ****************************       
**********************************************************************       
mww3_test_02/./work_PR1_c                     (0 files differ)               
mww3_test_02/./work_PR2_UNO_c                     (0 files differ)           
mww3_test_02/./work_PR3_UQ_MPI_a                     (0 files differ)        
mww3_test_02/./work_PR1_MPI_d                     (0 files differ)           
mww3_test_02/./work_PR3_UNO_MPI_b_c                     (0 files differ)     
mww3_test_02/./work_PR3_UNO_c_c                     (0 files differ)         
mww3_test_02/./work_PR3_UQ_MPI_c                     (0 files differ)        
mww3_test_02/./work_PR2_UNO_MPI_d                     (0 files differ)       
mww3_test_02/./work_PR2_UNO_d                     (0 files differ)           
mww3_test_02/./work_PR2_UQ_MPI_a                     (0 files differ)        
mww3_test_02/./work_PR3_UQ_MPI_a_c                     (0 files differ)      
mww3_test_02/./work_PR3_UNO_MPI_d_c                     (0 files differ)     
mww3_test_02/./work_PR1_d                     (0 files differ)               
mww3_test_02/./work_PR2_UQ_c                     (0 files differ)            
mww3_test_02/./work_PR3_UQ_b                     (0 files differ)            
mww3_test_02/./work_PR3_UQ_a                     (0 files differ)            
mww3_test_02/./work_PR1_a                     (0 files differ)               
mww3_test_02/./work_PR3_UNO_MPI_d                     (0 files differ)       
mww3_test_02/./work_PR3_UNO_a_c                     (0 files differ)         
mww3_test_02/./work_PR2_UQ_MPI_b                     (0 files differ)        
mww3_test_02/./work_PR3_UNO_d                     (0 files differ)           
mww3_test_02/./work_PR3_UNO_MPI_c_c                     (0 files differ)     
mww3_test_02/./work_PR3_UNO_MPI_a_c                     (0 files differ)     
mww3_test_02/./work_PR2_UQ_a                     (0 files differ)            
mww3_test_02/./work_PR3_UNO_MPI_b                     (0 files differ)       
mww3_test_02/./work_PR3_UNO_b_c                     (0 files differ)         
mww3_test_02/./work_PR1_b                     (0 files differ)               
mww3_test_02/./work_PR2_UNO_b                     (0 files differ)           
mww3_test_02/./work_PR3_UQ_MPI_c_c                     (0 files differ)      
mww3_test_02/./work_PR2_UQ_d                     (0 files differ)            
mww3_test_02/./work_PR3_UQ_c                     (0 files differ)            
mww3_test_02/./work_PR3_UNO_MPI_a                     (0 files differ)       
mww3_test_02/./work_PR1_MPI_c                     (0 files differ)           
mww3_test_02/./work_PR3_UNO_b                     (0 files differ)           
mww3_test_02/./work_PR1_MPI_b                     (0 files differ)           
mww3_test_02/./work_PR3_UQ_a_c                     (0 files differ)          
mww3_test_02/./work_PR3_UQ_MPI_b_c                     (0 files differ)      
mww3_test_02/./work_PR3_UQ_d_c                     (0 files differ)          
mww3_test_02/./work_PR1_MPI_a                     (0 files differ)           
mww3_test_02/./work_PR3_UQ_MPI_d_c                     (0 files differ)      
mww3_test_02/./work_PR3_UQ_MPI_d                     (0 files differ)        
mww3_test_02/./work_PR3_UQ_d                     (0 files differ)            
mww3_test_02/./work_PR3_UNO_d_c                     (0 files differ)         
mww3_test_02/./work_PR3_UQ_c_c                     (0 files differ)          
mww3_test_02/./work_PR2_UNO_MPI_b                     (0 files differ)       
mww3_test_02/./work_PR3_UNO_MPI_c                     (0 files differ)       
mww3_test_02/./work_PR2_UQ_b                     (0 files differ)            
mww3_test_02/./work_PR3_UNO_c                     (0 files differ)           
mww3_test_02/./work_PR3_UNO_a                     (0 files differ)           
mww3_test_02/./work_PR2_UQ_MPI_d                     (0 files differ)        
mww3_test_02/./work_PR2_UQ_MPI_c                     (0 files differ)        
mww3_test_02/./work_PR2_UNO_a                     (0 files differ)           
mww3_test_02/./work_PR2_UNO_MPI_c                     (0 files differ)       
mww3_test_02/./work_PR2_UNO_MPI_a                     (0 files differ)       
mww3_test_02/./work_PR3_UQ_b_c                     (0 files differ)          
mww3_test_02/./work_PR3_UQ_MPI_b                     (0 files differ)        
mww3_test_03/./work_PR1_MPI_e                     (1 files differ)           
mww3_test_03/./work_PR3_UQ_MPI_e_c                     (1 files differ)      
mww3_test_03/./work_PR2_UQ_MPI_e                     (1 files differ)        
mww3_test_03/./work_PR2_UNO_MPI_e                     (1 files differ)       
mww3_test_03/./work_PR2_UNO_MPI_d2                     (15 files differ)     
mww3_test_03/./work_PR1_MPI_d2                     (6 files differ)          
mww3_test_03/./work_PR3_UNO_MPI_d2_c                     (15 files differ)   
mww3_test_03/./work_PR3_UQ_MPI_d2_c                     (16 files differ)    
mww3_test_03/./work_PR3_UNO_MPI_d2                     (15 files differ)     
mww3_test_03/./work_PR2_UQ_MPI_d2                     (15 files differ)      
mww3_test_03/./work_PR3_UNO_MPI_e_c                     (1 files differ)     
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**********************************************************************       
************************ identical cases *****************************       
**********************************************************************

@MatthewMasarik-NOAA
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Awesome, thanks @thesser1 !

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@sbrus89 sbrus89 left a comment

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I was able to get this working on our systems.

@MatthewMasarik-NOAA
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Awesome. Thanks for your review @sbrus89. I'm curious if you compiled with gnu or other (intel)?

@sbrus89
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sbrus89 commented Mar 1, 2023

@MatthewMasarik-NOAA, I used Gnu 10.2.0

@MatthewMasarik-NOAA
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Great, thanks for confirming. And thanks for your work helping test this @sbrus89!

@aliabdolali
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It is great to have confirmation with different compilers.

@JessicaMeixner-NOAA
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Thank you @aliabdolali and @aronroland for adding the SCOTCH capability. Thank you to @AlexanderRichert-NOAA @aerorahul @MatthewMasarik-NOAA and the many others who helped get us through cmake, orion and other issues and get this PR past the finish line! Thank you to @ukmo-ccbunney @sbrus89 @thesser1 for your reviews! This is a huge accomplishment and we look forward to continuing to work on the outstanding issues resolving the scaling and mpi b4b (which are likely the cause of diffs between scotch and metis).

@JessicaMeixner-NOAA JessicaMeixner-NOAA merged commit ea0de58 into NOAA-EMC:develop Mar 1, 2023
@aliabdolali
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Yay, finally, this PR hit a record !!!!
Thanks to @ukmo-ccbunney @sbrus89 @MatthewMasarik-NOAA @JessicaMeixner-NOAA @aerorahul for checking our development.

@thesser1 thesser1 deleted the ww3_scotch_dev branch October 26, 2023 13:57
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Domain decomposition library (SCOTCH)
8 participants