Merge pull request #193 from fusion-energy/develop

fixing the docker image

.devcontainer/Dockerfile

@@ -9,13 +9,13 @@
 # To build this Dockerfile into a docker image:
 # docker build -t neutronics-workshop -f .devcontainer/Dockerfile .
 
-# for local testing I tend to use this build command
-# docker build -t neutronics-workshop 
-# and then run with this command
+# then run with this command
 # docker run -p 8888:8888 neutronics-workshop
 
-
+# remote image
 FROM ghcr.io/fusion-energy/neutronics-workshop:base as base
+# local image
+# FROM neutronics-workshop:base as base
 
 # Copy over the local repository files
 COPY tasks tasks/
@@ -28,5 +28,12 @@ FROM base as jupyter_cmd
 
 ENV PORT 8888
 
+# ENV PYTHONPATH="/MOAB/moab/pymoab"
+# RUN pip install gmsh
+# RUN apt-get install libxcursor-dev -y
+# RUN apt-get install libxinerama-dev -y
+
+# libXinerama.so.1: cannot open shared object file: No such file or directory
+
 # could switch to --ip='*'
 CMD ["jupyter", "lab", "--notebook-dir=/tasks", "--port=8888", "--no-browser", "--ip=0.0.0.0", "--allow-root"]

.devcontainer/base.Dockerfile

@@ -30,7 +30,8 @@
 # and then run with this command
 # docker run -it neutronics-workshop:base
 
-FROM mcr.microsoft.com/vscode/devcontainers/miniconda:0-3 as dependencies
+# FROM mcr.microsoft.com/vscode/devcontainers/miniconda:0-3 as dependencies
+FROM mcr.microsoft.com/vscode/devcontainers/python:0-3.9-bullseye as dependencies
 
 RUN apt-get --allow-releaseinfo-change update
 RUN apt-get --yes update && apt-get --yes upgrade
@@ -77,11 +78,19 @@ RUN apt-get --yes install libeigen3-dev \
                           libxft2
 
 
-RUN conda install -c conda-forge -c python python=3.8
+# RUN conda install -c conda-forge -c python python=3.8
 
-RUN conda install -c conda-forge mamba -y
-RUN mamba install -c fusion-energy -c cadquery -c conda-forge paramak==0.8.7 -y
+# RUN conda install -c conda-forge mamba -y
+# RUN conda install -c fusion-energy -c cadquery -c conda-forge paramak==0.8.7 -y
+RUN pip install cadquery  \
+                paramak
 
+RUN pip install gmsh
+# needed for gmsh
+RUN apt-get install libxcursor-dev -y
+# needed for gmsh
+RUN apt-get install libxinerama-dev -y
+# might be libxinerama1
 
 # python packages from the neutronics workflow
 RUN pip install neutronics_material_maker[density] \
@@ -93,7 +102,8 @@ RUN pip install neutronics_material_maker[density] \
                 spectrum_plotter \
                 openmc_source_plotter \
                 openmc_depletion_plotter \
-                openmc_data_downloader \
+                openmc_data_downloader>=0.6.0 \
+                openmc_data \
                 openmc_plot \
                 dagmc_geometry_slice_plotter
 
@@ -156,7 +166,8 @@ RUN if [ "$build_double_down" = "ON" ] ; \
 # Clone and install MOAB
 RUN mkdir MOAB && \
     cd MOAB && \
-    git clone  --single-branch --branch 5.4.1 --depth 1 https://bitbucket.org/fathomteam/moab.git && \
+    # newer versions of moab (5.4.0, 5.4.1) don't produce an importable pymoab package!
+    git clone  --single-branch --branch 5.3.1 --depth 1 https://bitbucket.org/fathomteam/moab.git && \
     mkdir build && \
     cd build && \
     cmake ../moab -DENABLE_HDF5=ON \
@@ -166,8 +177,13 @@ RUN mkdir MOAB && \
                   -DBUILD_SHARED_LIBS=ON \
                   -DENABLE_PYMOAB=ON \
                   -DCMAKE_INSTALL_PREFIX=/MOAB && \
-    make -j"$compile_cores" &&  \
-    make -j"$compile_cores" install
+    mkdir -p MOAB/lib/pymoab/lib/python3.9/site-packages && \
+    PYTHONPATH=/MOAB/lib/pymoab/lib/python3.9/site-packages:${PYTHONPATH} make -j && \
+    PYTHONPATH=/MOAB/lib/pymoab/lib/python3.9/site-packages:${PYTHONPATH} make install -j
+
+ENV PYTHONPATH="/MOAB/lib/python3.9/site-packages/pymoab-5.3.1-py3.9-linux-x86_64.egg/"
+
+RUN python -c "import pymoab"
 
 
 ENV PATH=$PATH:/MOAB/bin
@@ -209,10 +225,9 @@ ENV PATH=$PATH:/DAGMC/bin
 ENV LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/DAGMC/lib
 
 # installs OpenMc from source
-RUN cd /opt && \
-    # switch back to tagged version when 0.13.3 is released as develop depletion is used
-    # git clone --single-branch --branch v0.13.3 --depth 1 https://github.com/openmc-dev/openmc.git && \
-    git clone --single-branch --branch develop --depth 1 https://github.com/openmc-dev/openmc.git && \
+# switch back to tagged version when 0.13.3 is released as develop depletion is used
+# git clone --single-branch --branch v0.13.3 --depth 1 https://github.com/openmc-dev/openmc.git && \
+RUN git clone --single-branch --branch develop --depth 1 https://github.com/openmc-dev/openmc.git && \
     cd openmc && \
     mkdir build && \
     cd build && \
@@ -221,29 +236,23 @@ RUN cd /opt && \
           -DHDF5_PREFER_PARALLEL=OFF .. && \
     make -j"$compile_cores" && \
     make -j"$compile_cores" install && \
-    cd /opt/openmc/ && \
+    cd /openmc/ && \
     pip install .
 
 # installs TENDL and ENDF nuclear data. Performed after openmc install as
 # openmc is needed to write the cross_Sections.xml file
+
 # RUN pip install openmc_data_downloader && \
-#     openmc_data_downloader -d nuclear_data -l ENDFB-7.1-NNDC TENDL-2019 -p neutron photon -e all -i H3 --no-overwrite
+RUN openmc_data_downloader -d nuclear_data -l ENDFB-8.0-NNDC TENDL-2019 -p neutron photon -e all -i H3 --no-overwrite
 
 RUN pip install openmc_data && \
     mkdir -p /nuclear_data && \
-    download_nndc_chain -d nuclear_data -r b8.0 && \
-    download_nndc -d nuclear_data -r b8.0 --cleanup && \
-    rm -rf nndc-b8.0-download
-# The last line here deletes the downloaded compressed nuclear datafile
-# not sure why but cleanup is not working, trackign on issue
-# https://github.com/openmc-data-storage/openmc_data/issues/29
-
-
+    download_nndc_chain -d nuclear_data -r b8.0
 
 # install WMP nuclear data
 RUN wget https://github.com/mit-crpg/WMP_Library/releases/download/v1.1/WMP_Library_v1.1.tar.gz && \
     tar -xf WMP_Library_v1.1.tar.gz -C /  && \
     rm WMP_Library_v1.1.tar.gz
 
-ENV OPENMC_CROSS_SECTIONS=/nuclear_data/endfb-viii.0-hdf5/cross_sections.xml
-ENV OPENMC_CHAIN_FILE=/nuclear_data/cross_sections.xml
+ENV OPENMC_CROSS_SECTIONS=/nuclear_data/cross_sections.xml
+ENV OPENMC_CHAIN_FILE=/nuclear_data/chain-nndc-b8.0.xml

tasks/task_01_cross_sections/plotting_utils.py

@@ -27,7 +27,7 @@ def create_isotope_plot(isotopes, reaction):
         isotope_object = openmc.Nuclide(isotope_name)
 
         energy, cross_sections = openmc.calculate_cexs(
-            isotope_object, "nuclide", [reaction]
+            isotope_object, [reaction]
         )
         cross_section = cross_sections[0]
         if cross_section.sum() != 0.0:
@@ -78,7 +78,7 @@ def create_element_plot(elements, reaction):
             continue
 
         energy, cross_sections = openmc.calculate_cexs(
-            element_object, "element", [reaction]
+            element_object, [reaction]
         )
         cross_section = cross_sections[0]
         if cross_section.sum() != 0.0:
@@ -118,7 +118,7 @@ def create_material_plot(materials, reaction):
 
     for material in materials:
         # extracts energy and cross section for the material for the provided MT reaction mumber
-        energy, xs_data = openmc.calculate_cexs(material, "material", [MT_number])
+        energy, xs_data = openmc.calculate_cexs(material, [MT_number])
 
         # adds the energy dependnat cross sction to the plot
         fig.add_trace(

tasks/task_13_variance_reduction/generate_single_ww_and_apply.ipynb

@@ -249,7 +249,7 @@
     "\n",
     "\n",
     "model.settings.weight_windows = weight_windows\n",
-    "model.settings.max_split = 1_000_000\n",
+    "model.settings.max_split = 1_000 # might want to increase this to 1_000_000 and get a better result \n",
     "model.run()"
    ]
   },