Tests fail when adding some files to ADDITIONAL_APP_OBJECTS in the Makefile

[thiloschmid]

Dear moose community,

I am running into an issue when trying to couple an external framework to moose. The additional files are added in the Makefile via

# object files
ADDITIONAL_APP_OBJECTS += $(patsubst %.cpp, %.$(obj-suffix), $(additional_srcfiles))

# dependencies 
ADDITIONAL_APP_DEPS += $(patsubst %.cpp, %.$(obj-suffix).d, $(additional_srcfiles))

But after running make, the test fails with the following output.

(moose) me@cluster:~/Projects/chamois$ ./run_tests 
<frozen importlib._bootstrap>:228: RuntimeWarning: compiletime version 3.8 of module 'hit' does not match runtime version 3.9
test:kernels/simple_diffusion.test: Working Directory: /local/home/schmithi/Projects/chamois/test/tests/kernels/simple_diffusion
test:kernels/simple_diffusion.test: Running command: /local/home/schmithi/Projects/chamois/chamois-opt -i simple_diffusion.i --no-gdb-backtrace
test:kernels/simple_diffusion.test: 
test:kernels/simple_diffusion.test: Framework Information:
test:kernels/simple_diffusion.test: MOOSE Version:           git commit 4aee48977f on 2021-10-30
test:kernels/simple_diffusion.test: LibMesh Version:         
test:kernels/simple_diffusion.test: PETSc Version:           3.15.1
test:kernels/simple_diffusion.test: SLEPc Version:           3.15.1
test:kernels/simple_diffusion.test: Current Time:            Sat Oct 30 14:57:38 2021
test:kernels/simple_diffusion.test: Executable Timestamp:    Sat Oct 30 14:57:36 2021
test:kernels/simple_diffusion.test: 
test:kernels/simple_diffusion.test: Parallelism:
test:kernels/simple_diffusion.test:   Num Processors:          1
test:kernels/simple_diffusion.test:   Num Threads:             1
test:kernels/simple_diffusion.test: 
test:kernels/simple_diffusion.test: Mesh: 
test:kernels/simple_diffusion.test:   Parallel Type:           replicated
test:kernels/simple_diffusion.test:   Mesh Dimension:          2
test:kernels/simple_diffusion.test:   Spatial Dimension:       2
test:kernels/simple_diffusion.test:   Nodes:                   121
test:kernels/simple_diffusion.test:   Elems:                   100
test:kernels/simple_diffusion.test:   Num Subdomains:          1
test:kernels/simple_diffusion.test: 
test:kernels/simple_diffusion.test: Nonlinear System:
test:kernels/simple_diffusion.test:   Num DOFs:                121
test:kernels/simple_diffusion.test:   Num Local DOFs:          121
test:kernels/simple_diffusion.test:   Variables:               "u" 
test:kernels/simple_diffusion.test:   Finite Element Types:    "LAGRANGE" 
test:kernels/simple_diffusion.test:   Approximation Orders:    "FIRST" 
test:kernels/simple_diffusion.test: 
test:kernels/simple_diffusion.test: Execution Information:
test:kernels/simple_diffusion.test:   Executioner:             Steady
test:kernels/simple_diffusion.test:   Solver Mode:             Preconditioned JFNK
test:kernels/simple_diffusion.test:   PETSc Preconditioner:    hypre boomeramg 
test:kernels/simple_diffusion.test: 
test:kernels/simple_diffusion.test:  0 Nonlinear |R| = 3.082207e+00
test:kernels/simple_diffusion.test:       0 Linear |R| = 3.082207e+00
test:kernels/simple_diffusion.test:       1 Linear |R| = 1.034260e-01
test:kernels/simple_diffusion.test:       2 Linear |R| = 2.616261e-03
test:kernels/simple_diffusion.test:       3 Linear |R| = 9.194723e-05
test:kernels/simple_diffusion.test:       4 Linear |R| = 1.366911e-06
test:kernels/simple_diffusion.test:  1 Nonlinear |R| = 1.373820e-06
test:kernels/simple_diffusion.test:       0 Linear |R| = 1.373820e-06
test:kernels/simple_diffusion.test:       1 Linear |R| = 3.507042e-08
test:kernels/simple_diffusion.test:       2 Linear |R| = 4.049791e-10
test:kernels/simple_diffusion.test:       3 Linear |R| = 1.351613e-11
test:kernels/simple_diffusion.test:  2 Nonlinear |R| = 1.352021e-11
test:kernels/simple_diffusion.test:  Solve Converged!
test:kernels/simple_diffusion.test: double free or corruption (!prev)
test:kernels/simple_diffusion.test: Aborted
test:kernels/simple_diffusion.test: 
test:kernels/simple_diffusion.test: Framework Information:
test:kernels/simple_diffusion.test: MOOSE Version:           git commit 4aee48977f on 2021-10-30
test:kernels/simple_diffusion.test: LibMesh Version:         
test:kernels/simple_diffusion.test: PETSc Version:           3.15.1
test:kernels/simple_diffusion.test: SLEPc Version:           3.15.1
test:kernels/simple_diffusion.test: Current Time:            Sat Oct 30 14:57:38 2021
test:kernels/simple_diffusion.test: Executable Timestamp:    Sat Oct 30 14:57:36 2021
test:kernels/simple_diffusion.test: 
test:kernels/simple_diffusion.test: Parallelism:
test:kernels/simple_diffusion.test:   Num Processors:          1
test:kernels/simple_diffusion.test:   Num Threads:             1
test:kernels/simple_diffusion.test: 
test:kernels/simple_diffusion.test: Mesh: 
test:kernels/simple_diffusion.test:   Parallel Type:           replicated
test:kernels/simple_diffusion.test:   Mesh Dimension:          2
test:kernels/simple_diffusion.test:   Spatial Dimension:       2
test:kernels/simple_diffusion.test:   Nodes:                   121
test:kernels/simple_diffusion.test:   Elems:                   100
test:kernels/simple_diffusion.test:   Num Subdomains:          1
test:kernels/simple_diffusion.test: 
test:kernels/simple_diffusion.test: Nonlinear System:
test:kernels/simple_diffusion.test:   Num DOFs:                121
test:kernels/simple_diffusion.test:   Num Local DOFs:          121
test:kernels/simple_diffusion.test:   Variables:               "u" 
test:kernels/simple_diffusion.test:   Finite Element Types:    "LAGRANGE" 
test:kernels/simple_diffusion.test:   Approximation Orders:    "FIRST" 
test:kernels/simple_diffusion.test: 
test:kernels/simple_diffusion.test: Execution Information:
test:kernels/simple_diffusion.test:   Executioner:             Steady
test:kernels/simple_diffusion.test:   Solver Mode:             Preconditioned JFNK
test:kernels/simple_diffusion.test:   PETSc Preconditioner:    hypre boomeramg 
test:kernels/simple_diffusion.test: 
test:kernels/simple_diffusion.test:  0 Nonlinear |R| = 3.082207e+00
test:kernels/simple_diffusion.test:       0 Linear |R| = 3.082207e+00
test:kernels/simple_diffusion.test:       1 Linear |R| = 1.034260e-01
test:kernels/simple_diffusion.test:       2 Linear |R| = 2.616261e-03
test:kernels/simple_diffusion.test:       3 Linear |R| = 9.194723e-05
test:kernels/simple_diffusion.test:       4 Linear |R| = 1.366911e-06
test:kernels/simple_diffusion.test:  1 Nonlinear |R| = 1.373820e-06
test:kernels/simple_diffusion.test:       0 Linear |R| = 1.373820e-06
test:kernels/simple_diffusion.test:       1 Linear |R| = 3.507042e-08
test:kernels/simple_diffusion.test:       2 Linear |R| = 4.049791e-10
test:kernels/simple_diffusion.test:       3 Linear |R| = 1.351613e-11
test:kernels/simple_diffusion.test:  2 Nonlinear |R| = 1.352021e-11
test:kernels/simple_diffusion.test:  Solve Converged!
test:kernels/simple_diffusion.test: double free or corruption (!prev)
test:kernels/simple_diffusion.test: Aborted
test:kernels/simple_diffusion.test: 
test:kernels/simple_diffusion.test: 
test:kernels/simple_diffusion.test: Exit Code: 134
test:kernels/simple_diffusion.test: ################################################################################
test:kernels/simple_diffusion.test: Tester failed, reason: CRASH
test:kernels/simple_diffusion.test: 
test:kernels/simple_diffusion.test ............................................................ FAILED (CRASH)


Final Test Results:
--------------------------------------------------------------------------------------------------------------
test:kernels/simple_diffusion.test ............................................................ FAILED (CRASH)
--------------------------------------------------------------------------------------------------------------
Ran 1 tests in 0.2 seconds. Average test time 0.1 seconds, maximum test time 0.1 seconds.
0 passed, 0 skipped, 0 pending, 1 FAILED

I am not too experienced with building more complex projects. Other input files lead to a similar result. They almost complete and lead to this double free or corruption (!prev) error somewhere after the solver converges. I have not been able to track down the problem with the debugger since the stack is corrupted.

It seems weird to me that the simple diffusion test fails even though it should not depend on the third-party library. Is there some moose function that is overloaded in some unintended way?

I would appreciate any help toward resolving this issue.

[GiudGiud]

Hello

Can you please build in debug mode and get us a backtrace in a debugger?
instructions are here: https://mooseframework.inl.gov/application_development/debugging.html#!

Guillaume

[thiloschmid]

I was able to resolve the issue. My apologies, it had nothing to do with moose directly.