MOOSE Compiling Issue -Libmesh Configuration

[AhmedAlmetwally]

I downloaded MOOSE on MAC and activated it through conda, but libmesh did not load and I receive the following:

almeag-mac@FN601235 ~ % cd ~/projects/moose/test
make -j 4
./run_tests -j 4
/bin/sh: /Users/almeag-mac/projects/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /Users/almeag-mac/projects/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /Users/almeag-mac/projects/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /Users/almeag-mac/projects/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /Users/almeag-mac/projects/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /Users/almeag-mac/projects/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /Users/almeag-mac/projects/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /Users/almeag-mac/projects/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /Users/almeag-mac/projects/moose/libmesh/installed/libtool: No such file or directory
/bin/sh: /Users/almeag-mac/projects/moose/libmesh/installed/libtool: No such file or directory
/bin/sh: /Users/almeag-mac/projects/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /Users/almeag-mac/projects/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /Users/almeag-mac/projects/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
Using HIT from /Users/almeag-mac/projects/moose/framework/contrib/hit
/bin/sh: /Users/almeag-mac/projects/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
Compiling C++ (in opt mode) /Users/almeag-mac/projects/moose/framework/build/unity_src/src_Unity.C...
/bin/sh: /Users/almeag-mac/projects/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
Compiling C++ (in opt mode) /Users/almeag-mac/projects/moose/framework/build/unity_src/linesearches_Unity.C...
/bin/sh: /Users/almeag-mac/projects/moose/libmesh/installed/libtool: No such file or directory
/bin/sh: /Users/almeag-mac/projects/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
make: *** [/Users/almeag-mac/projects/moose/framework/build/unity_src/src_Unity..opt.lo] Error 127
make: *** Waiting for unfinished jobs....
/bin/sh: /Users/almeag-mac/projects/moose/libmesh/installed/libtool: No such file or directory
make: *** [/Users/almeag-mac/projects/moose/framework/build/unity_src/linesearches_Unity..opt.lo] Error 127
/bin/sh: /Users/almeag-mac/projects/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /Users/almeag-mac/projects/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /Users/almeag-mac/projects/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /Users/almeag-mac/projects/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /Users/almeag-mac/projects/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /Users/almeag-mac/projects/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /Users/almeag-mac/projects/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /Users/almeag-mac/projects/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /Users/almeag-mac/projects/moose/libmesh/installed/libtool: No such file or directory
/bin/sh: /Users/almeag-mac/projects/moose/libmesh/installed/libtool: No such file or directory
/bin/sh: /Users/almeag-mac/projects/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /Users/almeag-mac/projects/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /Users/almeag-mac/projects/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
Using HIT from /Users/almeag-mac/projects/moose/framework/contrib/hit
/bin/sh: /Users/almeag-mac/projects/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
Building and linking hit...
bash: -std=c++11: command not found
make: *** [hit] Error 127
failed to import pyhit - try running "make hit" in the $MOOSE_DIR/test directory.

Following the steps on: https://mooseframework.inl.gov/getting_started/installation/conda.html

[loganharbour]

Did you run

conda create --name moose moose-libmesh moose-tools
conda activate moose

as listed on the page you linked?

The fact that your install looks for libmesh within the moose directory and not a conda directory leads me to believe that you did not.

[AhmedAlmetwally]

It return anything.

[AhmedAlmetwally]

make: *** Waiting for unfinished jobs....
/bin/sh: /Users/almeag-mac/projects/moose/libmesh/installed/libtool: No such file or directory
make: *** [/Users/almeag-mac/projects/moose/framework/src/utils/RankFourTensor..opt.lo] Error 127
/bin/sh: /Users/almeag-mac/projects/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /Users/almeag-mac/projects/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /Users/almeag-mac/projects/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /Users/almeag-mac/projects/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /Users/almeag-mac/projects/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /Users/almeag-mac/projects/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /Users/almeag-mac/projects/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /Users/almeag-mac/projects/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /Users/almeag-mac/projects/moose/libmesh/installed/libtool: No such file or directory
/bin/sh: /Users/almeag-mac/projects/moose/libmesh/installed/libtool: No such file or directory
/bin/sh: /Users/almeag-mac/projects/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /Users/almeag-mac/projects/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /Users/almeag-mac/projects/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
Using HIT from /Users/almeag-mac/projects/moose/framework/contrib/hit
/bin/sh: /Users/almeag-mac/projects/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
Building and linking hit...
bash: -std=c++11: command not found
make: *** [hit] Error 127
failed to import pyhit - try running "make hit" in the $MOOSE_DIR/test directory.

[loganharbour]

You're still not properly activating the conda environment. If the conda environment is active, $LIBMESH_DIR will be set to a directory.

I suggest that you remove miniconda with rm -rf ~/miniconda3 and follow the directions again. You're missing a step somewhere.

[AhmedAlmetwally]

I use this command:
curl -L -O https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh
bash Miniconda3-latest-MacOSX-x86_64.sh -b -p ~/miniconda3

[loganharbour]

The remainder of the instructions are very important.

If LIBMESH_DIR is not set, you are most likely not following them in their entirety.

[GiudGiud]

Assuming the conda reinstall went fine (to check could you please run conda list moose, thanks!)

I think you're just missing the conda activate moose step

[AhmedAlmetwally]

almeag-mac@FN601235 test % conda activate moose

CommandNotFoundError: Your shell has not been properly configured to use 'conda activate'.
To initialize your shell, run

$ conda init <SHELL_NAME>

Currently supported shells are:

• bash
• fish
• tcsh
• xonsh
• zsh
• powershell

See 'conda init --help' for more information and options.

IMPORTANT: You may need to close and restart your shell after running 'conda init'.

[loganharbour]

Please follow the instructions - this is explained clearly in the end of the section "Install MOOSE Conda Packages" and there are even frequently asked questions about this issue on the page.

[GiudGiud]

@AhmedAlmetwally
did you do what the error message says?
conda init zsh
then close and reopen the shell.

Then conda activate moose should work.
Please let us know how this goes

[AhmedAlmetwally]

@GiudGiud @loganharbour, Thank you so much! It compiled now properly conda initiation.