Libmesh directory empty in my MOOSE download

[Am-Americium]

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Issue or question about MOOSE

I have followed the steps for downloading MOOSE on the INL HPC Cluster.

After attempting to run make -j in the phase field directory, I get the error attached. After looking in my moose/libmesh directory, I notice it's empty.

This may be a silly issue on my part, but did I miss a step upon downloading MOOSE that would update and fill that directory? If so, what is that step?

(Optional) code in question / simulation log / errors

/bin/sh: /scratch/longaide2/projects/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /scratch/longaide2/projects/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /scratch/longaide2/projects/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /scratch/longaide2/projects/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /scratch/longaide2/projects/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /scratch/longaide2/projects/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /scratch/longaide2/projects/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /scratch/longaide2/projects/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /scratch/longaide2/projects/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /scratch/longaide2/projects/moose/libmesh/installed/libtool: No such file or directory
/bin/sh: /scratch/longaide2/projects/moose/libmesh/installed/libtool: No such file or directory
/bin/sh: /scratch/longaide2/projects/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /scratch/longaide2/projects/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /scratch/longaide2/projects/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
WARNING: Failed to initialize PreMake for version checking; this may be ignored but may suggest an environment issue.
Traceback (most recent call last):
  File "/scratch/longaide2/projects/moose/framework/../scripts/premake.py", line 20, in __init__
    from versioner import Versioner
  File "/ibmstor/scratch/longaide2/projects/moose/scripts/versioner.py", line 25, in <module>
    import jinja2
ModuleNotFoundError: No module named 'jinja2'

Traceback (most recent call last):
  File "/scratch/longaide2/projects/moose/framework/../scripts/premake.py", line 261, in <module>
    PreMake().check()
  File "/scratch/longaide2/projects/moose/framework/../scripts/premake.py", line 27, in __init__
    self.versioner_meta = Versioner().version_meta()
UnboundLocalError: local variable 'Versioner' referenced before assignment
make: [/scratch/longaide2/projects/moose/framework/moose.mk:399: prebuild] Error 1 (ignored)
/bin/sh: /scratch/longaide2/projects/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
Compiling C++ (in opt mode) /scratch/longaide2/projects/moose/framework/build/unity_src/convergence_Unity.C...
/bin/sh: /scratch/longaide2/projects/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
Compiling C++ (in opt mode) /scratch/longaide2/projects/moose/framework/build/unity_src/hdgkernels_Unity.C...
/bin/sh: /scratch/longaide2/projects/moose/libmesh/installed/libtool: No such file or directory
/bin/sh: /scratch/longaide2/projects/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
make: *** [/scratch/longaide2/projects/moose/framework/build.mk:151: /scratch/longaide2/projects/moose/framework/build/unity_src/convergence_Unity..opt.lo] Error 127
make: *** Waiting for unfinished jobs....
/bin/sh: /scratch/longaide2/projects/moose/libmesh/installed/libtool: No such file or directory
make: *** [/scratch/longaide2/projects/moose/framework/build.mk:151: /scratch/longaide2/projects/moose/framework/build/unity_src/hd
gkernels_Unity..opt.lo] Error 127

Encountering Errors? Please include diagnostic output

No response

[GiudGiud]

Hello

Please follow the instructions here
https://mooseframework.inl.gov/getting_started/installation/hpc_install_moose.html

on HPC you use a script from the instructionrs to get the libmesh and petsc folders to populate

[Am-Americium]

I used those instructions and am still receiving this error. The ./run_tests returned with 0 failed tests as well.

[GiudGiud]

you can address this error

export PETSC_DIR="path to your petsc folder under moose"

[Am-Americium]

should I do this for each directory? like libmesh too?

[Am-Americium]

after running the above command, the update_and_rebuild petc command and am experiencing the same error

sorry, this is a weird issue to have. Would you maybe suggest uninstalling moose and redownloading?

[milljm]

If you are following the INL HPC instructions, there is no need to build PETSc or libMesh. You will be operating in a container that has these already built.

What you probably need to do, is clean out the previous failed build attempt.

cd /scratch/longaide2/projects/moose
git clean -xfd; git submodule foreach --recursive git clean -xfd

Next, following the instructions here: https://mooseframework.inl.gov/getting_started/installation/inl_hpc_install_moose.html

you will end up doing:

module load use.moose versioner
cd /scratch/longaide2/projects/moose
scripts/versioner.py moose-dev

This return a hash, which basically forms the naming suffix of the module you need to load. As an example:

module load use.moose moose-dev-openmpi/5e9be02
                                        ^^^^^^^ being what was returned in the previous step

Once this final module is loading, you should be able to run make.