moved all installations to /opt

Dockerfile

@@ -2,28 +2,16 @@ FROM aiidalab/full-stack:2025.1025
 
 USER root
 
-
-#RUN apt-get update -y && apt-get install -y cp2k && apt-get clean -y
-# Install required system dependencies, including MPI development libraries
 RUN apt-get update -y && apt-get install -y  cp2k libmpich-dev libopenmpi-dev  build-essential  && apt-get clean -y
 
-USER ${NB_USER}
-
-
-
-
-RUN mkdir /home/${NB_USER}/opt
-
 RUN pip install virtualenv
 
-ENV deepmd_root=/home/${NB_USER}/opt/deepmd-kit
-ENV deepmd_source_dir=/home/${NB_USER}/opt/deepmd-kit
-ENV tensorflow_venv=/home/${NB_USER}/opt/tensorflow_venv
-ENV deepmd_root=/home/${NB_USER}/opt/deepmd-kit
-
-RUN cd /home/${NB_USER}/opt && git clone https://github.com/deepmodeling/deepmd-kit.git deepmd-kit
-
+ENV deepmd_root=/opt/deepmd-kit
+ENV deepmd_source_dir=/opt/deepmd-kit
+ENV tensorflow_venv=/opt/tensorflow_venv
+ENV deepmd_root=/opt/deepmd-kit
 
+RUN cd /opt && git clone https://github.com/deepmodeling/deepmd-kit.git deepmd-kit
 
 RUN virtualenv -p python3 $tensorflow_venv
 
@@ -40,43 +28,38 @@ RUN cd $deepmd_source_dir/source/build && pwd && pip install -U cmake && cmake -
 
 RUN cd $deepmd_source_dir/source/build && make lammps
 
-
-RUN cd /home/${NB_USER}/opt &&  git clone https://github.com/lammps/lammps && cd lammps/src && cp -r $deepmd_source_dir/source/build/USER-DEEPMD . && make lib-pace args="-b" && make yes-molecule && make yes-reaxff && make yes-rigid && make yes-ml-pace && make yes-manybody && make lib-voronoi args="-b" && make yes-voronoi && make lib-plumed args="-b" CC=gcc CXX=g++ && make yes-plumed && make yes-kspace && make yes-extra-fix && make yes-user-deepmd && make serial
+RUN cd /opt &&  git clone https://github.com/lammps/lammps && cd lammps/src && cp -r $deepmd_source_dir/source/build/USER-DEEPMD . && make lib-pace args="-b" && make yes-molecule && make yes-reaxff && make yes-rigid && make yes-ml-pace && make yes-manybody && make lib-voronoi args="-b" && make yes-voronoi && make lib-plumed args="-b" CC=gcc CXX=g++ && make yes-plumed && make yes-kspace && make yes-extra-fix && make yes-user-deepmd && make serial
 
 RUN deactivate 
 
-USER root
+RUN cp /opt/lammps/src/lmp_serial /usr/bin/lmp_serial
 
-RUN cp /home/${NB_USER}/opt/lammps/src/lmp_serial /usr/bin/lmp_serial
-
-USER ${NB_USER}
+RUN rm -rf /opt/lammps/
 
 ENV JUPYTER_TERMINAL_IDLE_TIMEOUT=3600
 ENV ASE_LAMMPSRUN_COMMAND="/usr/bin/lmp_serial"
 
-RUN rm -rf /home/${NB_USER}/opt/lammps/
 
 RUN pip install nglview
 
 RUN pip install mdtraj
 
 RUN pip install  skmatter
 
-RUN cd opt && git clone https://github.com/lab-cosmo/librascal.git && cd librascal && pip install  .
+RUN cd /opt && git clone https://github.com/lab-cosmo/librascal.git && cd librascal && pip install  .
 
 RUN pip install scikit-learn optuna xgboost lightgbm sympy pandas
 
 RUN pip install torch  torchmetrics torchvision
 
-RUN cd /home/${NB_USER}/opt && git clone https://github.com/aoterodelaroza/critic2.git
+RUN cd /opt && git clone https://github.com/aoterodelaroza/critic2.git
 
-RUN cd /home/${NB_USER}/opt/critic2 && mkdir build && cd build && cmake .. && make 
+RUN cd /opt/critic2 && mkdir build && cd build && cmake .. && make 
 
 
 
 RUN pip install pymatgen scikit-image
 
-#RUN pip install --user aiida-cp2k
 
 RUN pip install  spglib
 
@@ -86,37 +69,16 @@ RUN pip install cp2k-spm-tools
 
 #### hyperqueue
 
-# Install HyperQueue binary
-#hq-v0.19.0-rc1-linux-arm64-linux.tar.gz
-#ARG HQ_VER
-#ARG HQ_COMPUTER
-#USER root
-#RUN cd /home/${NB_USER}/opt && wget -c -O hq.tar.gz https://github.com/It4innovations/hyperqueue/releases/download/v0.21.0/hq-v0.21.0-linux-arm64-linux.tar.gz && \
-#    tar xf hq.tar.gz -C /usr/local/bin/ && \
-#    rm hq.tar.gz
-#USER ${NB_USER}
-
-# Install the aiida-hyperqueue
-# XXX: fix me after release aiida-hyperqueue
-#RUN --mount=from=uv,source=/uv,target=/bin/uv \
-#    --mount=from=build_deps,source=${UV_CACHE_DIR},target=${UV_CACHE_DIR},rw \
-#     uv pip install --system --strict --cache-dir=${UV_CACHE_DIR} \
-#     "aiida-hyperqueue@git+https://github.com/aiidateam/aiida-hyperqueue"
 
-#RUN pip install "aiida-hyperqueue@git+https://github.com/aiidateam/aiida-hyperqueue"
-
-#ENV HQ_COMPUTER=$HQ_COMPUTER
-
-USER root
-RUN mv /home/jovyan/opt/critic2/build/src/critic2 /usr/local/bin/critic2
+RUN mv /opt/critic2/build/src/critic2 /usr/local/bin/critic2
 RUN chmod a+rx /usr/local/bin/critic2
-RUN rm -rf /home/jovyan/opt/critic2
+RUN rm -rf /opt/critic2
 
 ####
 # Copy from local computer to Docker
 COPY before-notebook.d/* /usr/local/bin/before-notebook.d/
 COPY configs /opt/configs
 RUN chmod a+rx /opt/configs
 RUN chmod a+rx /opt/configs/*
-
+RUN chown -R ${NB_USER}:users /home/jovyan
 USER ${NB_USER}