error: "PETSc was configured with MPICH but now appears to be compiling using a non-MPICH mpi.h" and missing modules pyaml, jinja2

[smpeyres]

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Issue or question about MOOSE

I am trying to compile MOOSE on Apple Silicon (M1), but I get this error on multiple occurrences after running make -j8 in tests. Seems that similar posts are trying to compile on HPC, not me. I completely removed conda and re-installed, current version is 24.9.1

I ran diagnostics.sh, and it looks like my python is not up to date and I missing some packages like pyaml and jinja2.

How do I update python and update these modules and fix this error? I attached the error and diagnostic output

(Optional) code in question / simulation log / errors

(moose) wirelessprv-10-192-133-5:test seanpeyres$ make -j8
WARNING: Failed to initialize PreMake for version checking; this may be ignored but may suggest an environment issue.

Traceback (most recent call last):
  File "/Users/seanpeyres/moose-projects/moose/framework/../scripts/premake.py", line 20, in __init__
    from versioner import Versioner
  File "/Users/seanpeyres/moose-projects/moose/scripts/versioner.py", line 25, in <module>
    import yaml
ModuleNotFoundError: No module named 'yaml'

Traceback (most recent call last):
  File "/Users/seanpeyres/moose-projects/moose/framework/../scripts/premake.py", line 261, in <module>
    PreMake().check()
    ^^^^^^^^^
  File "/Users/seanpeyres/moose-projects/moose/framework/../scripts/premake.py", line 27, in __init__
    self.versioner_meta = Versioner().version_meta()
                          ^^^^^^^^^
UnboundLocalError: cannot access local variable 'Versioner' where it is not associated with a value
make: [/Users/seanpeyres/moose-projects/moose/framework/moose.mk:399: prebuild] Error 1 (ignored)
Compiling C++ (in opt mode) /Users/seanpeyres/moose-projects/moose/framework/build/unity_src/linesearches_Unity.C...
Compiling C++ (in opt mode) /Users/seanpeyres/moose-projects/moose/framework/build/unity_src/mesh_Unity.C...
Compiling C++ (in opt mode) /Users/seanpeyres/moose-projects/moose/framework/build/unity_src/fvics_Unity.C...
Compiling C++ (in opt mode) /Users/seanpeyres/moose-projects/moose/framework/build/unity_src/auxkernels_Unity.C...
Compiling C++ (in opt mode) /Users/seanpeyres/moose-projects/moose/framework/build/unity_src/kernels_Unity.C...
Compiling C++ (in opt mode) /Users/seanpeyres/moose-projects/moose/framework/build/unity_src/executioners_Unity.C...
Compiling C++ (in opt mode) /Users/seanpeyres/moose-projects/moose/framework/build/unity_src/bounds_Unity.C...
Compiling C++ (in opt mode) /Users/seanpeyres/moose-projects/moose/framework/build/unity_src/scalarkernels_Unity.C...
In file included from /Users/seanpeyres/moose-projects/moose/framework/build/unity_src/mesh_Unity.C:2:
In file included from /Users/seanpeyres/moose-projects/moose/framework/src/mesh/AnnularMesh.C:10:
In file included from /Users/seanpeyres/moose-projects/moose/framework/build/header_symlinks/AnnularMesh.h:12:
In file included from /Users/seanpeyres/moose-projects/moose/framework/build/header_symlinks/MooseMesh.h:12:
In file included from /Users/seanpeyres/moose-projects/moose/framework/build/header_symlinks/MooseObject.h:13:
In file included from /Users/seanpeyres/moose-projects/moose/framework/build/header_symlinks/MooseUtils.h:13:
In file included from /Users/seanpeyres/moose-projects/moose/framework/build/header_symlinks/MooseTypes.h:26:
In file included from /Users/seanpeyres/miniforge/envs/moose/libmesh/include/libmesh/petsc_macro.h:56:
In file included from /Users/seanpeyres/miniforge/envs/moose/petsc/include/petsc.h:6:
In file included from /Users/seanpeyres/miniforge/envs/moose/petsc/include/petscbag.h:3:
/Users/seanpeyres/miniforge/envs/moose/petsc/include/petscsys.h:92:6: error: "PETSc was configured with MPICH but now appears to be compiling using a non-MPICH mpi.h"
    #error "PETSc was configured with MPICH but now appears to be compiling using a non-MPICH mpi.h"
     ^
In file included from /Users/seanpeyres/moose-projects/moose/framework/build/unity_src/executioners_Unity.C:2:
In file included from /Users/seanpeyres/moose-projects/moose/framework/src/executioners/EigenExecutionerBase.C:10:
In file included from /Users/seanpeyres/moose-projects/moose/framework/build/header_symlinks/EigenExecutionerBase.h:12:
In file included from /Users/seanpeyres/moose-projects/moose/framework/build/header_symlinks/Executioner.h:12:
In file included from /Users/seanpeyres/moose-projects/moose/framework/build/header_symlinks/MooseObject.h:13:
In file included from /Users/seanpeyres/moose-projects/moose/framework/build/header_symlinks/MooseUtils.h:13:
In file included from /Users/seanpeyres/moose-projects/moose/framework/build/header_symlinks/MooseTypes.h:26:
In file included from /Users/seanpeyres/miniforge/envs/moose/libmesh/include/libmesh/petsc_macro.h:56:
In file included from /Users/seanpeyres/miniforge/envs/moose/petsc/include/petsc.h:6:
In file included from /Users/seanpeyres/miniforge/envs/moose/petsc/include/petscbag.h:3:
/Users/seanpeyres/miniforge/envs/moose/petsc/include/petscsys.h:92:6: error: "PETSc was configured with MPICH but now appears to be compiling using a non-MPICH mpi.h"
    #error "PETSc was configured with MPICH but now appears to be compiling using a non-MPICH mpi.h"
     ^
In file included from /Users/seanpeyres/moose-projects/moose/framework/build/unity_src/kernels_Unity.C:2:
In file included from /Users/seanpeyres/moose-projects/moose/framework/src/kernels/ADConservativeAdvection.C:10:
In file included from /Users/seanpeyres/moose-projects/moose/framework/build/header_symlinks/ADConservativeAdvection.h:12:
In file included from /Users/seanpeyres/moose-projects/moose/framework/build/header_symlinks/ADKernel.h:12:
In file included from /Users/seanpeyres/moose-projects/moose/framework/build/header_symlinks/KernelBase.h:12:
In file included from /Users/seanpeyres/moose-projects/moose/framework/build/header_symlinks/ResidualObject.h:12:
In file included from /Users/seanpeyres/moose-projects/moose/framework/build/header_symlinks/MooseObject.h:13:
In file included from /Users/seanpeyres/moose-projects/moose/framework/build/header_symlinks/MooseUtils.h:13:
In file included from /Users/seanpeyres/moose-projects/moose/framework/build/header_symlinks/MooseTypes.h:26:
In file included from /Users/seanpeyres/miniforge/envs/moose/libmesh/include/libmesh/petsc_macro.h:56:
In file included from /Users/seanpeyres/miniforge/envs/moose/petsc/include/petsc.h:6:
In file included from /Users/seanpeyres/miniforge/envs/moose/petsc/include/petscbag.h:3:
/Users/seanpeyres/miniforge/envs/moose/petsc/include/petscsys.h:92:6: error: "PETSc was configured with MPICH but now appears to be compiling using a non-MPICH mpi.h"
In file included from /Users/seanpeyres/moose-projects/moose/framework/build/unity_src/scalarkernels_Unity.C:2:
In file included from /Users/seanpeyres/moose-projects/moose/framework/src/scalarkernels/ADScalarKernel.C:10:
In file included from /Users/seanpeyres/moose-projects/moose/framework/build/header_symlinks/ADScalarKernel.h:12:
In file included from /Users/seanpeyres/moose-projects/moose/framework/build/header_symlinks/ScalarKernelBase.h:12:
In file included from /Users/seanpeyres/moose-projects/moose/framework/build/header_symlinks/ResidualObject.h:12    #error "PETSc was configured with MPICH but now appears to be compiling using a non-MPICH mpi.h":

In file included from /Users/seanpeyres/moose-projects/moose/framework/build/header_symlinks/MooseObject.h     ^:
13:
In file included from /Users/seanpeyres/moose-projects/moose/framework/build/header_symlinks/MooseUtils.h:13:
In file included from /Users/seanpeyres/moose-projects/moose/framework/build/header_symlinks/MooseTypes.h:26:
In file included from /Users/seanpeyres/miniforge/envs/moose/libmesh/include/libmesh/petsc_macro.h:56:
In file included from /Users/seanpeyres/miniforge/envs/moose/petsc/include/petsc.h:6:
In file included from /Users/seanpeyres/miniforge/envs/moose/petsc/include/petscbag.h:3:
/Users/seanpeyres/miniforge/envs/moose/petsc/include/petscsys.h:92:6: error: "PETSc was configured with MPICH but now appears to be compiling using a non-MPICH mpi.h"
    #error "PETSc was configured with MPICH but now appears to be compiling using a non-MPICH mpi.h"
     ^
In file included from /Users/seanpeyres/moose-projects/moose/framework/build/unity_src/linesearches_Unity.C:2:
In file included from /Users/seanpeyres/moose-projects/moose/framework/src/linesearches/LineSearch.C:10:
In file included from /Users/seanpeyres/moose-projects/moose/framework/build/header_symlinks/LineSearch.h:12:
In file included from /Users/seanpeyres/moose-projects/moose/framework/build/header_symlinks/MooseObject.h:13:
In file included from /Users/seanpeyres/moose-projects/moose/framework/build/header_symlinks/MooseUtils.h:13:
In file included from /Users/seanpeyres/moose-projects/moose/framework/build/header_symlinks/MooseTypes.h:26:
In file included from /Users/seanpeyres/miniforge/envs/moose/libmesh/include/libmesh/petsc_macro.h:56:
In file included from /Users/seanpeyres/miniforge/envs/moose/petsc/include/petsc.h:6:
In file included from /Users/seanpeyres/miniforge/envs/moose/petsc/include/petscbag.h:3:
/Users/seanpeyres/miniforge/envs/moose/petsc/include/petscsys.h:92:6: error: "PETSc was configured with MPICH but now appears to be compiling using a non-MPICH mpi.h"
    #error "PETSc was configured with MPICH but now appears to be compiling using a non-MPICH mpi.h"
     ^
In file included from /Users/seanpeyres/moose-projects/moose/framework/build/unity_src/auxkernels_Unity.C:2:
In file included from /Users/seanpeyres/moose-projects/moose/framework/src/auxkernels/AdvectiveFluxAux.C:10:
In file included from /Users/seanpeyres/moose-projects/moose/framework/build/header_symlinks/AdvectiveFluxAux.h:12:
In file included from /Users/seanpeyres/moose-projects/moose/framework/build/header_symlinks/AuxKernel.h:12:
In file included from /Users/seanpeyres/moose-projects/moose/framework/build/header_symlinks/MooseObject.h:13:
In file included from /Users/seanpeyres/moose-projects/moose/framework/build/header_symlinks/MooseUtils.h:13:
In file included from /Users/seanpeyres/moose-projects/moose/framework/build/header_symlinks/MooseTypes.h:26:
In file included from /Users/seanpeyres/miniforge/envs/moose/libmesh/include/libmesh/petsc_macro.h:56:
In file included from /Users/seanpeyres/miniforge/envs/moose/petsc/include/petsc.h:6:
In file included from /Users/seanpeyres/miniforge/envs/moose/petsc/include/petscbag.h:3:
/Users/seanpeyres/miniforge/envs/moose/petsc/include/petscsys.h:92:6: error: "PETSc was configured with MPICH but now appears to be compiling using a non-MPICH mpi.h"
    #error "PETSc was configured with MPICH but now appears to be compiling using a non-MPICH mpi.h"
     ^
In file included from /Users/seanpeyres/moose-projects/moose/framework/build/unity_src/bounds_Unity.C:2:
In file included from /Users/seanpeyres/moose-projects/moose/framework/src/bounds/BoundsBase.C:10:
In file included from /Users/seanpeyres/moose-projects/moose/framework/build/header_symlinks/BoundsBase.h:12:
In file included from /Users/seanpeyres/moose-projects/moose/framework/build/header_symlinks/AuxKernel.h:12:
In file included from /Users/seanpeyres/moose-projects/moose/framework/build/header_symlinks/MooseObject.h:13:
In file included from /Users/seanpeyres/moose-projects/moose/framework/build/header_symlinks/MooseUtils.h:13:
In file included from /Users/seanpeyres/moose-projects/moose/framework/build/header_symlinks/MooseTypes.h:26:
In file included from /Users/seanpeyres/miniforge/envs/moose/libmesh/include/libmesh/petsc_macro.h:56:
In file included from /Users/seanpeyres/miniforge/envs/moose/petsc/include/petsc.h:6:
In file included from /Users/seanpeyres/miniforge/envs/moose/petsc/include/petscbag.h:3:
/Users/seanpeyres/miniforge/envs/moose/petsc/include/petscsys.h:92:6: error: "PETSc was configured with MPICH but now appears to be compiling using a non-MPICH mpi.h"
    #error "PETSc was configured with MPICH but now appears to be compiling using a non-MPICH mpi.h"
     ^
In file included from /Users/seanpeyres/moose-projects/moose/framework/build/unity_src/fvics_Unity.C:2:
In file included from /Users/seanpeyres/moose-projects/moose/framework/src/fvics/FVConstantIC.C:10:
In file included from /Users/seanpeyres/moose-projects/moose/framework/build/header_symlinks/FVConstantIC.h:12:
In file included from /Users/seanpeyres/moose-projects/moose/framework/build/header_symlinks/FVInitialConditionTempl.h:12:
In file included from /Users/seanpeyres/moose-projects/moose/framework/build/header_symlinks/FVInitialConditionBase.h:12:
In file included from /Users/seanpeyres/moose-projects/moose/framework/build/header_symlinks/MooseObject.h:13:
In file included from /Users/seanpeyres/moose-projects/moose/framework/build/header_symlinks/MooseUtils.h:13:
In file included from /Users/seanpeyres/moose-projects/moose/framework/build/header_symlinks/MooseTypes.h:26:
In file included from /Users/seanpeyres/miniforge/envs/moose/libmesh/include/libmesh/petsc_macro.h:56:
In file included from /Users/seanpeyres/miniforge/envs/moose/petsc/include/petsc.h:6:
In file included from /Users/seanpeyres/miniforge/envs/moose/petsc/include/petscbag.h:3:
/Users/seanpeyres/miniforge/envs/moose/petsc/include/petscsys.h:92:6: error: "PETSc was configured with MPICH but now appears to be compiling using a non-MPICH mpi.h"
    #error "PETSc was configured with MPICH but now appears to be compiling using a non-MPICH mpi.h"
     ^
1 error generated.
make: *** [/Users/seanpeyres/moose-projects/moose/framework/build.mk:151: /Users/seanpeyres/moose-projects/moose/framework/build/unity_src/linesearches_Unity.aarch64-apple-darwin20.0.0.opt.lo] Error 1
make: *** Waiting for unfinished jobs....
1 error generated.
1 error generated.
make: *** [/Users/seanpeyres/moose-projects/moose/framework/build.mk:151: /Users/seanpeyres/moose-projects/moose/framework/build/unity_src/executioners_Unity.aarch64-apple-darwin20.0.0.opt.lo] Error 1
make: *** [/Users/seanpeyres/moose-projects/moose/framework/build.mk:151: /Users/seanpeyres/moose-projects/moose/framework/build/unity_src/bounds_Unity.aarch64-apple-darwin20.0.0.opt.lo] Error 1
1 error generated.
make: *** [/Users/seanpeyres/moose-projects/moose/framework/build.mk:151: /Users/seanpeyres/moose-projects/moose/framework/build/unity_src/fvics_Unity.aarch64-apple-darwin20.0.0.opt.lo] Error 1
1 error generated.
make: *** [/Users/seanpeyres/moose-projects/moose/framework/build.mk:151: /Users/seanpeyres/moose-projects/moose/framework/build/unity_src/scalarkernels_Unity.aarch64-apple-darwin20.0.0.opt.lo] Error 1
1 error generated.
make: *** [/Users/seanpeyres/moose-projects/moose/framework/build.mk:151: /Users/seanpeyres/moose-projects/moose/framework/build/unity_src/kernels_Unity.aarch64-apple-darwin20.0.0.opt.lo] Error 1
1 error generated.
make: *** [/Users/seanpeyres/moose-projects/moose/framework/build.mk:151: /Users/seanpeyres/moose-projects/moose/framework/build/unity_src/mesh_Unity.aarch64-apple-darwin20.0.0.opt.lo] Error 1
1 error generated.
make: *** [/Users/seanpeyres/moose-projects/moose/framework/build.mk:151: /Users/seanpeyres/moose-projects/moose/framework/build/unity_src/auxkernels_Unity.aarch64-apple-darwin20.0.0.opt.lo] Error 1

Encountering Errors? Please include diagnostic output

(moose) wirelessprv-10-192-133-5:scripts seanpeyres$ bash diagnostics.sh
################################################################################
Influential Environment Variables

CC=mpicc
CC_FOR_BUILD=/Users/seanpeyres/miniforge/envs/moose/bin/arm64-apple-darwin20.0.0-clang
CFLAGS= -fPIC -fstack-protector-strong  -pipe -isystem /Users/seanpeyres/miniforge/envs/moose/include 
CONDA_CHANNEL=https://conda.software.inl.gov/public
CONDA_DEFAULT_ENV=moose
CONDA_EXE=/Users/seanpeyres/miniforge/bin/conda
CONDA_PREFIX=/Users/seanpeyres/miniforge/envs/moose
CONDA_PREFIX_1=/Users/seanpeyres/miniforge
CONDA_PROMPT_MODIFIER=(moose) 
CONDA_PYTHON_EXE=/Users/seanpeyres/miniforge/bin/python
CONDA_SHLVL=2
CONDA_TOOLCHAIN_BUILD=arm64-apple-darwin20.0.0
CONDA_TOOLCHAIN_HOST=arm64-apple-darwin20.0.0
CPPFLAGS= -isystem /Users/seanpeyres/miniforge/envs/moose/include -mmacosx-version-min=11.3 
CURL_CA_BUNDLE=
CXX=mpicxx
CXXFLAGS= -fPIC -fstack-protector-strong  -pipe -stdlib=libc++ -fvisibility-inlines-hidden -fmessage-length=0 -isystem /Users/seanpeyres/miniforge/envs/moose/include  -std=c++17
CXX_FOR_BUILD=/Users/seanpeyres/miniforge/envs/moose/bin/arm64-apple-darwin20.0.0-clang++
F77=mpif77
F90=mpif90
F95=/Users/seanpeyres/miniforge/envs/moose/bin/arm64-apple-darwin20.0.0-gfortran
FC=mpif90
FC_FOR_BUILD=/Users/seanpeyres/miniforge/envs/moose/bin/arm64-apple-darwin20.0.0-gfortran
FFLAGS=  -fPIC   -pipe -isystem /Users/seanpeyres/miniforge/envs/moose/include 
FI_PROVIDER=tcp
HDF5_DIR=/Users/seanpeyres/miniforge/envs/moose
LD=arm64-apple-darwin20.0.0-ld
LDFLAGS=-Wl,-headerpad_max_install_names  -Wl,-rpath,/Users/seanpeyres/miniforge/envs/moose/lib -L/Users/seanpeyres/miniforge/envs/moose/lib  -Wl,-ld_classic -Wl,-commons,use_dylibs
LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath /Users/seanpeyres/miniforge/envs/moose/lib -L/Users/seanpeyres/miniforge/envs/moose/lib
LIBMESH_DIR=/Users/seanpeyres/miniforge/envs/moose/libmesh
MOOSE_JOBS=6
MOOSE_NO_CODESIGN=true
PATH=/Users/seanpeyres/.cargo/bin:/Users/seanpeyres/.juliaup/bin:/opt/homebrew/bin:/Users/seanpeyres/miniforge/envs/moose/bin:/Users/seanpeyres/miniforge/condabin:/usr/local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/local/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/appleinternal/bin:/Library/TeX/texbin:/Users/seanpeyres/miniforge/envs/moose/wasp/bin
PETSC_DIR=/Users/seanpeyres/miniforge/envs/moose/petsc
REQUESTS_CA_BUNDLE=
SSL_CERT_FILE=
WASP_DIR=/Users/seanpeyres/miniforge/envs/moose/wasp
################################################################################
Compiler(s) (CC CXX FC F77 F90):

which $CC; /opt/homebrew/bin/mpicc
$CC --version; clang version 16.0.6
$CC -show; clang -I/opt/homebrew/Cellar/open-mpi/5.0.3_1/include -L/opt/homebrew/Cellar/open-mpi/5.0.3_1/lib -lmpi

which $CXX; /opt/homebrew/bin/mpicxx
$CXX --version; clang version 16.0.6
$CXX -show; clang++ -I/opt/homebrew/Cellar/open-mpi/5.0.3_1/include -L/opt/homebrew/Cellar/open-mpi/5.0.3_1/lib -lmpi

which $FC; /opt/homebrew/bin/mpif90
$FC --version; GNU Fortran (Homebrew GCC 14.2.0) 14.2.0
$FC -show; gfortran -I/opt/homebrew/Cellar/open-mpi/5.0.3_1/include -Wl,-flat_namespace -Wl,-commons,use_dylibs -Wl,-ld_classic -I/opt/homebrew/Cellar/open-mpi/5.0.3_1/lib -L/opt/homebrew/Cellar/open-mpi/5.0.3_1/lib -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi

which $F77; /opt/homebrew/bin/mpif77
$F77 --version; GNU Fortran (Homebrew GCC 14.2.0) 14.2.0
$F77 -show; gfortran -I/opt/homebrew/Cellar/open-mpi/5.0.3_1/include -Wl,-flat_namespace -Wl,-commons,use_dylibs -Wl,-ld_classic -I/opt/homebrew/Cellar/open-mpi/5.0.3_1/lib -L/opt/homebrew/Cellar/open-mpi/5.0.3_1/lib -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi

which $F90; /opt/homebrew/bin/mpif90
$F90 --version; GNU Fortran (Homebrew GCC 14.2.0) 14.2.0
$F90 -show; gfortran -I/opt/homebrew/Cellar/open-mpi/5.0.3_1/include -Wl,-flat_namespace -Wl,-commons,use_dylibs -Wl,-ld_classic -I/opt/homebrew/Cellar/open-mpi/5.0.3_1/lib -L/opt/homebrew/Cellar/open-mpi/5.0.3_1/lib -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi

OK
################################################################################
Python Sanity Checks

/usr/bin/env python3 --version; (reporting as: Python 3.12.5) matches
which python3 python;

/opt/homebrew/bin/python3 --version; == Python 3.12.5
FAIL: /Users/seanpeyres/miniforge/envs/moose/bin/python --version (reporting as Python 3.11.8)) != Python 3.12.5

This will likely result in the TestHarness failing. Or WASP/HIT parsing errors.
################################################################################
Python Modules (TestHarness, run-ability)


WARNING: missing module(s): pyaml jinja2 

Either install the above packages, or perhaps you have yet
to activate the moose environment: conda activate moose

Missing 'warning' Python modules may cause miscellaneous runtime issues.

WARNING: One or more Python issues present.
################################################################################
MOOSE Repository/Conda Version Checks

WARNING: Unable to run Conda tests due to missing Python modules


checks FAILED

[GiudGiud]

hello

conda install pyaml jinja2
should solve that problem

the other problem, with mpi, stems from having multiple mpi distributions installed on your system.
You should set CC, CXX, FC to the mpicc mpicxx and mpif90 brought in by conda.

Right now it must be finding the compilers from your systme

Guillaume

[smpeyres]

When I run conda install pyaml jinja2, I get the following output:

Channels:
 - https://conda.software.inl.gov/public
 - conda-forge
Platform: osx-arm64
Collecting package metadata (repodata.json): done
Solving environment: done

# All requested packages already installed.

When I run diagnostics.sh, the same error occurs.

Any thoughts?

[GiudGiud]

ah so conda is well setup
but you homebrew python is being found instead of the conda python

/opt/homebrew/bin/python3 --version; == Python 3.12.5

same remedy, set the PATH to find the conda python first

[smpeyres]

Okay, how do I do this?

Also, if I set the PATH to find conda python first, will it bother anything else? For example, if I naively try brew uninstall python, it warns me that there are a handful of modules/packages (gnuplot, scipy, matplotlib, etc...) that depend on python, so it doesn't uninstall it. I don't want these modules/packages to be unable to find the conda python.

[GiudGiud]

You might have to switch back and forth if other packages need your brew python.

This is the problem with brew. It does not compartmentalize at all. With conda you can de-activate the environment if you no longer want to use it, with brew you can't

[smpeyres]

Interesting. I have both PATH's in my bash_profile, and I just comment out the one I'm not using (in this case, brew). This seemed to work fine as make -j8 had no further issues and bash diagnostics.sh also reported that everything looked OK.

When I run the tests, I get a handful of errors for controls/web_server_control:

controls/web_server_control.control/bool ...................................................... FAILED (CRASH)
controls/web_server_control.control/real ...................................................... FAILED (CRASH)
controls/web_server_control.control/int ....................................................... FAILED (CRASH)
controls/web_server_control.control/string .................................................... FAILED (CRASH)
controls/web_server_control.control/vec_real .................................................. FAILED (CRASH)
controls/web_server_control.control/vec_int ................................................... FAILED (CRASH)
controls/web_server_control.control/vec_string ................................................ FAILED (CRASH)
controls/web_server_control.get_postprocessor ................................................. FAILED (CRASH)
controls/web_server_control.parallel_consistent .................................. [min_cpus=2] FAILED (CRASH)
controls/web_server_control.errors/set_controllable_no_exist ................. FAILED (EXPECTED ERROR MISSING)
controls/web_server_control.errors/postprocessor_no_exist .................... FAILED (EXPECTED ERROR MISSING)
controls/web_server_control.errors/set_controllable_unregistered_type ........ FAILED (EXPECTED ERROR MISSING)
controls/web_server_control.errors/set_controllable_bad_convert_json ......... FAILED (EXPECTED ERROR MISSING)
controls/web_server_control.errors/set_controllable_vector_non_array ......... FAILED (EXPECTED ERROR MISSING)
--------------------------------------------------------------------------------------------------------------
Ran 4446 tests in 469.0 seconds. Average test time 0.5 seconds, maximum test time 28.6 seconds.
4432 passed, 120 skipped, 0 pending, 14 FAILED

These failures don't look like the would inhibit the use of MOOSE, but I just want to make sure I'm not missing any other crucial dependencies. Please let me know if I should open a separate discussion for this.

Below is an example of how it shows up during the testing sequence:

controls/web_server_control.errors/set_controllable_bad_convert_json: Working Directory: /Users/seanpeyres/moose-projects/moose/test/tests/controls/web_server_control
controls/web_server_control.errors/set_controllable_bad_convert_json: Running command: RUNAPP_COMMAND="/Users/seanpeyres/moose-projects/moose/test/moose_test-opt -i wait_initial.i Outputs/json/type=JSON --error --error-override --libtorch-device cpu" /Users/seanpeyres/moose-projects/moose/test/tests/controls/web_server_control/errors.py set_controllable_bad_convert
controls/web_server_control.errors/set_controllable_bad_convert_json: MooseControl: Determined file socket /var/folders/gk/ymz0v5rs0z962fcgr2zm40pw0000gn/T/moose_control_h49yxm for communication
controls/web_server_control.errors/set_controllable_bad_convert_json: MooseControl: Spawning MOOSE with command "['/Users/seanpeyres/moose-projects/moose/test/moose_test-opt', '-i', 'wait_initial.i', 'Outputs/json/type=JSON', '--error', '--error-override', '--libtorch-device', 'cpu', 'Controls/web_server/file_socket=/var/folders/gk/ymz0v5rs0z962fcgr2zm40pw0000gn/T/moose_control_h49yxm']"
controls/web_server_control.errors/set_controllable_bad_convert_json: MooseControl: Waiting for the webserver to start on "http+unix:///var/folders/gk/ymz0v5rs0z962fcgr2zm40pw0000gn/T/moose_control_h49yxm"
controls/web_server_control.errors/set_controllable_bad_convert_json: Traceback (most recent call last):
controls/web_server_control.errors/set_controllable_bad_convert_json:   File "/Users/seanpeyres/miniforge/envs/moose/lib/python3.11/encodings/idna.py", line 165, in encode
controls/web_server_control.errors/set_controllable_bad_convert_json:     raise UnicodeError("label too long")
controls/web_server_control.errors/set_controllable_bad_convert_json: UnicodeError: label too long
controls/web_server_control.errors/set_controllable_bad_convert_json: 
controls/web_server_control.errors/set_controllable_bad_convert_json: The above exception was the direct cause of the following exception:
controls/web_server_control.errors/set_controllable_bad_convert_json: 
controls/web_server_control.errors/set_controllable_bad_convert_json: Traceback (most recent call last):
controls/web_server_control.errors/set_controllable_bad_convert_json:   File "/Users/seanpeyres/moose-projects/moose/test/tests/controls/web_server_control/errors.py", line 23, in <module>
controls/web_server_control.errors/set_controllable_bad_convert_json:     base_controller('web_server', run_control)
controls/web_server_control.errors/set_controllable_bad_convert_json:   File "/Users/seanpeyres/moose-projects/moose/test/tests/controls/web_server_control/base_controller.py", line 29, in base_controller
controls/web_server_control.errors/set_controllable_bad_convert_json:     control.initialize()
controls/web_server_control.errors/set_controllable_bad_convert_json:   File "/Users/seanpeyres/moose-projects/moose/python/MooseControl/MooseControl.py", line 287, in initialize
controls/web_server_control.errors/set_controllable_bad_convert_json:     if self.isListening():
controls/web_server_control.errors/set_controllable_bad_convert_json:        ^^^^^^^^^^^^^^^^^^
controls/web_server_control.errors/set_controllable_bad_convert_json:   File "/Users/seanpeyres/moose-projects/moose/python/MooseControl/MooseControl.py", line 214, in isListening
controls/web_server_control.errors/set_controllable_bad_convert_json:     r = self._requests_get(f'{self._url}/check')
controls/web_server_control.errors/set_controllable_bad_convert_json:         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
controls/web_server_control.errors/set_controllable_bad_convert_json:   File "/Users/seanpeyres/moose-projects/moose/python/MooseControl/MooseControl.py", line 143, in _requests_get
controls/web_server_control.errors/set_controllable_bad_convert_json:     return self._requests_wrapper('get', *args, **kwargs)
controls/web_server_control.errors/set_controllable_bad_convert_json:            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
controls/web_server_control.errors/set_controllable_bad_convert_json:   File "/Users/seanpeyres/moose-projects/moose/python/MooseControl/MooseControl.py", line 139, in _requests_wrapper
controls/web_server_control.errors/set_controllable_bad_convert_json:     return getattr(accessor, function_name)(*args, **kwargs)
controls/web_server_control.errors/set_controllable_bad_convert_json:            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
controls/web_server_control.errors/set_controllable_bad_convert_json:   File "/Users/seanpeyres/miniforge/envs/moose/lib/python3.11/site-packages/requests/sessions.py", line 602, in get
controls/web_server_control.errors/set_controllable_bad_convert_json:     return self.request("GET", url, **kwargs)
controls/web_server_control.errors/set_controllable_bad_convert_json:            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
controls/web_server_control.errors/set_controllable_bad_convert_json:   File "/Users/seanpeyres/miniforge/envs/moose/lib/python3.11/site-packages/requests/sessions.py", line 579, in request
controls/web_server_control.errors/set_controllable_bad_convert_json:     settings = self.merge_environment_settings(
controls/web_server_control.errors/set_controllable_bad_convert_json:                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
controls/web_server_control.errors/set_controllable_bad_convert_json:   File "/Users/seanpeyres/miniforge/envs/moose/lib/python3.11/site-packages/requests/sessions.py", line 760, in merge_environment_settings
controls/web_server_control.errors/set_controllable_bad_convert_json:     env_proxies = get_environ_proxies(url, no_proxy=no_proxy)
controls/web_server_control.errors/set_controllable_bad_convert_json:                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
controls/web_server_control.errors/set_controllable_bad_convert_json:   File "/Users/seanpeyres/miniforge/envs/moose/lib/python3.11/site-packages/requests/utils.py", line 832, in get_environ_proxies
controls/web_server_control.errors/set_controllable_bad_convert_json:     if should_bypass_proxies(url, no_proxy=no_proxy):
controls/web_server_control.errors/set_controllable_bad_convert_json:        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
controls/web_server_control.errors/set_controllable_bad_convert_json:   File "/Users/seanpeyres/miniforge/envs/moose/lib/python3.11/site-packages/requests/utils.py", line 816, in should_bypass_proxies
controls/web_server_control.errors/set_controllable_bad_convert_json:     bypass = proxy_bypass(parsed.hostname)
controls/web_server_control.errors/set_controllable_bad_convert_json:              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
controls/web_server_control.errors/set_controllable_bad_convert_json:   File "/Users/seanpeyres/miniforge/envs/moose/lib/python3.11/urllib/request.py", line 2660, in proxy_bypass
controls/web_server_control.errors/set_controllable_bad_convert_json:     return proxy_bypass_macosx_sysconf(host)
controls/web_server_control.errors/set_controllable_bad_convert_json:            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
controls/web_server_control.errors/set_controllable_bad_convert_json:   File "/Users/seanpeyres/miniforge/envs/moose/lib/python3.11/urllib/request.py", line 2637, in proxy_bypass_macosx_sysconf
controls/web_server_control.errors/set_controllable_bad_convert_json:     return _proxy_bypass_macosx_sysconf(host, proxy_settings)
controls/web_server_control.errors/set_controllable_bad_convert_json:            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
controls/web_server_control.errors/set_controllable_bad_convert_json:   File "/Users/seanpeyres/miniforge/envs/moose/lib/python3.11/urllib/request.py", line 2605, in _proxy_bypass_macosx_sysconf
controls/web_server_control.errors/set_controllable_bad_convert_json:     hostIP = socket.gethostbyname(hostonly)
controls/web_server_control.errors/set_controllable_bad_convert_json:              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
controls/web_server_control.errors/set_controllable_bad_convert_json: UnicodeError: encoding with 'idna' codec failed (UnicodeError: label too long)
controls/web_server_control.errors/set_controllable_bad_convert_json: ################################################################################
controls/web_server_control.errors/set_controllable_bad_convert_json: 
controls/web_server_control.errors/set_controllable_bad_convert_json: Unable to match the following pattern against the program's output:
controls/web_server_control.errors/set_controllable_bad_convert_json: 
controls/web_server_control.errors/set_controllable_bad_convert_json: The value "foo" of JSON type string is not of the expected JSON type bool
controls/web_server_control.errors/set_controllable_bad_convert_json: 
controls/web_server_control.errors/set_controllable_bad_convert_json: ################################################################################
controls/web_server_control.errors/set_controllable_bad_convert_json: Tester failed, reason: EXPECTED ERROR MISSING
controls/web_server_control.errors/set_controllable_bad_convert_json: 
controls/web_server_control.errors/set_controllable_bad_convert_json ......... FAILED (EXPECTED ERROR MISSING)

[GiudGiud]

you can skip that one for now, unless you are planning to use it specifically.
it would require some modifications to get this 'label' shorter

[smpeyres]

Don't plan on it, so I'll stop here. Thank you for the help!

[bplcn]

Hi,

I face the same error "PETSc was configured with MPICH but now appears to be compiling using a non-MPICH mpi.h" when install moose on M3 Mac.

/opt/homebrew/Caskroom/miniconda/base/envs/moose/petsc/include/petscsys.h:94:6: error: "PETSc was configured with MPICH but now appears to be compiling using a non-MPICH mpi.h"

And the complier of the mpi is

$CC -show; clang -I/opt/homebrew/Cellar/open-mpi/5.0.6/include -L/opt/homebrew/Cellar/open-mpi/5.0.6/lib -lmpi

How to switch the mpi complier ? Thank you

[GiudGiud]

You should follow the install from source instruction on the website

you ll want to set environment variables CC CXX FC F77 F90

[GiudGiud]

it is crucial that you use the same set of compilers for petsc, libmesh and MOOSE. Any deviation will fail the build. The environment variables will help with that.
Considering that you are using Brew, you may have two sets of compilers (at least) on your system.

[bplcn]

it is crucial that you use the same set of compilers for petsc, libmesh and MOOSE. Any deviation will fail the build. The environment variables will help with that. Considering that you are using Brew, you may have two sets of compilers (at least) on your system.

Following you advice, I tried to uninstall the open-mpi and the problem is fixed. Thank you for your help!