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Singularity Documentation: https://docs.sylabs.io/guides/4.3latest/user-guide/
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Initial account setup
- Create an account on sylabs (via google/ucar email)
- Generate access token - Once logged in, go to the top right in the drop down menu under your user name and click "Access Tokens". Enter a label/alias, ie "Hercules", and click "Create Access Token". You will be prompted for this token when you first create a container using the
--remoteoption.
Environment setup
Load the singularity module with: module load singularity
Building a singularity container
Singularity containers can be built using a .def file. This allows for easy reproducibility and standardization. You can find more information on this file setup in the Singularity Documentation. Below is a simple .def file used for a bare bones container
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TODO
Running a container
that is used to run WeatherBenchX.
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Bootstrap: docker
From: ubuntu:22.04
%labels
Maintainer AGriffin
Purpose WeatherBenchX
%post
export DEBIAN_FRONTEND=noninteractive
# Install dependencies
apt-get update && apt-get install -y \
software-properties-common \
curl \
wget \
build-essential \
git \
vim \
libffi-dev \
libssl-dev \
libbz2-dev \
libreadline-dev \
libsqlite3-dev \
zlib1g-dev \
libncursesw5-dev \
xz-utils \
tk-dev \
libxml2-dev \
libxmlsec1-dev \
liblzma-dev \
ca-certificates \
&& apt-get clean
# Add deadsnakes PPA and install Python 3.11 and venv
add-apt-repository ppa:deadsnakes/ppa -y
apt-get update && apt-get install -y \
python3.11 \
python3.11-venv \
python3.11-dev \
python3.11-distutils \
&& apt-get clean
# Point python3 to python3.11
update-alternatives --install /usr/bin/python3 python3 /usr/bin/python3.11 1
# Create the virtual environment
python3 -m venv /venv_wb
# Install WeatherBenchX and dependencies
/venv_wb/bin/pip install --upgrade pip setuptools wheel
git clone https://github.com/google-research/weatherbenchX /weatherbenchX
cd /weatherbenchX
/venv_wb/bin/pip install -e .
/venv_wb/bin/pip install netCDF4
%environment
# Activate virtual environment at runtime
source /venv_wb/bin/activate
export PATH="/venv_wb/bin:$PATH"
%runscript
echo "Singularity container for WeatherBenchX"
exec /bin/bash |
In order to build a container on a remote host or HPC, you need to use the --remote flag since we typically do not have admin privileges. An example build command using the definition file above on Hercules is: singularity build --remote wb_container.sif /work2/noaa/jcsda/agriffin/JEDI_WB/wb_container/wb_container.def
Running a container
Running a container is done by using the singularity exec command. The singularity exec command will run a specific command against an instance. An example of how we can use this inside an EWOK task is the line in the runtime file for weather bench scores (src/runtime/wbScoresRun.sh):
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singularity exec -B $WORKDIR:/$WORKDIR -B $JEDI_WORKFLOW:/jedi-workflow -B /work2/noaa/jcsda/cgas/jedi/wb_files:/work2/noaa/jcsda/cgas/jedi/wb_files /work2/noaa/jcsda/agriffin/JEDI_WB/wb_container/wb_container.sif bash -c "cd $WORKDIR && python3 /jedi-workflow/ewok/src/runtime/evaluation_deterministic.py" |
Note, -B will "bind"/mount the directories you need onto the container.
Note, you can also run singularity shell work2/noaa/jcsda/agriffin/JEDI_WB/wb_container/wb_container.sif to spawn a new shell within your container.TODO