New PETSC ERROR when running optimization code

[Adam Haynes]

Hello,

After updating my homebrew and updating my Mac to Sonoma 14.5, I have been unable to run an optimization script as I get the following error:

[0]PETSC ERROR: ------------------------------------------------------------------------

[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range

[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger

[0]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind and https://petsc.org/release/faq/

[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run 

[0]PETSC ERROR: to get more information on the crash.

[0]PETSC ERROR: Run with -malloc_debug to check if memory corruption is causing the crash.

application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0

[unset]: PMIU_write error; fd=-1 buf=:cmd=abort exitcode=59 message=application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0

:

system msg for write_line failure : Bad file descriptor

I am running on my local machine and have been doing so successfully until the updates. 

The input file is created within the optimization script.

Also, if anyone has a cleaner/more straightforward optimization script that optimizes multiple parameters at once and would like to share, I'd appreciate it. 

Adam

[Hammond, Glenn E]

Adam,

 

We are looking into this.

 

Glenn

 

From: 'Adam Haynes' via pflotran-users <pflotra...@googlegroups.com>
Sent: Monday, June 3, 2024 3:34 PM
To: pflotran-users <pflotra...@googlegroups.com>
Subject: [pflotran-users: 7781] New PETSC ERROR when running optimization code

 

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[Hammond, Glenn E]

Adam,

 

Please pull the latest source code, recompile and follow the guidance in the error message when you run the simulation.

 

Glenn

 

From: 'Adam Haynes' via pflotran-users <pflotra...@googlegroups.com>
Sent: Monday, June 3, 2024 3:34 PM
To: pflotran-users <pflotra...@googlegroups.com>
Subject: [pflotran-users: 7781] New PETSC ERROR when running optimization code

 

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

 

Hello,

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[madelain...@gmail.com]

Hello all, 

I am experiencing this same PETSc Segmentation Violation error and was wondering if there are any further updates on how to address this error? I recently updated my pflotran version to maint/v5.0 using petsc v3.20.2. I have attached my output log with the error information as well as the input file. It appears to be an issue with the write to the HDF5 file because the model runs when I comment out the output card. 

Thank you for any help or troubleshooting tips. 

Best,

Madelaine

[Hammond, Glenn E]

Madelaine,

 

The error in Adam’s simulation was due to the SUBSURFACE_TRANSPORT process model being invoked without a CHEMISTRY block in the SUBSURFACE section. I added error messaging to catch this issue before the code crashes.

 

To run the input deck that you sent, I need the supporting files: mesh.ugi, bedform_mesh.ss, and fehlman_bedforms_1m_water.h5

 

Please send them to pflotran-dev.

 

Glenn

 

To view this discussion on the web visit https://groups.google.com/d/msgid/pflotran-users/952b3607-adc0-4aac-905b-17069732d010n%40googlegroups.com.

[madelain...@gmail.com]

Hello Glenn, 

Thank you for the clarification. I have sent the requested files to the pflotran-dev email address. 

Thanks again,

Madelaine