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Amber-MD / cpptraj

Biomolecular simulation trajectory/data analysis.
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WIP - Playing with conda env for now (DO NOT MERGE) #1069

Closed hainm closed 8 months ago

hainm commented 8 months ago

um, there are two conda programs now. 

Run # $CONDA is an environment variable pointing to the root of the miniconda directory
  # $CONDA is an environment variable pointing to the root of the miniconda directory
  echo $CONDA/bin >> $GITHUB_PATH
  shell: /usr/bin/bash -e {0}
  env:
    pythonLocation: /opt/hostedtoolcache/Python/3.10.13/x64
    PKG_CONFIG_PATH: /opt/hostedtoolcache/Python/3.10.13/x64/lib/pkgconfig
    Python_ROOT_DIR: /opt/hostedtoolcache/Python/3.10.13/x64
    Python2_ROOT_DIR: /opt/hostedtoolcache/Python/3.10.13/x64
    Python3_ROOT_DIR: /opt/hostedtoolcache/Python/3.10.13/x64
    LD_LIBRARY_PATH: /opt/hostedtoolcache/Python/3.10.13/x64/lib
Run which conda
/usr/share/miniconda/bin/conda
drroe commented 8 months ago

Well $CONDA/bin/conda appears to be the one segfaulting: https://github.com/Amber-MD/cpptraj/actions/runs/8177232131/job/22358432147?pr=1068

Do you think I should try the /usr/share/miniconda one? Or something else? I'm really in the weeds here.

On Wed, Mar 6, 2024 at 1:24 PM Hai Nguyen @.***> wrote:

um, there are two conda programs now.

Run # $CONDA is an environment variable pointing to the root of the miniconda directory

$CONDA is an environment variable pointing to the root of the miniconda directory

echo $CONDA/bin >> $GITHUB_PATH shell: /usr/bin/bash -e {0} env: pythonLocation: /opt/hostedtoolcache/Python/3.10.13/x64 PKG_CONFIG_PATH: /opt/hostedtoolcache/Python/3.10.13/x64/lib/pkgconfig Python_ROOT_DIR: /opt/hostedtoolcache/Python/3.10.13/x64 Python2_ROOT_DIR: /opt/hostedtoolcache/Python/3.10.13/x64 Python3_ROOT_DIR: /opt/hostedtoolcache/Python/3.10.13/x64 LD_LIBRARY_PATH: /opt/hostedtoolcache/Python/3.10.13/x64/lib

Run which conda /usr/share/miniconda/bin/conda

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hainm commented 8 months ago

Yeah we should use the same version to run.

drroe commented 8 months ago

So actually that is the one that fails:

$ /usr/share/miniconda/bin/conda env update --file devtools/ci/environment.yml --name base

See https://github.com/Amber-MD/cpptraj/actions/runs/8177232131/job/22358432147?pr=1068

Is there somewhere else I should be looking?

On Wed, Mar 6, 2024 at 2:01 PM Hai Nguyen @.***> wrote:

Yeah we should use the same version to run.

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hainm commented 8 months ago

Is there somewhere else I should be looking?

I will do this. cheers.

hainm commented 8 months ago

Is there somewhere else I should be looking?

I will do this. cheers.

@drroe green now. Please include the change in this PR to yours. cheers.

drroe commented 8 months ago

Thanks Hai, you're awesome!

hainm commented 8 months ago

Yay, i was just trying to soothe your Python pain. 😂

On Thu, Mar 7, 2024 at 9:27 AM Daniel R. Roe @.***> wrote:

Thanks Hai, you're awesome!

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