Setup issue: Test timeout, LibMesh version blank. #26345

calebfowler-tamu · 2023-12-14T21:35:57Z

calebfowler-tamu
Dec 14, 2023

I am trying to setup MOOSE on a laptop for personal research and study. I have been able to follow the instructions here: https://mooseframework.inl.gov/getting_started/installation/conda.html successfully through cloning MOOSE.

In making the test script by make -j 6 I was running into issues that weren't giving much info, so I switched to make -j 1 as I saw recommended on a number of other posts to avoid running out of memory.

This was the printed error when make failed:
Compiling C++ (in opt mode) /home/calebfowler/mooseWorkspace/moose/framework/build/unity_src/variables_Unity.C... x86_64-conda-linux-gnu-c++: fatal error: Killed signal terminated program cc1plus compilation terminated.

But proceeding from there, I eventually hadthe test 'fvkernels/mms/harmonic_interpolation.average/tris' timeout, giving the full output which I'll comment below. I noticed that no version was listed for LibMesh.
fvkernels/mms/harmonic_interpolation.average/tris: Working Directory: /home/calebfowler/mooseWorkspace/moose/test/tests/fvkernels/mms/harmonic_interpolation fvkernels/mms/harmonic_interpolation.average/tris: Running command: python3 -m unittest -v test.TestAverageTriangles fvkernels/mms/harmonic_interpolation.average/tris: Framework Information: fvkernels/mms/harmonic_interpolation.average/tris: MOOSE Version: git commit bde1548eec on 2023-12-14 fvkernels/mms/harmonic_interpolation.average/tris: LibMesh Version: fvkernels/mms/harmonic_interpolation.average/tris: PETSc Version: 3.20.1 fvkernels/mms/harmonic_interpolation.average/tris: SLEPc Version: 3.20.0 fvkernels/mms/harmonic_interpolation.average/tris: Current Time: Thu Dec 14 15:06:04 2023 fvkernels/mms/harmonic_interpolation.average/tris: Executable Timestamp: Thu Dec 14 14:59:51 2023

As such, I have tried rebuilding LibMes, following the instructions here, to no avail. Some of the critical output is listed below https://mooseframework.inl.gov/getting_started/installation/build_libmesh.html.
No LSB modules are available. Submodule 'libmesh' (https://github.com/libMesh/libmesh) registered for path 'libmesh' Cloning into '/home/calebfowler/mooseWorkspace/moose/libmesh'...

checking for built-in XDR support... yes checking for boostlib >= 1.57.0... configure: We could not detect the boost libraries (version 1.57 or higher). If you have a staged boost library (still not installed) please specify $BOOST_ROOT in your environment and do not give a PATH to --with-boost option. If you are sure you have boost installed, then check your version number looking in <boost/version.hpp>. See http://randspringer.de/boost for more documentation. <<< External boost installation *not* found... will try to configure for libmesh's internal boost >>> checking for boostlib >= 1.57.0... yes <<< Using libmesh-provided boost in ./contrib >>> checking for boost::movelib::unique_ptr support... yes note: Checking /lib and /include for MPI note: Could not find /lib/libmpi(.a/.so/.dylib) mpicxx Compiler Supports MPI configure: error: *** PETSc was not found, but --enable-petsc-required was specified. Running make -j 6... make: *** No targets specified and no makefile found. Stop.

Answered by GiudGiud

Dec 14, 2023

Hello

Switching to make -j 1 was the right call. Now you can see if make -j 2 ... works, just to save a little time in the future.

You are building on your laptop so probably using mamba to get petsc and libmesh (as a moose-petsc and moose-petsc package).
So you should not run the script to install libmesh from moose/scripts.

A timeout can just mean your laptop is slower than any machine we test with.

Guillaume

View full answer

calebfowler-tamu · 2023-12-14T21:38:35Z

calebfowler-tamu
Dec 14, 2023
Author

fvkernels/mms/harmonic_interpolation.average/tris: Working Directory: /home/calebfowler/mooseWorkspace/moose/test/tests/fvkernels/mms/harmonic_interpolation fvkernels/mms/harmonic_interpolation.average/tris: Running command: python3 -m unittest -v test.TestAverageTriangles fvkernels/mms/harmonic_interpolation.average/tris: Framework Information: fvkernels/mms/harmonic_interpolation.average/tris: MOOSE Version: git commit bde1548eec on 2023-12-14 fvkernels/mms/harmonic_interpolation.average/tris: LibMesh Version: fvkernels/mms/harmonic_interpolation.average/tris: PETSc Version: 3.20.1 fvkernels/mms/harmonic_interpolation.average/tris: SLEPc Version: 3.20.0 fvkernels/mms/harmonic_interpolation.average/tris: Current Time: Thu Dec 14 15:06:04 2023 fvkernels/mms/harmonic_interpolation.average/tris: Executable Timestamp: Thu Dec 14 14:59:51 2023 fvkernels/mms/harmonic_interpolation.average/tris: fvkernels/mms/harmonic_interpolation.average/tris: Parallelism: fvkernels/mms/harmonic_interpolation.average/tris: Num Processors: 1 fvkernels/mms/harmonic_interpolation.average/tris: Num Threads: 1 fvkernels/mms/harmonic_interpolation.average/tris: fvkernels/mms/harmonic_interpolation.average/tris: Mesh: fvkernels/mms/harmonic_interpolation.average/tris: Parallel Type: replicated fvkernels/mms/harmonic_interpolation.average/tris: Mesh Dimension: 2 fvkernels/mms/harmonic_interpolation.average/tris: Spatial Dimension: 2 fvkernels/mms/harmonic_interpolation.average/tris: Nodes: 9 fvkernels/mms/harmonic_interpolation.average/tris: Elems: 8 fvkernels/mms/harmonic_interpolation.average/tris: Num Subdomains: 2 fvkernels/mms/harmonic_interpolation.average/tris: fvkernels/mms/harmonic_interpolation.average/tris: Nonlinear System: fvkernels/mms/harmonic_interpolation.average/tris: Num DOFs: 8 fvkernels/mms/harmonic_interpolation.average/tris: Num Local DOFs: 8 fvkernels/mms/harmonic_interpolation.average/tris: Variables: "v" fvkernels/mms/harmonic_interpolation.average/tris: Finite Element Types: "MONOMIAL" fvkernels/mms/harmonic_interpolation.average/tris: Approximation Orders: "CONSTANT" fvkernels/mms/harmonic_interpolation.average/tris: fvkernels/mms/harmonic_interpolation.average/tris: Execution Information: fvkernels/mms/harmonic_interpolation.average/tris: Executioner: Steady fvkernels/mms/harmonic_interpolation.average/tris: Solver Mode: NEWTON fvkernels/mms/harmonic_interpolation.average/tris: MOOSE Preconditioner: SMP (auto) fvkernels/mms/harmonic_interpolation.average/tris: fvkernels/mms/harmonic_interpolation.average/tris: fvkernels/mms/harmonic_interpolation.average/tris: Postprocessor Values: fvkernels/mms/harmonic_interpolation.average/tris: +----------------+----------------+----------------+ fvkernels/mms/harmonic_interpolation.average/tris: | time | error | h | fvkernels/mms/harmonic_interpolation.average/tris: +----------------+----------------+----------------+ fvkernels/mms/harmonic_interpolation.average/tris: | 0.000000e+00 | 0.000000e+00 | 0.000000e+00 | fvkernels/mms/harmonic_interpolation.average/tris: +----------------+----------------+----------------+ fvkernels/mms/harmonic_interpolation.average/tris: fvkernels/mms/harmonic_interpolation.average/tris: 0 Nonlinear |R| = 1.594123e+02 fvkernels/mms/harmonic_interpolation.average/tris: 0 Linear |R| = 1.594123e+02 fvkernels/mms/harmonic_interpolation.average/tris: 1 Linear |R| = 2.738872e-02 fvkernels/mms/harmonic_interpolation.average/tris: 2 Linear |R| = 1.178621e-06 fvkernels/mms/harmonic_interpolation.average/tris: 1 Nonlinear |R| = 1.178621e-06 fvkernels/mms/harmonic_interpolation.average/tris: Solve Converged! fvkernels/mms/harmonic_interpolation.average/tris: fvkernels/mms/harmonic_interpolation.average/tris: Postprocessor Values: fvkernels/mms/harmonic_interpolation.average/tris: +----------------+----------------+----------------+ fvkernels/mms/harmonic_interpolation.average/tris: | time | error | h | fvkernels/mms/harmonic_interpolation.average/tris: +----------------+----------------+----------------+ fvkernels/mms/harmonic_interpolation.average/tris: | 0.000000e+00 | 0.000000e+00 | 0.000000e+00 | fvkernels/mms/harmonic_interpolation.average/tris: | 1.000000e+00 | 5.811146e-02 | 7.071068e-01 | fvkernels/mms/harmonic_interpolation.average/tris: +----------------+----------------+----------------+ fvkernels/mms/harmonic_interpolation.average/tris: fvkernels/mms/harmonic_interpolation.average/tris: Framework Information: fvkernels/mms/harmonic_interpolation.average/tris: MOOSE Version: git commit bde1548eec on 2023-12-14 fvkernels/mms/harmonic_interpolation.average/tris: LibMesh Version: fvkernels/mms/harmonic_interpolation.average/tris: PETSc Version: 3.20.1 fvkernels/mms/harmonic_interpolation.average/tris: SLEPc Version: 3.20.0 fvkernels/mms/harmonic_interpolation.average/tris: Current Time: Thu Dec 14 15:06:04 2023 fvkernels/mms/harmonic_interpolation.average/tris: Executable Timestamp: Thu Dec 14 14:59:51 2023 fvkernels/mms/harmonic_interpolation.average/tris: fvkernels/mms/harmonic_interpolation.average/tris: Parallelism: fvkernels/mms/harmonic_interpolation.average/tris: Num Processors: 1 fvkernels/mms/harmonic_interpolation.average/tris: Num Threads: 1 fvkernels/mms/harmonic_interpolation.average/tris: fvkernels/mms/harmonic_interpolation.average/tris: Mesh: fvkernels/mms/harmonic_interpolation.average/tris: Parallel Type: replicated fvkernels/mms/harmonic_interpolation.average/tris: Mesh Dimension: 2 fvkernels/mms/harmonic_interpolation.average/tris: Spatial Dimension: 2 fvkernels/mms/harmonic_interpolation.average/tris: Nodes: 25 fvkernels/mms/harmonic_interpolation.average/tris: Elems: 32 fvkernels/mms/harmonic_interpolation.average/tris: Num Subdomains: 2 fvkernels/mms/harmonic_interpolation.average/tris: fvkernels/mms/harmonic_interpolation.average/tris: Nonlinear System: fvkernels/mms/harmonic_interpolation.average/tris: Num DOFs: 32 fvkernels/mms/harmonic_interpolation.average/tris: Num Local DOFs: 32 fvkernels/mms/harmonic_interpolation.average/tris: Variables: "v" fvkernels/mms/harmonic_interpolation.average/tris: Finite Element Types: "MONOMIAL" fvkernels/mms/harmonic_interpolation.average/tris: Approximation Orders: "CONSTANT" fvkernels/mms/harmonic_interpolation.average/tris: fvkernels/mms/harmonic_interpolation.average/tris: Execution Information: fvkernels/mms/harmonic_interpolation.average/tris: Executioner: Steady fvkernels/mms/harmonic_interpolation.average/tris: Solver Mode: NEWTON fvkernels/mms/harmonic_interpolation.average/tris: MOOSE Preconditioner: SMP (auto) fvkernels/mms/harmonic_interpolation.average/tris: fvkernels/mms/harmonic_interpolation.average/tris: fvkernels/mms/harmonic_interpolation.average/tris: Postprocessor Values: fvkernels/mms/harmonic_interpolation.average/tris: +----------------+----------------+----------------+ fvkernels/mms/harmonic_interpolation.average/tris: | time | error | h | fvkernels/mms/harmonic_interpolation.average/tris: +----------------+----------------+----------------+ fvkernels/mms/harmonic_interpolation.average/tris: | 0.000000e+00 | 0.000000e+00 | 0.000000e+00 | fvkernels/mms/harmonic_interpolation.average/tris: +----------------+----------------+----------------+ fvkernels/mms/harmonic_interpolation.average/tris: fvkernels/mms/harmonic_interpolation.average/tris: 0 Nonlinear |R| = 2.104827e+02 fvkernels/mms/harmonic_interpolation.average/tris: 0 Linear |R| = 2.104827e+02 fvkernels/mms/harmonic_interpolation.average/tris: 1 Linear |R| = 1.188994e-01 fvkernels/mms/harmonic_interpolation.average/tris: 2 Linear |R| = 7.903575e-04 fvkernels/mms/harmonic_interpolation.average/tris: 1 Nonlinear |R| = 7.903575e-04 fvkernels/mms/harmonic_interpolation.average/tris: 0 Linear |R| = 7.903575e-04 fvkernels/mms/harmonic_interpolation.average/tris: 1 Linear |R| = 2.142164e-06 fvkernels/mms/harmonic_interpolation.average/tris: 2 Linear |R| = 2.994724e-09 fvkernels/mms/harmonic_interpolation.average/tris: 2 Nonlinear |R| = 2.994729e-09 fvkernels/mms/harmonic_interpolation.average/tris: Solve Converged! fvkernels/mms/harmonic_interpolation.average/tris: fvkernels/mms/harmonic_interpolation.average/tris: Postprocessor Values: fvkernels/mms/harmonic_interpolation.average/tris: +----------------+----------------+----------------+ fvkernels/mms/harmonic_interpolation.average/tris: | time | error | h | fvkernels/mms/harmonic_interpolation.average/tris: +----------------+----------------+----------------+ fvkernels/mms/harmonic_interpolation.average/tris: | 0.000000e+00 | 0.000000e+00 | 0.000000e+00 | fvkernels/mms/harmonic_interpolation.average/tris: | 1.000000e+00 | 4.064836e-02 | 3.535534e-01 | fvkernels/mms/harmonic_interpolation.average/tris: +----------------+----------------+----------------+ fvkernels/mms/harmonic_interpolation.average/tris: fvkernels/mms/harmonic_interpolation.average/tris: Framework Information: fvkernels/mms/harmonic_interpolation.average/tris: MOOSE Version: git commit bde1548eec on 2023-12-14 fvkernels/mms/harmonic_interpolation.average/tris: LibMesh Version: fvkernels/mms/harmonic_interpolation.average/tris: PETSc Version: 3.20.1 fvkernels/mms/harmonic_interpolation.average/tris: SLEPc Version: 3.20.0 fvkernels/mms/harmonic_interpolation.average/tris: Current Time: Thu Dec 14 15:06:05 2023 fvkernels/mms/harmonic_interpolation.average/tris: Executable Timestamp: Thu Dec 14 14:59:51 2023 fvkernels/mms/harmonic_interpolation.average/tris: fvkernels/mms/harmonic_interpolation.average/tris: Parallelism: fvkernels/mms/harmonic_interpolation.average/tris: Num Processors: 1 fvkernels/mms/harmonic_interpolation.average/tris: Num Threads: 1 fvkernels/mms/harmonic_interpolation.average/tris: fvkernels/mms/harmonic_interpolation.average/tris: Mesh: fvkernels/mms/harmonic_interpolation.average/tris: Parallel Type: replicated fvkernels/mms/harmonic_interpolation.average/tris: Mesh Dimension: 2 fvkernels/mms/harmonic_interpolation.average/tris: Spatial Dimension: 2 fvkernels/mms/harmonic_interpolation.average/tris: Nodes: 81 fvkernels/mms/harmonic_interpolation.average/tris: Elems: 128 fvkernels/mms/harmonic_interpolation.average/tris: Num Subdomains: 2 fvkernels/mms/harmonic_interpolation.average/tris: fvkernels/mms/harmonic_interpolation.average/tris: Nonlinear System: fvkernels/mms/harmonic_interpolation.average/tris: Num DOFs: 128 fvkernels/mms/harmonic_interpolation.average/tris: Num Local DOFs: 128 fvkernels/mms/harmonic_interpolation.average/tris: Variables: "v" fvkernels/mms/harmonic_interpolation.average/tris: Finite Element Types: "MONOMIAL" fvkernels/mms/harmonic_interpolation.average/tris: Approximation Orders: "CONSTANT" fvkernels/mms/harmonic_interpolation.average/tris: fvkernels/mms/harmonic_interpolation.average/tris: Execution Information: fvkernels/mms/harmonic_interpolation.average/tris: Executioner: Steady fvkernels/mms/harmonic_interpolation.average/tris: Solver Mode: NEWTON fvkernels/mms/harmonic_interpolation.average/tris: MOOSE Preconditioner: SMP (auto) fvkernels/mms/harmonic_interpolation.average/tris: fvkernels/mms/harmonic_interpolation.average/tris: fvkernels/mms/harmonic_interpolation.average/tris: Postprocessor Values: fvkernels/mms/harmonic_interpolation.average/tris: +----------------+----------------+----------------+ fvkernels/mms/harmonic_interpolation.average/tris: | time | error | h | fvkernels/mms/harmonic_interpolation.average/tris: +----------------+----------------+----------------+ fvkernels/mms/harmonic_interpolation.average/tris: | 0.000000e+00 | 0.000000e+00 | 0.000000e+00 | fvkernels/mms/harmonic_interpolation.average/tris: +----------------+----------------+----------------+ fvkernels/mms/harmonic_interpolation.average/tris: fvkernels/mms/harmonic_interpolation.average/tris: 0 Nonlinear |R| = 2.853799e+02 fvkernels/mms/harmonic_interpolation.average/tris: 0 Linear |R| = 2.853799e+02 fvkernels/mms/harmonic_interpolation.average/tris: 1 Linear |R| = 6.025500e-01 fvkernels/mms/harmonic_interpolation.average/tris: 2 Linear |R| = 7.192565e-03 fvkernels/mms/harmonic_interpolation.average/tris: 3 Linear |R| = 5.581953e-05 fvkernels/mms/harmonic_interpolation.average/tris: 1 Nonlinear |R| = 5.581953e-05 fvkernels/mms/harmonic_interpolation.average/tris: 0 Linear |R| = 5.581953e-05 fvkernels/mms/harmonic_interpolation.average/tris: 1 Linear |R| = 6.546158e-07 fvkernels/mms/harmonic_interpolation.average/tris: 2 Linear |R| = 5.134356e-09 fvkernels/mms/harmonic_interpolation.average/tris: 3 Linear |R| = 4.753799e-11 fvkernels/mms/harmonic_interpolation.average/tris: 2 Nonlinear |R| = 4.753939e-11 fvkernels/mms/harmonic_interpolation.average/tris: Solve Converged! fvkernels/mms/harmonic_interpolation.average/tris: fvkernels/mms/harmonic_interpolation.average/tris: Postprocessor Values: fvkernels/mms/harmonic_interpolation.average/tris: +----------------+----------------+----------------+ fvkernels/mms/harmonic_interpolation.average/tris: | time | error | h | fvkernels/mms/harmonic_interpolation.average/tris: +----------------+----------------+----------------+ fvkernels/mms/harmonic_interpolation.average/tris: | 0.000000e+00 | 0.000000e+00 | 0.000000e+00 | fvkernels/mms/harmonic_interpolation.average/tris: | 1.000000e+00 | 2.295142e-02 | 1.767767e-01 | fvkernels/mms/harmonic_interpolation.average/tris: +----------------+----------------+----------------+ fvkernels/mms/harmonic_interpolation.average/tris: fvkernels/mms/harmonic_interpolation.average/tris: Framework Information: fvkernels/mms/harmonic_interpolation.average/tris: MOOSE Version: git commit bde1548eec on 2023-12-14 fvkernels/mms/harmonic_interpolation.average/tris: LibMesh Version: fvkernels/mms/harmonic_interpolation.average/tris: PETSc Version: 3.20.1 fvkernels/mms/harmonic_interpolation.average/tris: SLEPc Version: 3.20.0 fvkernels/mms/harmonic_interpolation.average/tris: Current Time: Thu Dec 14 15:06:05 2023 fvkernels/mms/harmonic_interpolation.average/tris: Executable Timestamp: Thu Dec 14 14:59:51 2023 fvkernels/mms/harmonic_interpolation.average/tris: fvkernels/mms/harmonic_interpolation.average/tris: Parallelism: fvkernels/mms/harmonic_interpolation.average/tris: Num Processors: 1 fvkernels/mms/harmonic_interpolation.average/tris: Num Threads: 1 fvkernels/mms/harmonic_interpolation.average/tris: fvkernels/mms/harmonic_interpolation.average/tris: Mesh: fvkernels/mms/harmonic_interpolation.average/tris: Parallel Type: replicated fvkernels/mms/harmonic_interpolation.average/tris: Mesh Dimension: 2 fvkernels/mms/harmonic_interpolation.average/tris: Spatial Dimension: 2 fvkernels/mms/harmonic_interpolation.average/tris: Nodes: 289 fvkernels/mms/harmonic_interpolation.average/tris: Elems: 512 fvkernels/mms/harmonic_interpolation.average/tris: Num Subdomains: 2 fvkernels/mms/harmonic_interpolation.average/tris: fvkernels/mms/harmonic_interpolation.average/tris: Nonlinear System: fvkernels/mms/harmonic_interpolation.average/tris: Num DOFs: 512 fvkernels/mms/harmonic_interpolation.average/tris: Num Local DOFs: 512 fvkernels/mms/harmonic_interpolation.average/tris: Variables: "v" fvkernels/mms/harmonic_interpolation.average/tris: Finite Element Types: "MONOMIAL" fvkernels/mms/harmonic_interpolation.average/tris: Approximation Orders: "CONSTANT" fvkernels/mms/harmonic_interpolation.average/tris: fvkernels/mms/harmonic_interpolation.average/tris: Execution Information: fvkernels/mms/harmonic_interpolation.average/tris: Executioner: Steady fvkernels/mms/harmonic_interpolation.average/tris: Solver Mode: NEWTON fvkernels/mms/harmonic_interpolation.average/tris: MOOSE Preconditioner: SMP (auto) fvkernels/mms/harmonic_interpolation.average/tris: fvkernels/mms/harmonic_interpolation.average/tris: fvkernels/mms/harmonic_interpolation.average/tris: Postprocessor Values: fvkernels/mms/harmonic_interpolation.average/tris: +----------------+----------------+----------------+ fvkernels/mms/harmonic_interpolation.average/tris: | time | error | h | fvkernels/mms/harmonic_interpolation.average/tris: +----------------+----------------+----------------+ fvkernels/mms/harmonic_interpolation.average/tris: | 0.000000e+00 | 0.000000e+00 | 0.000000e+00 | fvkernels/mms/harmonic_interpolation.average/tris: +----------------+----------------+----------------+ fvkernels/mms/harmonic_interpolation.average/tris: fvkernels/mms/harmonic_interpolation.average/tris: 0 Nonlinear |R| = 3.941863e+02 fvkernels/mms/harmonic_interpolation.average/tris: 0 Linear |R| = 3.941863e+02 fvkernels/mms/harmonic_interpolation.average/tris: 1 Linear |R| = 1.085823e+00 fvkernels/mms/harmonic_interpolation.average/tris: 2 Linear |R| = 2.897496e-02 fvkernels/mms/harmonic_interpolation.average/tris: 3 Linear |R| = 4.281595e-04 fvkernels/mms/harmonic_interpolation.average/tris: 1 Nonlinear |R| = 4.281595e-04 fvkernels/mms/harmonic_interpolation.average/tris: 0 Linear |R| = 4.281595e-04 fvkernels/mms/harmonic_interpolation.average/tris: 1 Linear |R| = 8.778613e-06 fvkernels/mms/harmonic_interpolation.average/tris: 2 Linear |R| = 2.135415e-07 fvkernels/mms/harmonic_interpolation.average/tris: 3 Linear |R| = 3.446505e-09 fvkernels/mms/harmonic_interpolation.average/tris: 2 Nonlinear |R| = 3.446498e-09 fvkernels/mms/harmonic_interpolation.average/tris: Solve Converged! fvkernels/mms/harmonic_interpolation.average/tris: fvkernels/mms/harmonic_interpolation.average/tris: Postprocessor Values: fvkernels/mms/harmonic_interpolation.average/tris: +----------------+----------------+----------------+ fvkernels/mms/harmonic_interpolation.average/tris: | time | error | h | fvkernels/mms/harmonic_interpolation.average/tris: +----------------+----------------+----------------+ fvkernels/mms/harmonic_interpolation.average/tris: | 0.000000e+00 | 0.000000e+00 | 0.000000e+00 | fvkernels/mms/harmonic_interpolation.average/tris: | 1.000000e+00 | 1.192730e-02 | 8.838835e-02 | fvkernels/mms/harmonic_interpolation.average/tris: +----------------+----------------+----------------+ fvkernels/mms/harmonic_interpolation.average/tris: fvkernels/mms/harmonic_interpolation.average/tris: Framework Information: fvkernels/mms/harmonic_interpolation.average/tris: MOOSE Version: git commit bde1548eec on 2023-12-14 fvkernels/mms/harmonic_interpolation.average/tris: LibMesh Version: fvkernels/mms/harmonic_interpolation.average/tris: PETSc Version: 3.20.1 fvkernels/mms/harmonic_interpolation.average/tris: SLEPc Version: 3.20.0 fvkernels/mms/harmonic_interpolation.average/tris: Current Time: Thu Dec 14 15:06:05 2023 fvkernels/mms/harmonic_interpolation.average/tris: Executable Timestamp: Thu Dec 14 14:59:51 2023 fvkernels/mms/harmonic_interpolation.average/tris: fvkernels/mms/harmonic_interpolation.average/tris: Parallelism: fvkernels/mms/harmonic_interpolation.average/tris: Num Processors: 1 fvkernels/mms/harmonic_interpolation.average/tris: Num Threads: 1 fvkernels/mms/harmonic_interpolation.average/tris: fvkernels/mms/harmonic_interpolation.average/tris: Mesh: fvkernels/mms/harmonic_interpolation.average/tris: Parallel Type: replicated fvkernels/mms/harmonic_interpolation.average/tris: Mesh Dimension: 2 fvkernels/mms/harmonic_interpolation.average/tris: Spatial Dimension: 2 fvkernels/mms/harmonic_interpolation.average/tris: Nodes: 1089 fvkernels/mms/harmonic_interpolation.average/tris: Elems: 2048 fvkernels/mms/harmonic_interpolation.average/tris: Num Subdomains: 2 fvkernels/mms/harmonic_interpolation.average/tris: fvkernels/mms/harmonic_interpolation.average/tris: Nonlinear System: fvkernels/mms/harmonic_interpolation.average/tris: Num DOFs: 2048 fvkernels/mms/harmonic_interpolation.average/tris: Num Local DOFs: 2048 fvkernels/mms/harmonic_interpolation.average/tris: Variables: "v" fvkernels/mms/harmonic_interpolation.average/tris: Finite Element Types: "MONOMIAL" fvkernels/mms/harmonic_interpolation.average/tris: Approximation Orders: "CONSTANT" fvkernels/mms/harmonic_interpolation.average/tris: fvkernels/mms/harmonic_interpolation.average/tris: Execution Information: fvkernels/mms/harmonic_interpolation.average/tris: Executioner: Steady fvkernels/mms/harmonic_interpolation.average/tris: Solver Mode: NEWTON fvkernels/mms/harmonic_interpolation.average/tris: MOOSE Preconditioner: SMP (auto) fvkernels/mms/harmonic_interpolation.average/tris: fvkernels/mms/harmonic_interpolation.average/tris: fvkernels/mms/harmonic_interpolation.average/tris: Postprocessor Values: fvkernels/mms/harmonic_interpolation.average/tris: +----------------+----------------+----------------+ fvkernels/mms/harmonic_interpolation.average/tris: | time | error | h | fvkernels/mms/harmonic_interpolation.average/tris: +----------------+----------------+----------------+ fvkernels/mms/harmonic_interpolation.average/tris: | 0.000000e+00 | 0.000000e+00 | 0.000000e+00 | fvkernels/mms/harmonic_interpolation.average/tris: +----------------+----------------+----------------+ fvkernels/mms/harmonic_interpolation.average/tris: fvkernels/mms/harmonic_interpolation.average/tris: 0 Nonlinear |R| = 5.505286e+02 fvkernels/mms/harmonic_interpolation.average/tris: 0 Linear |R| = 5.505286e+02 fvkernels/mms/harmonic_interpolation.average/tris: 1 Linear |R| = 1.178934e+00 fvkernels/mms/harmonic_interpolation.average/tris: 2 Linear |R| = 3.070637e-02 fvkernels/mms/harmonic_interpolation.average/tris: 3 Linear |R| = 1.068884e-03 fvkernels/mms/harmonic_interpolation.average/tris: 1 Nonlinear |R| = 1.068884e-03 fvkernels/mms/harmonic_interpolation.average/tris: 0 Linear |R| = 1.068884e-03 fvkernels/mms/harmonic_interpolation.average/tris: 1 Linear |R| = 3.484288e-05 fvkernels/mms/harmonic_interpolation.average/tris: 2 Linear |R| = 7.812917e-07 fvkernels/mms/harmonic_interpolation.average/tris: 3 Linear |R| = 1.678239e-08 fvkernels/mms/harmonic_interpolation.average/tris: 4 Linear |R| = 4.068220e-10 fvkernels/mms/harmonic_interpolation.average/tris: 2 Nonlinear |R| = 4.068274e-10 fvkernels/mms/harmonic_interpolation.average/tris: Solve Converged! fvkernels/mms/harmonic_interpolation.average/tris: fvkernels/mms/harmonic_interpolation.average/tris: Postprocessor Values: fvkernels/mms/harmonic_interpolation.average/tris: +----------------+----------------+----------------+ fvkernels/mms/harmonic_interpolation.average/tris: | time | error | h | fvkernels/mms/harmonic_interpolation.average/tris: +----------------+----------------+----------------+ fvkernels/mms/harmonic_interpolation.average/tris: | 0.000000e+00 | 0.000000e+00 | 0.000000e+00 | fvkernels/mms/harmonic_interpolation.average/tris: | 1.000000e+00 | 6.037172e-03 | 4.419417e-02 | fvkernels/mms/harmonic_interpolation.average/tris: +----------------+----------------+----------------+ fvkernels/mms/harmonic_interpolation.average/tris: fvkernels/mms/harmonic_interpolation.average/tris: test (test.TestAverageTriangles) ... fvkernels/mms/harmonic_interpolation.average/tris ................................ [FINISHED] FAILED (TIMEOUT)

0 replies

GiudGiud · 2023-12-14T21:39:55Z

GiudGiud
Dec 14, 2023
Collaborator

Hello

Switching to make -j 1 was the right call. Now you can see if make -j 2 ... works, just to save a little time in the future.

You are building on your laptop so probably using mamba to get petsc and libmesh (as a moose-petsc and moose-petsc package).
So you should not run the script to install libmesh from moose/scripts.

A timeout can just mean your laptop is slower than any machine we test with.

Guillaume

0 replies

nhnkkhang · 2023-12-16T16:55:05Z

nhnkkhang
Dec 16, 2023

I have the same issue. I used INL HPC, follow the instruction here: https://mooseframework.inl.gov/moose/getting_started/installation/inl_hpc_install_moose.html. I can run the ./update_and_rebuild_petsc.sh, but when I run: ./update_and_rebuild_libmesh.sh, it return like this

configure: error: cannot find flags to link with the Boost system library (libboost-system)
configure: error: ../../../contrib/metaphysicl/configure failed for contrib/metaphysicl
Running make -j 6...
make: *** No targets specified and no makefile found.  Stop.
` . Then I still tried to build moose and run to the same error: 
`In file included from /home/nguykhan/Work_Moose/moose/framework/build/unity_src/userobjects_Unity.C:55:
/home/nguykhan/Work_Moose/moose/framework/src/userobjects/NodalPatchRecoveryBase.C:18:10: fatal error: libmesh/parallel_eigen.h: No such file or directory
   18 | #include "libmesh/parallel_eigen.h"
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make: *** [/home/nguykhan/Work_Moose/moose/framework/build.mk:150: /home/nguykhan/Work_Moose/moose/framework/build/unity_src/userobjects_Unity.x86_64-pc-linux-gnu.opt.lo] Error 1
make: *** Waiting for unfinished jobs....
In file included from /home/nguykhan/Work_Moose/moose/framework/build/unity_src/utils_Unity.C:2:
/home/nguykhan/Work_Moose/moose/framework/src/utils/ADFParser.C: In member function 'bool ADFParser::JITCompile()':
/home/nguykhan/Work_Moose/moose/framework/src/utils/ADFParser.C:36:30: error: no matching function for call to 'ADFParser::JITCompileHelper(const char [7], const char [1], std::__cxx11::basic_string<char>, const long unsigned int&)'
   36 |     result = JITCompileHelper(
      |              ~~~~~~~~~~~~~~~~^
   37 |         "ADReal", "", "#include \"" + std::string(include_path_env) + "\"\n", type_hash);
      |         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/nguykhan/Work_Moose/moose/framework/build/header_symlinks/ADFParser.h:15,
                 from /home/nguykhan/Work_Moose/moose/framework/src/utils/ADFParser.C:10:
/apps/local/libmesh/1.8.0/include/libmesh/fparser_ad.hh:147:8: note: candidate: 'bool FunctionParserADBase<Value_t>::JITCompileHelper(const std::string&, const std::string&, const std::string&) [with Value_t = double; std::string = std::__cxx11::basic_string<char>]'
  147 |   bool JITCompileHelper(const std::string & Value_t_name,
      |        ^~~~~~~~~~~~~~~~
/apps/local/libmesh/1.8.0/include/libmesh/fparser_ad.hh:147:8: note:   candidate expects 3 arguments, 4 provided
/home/nguykhan/Work_Moose/moose/framework/src/utils/ADFParser.C:44:32: error: no matching function for call to 'ADFParser::JITCompileHelper(const char [7], const char [1], std::__cxx11::basic_string<char>, const long unsigned int&)'
   44 |       result = JITCompileHelper("ADReal", "", "#include \"" + include_path + "\"\n", type_hash);
      |                ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/apps/local/libmesh/1.8.0/include/libmesh/fparser_ad.hh:147:8: note: candidate: 'bool FunctionParserADBase<Value_t>::JITCompileHelper(const std::string&, const std::string&, const std::string&) [with Value_t = double; std::string = std::__cxx11::basic_string<char>]'
  147 |   bool JITCompileHelper(const std::string & Value_t_name,
      |        ^~~~~~~~~~~~~~~~
/apps/local/libmesh/1.8.0/include/libmesh/fparser_ad.hh:147:8: note:   candidate expects 3 arguments, 4 provided
/home/nguykhan/Work_Moose/moose/framework/src/utils/ADFParser.C:47:32: error: no matching function for call to 'ADFParser::JITCompileHelper(const char [7], const char [307], const char [21], const long unsigned int&)'
   47 |       result = JITCompileHelper("ADReal", ADFPARSER_INCLUDES, "#include \"ADReal.h\"\n", type_hash);
      |                ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/apps/local/libmesh/1.8.0/include/libmesh/fparser_ad.hh:147:8: note: candidate: 'bool FunctionParserADBase<Value_t>::JITCompileHelper(const std::string&, const std::string&, const std::string&) [with Value_t = double; std::string = std::__cxx11::basic_string<char>]'
  147 |   bool JITCompileHelper(const std::string & Value_t_name,
      |        ^~~~~~~~~~~~~~~~
/apps/local/libmesh/1.8.0/include/libmesh/fparser_ad.hh:147:8: note:   candidate expects 3 arguments, 4 provided
In file included from /home/nguykhan/Work_Moose/moose/framework/build/unity_src/variables_Unity.C:7:
/home/nguykhan/Work_Moose/moose/framework/src/variables/MooseVariableData.C: In constructor 'MooseVariableData<OutputType>::MooseVariableData(const MooseVariableField<OutputType>&, SystemBase&, THREAD_ID, Moose::ElementType, const libMesh::QBase* const&, const libMesh::QBase* const&, const libMesh::Node* const&, const libMesh::Elem* const&)':
/home/nguykhan/Work_Moose/moose/framework/src/variables/MooseVariableData.C:79:61: error: 'RAVIART_THOMAS' was not declared in this scope
   79 |       _fe_type.family == MONOMIAL_VEC || _fe_type.family == RAVIART_THOMAS)
      |                                                             ^~~~~~~~~~~~~~
In file included from /home/nguykhan/Work_Moose/moose/framework/build/unity_src/systems_Unity.C:2:
/home/nguykhan/Work_Moose/moose/framework/src/systems/AuxiliarySystem.C: In member function 'virtual void AuxiliarySystem::addVariable(const std::string&, const std::string&, InputParameters&)':
/home/nguykhan/Work_Moose/moose/framework/src/systems/AuxiliarySystem.C:234:61: error: 'RAVIART_THOMAS' was not declared in this scope
  234 |         fe_type.family == MONOMIAL_VEC || fe_type.family == RAVIART_THOMAS)
      |                                                             ^~~~~~~~~~~~~~
In file included from /home/nguykhan/Work_Moose/moose/framework/build/unity_src/base_Unity.C:4:
/home/nguykhan/Work_Moose/moose/framework/src/base/Assembly.C: In member function 'void Assembly::buildVectorFE(libMesh::FEType) const':
/home/nguykhan/Work_Moose/moose/framework/src/base/Assembly.C:474:24: error: 'RAVIART_THOMAS' was not declared in this scope
  474 |     if (type.family == RAVIART_THOMAS)
      |                        ^~~~~~~~~~~~~~
/home/nguykhan/Work_Moose/moose/framework/src/base/Assembly.C: In member function 'void Assembly::buildVectorFaceFE(libMesh::FEType) const':
/home/nguykhan/Work_Moose/moose/framework/src/base/Assembly.C:507:24: error: 'RAVIART_THOMAS' was not declared in this scope
  507 |     if (type.family == RAVIART_THOMAS)
      |                        ^~~~~~~~~~~~~~
/home/nguykhan/Work_Moose/moose/framework/src/base/Assembly.C: In member function 'void Assembly::buildVectorNeighborFE(libMesh::FEType) const':
/home/nguykhan/Work_Moose/moose/framework/src/base/Assembly.C:536:24: error: 'RAVIART_THOMAS' was not declared in this scope
  536 |     if (type.family == RAVIART_THOMAS)
      |                        ^~~~~~~~~~~~~~
/home/nguykhan/Work_Moose/moose/framework/src/base/Assembly.C: In member function 'void Assembly::buildVectorFaceNeighborFE(libMesh::FEType) const':
/home/nguykhan/Work_Moose/moose/framework/src/base/Assembly.C:566:24: error: 'RAVIART_THOMAS' was not declared in this scope
  566 |     if (type.family == RAVIART_THOMAS)
      |                        ^~~~~~~~~~~~~~
In file included from /home/nguykhan/Work_Moose/moose/framework/build/unity_src/systems_Unity.C:12:
/home/nguykhan/Work_Moose/moose/framework/src/systems/SystemBase.C: In member function 'virtual void SystemBase::addVariable(const std::string&, const std::string&, InputParameters&)':
/home/nguykhan/Work_Moose/moose/framework/src/systems/SystemBase.C:734:61: error: 'RAVIART_THOMAS' was not declared in this scope
  734 |         fe_type.family == MONOMIAL_VEC || fe_type.family == RAVIART_THOMAS)
      |                                                             ^~~~~~~~~~~~~~
make: *** [/home/nguykhan/Work_Moose/moose/framework/build.mk:150: /home/nguykhan/Work_Moose/moose/framework/build/unity_src/variables_Unity.x86_64-pc-linux-gnu.opt.lo] Error 1
make: *** [/home/nguykhan/Work_Moose/moose/framework/build.mk:150: /home/nguykhan/Work_Moose/moose/framework/build/unity_src/base_Unity.x86_64-pc-linux-gnu.opt.lo] Error 1
make: *** [/home/nguykhan/Work_Moose/moose/framework/build.mk:150: /home/nguykhan/Work_Moose/moose/framework/build/unity_src/systems_Unity.x86_64-pc-linux-gnu.opt.lo] Error 1
make: *** [/home/nguykhan/Work_Moose/moose/framework/build.mk:150: /home/nguykhan/Work_Moose/moose/framework/build/unity_src/utils_Unity.x86_64-pc-linux-gnu.opt.lo] Error 1

What should I do in this case?

2 replies

GiudGiud Dec 16, 2023
Collaborator

Hello

Which MPI modules did you load?
You can type 'module list' or run the diagnostics script in moose/scripts to get that

Guillaume

nhnkkhang Dec 16, 2023

Thank you for your support!
I resolved the issue. Apparently, I have a local libmesh (different version with MOOSE), that caused the issue.

lvkas521424 · 2024-04-21T10:38:41Z

lvkas521424
Apr 21, 2024

Hello, @GiudGiud also encountered the issue of "XDR not found" while installing on HPC,
Running make - j 6
Make: * * * * No targets specified and no makefiles found stop

lvkas

1 reply

GiudGiud Apr 21, 2024
Collaborator

Hello

You can pass a flag to install without it. It's tied to checkpointing, XDR is the binary format
we are actually supporting a non-binary (ascii) format that had the same performance pretty much

Or you need to install libtirpc-devel on your cluster.

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Setup issue: Test timeout, LibMesh version blank. #26345

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Setup issue: Test timeout, LibMesh version blank. #26345

calebfowler-tamu Dec 14, 2023

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