MOOSE installation on HPC by using Singularity (like Docker)

[hokonkim]

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Question

Hello, MOOSE Communities.

I'm trying to install MOOSE on HPC by using Singularity (like Docker).

I use this command to generate Singularity Image Format.
singularity build --fakeroot moose-dev.sif docker://idaholab/moose-dev:latest

After that, I tried this command to bind directory.
singularity shell -B /scratch/a1960a01/projects:/projects /scratch/a1960a01/moose-dev.sif

Then, I tried to test MOOSE and got an error message like below.

I tried
source /environment
but it didn't work for me.

I think I followed a guideline from MOOSE website, but I'm stuck at this point.
Please let me know a solution.
Thank you.

[GiudGiud]

hello

That error means it is not finding libmesh.
If libmesh is compiled at a different location you need to set LIBMESH_DIR to point to it

Which instructions are you following?

Guillaume

[hokonkim]

I tried to follow this one.
https://mooseframework.inl.gov/getting_started/installation/docker.html

[hokonkim]

@GiudGiud
I modified ~/.bashrc like below.

source /opt/rh/gcc-toolset-13/enable
export LD_LIBRARY_PATH=/opt/rh/gcc-toolset-13/root/usr/lib64:$LD_LIBRARY_PATH

export LIBMESH_DIR=/opt/libmesh
export PATH=$LIBMESH_DIR/bin:$PATH
export LD_LIBRARY_PATH=$LIBMESH_DIR/lib:$LD_LIBRARY_PATH

export PATH=/opt/miniforge3/bin:$PATH

export PATH=/opt/openmpi/bin:$PATH

export WASP_DIR=/opt/wasp
export CXXFLAGS="-I$WASP_DIR/include $CXXFLAGS"
export CFLAGS="-I$WASP_DIR/include $CFLAGS"

make -j 4 works for me.

However, when trying `./run_tests -j 4'
I got an error like this.

./run_tests -j 4
Building and linking /scratch/a1960a01/projects/moose/framework/contrib/hit/hit.so...
make[1]: Entering directory '/scratch/a1960a01/projects/moose/framework/contrib/hit'
Building hit for python with python3-config
make[1]: 'hit' is up to date.
make[1]: Leaving directory '/scratch/a1960a01/projects/moose/framework/contrib/hit'
Traceback (most recent call last):
  File "/scratch/a1960a01/projects/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 "/scratch/a1960a01/projects/moose/python/pyhit/__init__.py", line 18, in <module>
    import hit
ImportError: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.32' not found (required by /scratch/a1960a01/projects/moose/python/pyhit/../../framework/contrib/hit/hit.so)

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/scratch/a1960a01/projects/moose/test/./run_tests", line 6, in <module>
    from TestHarness import TestHarness
  File "/scratch/a1960a01/projects/moose/python/TestHarness/__init__.py", line 9, in <module>
    from .TestHarness import TestHarness
  File "/scratch/a1960a01/projects/moose/python/TestHarness/TestHarness.py", line 24, in <module>
    from FactorySystem.Factory import Factory
  File "/scratch/a1960a01/projects/moose/python/FactorySystem/__init__.py", line 13, in <module>
    from .Parser import Parser
  File "/scratch/a1960a01/projects/moose/python/FactorySystem/Parser.py", line 13, in <module>
    import pyhit
  File "/scratch/a1960a01/projects/moose/python/pyhit/__init__.py", line 22, in <module>
    import hit
ImportError: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.32' not found (required by /scratch/a1960a01/projects/moose/python/pyhit/../../framework/contrib/hit/hit.so)

[GiudGiud]

looks like hit gets compiled when needed, which is expected, when running run_tests

however it does not get compiled properly, referring to a version of /lib64/libstdc++.so.6 that is not found.
Maybe clean the directory (git clean -Xfd), then make sure to export the compiler variables (FC, CC, CXX)

I would also recommend looking through old posts for GLIBCXX related issues

[hokonkim]

For whom will have a similar issue like me,
Here are my solution.

I checked again many posts for GLIBCXX and found a link below.
#27377
Based on @GiudGiud comments and the link,

I modified my ~/.bashrc

# ===== Path & Library Path Configuration =====
# Executable search path (PATH)
export PATH=/opt/moose/bin:/opt/miniforge3/bin:/opt/openmpi/bin:/opt/libmesh/bin:$PATH
# Shared library search path (LD_LIBRARY_PATH)
# Prioritize gcc-toolset-13 libraries to resolve GLIBCXX errors
export LD_LIBRARY_PATH=/opt/rh/gcc-toolset-13/root/usr/lib64:/opt/rh/gcc-toolset-13/root/usr/lib:/opt/openmpi/lib:/opt/libmesh/lib:$LD_LIBRARY_PATH

# ===== Compiler & Dependency Settings =====
# Enable gcc-toolset-13 environment
source /opt/rh/gcc-toolset-13/enable
# Explicitly set compilers
export CC=gcc
export CXX=g++
export FC=gfortran
# Set dependency directories
export LIBMESH_DIR=/opt/libmesh
export PETSC_DIR=/opt/petsc
export WASP_DIR=/opt/wasp
# Add compiler flags
export CXXFLAGS="-I$WASP_DIR/include $CXXFLAGS"
export CFLAGS="-I$WASP_DIR/include $CFLAGS"
# Fix locale warnings
export LC_ALL=C

# ===== Python/Conda Environment =====
source activate /opt/miniforge3/envs/moose

Also, don't forget at MOOSE foler (projects/moose) before compiling
git clean -Xfd

Summary.

1. Modify ~/.bashrc
2. source ~/.bashrc
3. git clean -Xfd at MOOSE folder (projects/moose)
4. make -j 4 (projects/moose/test)
5. ./run_tests -j 4 (projects/moose/test)