Issue with PETSc

[Hyo Heo]

Hi,

I have tried to run with using mpirun option, but some errors.

The error messages as bellows.

[0]PETSC ERROR: Arguments are incompatible
[0]PETSC ERROR: Bag in file has different number of entries 23 then passed in bag 2

[0]PETSC ERROR: #1 PetscBagLoad() at /home/hheo/petsc/src/sys/classes/bag/bag.c:841
[0]PETSC ERROR: #2 User provided function() at User file:0

Thank you in advance for your help.

Thanks

[Hammond, Glenn E]

Please send your input deck and instructions on how to replicate the error to pflotr...@goolgegroups.com.  Please include the commit hash (use output from ‘git log -1’) and the number of processes employed.

 

Thanks,

 

Glenn

 

From: pflotra...@googlegroups.com <pflotra...@googlegroups.com> On Behalf Of Hyo Heo
Sent: Friday, July 8, 2022 7:12 AM
To: pflotran-users <pflotra...@googlegroups.com>
Subject: [pflotran-users: 6737] Issue with PETSc

 

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[Hyo Heo]

 Hi,

Attached files are my input deck, commit hash, and error messages shown when I tried to run.

The mpirun option is valid for other input deck such as regional doublet input deck provided from yours, but not my input deck.

The number of process exployed was 4.

Thank you in advance for your help.

Feel free to contact me if you have some questions.

Thanks, 

Hyo

 

2022년 7월 9일 토요일 오전 12시 44분 40초 UTC+9에 Hammond, Glenn E님이 작성:

Please send your input deck and instructions on how to replicate the error to pflotr...@goolgegroups.com.  Please include the commit hash (use output from ‘git log -1’) and the number of processes employed.

 

Thanks,

 

Glenn

 

From: pflotran-users@googlegroups.com <pflotran-users@googlegroups.com> On Behalf Of Hyo Heo
Sent: Friday, July 8, 2022 7:12 AM
To: pflotran-users <pflotran-users@googlegroups.com>
Subject: [pflotran-users: 6737] Issue with PETSc

 

Check twice before you click! This email originated from outside PNNL.

 

Hi,

 

I have tried to run with using mpirun option, but some errors.

The error messages as bellows.

 

[0]PETSC ERROR: Arguments are incompatible
[0]PETSC ERROR: Bag in file has different number of entries 23 then passed in bag 2

 

[0]PETSC ERROR: #1 PetscBagLoad() at /home/hheo/petsc/src/sys/classes/bag/bag.c:841
[0]PETSC ERROR: #2 User provided function() at User file:0

 

Thank you in advance for your help.

 

Thanks

 

 

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[Hammond, Glenn E]

Hyo,

 

Thank you for sending the .chk and .dat files.

 

I can only replicate the error with the gm.chk file that you sent.

 

When I run the simulation to completion with checkpointing turned on, but without RESTART (I generate my own checkpoint files), and then I restart with the checkpoint files that I have generated, the simulation runs fine. I tried all combinations of 1 vs 4 cores for the checkpoint generation and restart.

 

I believe that your .chk file is corrupted, but I cannot explain how. And if regenerating the .chk files still produces the corruption, I have no answers….

 

Let’s try the following: Please try using ‘FORMAT HDF5’ with checkpointing and see if that resolves the issue.  Please let me know the results.

 

Thanks,

 

Glenn

 

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[Hyo Heo]

Hi Glenn,

The solution you gave was good, the issue was resolved with it.

After I generated my own checkpoint files in .h5 format, it did work well when I applied the mpirun option.

Thank you for your helps and advices.

Thanks,

Hyo 

2022년 7월 15일 금요일 오전 9시 9분 56초 UTC+9에 Hammond, Glenn E님이 작성: