Using MOOSE with Docker and Moltres Submodule

[Jeremyb8707bigbrain]

Check these boxes if you have followed the posting rules.

• I have consulted the Posting Guidelines.
• I have searched the Discussions Forum and MOOSE Framework Troubleshooting and have not found what I was looking for
• Q&A Getting Started is the most appropriate category for my question (trouble installing, beginner user, ...)

Issue or question about MOOSE

I am on Windows 11 using Docker to run Moltres, which has MOOSE as a submodule. Before I was able to get this working but it seems now it has been quite a challenge.

I am using the idaholab/moose:latest image for my docker, in which I download Moltres, which subsequently downloads MOOSE as a submodule. I know it is not ideal but for a Windows machine this is the best I am working with.

I am able to use MOOSE perfectly well on its own, but when it gets introduced as a submodule it seems to not want to work. A lot of the fixes I have seen use Conda, which I dont have as a Windows user. My main issue I am encountering is that the libmesh folder is entirely empty. So when trying to build, it goes haywire. It seems that either the image or Moltres is missing the "hit" dependency. The Moltres Installation Documentation (https://arfc.github.io/moltres/getting_started/installation.html) suggests using a Conda Environment (obviously). I was wondering if the Docker part of this is messing it up.

Bottomline is, the environment just is all out of wack and I was wondering if anyone knew a workaround to use Moltres on Docker (which I have done before but obviously cant remember how to do now). Pictures attached detail what my docker container looks like, as you can see with the first image the libmesh folder is absolutely empty.

I also was wondering if there was a way to get moltres to use the files that the image has already provided instead of its own submodule?

(Optional) code in question / simulation log / errors

sh-4.4# make -j8
/bin/sh: /moltres/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /moltres/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /moltres/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /moltres/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /moltres/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /moltres/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /moltres/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /moltres/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /moltres/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /moltres/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /moltres/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /moltres/moose/libmesh/installed/libtool: No such file or directory
/bin/sh: /moltres/moose/libmesh/installed/libtool: No such file or directory
/bin/sh: /moltres/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /moltres/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /moltres/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /moltres/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /moltres/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /moltres/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /moltres/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /moltres/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /moltres/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /moltres/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /moltres/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /moltres/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /moltres/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /moltres/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /moltres/moose/libmesh/installed/libtool: No such file or directory
/bin/sh: /moltres/moose/libmesh/installed/libtool: No such file or directory
/bin/sh: /moltres/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /moltres/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /moltres/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /moltres/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
bash: -I/moltres/moose/framework/contrib/hit/include: No such file or directory
make: *** [/moltres/moose/framework/moose.mk:233: hit] Error 127
Traceback (most recent call last):
  File "/moltres/moose/python/pyhit/__init__.py", line 13, in <module>
    import hit
ModuleNotFoundError: No module named 'hit'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/moltres/moose/python/pyhit/__init__.py", line 18, in <module>
    import hit
ModuleNotFoundError: No module named 'hit'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/moltres/moose/framework/scripts/find_dep_apps.py", line 16, in <module>
    from TestHarness import findDepApps
  File "/moltres/moose/python/TestHarness/__init__.py", line 9, in <module>
    from .TestHarness import TestHarness
  File "/moltres/moose/python/TestHarness/TestHarness.py", line 25, in <module>
    from FactorySystem.Factory import Factory
  File "/moltres/moose/python/FactorySystem/__init__.py", line 13, in <module>
    from .Parser import Parser
  File "/moltres/moose/python/FactorySystem/Parser.py", line 13, in <module>
    import pyhit
  File "/moltres/moose/python/pyhit/__init__.py", line 22, in <module>
    import hit
ModuleNotFoundError: No module named 'hit'
Building and linking /moltres/moose/framework/contrib/capabilities/capabilities.so...
bash: -DMOOSESTRINGUTILS_NO_LIBMESH: command not found
make: *** [/moltres/moose/framework/moose.mk:243: /moltres/moose/framework/contrib/capabilities/capabilities.so] Error 127
make: *** Waiting for unfinished jobs....

Encountering Errors? Please include diagnostic output

sh-4.4# scripts/diagnostics.sh
####################################################################################################
Influential Environment Variables

CONDA_CHANNEL=https://conda.software.inl.gov/public
CURL_CA_BUNDLE=
LD_LIBRARY_PATH=/.singularity.d/libs
MOOSE_JOBS=6
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
REQUESTS_CA_BUNDLE=
SSL_CERT_FILE=
####################################################################################################
Compiler(s) (CC CXX FC F77 F90):

CC      not set
CXX     not set
FC      not set
F77     not set
F90     not set

FAIL: One or more compiler environment variables not set, or set incorrectly
####################################################################################################
Python Sanity Checks

/usr/bin/env python3 --version; (reporting as: Python 3.12.11) matches
which python3 python;

/usr/bin/python3 --version; == Python 3.12.11
/usr/bin/python --version; == Python 3.12.11

OK
####################################################################################################
Python Modules (TestHarness, run-ability)


FAIL:    missing module(s): packaging 

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

Missing 'failing' Python modules will prevent you from building MOOSE.

FAIL: One or more Python issues present.


checks FAILED

[GiudGiud]

Hello

/bin/sh: /moltres/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory

this means it didnt find libmesh. Try to set LIBMESH_DIR to where libmesh is on the system

FAIL:    missing module(s): packaging 

you can conda install this package to remove this error

[Jeremyb8707bigbrain]

now im more confused, im going off the official documentation for how to setup docker with the moose-dev image, which says it comes with the libmesh configured properly. I follow every step and I still get the same exact errors as I did with my moltres.

[Jeremyb8707bigbrain]

I think this comes down to the issue of not having a conda environment perhaps? This worked for me before a while back but now it just seems like it doesnt want to work. Again, my conda command does not work.

[Jeremyb8707bigbrain]

I submodule updated moose to see if thatll help, which looks like it did but libmesh wont configure properly? I swore docker came with all of this stuff

sh-4.4# ./configure

----------- Configuring libMesh -------------

checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking target system type... x86_64-pc-linux-gnu
checking for a BSD-compatible install... /usr/bin/install -c
checking whether sleep supports fractional seconds... yes
checking filesystem timestamp resolution... 0.01
checking whether build environment is sane... yes
checking for a race-free mkdir -p... /usr/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking xargs -n works... yes
checking whether UID '0' is supported by ustar format... yes
checking whether GID '0' is supported by ustar format... yes
checking how to create a ustar tar archive... gnutar
checking whether to enable maintainer-specific portions of Makefiles... no
checking for src/base/libmesh.C... yes
checking for perl... /usr/bin/perl
note: MPI library path not given...
note: MPI library path not given...
checking for petscarch... no
checking whether make supports the include directive... yes (GNU style)
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc option to enable C11 features... none needed
checking whether gcc understands -c and -o together... yes
checking dependency style of gcc... gcc3
checking for mpif90... no
checking for gfortran... no
checking for ifort... no
checking for pgf90... no
checking for xlf95... no
checking whether the compiler supports GNU Fortran... no
checking whether accepts -g... no

No valid Fortran compiler <<<
checking for mpif77... no
checking for gfortran... no
checking for g77... no
checking for ifort... no
checking for f77... no
checking for xlf... no
checking for frt... no
checking for pgf77... no
checking for fort77... no
checking for fl32... no
checking for af77... no
checking for f90... no
checking for xlf90... no
checking for pgf90... no
checking for epcf90... no
checking for f95... no
checking for fort... no
checking for xlf95... no
checking for ifc... no
checking for efc... no
checking for pgf95... no
checking for lf95... no
checking whether the compiler supports GNU Fortran 77... no
checking whether accepts -g... no
No valid Fortran 77 compiler <<<
checking whether the compiler supports GNU C++... no
checking whether g++ accepts -g... no
checking for g++ option to enable C++11 features... unsupported
checking for g++ option to enable C++98 features... unsupported
checking dependency style of g++... none
WARNING:
Unrecognized compiler: "g++" <<<
You will likely need to modify
Make.common directly to specify
proper compiler flags
checking for a sed that does not truncate output... /usr/bin/sed
checking for C++ compiler vendor... unknown
configure: Seeking a C++ standard between "2017" and "2017"
checking whether g++ supports C++17 features by default... no
checking whether g++ supports C++17 features with -std=gnu++17... no
checking whether g++ supports C++17 features with -std=gnu++1z... no
checking whether g++ supports C++17 features with -std=c++17... no
checking whether g++ supports C++17 features with +std=c++17... no
checking whether g++ supports C++17 features with -h std=c++17... no
checking whether g++ supports C++17 features with -std=c++1z... no
checking whether g++ supports C++17 features with +std=c++1z... no
checking whether g++ supports C++17 features with -h std=c++1z... no
configure: error: *** A compiler with support for C++17 language features is required.``

[lindsayad]

@loganharbour do you have any thoughts on the docker stuff? When I hear moose-dev image, I would assume that comes with a LIBMESH_DIR set

[Jeremyb8707bigbrain]

@lindsayad I was curious if these errors are caused by the newest version of moose-dev, soley because I got a buddy to try the exact steps on the official MOOSE site and he got the same errors I did, no libmesh.

[loganharbour]

How are you entering the container? You should enter it within the bash shell (I see you're using /bin/sh above); something like:

docker run --rm -it idaholab/moose-dev:2025.12.08 /bin/bash

I think the problem here is that the main environment isn't getting sourced. We do a conversion from apptainer back to docker, which I think is losing that environment. I should have a fix up for this in the latest package update in https://github.com/idaholab/moose/pulls/maythuwin1313.

Once you enter the bash shell, if you don't see a shell prompt that looks like this:

moose-dev-openmpi-x86_64:2025.12.08 <removed>
$

it means that the environment wasn't sourced properly. You might also need to run (once entering the shell):

source /.singularity.d/env/90-environment.sh

[Jeremyb8707bigbrain]

While im here did you want to test anything else?

[loganharbour]

You should be able to build your application within that environment now, without needing to build libmesh, petsc, any of that. Should just change into the app directory and run make

[Jeremyb8707bigbrain]

Do you want me to run make through powershell or Docker Desktop 🤔

[loganharbour]

As long as you're in an environment in which you see that custom prompt (and thus LIBMESH_DIR, and everything else should be set), you should be able to build there.

Which probably means power shell. Within docker desktop, you should also be able to configure starting the container within /bin/bash. How are you spawning the container within docker desktop? Can you send a screenshot? I can try to replicate it on my side.

[Jeremyb8707bigbrain]

What I normally do is create my container through powershell like that and create a bind mount so I can get my files in there, but I usually leave the /bin/bash off at the end.

Whenever I create the container it automatically populates inside of docker desktop, here.

And usually since I want cleaner access to files and stuff I close powershell, restart the container on dockerdesktop and have access to all the files like this.