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Important notice: in the following a generic name `lmgc90_user_xxxx` is used in the instruction, but each time the `xxxx` is met, it must be replaced by the real name of the version used. For example the `2020.rc1` or `2020`.
# Singularity
Here are provided some very basics directions on how to use LMGC90 in a Singularity container.
On how to install and use Singularity properly, check their [official website](https://apptainer.org/).
For a direct use, download the image file:
* [lmgc90_user_2024_rc1.sif](https://seafile.lmgc.univ-montp2.fr/f/0213f8323051431d8744/?dl=1)
* [lmgc90_user_2023.sif](https://seafile.lmgc.univ-montp2.fr/f/577871f9c9344a7a8711/?dl=1)
* [lmgc90_user_2023_rc2.sif](https://seafile.lmgc.univ-montp2.fr/f/ffa27bb6a3e04016a72b/?dl=1)
* [lmgc90_user_2023_rc1.sif](https://seafile.lmgc.univ-montp2.fr/f/1c75255d95f5460c9dee/?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_xxxx.sif python command.py
```
It is preferred to stay in the same image ; for example in order to
run several python commands:
```cmd
singularity shell lmgc90_user_xxxx.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:jammy
%files
lmgc90_user_xxxx /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 cython3 python-is-python3
apt install -y python3-scipy python3-matplotlib python3-pandas python3-vtk9 python3-igraph
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_xxxx.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.
```file
FROM ubuntu:jammy
# install packages
RUN apt update -y
RUN apt upgrade -y
RUN DEBIAN_FRONTEND=noninteractive apt-get install -y tzdata
RUN apt install -y git cmake gcc g++ gfortran liblapack-dev swig python3-dev python3-numpy cython3 python-is-python3
RUN apt install -y python3-scipy python3-matplotlib python3-pandas python3-vtk9 python3-igraph
RUN apt install -y libhdf5-dev hdf5-tools python3-h5py
# get the sources
COPY lmgc90_user_xxxx /root/lmgc90
# build the sources
WORKDIR /root/lmgc90/build
RUN cmake ../ -DWITH_HDF5=ON -DNO_INSTALL=FALSE -DWITH_OPENMP=True
RUN make && make install
# clean build and source directories
WORKDIR /root/compute
RUN rm -rf /root/lmgc90
```
Then build the docker image with (again replace the `xxxx` by your revision), do not forget the ending dot character:
```cmd
docker build -t lmgc90_user:xxxx -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:2022.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:xxxx /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
Important notice: in the following a generic name `lmgc90_user_xxxx` is used in the instruction, but each time the `xxxx` is met, it must be replaced by the real name of the version used. For example the `2020.rc1` or `2020`.
# Singularity
Here are provided some very basics directions on how to use LMGC90 in a Singularity container.
On how to install and use Singularity properly, check their [official website](https://apptainer.org/).
For a direct use, download the image file:
* [lmgc90_user_2024_rc1.sif](https://seafile.lmgc.univ-montp2.fr/f/0213f8323051431d8744/?dl=1) (m5sum e58a398352a64b41567e0aaf816863df)
* [lmgc90_user_2023.sif](https://seafile.lmgc.univ-montp2.fr/f/577871f9c9344a7a8711/?dl=1)
* [lmgc90_user_2023_rc2.sif](https://seafile.lmgc.univ-montp2.fr/f/ffa27bb6a3e04016a72b/?dl=1)
* [lmgc90_user_2023_rc1.sif](https://seafile.lmgc.univ-montp2.fr/f/1c75255d95f5460c9dee/?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_xxxx.sif python command.py
```
It is preferred to stay in the same image ; for example in order to
run several python commands:
```cmd
singularity shell lmgc90_user_xxxx.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:jammy
%files
lmgc90_user_xxxx /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 cython3 python-is-python3
apt install -y python3-scipy python3-matplotlib python3-pandas python3-vtk9 python3-igraph
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_xxxx.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.
```file
FROM ubuntu:jammy
# install packages
RUN apt update -y
RUN apt upgrade -y
RUN DEBIAN_FRONTEND=noninteractive apt-get install -y tzdata
RUN apt install -y git cmake gcc g++ gfortran liblapack-dev swig python3-dev python3-numpy cython3 python-is-python3
RUN apt install -y python3-scipy python3-matplotlib python3-pandas python3-vtk9 python3-igraph
RUN apt install -y libhdf5-dev hdf5-tools python3-h5py
# get the sources
COPY lmgc90_user_xxxx /root/lmgc90
# build the sources
WORKDIR /root/lmgc90/build
RUN cmake ../ -DWITH_HDF5=ON -DNO_INSTALL=FALSE -DWITH_OPENMP=True
RUN make && make install
# clean build and source directories
WORKDIR /root/compute
RUN rm -rf /root/lmgc90
```
Then build the docker image with (again replace the `xxxx` by your revision), do not forget the ending dot character:
```cmd
docker build -t lmgc90_user:xxxx -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:2022.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:xxxx /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
```
\ No newline at end of file