Using standard user for the container

Dockerfile

@@ -31,17 +31,6 @@
 # Importing Ubuntu image
 FROM ubuntu:18.04
 
-# Build arguments
-ARG PREFIX
-
-# Environment variables
-ENV DEBIAN_FRONTEND noninteractive
-ENV QUIP_ARCH linux_x86_64_gfortran
-ENV QUIP_STRUCTS_DIR $PREFIX/QUIP/structs
-ENV QUIP_INSTALLDIR $PREFIX/QUIP/bin
-USER $USER
-WORKDIR /root/
-
 # Updating distro
 RUN \
   apt-get update && \
@@ -55,54 +44,71 @@ RUN \
   apt-get autoclean && \
   apt-get autoremove
 
+# Installing Python3 modules
+RUN pip3 install numpy matplotlib vtk
+RUN pip3 install mayavi
+
+# Adding standard user
+RUN adduser --disabled-password --gecos '' --uid 1000 --gid 100 favad
+
+# Environment variables
+ENV DEBIAN_FRONTEND noninteractive
+ENV HOME /home/favad
+ENV PREF $HOME/software
+ENV QUIP_ARCH linux_x86_64_gfortran
+ENV QUIP_STRUCTS_DIR $PREF/QUIP/structs
+ENV QUIP_INSTALLDIR $PREF/QUIP/bin
+
 # Copying software source files
 COPY ./software /tmp/software
+RUN chown -R favad /tmp/software
 
-# Creating installation folder
-RUN mkdir -p $PREFIX
+# Copying sample files
+COPY ./sample $HOME/sample
+RUN  chown -R favad $HOME/sample
 
-# Installing Python3 modules
-RUN pip3 install numpy matplotlib vtk 
-RUN pip3 install mayavi
+# Switching to standard user
+USER favad
+WORKDIR $HOME
+
+# Creating installation folder
+RUN mkdir -p $PREF
 
 # Installing QUIP
 RUN \
-  tar xvzf /tmp/software/QUIP.tar.gz -C $PREFIX/. && \
-  cd $PREFIX/QUIP/ && \
-  tar xvzf /tmp/software/GAP.tar.gz -C $PREFIX/QUIP/src/. && \
+  tar xvzf /tmp/software/QUIP.tar.gz -C $PREF/. && \
+  cd $PREF/QUIP/ && \
+  tar xvzf /tmp/software/GAP.tar.gz -C $PREF/QUIP/src/. && \
   (echo ; echo ; echo ; echo ; echo ; echo ; echo ; echo ; echo ; echo ; echo ; echo y ; echo ; echo ; echo ; echo ; echo ; echo ; echo ; echo ; echo ; echo ; echo ; echo ; echo ) | make config && \
   make && \
   make install 
 
 # Installing VORO++
 RUN \
-  mkdir -p $PREFIX/voro++ && \
-  tar xvzf /tmp/software/voro++-0.4.6.tar.gz -C $PREFIX/voro++ --strip-components 1 && \
-  cd $PREFIX/voro++/ && \
-  sed -i "21s|.*|PREFIX=$PREFIX/voro++|" ./config.mk && \
+  mkdir -p $PREF/voro++ && \
+  tar xvzf /tmp/software/voro++-0.4.6.tar.gz -C $PREF/voro++ --strip-components 1 && \
+  cd $PREF/voro++/ && \
+  sed -i "21s|.*|PREFIX=$PREF/voro++|" ./config.mk && \
   make && \
   make install
 
 # Installing KDTREE2
 RUN \
-  tar xvzf /tmp/software/kdtree2.tar.gz -C $PREFIX/. && \
-  cd $PREFIX/kdtree2/ && \
+  tar xvzf /tmp/software/kdtree2.tar.gz -C $PREF/. && \
+  cd $PREF/kdtree2/ && \
   gfortran -c kdtree2.f90 && \
   gfortran -o kdtree2_iaea_v03.x kdtree2_iaea_v03.f90 kdtree2.o
 
 # Installing VisIt
 RUN \
-  mkdir -p $PREFIX/visit/ && \
+  mkdir -p $PREF/visit/ && \
   cd /tmp/software/ && \
-  chmod 755 /tmp/software/visit-install2_13_3 && \
-  (echo 1) | bash ./visit-install2_13_3 2.13.3 linux-x86_64-ubuntu18-wmesa $PREFIX/visit/
+  chmod 755 ./visit-install2_13_3 && \
+  (echo 1) | bash ./visit-install2_13_3 2.13.3 linux-x86_64-ubuntu18-wmesa $PREF/visit/
 
 # Removing installation packages
 RUN rm -rf /tmp/software/
 
-# Copying sample files
-COPY ./sample /root/sample
-
 # Run bash when the container launches
 CMD ["/bin/bash"]
 

README.md

@@ -55,15 +55,15 @@ If these optional parameters are not specified, the build process will ask for t
 Once the Docker image has been created and the [Docker daemon is running](https://docs.docker.com/config/daemon/), you can shell into the container mounting a local folder where the output files will be stored, using:
 
 ```shell
-sudo docker run -t -i --volume $HOME/favad_output/:/root/sample/output/ favad /bin/bash
+sudo docker run -t -i --volume $HOME/favad_output/:/home/favad/sample/output/ favad /bin/bash
 ```
 
 Using the previous command, the ouput files generated inside the Docker container will be available in $HOME/faved_output/ of your local machine. Please note that the content of this folder will be overwritten, if the folder is not empty.
 
 At this point you can run the workflow for fingerprinting and visualizing defects on the sample dataset inside the Docker container:
 ```shell
-cd /root/sample/
-python3 FaVaD.py -p /root/sample/parameters.txt
+cd /home/favad/sample/
+python3 FaVaD.py -p /home/favad/sample/parameters.txt
 ```
 
 ---

build.sh

@@ -113,10 +113,10 @@ echo
 echo "Build complete!"
 echo
 echo "You can run the image interactively mounting an ouput folder (use the full path) with:"
-echo "  sudo docker run -t -i --volume $HOME/favad_output/:/root/sample/output/ favad /bin/bash"
+echo "  sudo docker run -t -i --volume $HOME/favad_output/:/home/favad/sample/output/ favad /bin/bash"
 echo "and, once in the container" 
-echo "  cd /root/sample/"
-echo "  python3 FaVaD.py -p /root/sample/parameters.txt"
+echo "  cd /home/favad/sample/"
+echo "  python3 FaVaD.py -p /home/favad/sample/parameters.txt"
 echo
 
 # Disarming trap and exit

sample/parameters.txt

@@ -6,36 +6,36 @@
 # General Parameters
 ####################
 # Output folder
-OUTPUT_PATH = /root/sample/output/
+OUTPUT_PATH = /home/favad/sample/output/
 
 
 ####################
 # Calculation of DVs
 ####################
 # Path to QUIP executable
-QUIP_PATH = /root/software/QUIP/bin/quip
+QUIP_PATH = /home/favad/software/QUIP/bin/quip
 
 # Input xyz file for QUIP (damaged sample)
-QUIP_XYZ = /root/sample/input/fe_sample.xyz
+QUIP_XYZ = /home/favad/sample/input/fe_sample.xyz
 
 # Input reference descriptor vectors
-BCC_VEC = /root/sample/input/bcc_vector.dat
-INT_VEC = /root/sample/input/interstitial_vector.dat
-VAC_VEC = /root/sample/input/vacancy_vector.dat
-TYPA_VEC = /root/sample/input/typea_vector.dat
+BCC_VEC = /home/favad/sample/input/bcc_vector.dat
+INT_VEC = /home/favad/sample/input/interstitial_vector.dat
+VAC_VEC = /home/favad/sample/input/vacancy_vector.dat
+TYPA_VEC = /home/favad/sample/input/typea_vector.dat
 
 # Path to VORO++ executable
-VORO_PATH = /root/software/voro++/bin/voro++
+VORO_PATH = /home/favad/software/voro++/bin/voro++
 
 
 ##########################################
 # Calculation of the nearest atom location
 ##########################################
 # Path to kdtree executable
-KDTREE_PATH = /root/software/kdtree2/kdtree2_iaea_v03.x
+KDTREE_PATH = /home/favad/software/kdtree2/kdtree2_iaea_v03.x
 
 # Input parameter file for kdtree
-KDTREE_PAR = /root/sample/input/void_code_input.txt
+KDTREE_PAR = /home/favad/sample/input/void_code_input.txt
 # Threshold constant for identification of a voids
 KDTREE_THR = 3.00
 
@@ -44,12 +44,12 @@ KDTREE_THR = 3.00
 # Visualization
 ###############
 # Path to visit executable
-VISIT_PATH = /root/software/visit/bin/visit
+VISIT_PATH = /home/favad/software/visit/bin/visit
 
 # Path to VisIt visualization script
-VISIT_SCRIPT = /root/sample/input/vis.py
+VISIT_SCRIPT = /home/favad/sample/input/vis.py
 # Name for the final frames and movie
 VIS_NAME = fe_sample
 # Path to the bash script for the movie creation
-MOVIE_SCRIPT = /root/sample/input/movie.sh
+MOVIE_SCRIPT = /home/favad/sample/input/movie.sh