Trouble creating geometry and diffusion (STEP 1) when following Workshop 2023 Video

[ColinMG2]

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!

[GiudGiud]

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

[GiudGiud]

It looks like the paraview forum recommends installing Paraview on windows and moving files from linux to windows for visualization
https://discourse.paraview.org/t/paraview-installation-error-in-linux-subsystem-windows-10/1381/6

looks like the GL1 error could be fixed by installing more packages though
https://stackoverflow.com/questions/55313610/importerror-libgl-so-1-cannot-open-shared-object-file-no-such-file-or-directo

[ColinMG2]

The suggestion for installing Paraview on windows works now very well. I will just copy the files from linux to windows for visualization like you suggested for now. However, after looking at the link you found for the GL1 error, I seem to be having trouble:

(paraview) cmg88@COLIN-DESKTOP:~$ apt install libgl1-mesa-glx
E: Could not open lock file /var/lib/dpkg/lock-frontend - open (13: Permission denied)
E: Unable to acquire the dpkg frontend lock (/var/lib/dpkg/lock-frontend), are you root?

[GiudGiud]

(paraview) cmg88@COLIN-DESKTOP:~$ apt install libgl1-mesa-glx
E: Could not open lock file /var/lib/dpkg/lock-frontend - open (13: Permission denied)
E: Unable to acquire the dpkg frontend lock (/var/lib/dpkg/lock-frontend), are you root?

do you have admin rights on this machine?
I think you could sudo apt install libgl1-mesa-glx

[ColinMG2]

Yes I have admin rights on this machine. However, when I ran into the same issue after running sudo apt install libgl1-mesa-glx

(paraview) cmg88@COLIN-DESKTOP:$ sudo apt install libgl1-mesa-glx
[sudo] password for cmg88:
Reading package lists... Done
Building dependency tree... Done
Reading state information... Done
The following additional packages will be installed:
libdrm-amdgpu1 libdrm-intel1 libdrm-nouveau2 libdrm-radeon1 libgl1 libgl1-amber-dri libgl1-mesa-dri
libglapi-mesa libglx-mesa0 libglx0 libllvm15 libpciaccess0 libsensors-config libsensors5 libx11-xcb1
libxshmfence1 libxxf86vm1
Suggested packages:
lm-sensors
The following NEW packages will be installed:
libdrm-amdgpu1 libdrm-intel1 libdrm-nouveau2 libdrm-radeon1 libgl1 libgl1-amber-dri libgl1-mesa-dri
libgl1-mesa-glx libglapi-mesa libglx-mesa0 libglx0 libllvm15 libpciaccess0 libsensors-config libsensors5
libx11-xcb1 libxshmfence1 libxxf86vm1
0 upgraded, 18 newly installed, 0 to remove and 6 not upgraded.
Need to get 5584 B/39.0 MB of archives.
After this operation, 168 MB of additional disk space will be used.
Do you want to continue? [Y/n] y
Get:1 http://archive.ubuntu.com/ubuntu jammy-updates/universe amd64 libgl1-mesa-glx amd64 23.0.4-0ubuntu122.04.1 [5584 B]
Fetched 5584 B in 0s (26.2 kB/s)
Selecting previously unselected package libdrm-amdgpu1:amd64.
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(paraview) cmg88@COLIN-DESKTOP:$ paraview step1_colin_in.e
paraview: error while loading shared libraries: libEGL.so.1: cannot open shared object file: No such file or directory
(paraview) cmg88@COLIN-DESKTOP:~$ open step1_colin_in.e
Warning: unknown mime-type for "step1_colin_in.e" -- using "application/octet-stream"
Error: no such file "step1_colin_in.e"

[GiudGiud]

different error now

paraview: error while loading shared libraries: libEGL.so.1: cannot open shared object file: No such file or directory

you should google this one to find which package you are missing