PETSc Segmentation Violation Error

[Madelaine Griesel]

Hello, 

I recently updated my pflotran version to maint/v5.0 using petsc v3.20.2 and I am getting an PETSc error message about Segmentation Violation error. It appears to be an issue with the write to the HDF5 file because the model runs when I comment out the output card. 

I have inserted links below to the input files as well as the log with the error message. Please let me know if the links do not work.  

Thank you for your time, 
Madelaine

mesh.ugi
fehlman_bedforms_1m_water.h5
bedform_surface.ss
pflotran.in

pflotran.log-26226468

[Hammond, Glenn E]

Madelaine,

 

I cannot replicate the issue with v5.0 or the master branch compiled as debug or optimized, serial or parallel. I suspect that something is corrupted with the HDF5 installation, but that is speculation. Are you running this on a Linux box or a larger machine?

 

Glenn

 

From: pflotr...@googlegroups.com <pflotr...@googlegroups.com> On Behalf Of Madelaine Griesel
Sent: Tuesday, June 11, 2024 8:57 AM
To: pflotr...@googlegroups.com
Subject: [pflotran-dev: 6259] PETSc Segmentation Violation Error

 

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[Madelaine Griesel]

Hi Glenn, 

I am running this on the MIT Lincoln Labs Supercloud. For context, the Supercloud administrator recommended we use an open MPI module instead of MPICH to configure PETSc, which also includes an HDF5 download. Here is the configure command I used: 

./configure --CFLAGS='-O3' --CXXFLAGS='-O3' --FFLAGS='-O3' --with-debugging=no --with-mpi-dir=/usr/local/pkg/openmpi/4.1.5/ --download-hdf5=yes --download-hdf5-fortran-bindings=yes --download-fblaslapack=yes --download-metis=yes --download-parmetis=yes --force

Thank you,

Madelaine

[Hammond, Glenn E]

Open MPI should be fine. Do you have another machine on which you can confirm that PFLOTRAN compiles and the input deck fails? That will help rule out the MIT Supercloud installation being an issue.

 

Glenn

 

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[Madelaine Griesel]

Hello Glenn, 

I was able to successfully compile PFLOTRAN and run a model with my input deck on another machine. Thus, it seems like an issue with the Supercloud installation. I'll reach out to their team. 

Thank you for your advice and time, 

Madelaine