|
|
|
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 |
