From c16527091433a2cb082e6a7ab345d6683c938491 Mon Sep 17 00:00:00 2001 From: bliven_s Date: Tue, 5 Nov 2019 15:48:03 +0100 Subject: [PATCH] Check in older anaconda versions. Version 2019.03 was an alpha version but got deployed. This updates it to use the current modulefile. --- .../config-2018.12.sh => 2019.03/config.sh} | 0 .../2019.07/conda-env-defs/cryocare/README.md | 20 +++++++++++ .../conda-env-defs/cryocare/cryocare.yml | 33 +++++++++++++++++++ .../etc/conda/activate.d/cryocare-env.sh | 16 +++++++++ .../etc/conda/deactivate.d/cryocare-env.sh | 14 ++++++++ .../share/jupyter/kernels/python3/kernel.json | 13 ++++++++ Programming/anaconda/files/variants | 2 +- 7 files changed, 97 insertions(+), 1 deletion(-) rename Programming/anaconda/{files/config-2018.12.sh => 2019.03/config.sh} (100%) create mode 100644 Programming/anaconda/2019.07/conda-env-defs/cryocare/README.md create mode 100644 Programming/anaconda/2019.07/conda-env-defs/cryocare/cryocare.yml create mode 100644 Programming/anaconda/2019.07/conda-env-defs/cryocare/etc/conda/activate.d/cryocare-env.sh create mode 100644 Programming/anaconda/2019.07/conda-env-defs/cryocare/etc/conda/deactivate.d/cryocare-env.sh create mode 100644 Programming/anaconda/2019.07/conda-env-defs/cryocare/share/jupyter/kernels/python3/kernel.json diff --git a/Programming/anaconda/files/config-2018.12.sh b/Programming/anaconda/2019.03/config.sh similarity index 100% rename from Programming/anaconda/files/config-2018.12.sh rename to Programming/anaconda/2019.03/config.sh diff --git a/Programming/anaconda/2019.07/conda-env-defs/cryocare/README.md b/Programming/anaconda/2019.07/conda-env-defs/cryocare/README.md new file mode 100644 index 0000000..82f85e5 --- /dev/null +++ b/Programming/anaconda/2019.07/conda-env-defs/cryocare/README.md @@ -0,0 +1,20 @@ +# 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 $CONDA_PREFIX/etc/conda/deactivate.d/ + +## Package notes + +- cudatoolkit version is fixed because it needs to match merlin6's CUDA module + (required by the MotionCor2 package). +- This environment installs packages for gpu support, but these currently don't + seem to be working on merlin. + diff --git a/Programming/anaconda/2019.07/conda-env-defs/cryocare/cryocare.yml b/Programming/anaconda/2019.07/conda-env-defs/cryocare/cryocare.yml new file mode 100644 index 0000000..36002c2 --- /dev/null +++ b/Programming/anaconda/2019.07/conda-env-defs/cryocare/cryocare.yml @@ -0,0 +1,33 @@ +name: cryocare +channels: + - conda-forge + - defaults +dependencies: + - python=3.7 + - dask + - dask-jobqueue + - deap + - docopt + - graphviz + - ipython + - ipywidgets + - keras + - matplotlib + - mrcfile + - nb_conda_kernels + - numpy + - pandas + - plotly + - pytables + - python-graphviz + - scikit-learn + - scipy + - seaborn + - tensorflow=1.13.1 + - tensorflow-gpu + - tifffile + - cudatoolkit=9.2 + - cudnn + - pip: + - csbdeep + - pixiedust diff --git a/Programming/anaconda/2019.07/conda-env-defs/cryocare/etc/conda/activate.d/cryocare-env.sh b/Programming/anaconda/2019.07/conda-env-defs/cryocare/etc/conda/activate.d/cryocare-env.sh new file mode 100644 index 0000000..f7e7986 --- /dev/null +++ b/Programming/anaconda/2019.07/conda-env-defs/cryocare/etc/conda/activate.d/cryocare-env.sh @@ -0,0 +1,16 @@ +#!/bin/bash +echo "Running hook for adding PSI modules" >&2 +if [[ x$(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 "$@") + } +fi + +module use unstable +module use EM +module load cuda/9.2.148 MotionCor2/1.2.0 IMOD/4.9.5 +echo "DEBUG: loaded modules after addition:" >&2 +module list >&2 diff --git a/Programming/anaconda/2019.07/conda-env-defs/cryocare/etc/conda/deactivate.d/cryocare-env.sh b/Programming/anaconda/2019.07/conda-env-defs/cryocare/etc/conda/deactivate.d/cryocare-env.sh new file mode 100644 index 0000000..aab07f4 --- /dev/null +++ b/Programming/anaconda/2019.07/conda-env-defs/cryocare/etc/conda/deactivate.d/cryocare-env.sh @@ -0,0 +1,14 @@ +echo "Running hook for removing PSI modules" >&2 +if [[ x$(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 diff --git a/Programming/anaconda/2019.07/conda-env-defs/cryocare/share/jupyter/kernels/python3/kernel.json b/Programming/anaconda/2019.07/conda-env-defs/cryocare/share/jupyter/kernels/python3/kernel.json new file mode 100644 index 0000000..d1725d9 --- /dev/null +++ b/Programming/anaconda/2019.07/conda-env-defs/cryocare/share/jupyter/kernels/python3/kernel.json @@ -0,0 +1,13 @@ +{ + "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" +} diff --git a/Programming/anaconda/files/variants b/Programming/anaconda/files/variants index aeb4876..b061e38 100644 --- a/Programming/anaconda/files/variants +++ b/Programming/anaconda/files/variants @@ -1,3 +1,3 @@ anaconda/2018.12 unstable +anaconda/2019.03 unstable anaconda/2019.07 unstable -