fixufixupp

conda_enviroment.yml

-FROM nvidia/cuda:10.1-devel-ubuntu18.04
-
-RUN apt-get update --fix-missing && apt-get install -y build-essential wget git graphviz pandoc ffmpeg zip locales
-RUN locale-gen en_US.UTF-8
-ENV LANG en_US.UTF-8
-ENV LANGUAGE en_US:en
-ENV LC_ALL en_US.UTF-8
-
-# --- Miniconda
-RUN wget --quiet https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda.sh && \
-    /bin/bash ~/miniconda.sh -b -p /opt/conda && \
-     rm ~/miniconda.sh
-ENV PATH /opt/conda/bin:$PATH
-
-# --- Install packages into conda using environment file
-ADD conda_environment.yml
-RUN conda update -n base conda && \
-    conda env create -f conda_environment.yml
-
-# --- Disable gmpy backend of sympy, because of serialization bug
-ENV MPMATH_NOGMPY=1
-ENV PATH /opt/conda/envs/pystencils_dev/bin/:$PATH
-
-

conda_environment.yml

+# Development environment with all dependencies to run tests and build documentation
+
+name: pystencils_machine_learning
+channels:
+  - lssfau # for walberla package
+dependencies:
+  # Basic dependencies:
+  - python >= 3.6
+  - pip
+  - numpy
+  - sympy >= 1.1
+  - appdirs # to find default cache directory on each platform
+  - joblib # caching on hard-disk, this is optional, but if not installed lbmpy is really slow
+  - jinja2 # for walberla kernel generation
+  - cython # speed up boundary list computation (optional)
+  # Display and postprocessing
+  - jupyter # a lot of documentation and tutorials are in notebook format
+  - matplotlib
+  - imageio
+  - pandas
+  - scipy
+  # Test suite dependencies
+  - pytest
+  - pytest-cov
+  - pytest-xdist
+  - flake8
+  # Documentation dependencies
+  - sphinx
+  - sphinx_rtd_theme
+  - pandoc
+  # Other
+  - walberla # for distributed memory parallelization
+  - llvmlite # alternative jit backend
+  - gitpython # benchmarks reports include git hash
+  - psutil # for information about available / total RAM
+  - pip:
+      - islpy # used to optimize staggered kernels
+      - py-cpuinfo # get cpu info like cache sizes, supported vector instruction sets, ...
+      - graphviz  # can show abstract syntax trees as formatted graphs
+      - ipy_table  # HTML tables for jupyter notebooks
+      - pyevtk # VTK output for serial simulations
+      - blitzdb # file-based No-SQL database to store simulation results
+      - pycuda # run kernels on GPU (remove this if CUDA is not installed!)
+      - kerncraft # automatic performance analysis and benchmark
+      - influxdb # for reporting of benchmark results into time series database
+      - scikit-image # for phase field angle evaluations, when version 0.14.2 is available from conda it can be moved back
+      # Documentation
+      - nbsphinx # include notebooks into sphinx documentation
+      - sphinxcontrib-bibtex # add citations to sphinx doc
+      - sphinx_autodoc_typehints
+      # Machine learning dependencies
+      - pampy
+      - tqdm
+      - torch
+      - tensorflow-gpu

machine_learning.Dockerfile

@@ -13,9 +13,9 @@ RUN wget --quiet https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86
 ENV PATH /opt/conda/bin:$PATH
 
 # --- Install packages into conda using environment file
-ADD conda_environment_dev.yml conda_environment_machine_learning.yml
+ADD conda_environment.yml conda_environment.yml
 RUN conda update -n base conda && \
-    conda env create -f conda_environment_machine_learning.yml
+    conda env create -f conda_environment.yml
 
 # --- Disable gmpy backend of sympy, because of serialization bug
 ENV MPMATH_NOGMPY=1