make mpie-cmti standalone

.github/workflows/testing.yml

@@ -43,12 +43,6 @@ jobs:
           tail --lines=+5 base/environment.yml >> experimental/environment.yml
           docker build -t pyiron/experimental:latest experimental/
           docker tag pyiron/experimental:latest pyiron/experimental:"$(date +%F)"
-      - name: Build pyiron/mpie_cmti
-        timeout-minutes: 5
-        run: |
-          tail --lines=+5 pyiron/environment.yml >> mpie_cmti/environment.yml
-          docker build -t pyiron/mpie_cmti:latest mpie_cmti/
-          docker tag pyiron/mpie_cmti:latest pyiron/mpie_cmti:"$(date +%F)"
       # Testing
       - run: docker images
       - name: Test pyiron/continuum
@@ -71,6 +65,16 @@ jobs:
       - run: docker run -v $(pwd)/environment:/home/jovyan/ --rm pyiron/pyiron /bin/bash -c 'source /opt/conda/bin/activate; conda env export > /home/jovyan/pyiron_pyiron_$(date +%F).yml;' 
       - run: docker run -v $(pwd)/environment:/home/jovyan/ --rm pyiron/potentialworkshop /bin/bash -c 'source /opt/conda/bin/activate; conda env export > /home/jovyan/pyiron_potentialworkshop_$(date +%F).yml;' 
       - run: docker run -v $(pwd)/environment:/home/jovyan/ --rm pyiron/experimental /bin/bash -c 'source /opt/conda/bin/activate; conda env export > /home/jovyan/pyiron_experimental_$(date +%F).yml;'
-      - run: docker run -v $(pwd)/environment:/home/jovyan/ --rm pyiron/mpie_cmti /bin/bash -c 'source /opt/conda/bin/activate; conda env export > /home/jovyan/mpie_cmti_$(date +%F).yml;'
       - run: ls -al environment
-
+  build_cmti:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Build pyiron/mpie_cmti
+        timeout-minutes: 15
+        run: |
+          docker build -t pyiron/mpie_cmti:latest mpie_cmti/
+          docker tag pyiron/mpie_cmti:latest pyiron/mpie_cmti:"$(date +%F)"
+      - run: docker images
+      - run: mkdir -p environment; chmod 777 environment
+      - run: docker run -v $(pwd)/environment:/home/jovyan/ --rm pyiron/mpie_cmti /bin/bash -c 'source /opt/conda/bin/activate; conda env export > /home/jovyan/mpie_cmti_$(date +%F).yml;'

mpie_cmti/Dockerfile

@@ -1,16 +1,52 @@
-ARG ROOT_CONTAINER=pyiron/pyiron:latest
-ARG BASE_CONTAINER=$ROOT_CONTAINER
-FROM $BASE_CONTAINER
+ARG ROOT_IMAGE=jupyter/base-notebook:ubuntu-22.04@sha256:0ec801994602a53d3917d0f07ccf4474a1ddf5ae419483b24681a3c42abc4ce5 AS root_image
+FROM $ROOT_IMAGE
 
-MAINTAINER Jan Janssen <[email protected]>
+MAINTAINER Jan Janssen <[email protected]>, Marian Bruns <[email protected]>
 
-USER $DOCKER_UID
-WORKDIR $HOME
+ARG DOCKER_UID="1000"
+ARG DOCKER_GID="100"
+
+# Configure environment
+ENV CONDA_DIR=/opt/conda \
+    SHELL=/bin/bash \
+    LC_ALL=en_US.UTF-8 \
+    LANG=en_US.UTF-8 \
+    LANGUAGE=en_US.UTF-8 \
+    DOCKER_UID=$DOCKER_UID \
+    DOCKER_GID=$DOCKER_GID \
+    HOME=/home/$NB_USER \
+    OMPI_MCA_plm=isolated \
+    OMPI_MCA_rmaps_base_oversubscribe=yes \
+    OMPI_MCA_btl_vader_single_copy_mechanism=none
+
+# apt installation as root
+USER root
+
+# copy list of apt packages to be installed  
+COPY apt.txt /tmp/
+
+# install the packages and clean up
+RUN apt-get update -y &&\
+    xargs -a /tmp/apt.txt apt-get install -y &&\
+    apt-get clean &&\
+    rm /tmp/apt.txt 
+
+# install conda packages as $DOCKER_USER
+USER ${DOCKER_UID}
+WORKDIR ${HOME}
 ARG PYTHON_VERSION=default
 
 COPY . ${HOME}/
 RUN mamba env update -n base -f ${HOME}/environment.yml && \
     mamba clean --all -f -y && \
     mamba list
 
+# Fix permissions on /etc/jupyter as root
+USER root
+RUN fix-permissions /etc/jupyter/ &&\
+    fix-permissions ${HOME} && \
+    fix-permissions ${CONDA_DIR}
+
+# switch back to DOCKER_USER
+USER $DOCKER_UID
 WORKDIR $HOME

mpie_cmti/apt.txt

@@ -0,0 +1,2 @@
+libgl1-mesa-glx
+patch

mpie_cmti/environment.yml

@@ -5,29 +5,40 @@ dependencies:
 - aimsgb =1.1.1
 - atomicrex =1.0.4
 - bader =1.0.5
+- bokeh =3.6.1
 - calphy =1.3.11
 - fitsnap3 =3.1.0.4
+- flux-core =0.64.0
+- git =2.46.0
+- gpaw =24.6.0=*openmpi*
+- jupyter-server-proxy =4.4.0
+- lammps =2023.08.02=*openmpi*
+- llama-index =0.12.1
+- matgl =1.1.2
+- maxvolpy =0.3.8
+- mkl =2023.2.0
+- mlip =2.0
 - nbgitpuller =1.2.1
+- netcdf4 =1.7.1
+- nglview =3.1.2
+- numba =0.60.0
+- openkim-models =2021.01.28
+- psycopg2 =2.9.9
+- pyiron =0.5.2
+- pyiron-data =0.0.30
+- pyiron_atomistics =0.6.17
+- pyiron_base =0.10.8
 - pyiron_contrib =0.1.18
+- pyiron_gpl =0.0.5
+- pyiron_gui =0.0.12
 - pyiron_potentialfit =0.3.7
 - pyiron_workflow =0.11.2
-- pyiron_gui =0.0.12
 - pyironflow =0.0.4
-- matgl =1.1.2
-- mlip =2.0
-- sqsgenerator =0.3
-- pyiron_gpl =0.0.5
 - python-ace =0.3.0
 - pytorch =2.1.2
 - pyxtal =1.0.5
 - runner =1.3
+- sphinxdft =3.1
+- sqsgenerator =0.3
 - structdbrest =0.0.1
 - tensorflow =2.17.0
-- psycopg2 =2.9.9
-- numba =0.60.0
-- llama-index =0.12.1
-- jupyter-server-proxy =4.4.0
-- flux-core =0.64.0
-- netcdf4 =1.7.1
-- maxvolpy =0.3.8
-- bokeh =3.6.1