container.md

 # Singularity
 
-# Docker
+Here are provided some very basics directions on how to use LMGC90 in a Singularity container.
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+On how to install and use Singularity properly, check their [official website](https://sylabs.io/guides/3.6/user-guide/).
+
+For a direct use, download the image file:
+* [lmgc90_user_2020_rc1.sif](https://seafile.lmgc.univ-montp2.fr/f/989e8b26d2d14e4aac08/?dl=1)
+
+On a server or computer with singularity installed, you can directly use the
+singularity image to run a single command with:
+```cmd
+cd path_to_example
+singularity run lmgc90_user_2020_rc1.sif python command.py
+```
+
+If it is prefered to stay in the image, for example in order to
+run python several commands, then run:
+```cmd
+singularity shell lmgc90_user_2020_rc1.sif
+python gen_sample.py --novisu && python command.py
+exit
+```
+Beware, the `pylmgc90.pre.visuAvatars` function CANNOT work in this environment !!!
+
+In case it is desired to build image, the use the following content
+to create a `lmgc90.def` file (beware to beforehand adapt the path
+to the source directory of lmgc90 in the `files` section:
+```file
+Bootstrap: docker
+From: ubuntu:focal
+
+%files
+    lmgc90_user_2020.rc1 /root/lmgc90
+
+%environment
+    export SHELL=/bin/bash
+
+%post
+
+    # install packages
+    export DEBIAN_FRONTEND=noninteractive
+    apt update && apt -y upgrade
+    apt install -y git cmake gcc g++ gfortran liblapack-dev swig python3-dev python3-numpy python3-scipy python3-vtk7 python-is-python3
+    apt install -y cython3
+    apt install -y libhdf5-dev hdf5-tools python3-h5py
+
+    # build the sources
+    cd /root/lmgc90/build
+    cmake ../ -DWITH_HDF5=ON -DNO_INSTALL=FALSE
+    make && make install
+
+    # clean build and source directories
+    rm -rf /root/lmgc90
+```
+Then the image file can be created with:
+```cmd
+singularity build --fakeroot lmgc90_user_2020_rc1.sif lmgc90.def
+```
+
+
+# Docker
+
+Here are provided some very basics directions on how to use LMGC90 in a Docker container.
+On how to install and use Docker properly, check their [official website](https://docs.docker.com/).
+
+To build an image, use the following content to create a `docker_lmgc90` file.
+Of course the `lmgc90_user_2020_rc1` must be replaced by the actual
+path to the sources of lmgc90 to use:
+```file
+FROM ubuntu:focal
+
+# install packages
+RUN apt-get update  -y
+RUN apt-get upgrade -y
+
+RUN DEBIAN_FRONTEND=noninteractive apt-get install -y tzdata
+RUN apt-get install -y git cmake gcc g++ gfortran liblapack-dev swig python3-dev python3-numpy python3-scipy python3-vtk7 python-is-python3
+RUN apt-get install -y cython3
+RUN apt-get install -y libhdf5-dev hdf5-tools python3-h5py
+
+# get the sources
+COPY lmgc90_user_2020_rc1 /root/lmgc90
+
+# build the sources
+WORKDIR /root/lmgc90/build
+RUN cmake ../ -DWITH_HDF5=ON -DNO_INSTALL=FALSE
+RUN make && make install
+
+# clean build and source directories
+WORKDIR /root/compute
+RUN rm -rf /root/lmgc90
+```
+
+Then build the docker image with (again adapt `lmgc90_user:2020.rc1`
+with something relevant to your sources directory):
+```cmd
+docker build -t lmgc90_user:2020.rc1 -f docker_lmgc90 .
+```
+
+Then, next to a `example` directory containing a `gen_sample.py` (with
+NO `visuAvatars` command) and a `command.py`, a docker container
+can be run sharing the `example` directory and run a single command with:
+```cmd
+docker run -it -v $PWD/example:/root/compute lmgc90_user:2020.rc1 python command.py
+```
+To stay in the container for, let's say run python in interactive mode, or run 
+several commands, preferably use:
+```cmd
+docker run -it -v $PWD/example:/root/compute lmgc90_user:2020.rc1 /bin/bash
+python gen_sample.py --novisu
+python command.py
+exit
+```
+
+When using docker, it is good practice to sometime clean the
+container leftovers with:
+```cmd
+docker container prune
+```
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