Trouble creating geometry and diffusion (STEP 1) when following Workshop 2023 Video #27497
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ColinMG2
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Replies: 1 comment 39 replies
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Hello You ran out of memory when building the executable Use a lower processor count to build For example make -j2 for two processors Guillaume |
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I am following the steps on the Summer 2023 Workshop video to learn on how to get started running things in moose and I ran into trouble when trying to compile in the "step01_diffusion" directory.
(moose) cmg88@COLIN-DESKTOP:~/projects/moose/tutorials/darcy_thermo_mech/step01_diffusion$ make -j 10
Creating Unity Directory /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/../..//modules/ray_tracing/build/unity_src
Rebuilding symlinks in /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/../..//modules/ray_tracing/build/header_symlinks
Creating Unity Directory /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/../..//modules/heat_transfer/build/unity_src
Rebuilding symlinks in /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/../..//modules/heat_transfer/build/header_symlinks
Rebuilding symlinks in /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/../..//modules/solid_mechanics/build/header_symlinks
Creating Unity Directory /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/../..//modules/solid_mechanics/build/unity_src
Creating Unity Directory /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/../..//modules/phase_field/build/unity_src
Rebuilding symlinks in /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/../..//modules/phase_field/build/header_symlinks
Creating Unity Directory /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/step01_diffusion/build/unity_src
Rebuilding symlinks in /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/step01_diffusion/build/header_symlinks
Creating Resource file /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/step01_diffusion/darcy_thermo_mech.yaml
Creating Unity /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/../..//modules/ray_tracing/build/unity_src/postprocessors_Unity.C
Creating Unity /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/../..//modules/ray_tracing/build/unity_src/utils_Unity.C
Creating Unity /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/../..//modules/ray_tracing/build/unity_src/userobjects_Unity.C
Creating Unity /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/../..//modules/ray_tracing/build/unity_src/actions_Unity.C
Creating Unity /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/../..//modules/ray_tracing/build/unity_src/base_Unity.C
Creating Unity /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/../..//modules/ray_tracing/build/unity_src/vectorpostprocessors_Unity.C
Creating Unity /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/../..//modules/ray_tracing/build/unity_src/raybcs_Unity.C
Creating Unity /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/../..//modules/ray_tracing/build/unity_src/raykernels_Unity.C
Creating Unity /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/../..//modules/ray_tracing/build/unity_src/raytracing_Unity.C
Creating Unity /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/../..//modules/ray_tracing/build/unity_src/outputs_Unity.C
Creating Unity /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/../..//modules/heat_transfer/build/unity_src/interfacekernels_Unity.C
Creating Unity /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/../..//modules/heat_transfer/build/unity_src/meshgenerators_Unity.C
Creating Unity /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/../..//modules/heat_transfer/build/unity_src/dirackernels_Unity.C
Creating Unity /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/../..//modules/heat_transfer/build/unity_src/fvbcs_Unity.C
Creating Unity /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/../..//modules/heat_transfer/build/unity_src/postprocessors_Unity.C
Creating Unity /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/../..//modules/heat_transfer/build/unity_src/userobjects_Unity.C
Creating Unity /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/../..//modules/heat_transfer/build/unity_src/actions_Unity.C
Creating Unity /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/../..//modules/heat_transfer/build/unity_src/physics_Unity.C
Creating Unity /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/../..//modules/heat_transfer/build/unity_src/base_Unity.C
Creating Unity /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/../..//modules/heat_transfer/build/unity_src/fvkernels_Unity.C
Creating Unity /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/../..//modules/heat_transfer/build/unity_src/vectorpostprocessors_Unity.C
Creating Unity /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/../..//modules/heat_transfer/build/unity_src/materials_Unity.C
Creating Unity /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/../..//modules/heat_transfer/build/unity_src/raybcs_Unity.C
Creating Unity /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/../..//modules/heat_transfer/build/unity_src/bcs_Unity.C
Creating Unity /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/../..//modules/heat_transfer/build/unity_src/functormaterials_Unity.C
Creating Unity /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/../..//modules/heat_transfer/build/unity_src/kernels_Unity.C
Creating Unity /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/../..//modules/heat_transfer/build/unity_src/constraints_Unity.C
Creating Unity /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/../..//modules/heat_transfer/build/unity_src/auxkernels_Unity.C
Creating Unity /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/../..//modules/solid_mechanics/build/unity_src/interfacekernels_Unity.C
Creating Unity /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/../..//modules/solid_mechanics/build/unity_src/postprocessors_Unity.C
Creating Unity /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/../..//modules/solid_mechanics/build/unity_src/utils_Unity.C
Creating Unity /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/../..//modules/solid_mechanics/build/unity_src/userobjects_Unity.C
Creating Unity /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/../..//modules/solid_mechanics/build/unity_src/actions_Unity.C
Creating Unity /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/../..//modules/solid_mechanics/build/unity_src/controls_Unity.C
Creating Unity /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/../..//modules/solid_mechanics/build/unity_src/loops_Unity.C
Creating Unity /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/../..//modules/solid_mechanics/build/unity_src/physics_Unity.C
Creating Unity /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/../..//modules/solid_mechanics/build/unity_src/neml2_Unity.C
Creating Unity /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/../..//modules/solid_mechanics/build/unity_src/base_Unity.C
Creating Unity /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/../..//modules/solid_mechanics/build/unity_src/vectorpostprocessors_Unity.C
Creating Unity /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/../..//modules/solid_mechanics/build/unity_src/dampers_Unity.C
Creating Unity /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/../..//modules/solid_mechanics/build/unity_src/materials_Unity.C
Creating Unity /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/../..//modules/solid_mechanics/build/unity_src/bcs_Unity.C
Creating Unity /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/../..//modules/solid_mechanics/build/unity_src/ics_Unity.C
Creating Unity /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/../..//modules/solid_mechanics/build/unity_src/nodalkernels_Unity.C
Creating Unity /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/../..//modules/solid_mechanics/build/unity_src/scalarkernels_Unity.C
Creating Unity /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/../..//modules/solid_mechanics/build/unity_src/kernels_Unity.C
Creating Unity /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/../..//modules/solid_mechanics/build/unity_src/constraints_Unity.C
Creating Unity /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/../..//modules/solid_mechanics/build/unity_src/auxkernels_Unity.C
Creating Unity /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/../..//modules/phase_field/build/unity_src/markers_Unity.C
Creating Unity /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/../..//modules/phase_field/build/unity_src/interfacekernels_Unity.C
Creating Unity /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/../..//modules/phase_field/build/unity_src/meshgenerators_Unity.C
Creating Unity /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/../..//modules/phase_field/build/unity_src/postprocessors_Unity.C
Creating Unity /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/../..//modules/phase_field/build/unity_src/utils_Unity.C
Creating Unity /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/../..//modules/phase_field/build/unity_src/userobjects_Unity.C
Creating Unity /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/../..//modules/phase_field/build/unity_src/actions_Unity.C
Creating Unity /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/../..//modules/phase_field/build/unity_src/functions_Unity.C
Creating Unity /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/../..//modules/phase_field/build/unity_src/base_Unity.C
Creating Unity /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/../..//modules/phase_field/build/unity_src/mesh_Unity.C
Creating Unity /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/../..//modules/phase_field/build/unity_src/vectorpostprocessors_Unity.C
Creating Unity /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/../..//modules/phase_field/build/unity_src/materials_Unity.C
Creating Unity /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/../..//modules/phase_field/build/unity_src/ics_Unity.C
Creating Unity /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/../..//modules/phase_field/build/unity_src/kernels_Unity.C
Creating Unity /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/../..//modules/phase_field/build/unity_src/auxkernels_Unity.C
Compiling C++ with suffix (in opt mode) /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/../..//modules/module_loader/src/ModulesApp.C...
Creating Unity /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/step01_diffusion/build/unity_src/base_Unity.C
Compiling C++ (in opt mode) /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/../..//modules/ray_tracing/build/unity_src/postprocessors_Unity.C...
Compiling C++ (in opt mode) /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/../..//modules/ray_tracing/build/unity_src/utils_Unity.C...
Compiling C++ (in opt mode) /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/../..//modules/ray_tracing/build/unity_src/userobjects_Unity.C...
Compiling C++ (in opt mode) /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/../..//modules/ray_tracing/build/unity_src/actions_Unity.C...
Compiling C++ (in opt mode) /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/../..//modules/ray_tracing/build/unity_src/base_Unity.C...
Compiling C++ (in opt mode) /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/../..//modules/ray_tracing/build/unity_src/vectorpostprocessors_Unity.C...
Compiling C++ (in opt mode) /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/../..//modules/ray_tracing/build/unity_src/raybcs_Unity.C...
Compiling C++ (in opt mode) /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/../..//modules/ray_tracing/build/unity_src/raykernels_Unity.C...
Compiling C++ (in opt mode) /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/../..//modules/ray_tracing/build/unity_src/raytracing_Unity.C...
Compiling C++ (in opt mode) /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/../..//modules/ray_tracing/build/unity_src/outputs_Unity.C...
Compiling C++ (in opt mode) /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/../..//modules/heat_transfer/build/unity_src/interfacekernels_Unity.C...
{standard input}: Assembler messages:
{standard input}:1509: Warning: end of file not at end of a line; newline inserted
{standard input}:1510: Error: expecting operand after ','; got nothing
{standard input}: Error: open CFI at the end of file; missing .cfi_endproc directive
x86_64-conda-linux-gnu-c++: fatal error: Killed signal terminated program cc1plus
compilation terminated.
make: *** [/home/cmg88/projects/moose/tutorials/darcy_thermo_mech/../..//framework/build.mk:150: /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/../..//modules/ray_tracing/build/unity_src/vectorpostprocessors_Unity.x86_64-conda-linux-gnu.opt.lo] Error 1
make: *** Waiting for unfinished jobs....
This is the output it gave me. In addition, I ran tests to see if it would work and it said that 2 tests failed since it says "Application not Found." Most likely because something went wrong when trying to compile
(moose) cmg88@COLIN-DESKTOP:~/projects/moose/tutorials/darcy_thermo_mech/step01_diffusion$ ./run_tests
Error in launching a new task []
kernels/simple_diffusion.test: Working Directory: /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/step01_diffusion/tests/kernels/simple_diffusion
kernels/simple_diffusion.test: Running command:
kernels/simple_diffusion.test: Python exception encountered:
kernels/simple_diffusion.test:
kernels/simple_diffusion.test: Traceback (most recent call last):
kernels/simple_diffusion.test: File "/home/cmg88/projects/moose/python/TestHarness/schedulers/RunParallel.py", line 54, in run
kernels/simple_diffusion.test: job.run()
kernels/simple_diffusion.test: File "/home/cmg88/projects/moose/python/TestHarness/schedulers/Job.py", line 231, in run
kernels/simple_diffusion.test: self.__tester.run(self.timer, self.options)
kernels/simple_diffusion.test: File "/home/cmg88/projects/moose/python/TestHarness/testers/Tester.py", line 483, in run
kernels/simple_diffusion.test: self.runCommand(timer, options)
kernels/simple_diffusion.test: File "/home/cmg88/projects/moose/python/TestHarness/testers/Tester.py", line 447, in runCommand
kernels/simple_diffusion.test: exit_code = self.spawnSubprocessFromOptions(timer, options)
kernels/simple_diffusion.test: File "/home/cmg88/projects/moose/python/TestHarness/testers/Tester.py", line 409, in spawnSubprocessFromOptions
kernels/simple_diffusion.test: process = subprocess.Popen(*popen_args, **popen_kwargs)
kernels/simple_diffusion.test: File "/home/cmg88/miniforge/envs/moose/lib/python3.10/subprocess.py", line 971, in init
kernels/simple_diffusion.test: self._execute_child(args, executable, preexec_fn, close_fds,
kernels/simple_diffusion.test: File "/home/cmg88/miniforge/envs/moose/lib/python3.10/subprocess.py", line 1717, in _execute_child
kernels/simple_diffusion.test: executable = args[0]
kernels/simple_diffusion.test: IndexError: list index out of range
kernels/simple_diffusion.test:
kernels/simple_diffusion.test ................................................. FAILED (Application not found)
Error in launching a new task []
problems.step: Working Directory: /home/cmg88/projects/moose/tutorials/darcy_thermo_mech/step01_diffusion/problems
problems.step: Running command:
problems.step: Python exception encountered:
problems.step:
problems.step: Traceback (most recent call last):
problems.step: File "/home/cmg88/projects/moose/python/TestHarness/schedulers/RunParallel.py", line 54, in run
problems.step: job.run()
problems.step: File "/home/cmg88/projects/moose/python/TestHarness/schedulers/Job.py", line 231, in run
problems.step: self.__tester.run(self.timer, self.options)
problems.step: File "/home/cmg88/projects/moose/python/TestHarness/testers/Tester.py", line 483, in run
problems.step: self.runCommand(timer, options)
problems.step: File "/home/cmg88/projects/moose/python/TestHarness/testers/Tester.py", line 447, in runCommand
problems.step: exit_code = self.spawnSubprocessFromOptions(timer, options)
problems.step: File "/home/cmg88/projects/moose/python/TestHarness/testers/Tester.py", line 409, in spawnSubprocessFromOptions
problems.step: process = subprocess.Popen(*popen_args, **popen_kwargs)
problems.step: File "/home/cmg88/miniforge/envs/moose/lib/python3.10/subprocess.py", line 971, in init
problems.step: self._execute_child(args, executable, preexec_fn, close_fds,
problems.step: File "/home/cmg88/miniforge/envs/moose/lib/python3.10/subprocess.py", line 1717, in _execute_child
problems.step: executable = args[0]
problems.step: IndexError: list index out of range
problems.step:
problems.step ................................................................. FAILED (Application not found)
Final Test Results:
kernels/simple_diffusion.test ................................................. FAILED (Application not found)
problems.step ................................................................. FAILED (Application not found)
Ran 2 tests in 0.3 seconds. Average test time 0.0 seconds, maximum test time 0.0 seconds.
0 passed, 0 skipped, 0 pending, 2 FAILED
Any suggestions on how I can get around this issue? Thanks!
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