Compilation issues

[Emmanuel-324]

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Question

I am trying to recompile my application after my new installation in a conda environment(my previous installation was in an HPC cluster, just for context). Note I did not have these issues with the previous installation type.

After making make -j8, I get the error below

(moose) [emmanuel324@tinkercliffs1 emmanuel324]$ 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 "/home/emmanuel324/projects/moose/framework/../scripts/premake.py", line 20, in __init__
    from versioner import Versioner
  File "/home/emmanuel324/projects/moose/scripts/versioner.py", line 24, in <module>
    import yaml
ModuleNotFoundError: No module named 'yaml'
Traceback (most recent call last):
  File "/home/emmanuel324/projects/moose/framework/../scripts/premake.py", line 261, in <module>
    PreMake().check()
  File "/home/emmanuel324/projects/moose/framework/../scripts/premake.py", line 27, in __init__
    self.versioner_meta = Versioner().version_meta()
UnboundLocalError: local variable 'Versioner' referenced before assignment
make: [/home/emmanuel324/projects/moose/framework/moose.mk:399: prebuild] Error 1 (ignored)
Compiling C++ (in opt mode) /home/emmanuel324/projects/emmanuel324/build/unity_src/materials_Unity.C...
In file included from /home/emmanuel324/projects/emmanuel324/src/materials/BarrierFunctionMaterial_abs.C:10,
                 from /home/emmanuel324/projects/emmanuel324/build/unity_src/materials_Unity.C:2:
/home/emmanuel324/projects/emmanuel324/build/header_symlinks/BarrierFunctionMaterial_abs.h:13:10: fatal error: OrderParameterFunctionMaterial.h: No such file or directory
   13 | #include "OrderParameterFunctionMaterial.h"
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make: *** [/home/emmanuel324/projects/moose/framework/build.mk:151: /home/emmanuel324/projects/emmanuel324/build/unity_src/materials_Unity.x86_64-conda-linux-gnu.opt.lo] Error 1

Even though the OrderParameterFunctionMaterial.h is present in my repository.

And below is how I load my conda environment but it seems there is some wrong according to :WARNING: Failed to initialize PreMake for version checking; this may be ignored but may suggest an environment issue. Traceback (most recent call last): File "/home/emmanuel324/projects/moose/framework/../scripts/premake.py", line 20, in __init__ from versioner import Versioner File "/home/emmanuel324/projects/moose/scripts/versioner.py", line 24, in <module> import yaml ModuleNotFoundError: No module named 'yaml'

loading parameters:

module reset
module load apps site/tinkercliffs/easybuild/setup
module load OpenMPI CMake
export CC=mpicc CXX=mpicxx FC=mpif90 F90=mpif90 F77=mpif77
module load Miniforge3/24.1.2-0
conda activate moose

Note I am new to conda environment

[Emmanuel-324]

Below is the current error I get
@GiudGiud @milljm

/home/emmanuel324/mambaforge3/envs/moose/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /home/emmanuel324/projects/emmanuel324/lib/libemmanuel324-opt.so: undefined reference to `OrderParameterFunctionMaterial::OrderParameterFunctionMaterial(Input
Parameters const&)'
/home/emmanuel324/mambaforge3/envs/moose/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /home/emmanuel324/projects/emmanuel324/lib/libemmanuel324-opt.so: undefined reference to `OrderParameterFunctionMaterial::validParams()'
/home/emmanuel324/mambaforge3/envs/moose/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /home/emmanuel324/projects/emmanuel324/lib/libemmanuel324-opt.so: undefined reference to `InputParameters validParams<OrderParameterFunctionMaterial>()'

[GiudGiud]

It’s ok as a first install. It won't work very well beyond a few nodes.

On a cluster you are supposed to use your admin installed MPI modules not the conda binary MPI

[milljm]

I didn't want to comment here, but I just can't help myself. If this is the same HPC Cluster as this: Exodus error #29634, your HPC Admin gave horrible advice 😢

Our Conda packages will work. But not nearly as well as using HPC's custom built MPI stack made specifically for that cluster.

However, maybe I am wrong, and they will work just fine. I don't think anyone on my team has performed a case study on how poorly Conda MPI stack scales against INL's MVAPICH/OpenMPI stack.

[Emmanuel-324]

Even though the installation was successful and every test passed and yes, I have enabled all the modules yet, I get this error

*** ERROR ***
A 'RankTwoScalarAux' is not a registered object.

If you are trying to find this object in a dynamically loaded library, make sure that
the library can be found either in your "Problem/library_path" parameter or in the
MOOSE_LIBRARY_PATH environment variable.�[39m

[Emmanuel-324]

I didn't want to comment here, but I just can't help myself. If this is the same HPC Cluster as this: Exodus error #29634, your HPC Admin gave horrible advice 😢

Our Conda packages will work. But not nearly as well as using HPC's custom built MPI stack made specifically for that cluster.

However, maybe I am wrong, and they will work just fine. I don't think anyone on my team has performed a case study on how poorly Conda MPI stack scales against INL's MVAPICH/OpenMPI stack.

Yes unfortunately that is the response I got. If I "module load Miniforge3/24.1.2-0" anytime I submit a job would that overwrite the conda MPI packages(the one I used: curl -L -O https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh
bash Miniforge3-Linux-x86_64.sh -b -p ~/miniforge) or do I have to start the installation process again(with: module load Miniforge3/24.1.2-0) to get my clusters custom MPI packages.

[GiudGiud]

A 'RankTwoScalarAux' is not a registered object.

That's a solid mechanics object. Your compilation did not work as expected.
You need to git clean -Xfd your version of moose (after saving all your work), then recompile