Commit c1652709 authored by bliven_s's avatar bliven_s

Check in older anaconda versions.

Version 2019.03 was an alpha version but got deployed. This updates it
to use the current modulefile.
parent 186d4b65
# INSTALLATION
IMPORTANT! DON'T INSTALL WITH AURISTOR. Use an OpenAFS system (e.g. pmod6)
CONDA_COPY_ALWAYS=1 conda env create --file cryocare.yml
conda activate cryocare
Now configure jupyter
cp share/jupyter/kernels/python3/kernel.json $CONDA_PREFIX/share/jupyter/kernels/python3/
cp etc/conda/activate.d/cryocare-env.sh $CONDA_PREFIX/etc/conda/activate.d/
cp etc/conda/deactivate.d/cryocare-env.sh $CONDA_PREFIX/etc/conda/deactivate.d/
## Package notes
- cudatoolkit version is fixed because it needs to match merlin6's CUDA module
(required by the MotionCor2 package).
- This environment installs packages for gpu support, but these currently don't
seem to be working on merlin.
name: cryocare
channels:
- conda-forge
- defaults
dependencies:
- python=3.7
- dask
- dask-jobqueue
- deap
- docopt
- graphviz
- ipython
- ipywidgets
- keras
- matplotlib
- mrcfile
- nb_conda_kernels
- numpy
- pandas
- plotly
- pytables
- python-graphviz
- scikit-learn
- scipy
- seaborn
- tensorflow=1.13.1
- tensorflow-gpu
- tifffile
- cudatoolkit=9.2
- cudnn
- pip:
- csbdeep
- pixiedust
#!/bin/bash
echo "Running hook for adding PSI modules" >&2
if [[ x$(command -v module) = x ]]; then
echo "setting up module env" >&2
# source /opt/psi/config/profile.bash
module() {
unset BASH_ENV;
eval $("${PMODULES_HOME}/bin/modulecmd" bash "$@")
}
fi
module use unstable
module use EM
module load cuda/9.2.148 MotionCor2/1.2.0 IMOD/4.9.5
echo "DEBUG: loaded modules after addition:" >&2
module list >&2
echo "Running hook for removing PSI modules" >&2
if [[ x$(command -v module) = x ]]; then
echo "setting up module env" >&2
# source /opt/psi/config/profile.bash
module() {
unset BASH_ENV;
eval $("${PMODULES_HOME}/bin/modulecmd" bash "$@")
}
fi
echo "DEBUG: loaded modules prior to removal" >&2
module list >&2
module unload cuda/9.2.148 MotionCor2/1.2.0 IMOD/4.9.5 >&2
echo "DEBUG: loaded modules after removal" >&2
module list >&2
{
"argv": [
"/opt/psi/Programming/anaconda/2019.07/admintools/kernelwrapper.sh",
"cryocare",
"/opt/psi/Programming/anaconda/2019.07/conda/envs/cryocare/bin/python",
"-m",
"ipykernel_launcher",
"-f",
"{connection_file}"
],
"display_name": "Python 3",
"language": "python"
}
anaconda/2018.12 unstable
anaconda/2019.03 unstable
anaconda/2019.07 unstable
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