diff --git a/Programming/anaconda/2019.07/conda-env-defs/cryocare/README.md b/Programming/anaconda/2019.07/conda-env-defs/cryocare/README.md index 82f85e5..51bb1c9 100644 --- a/Programming/anaconda/2019.07/conda-env-defs/cryocare/README.md +++ b/Programming/anaconda/2019.07/conda-env-defs/cryocare/README.md @@ -13,8 +13,10 @@ Now configure jupyter ## 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. +- cudatoolkit version should ideally match merlin6's CUDA module + (required by the MotionCor2 package). However, tensorflow needs cuda 10.0 while + no MotionCor2 binary is available. For now, having a different version in + conda and modules is working OK, but it could cause problems with future compilation. +- You can test GPU support by running this command on a GPU machine: + `python -c 'import tensorflow as tf; print(tf.test.is_gpu_available())'` diff --git a/Programming/anaconda/2019.07/conda-env-defs/cryocare/cryocare.yml b/Programming/anaconda/2019.07/conda-env-defs/cryocare/cryocare.yml index 36002c2..4f2cc05 100644 --- a/Programming/anaconda/2019.07/conda-env-defs/cryocare/cryocare.yml +++ b/Programming/anaconda/2019.07/conda-env-defs/cryocare/cryocare.yml @@ -4,30 +4,23 @@ channels: - defaults dependencies: - python=3.7 + # Explicit cryocare dependencies from singularity + - tensorflow-gpu=1.15.0 + - keras + - tifffile + - mrcfile + + # Other dev packages + - jupyter - 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 + - plotly + - pytables + - pip - pip: - csbdeep - pixiedust