About

This page provides instructions for installing NetworkX.

It was tested for networkx/2.8.8

The instructions below will install networkx in a Python virtual environment which in this example is called nx_venv. They are based on instructions provided here: https://networkx.org/documentation/stable/install.html

If you notice any issues, please let us know.

1 About
2 ALICE
- 2.1 Intel nodes
- 2.2 AMD nodes
3 SHARK

ALICE

ALICE has two system-wide software stacks, i.e., one for nodes with Intel CPUs and one for nodes with AMD CPUs.

Because the login nodes have Intel CPUs, installing software for AMD nodes works slightly different.

Intel nodes

Make sure that you have a clean module environment
You can either copy the commands or safe them in a shell script and execute them
You can run the instructions on the login nodes
Adjust the path (line 6) as needed

#!/bin/bash
module purge
module load ALICE/default
module load Python/3.8.6-GCCcore-10.2.0

# Set the path as needed
venv_path='/path/to/nx_venv'

############################
# Commands below should work
# without modifications
############################

# Create virtual environment
python -m venv $venv_path

# Source the virtual environment
source $venv_path/bin/activate

# Some prerequisites
# Update pip and setuptools and install wheel
pip install --upgrade pip
pip install --upgrade setuptools
pip install wheel

# Install networkx with default packages
pip install networkx[default]

# Test it
python -c "import networkx as nx; print(nx.__version__); G = nx.Graph(); G.add_node(1); print(list(G.nodes))"

If you need additional extra packages

for pyyaml, lxml and pydot, you can just add pip install pyyaml lxml pydot to the after line 27
for gdal, you can load the corresponding module (module load GDAL/3.2.1-foss-2020b)
for pygraphviz, this package needs Graphviz which is not yet installed system-wide

AMD nodes

Save the commands below in a file (e.g., install_networkx_amd.slurm that can be submitted to slurm using sbatch install_networkx_amd.slurm
- Alternatively, create an interactive job with salloc, ssh to the allocated node and install everything manually. Make sure that you start from a clean module environment.
Adjust the path (line 13) as needed:

#!/bin/bash
#SBATCH --job-name=install_networkx_amd
#SBATCH --output=%x_%j.out
#SBATCH --partition="amd-short"
#SBATCH --time=00:05:00
#SBATCH --ntasks=1
#SBATCH --mem=1G

module load ALICE/default
module load Python/3.8.6-GCCcore-10.2.0

# Adjust path the path as needed
venv_path='/path/to/nx_venv'

############################
# Commands below should work
# without modifications
############################

if [ -d $venv_path ]; then
  echo "#### Virtual environment $venv_path already exists. Continuing"
else
  echo "#### Creating virtual environment $venv_path"
  python -m venv $venv_path
fi

echo "#### Switching to venv"
source $venv_path/bin/activate

echo "#### Updating pip"
pip install --upgrade pip
pip install --upgrade setuptools

echo "#### Installing packages"

echo "## Installing wheel"
pip install wheel

echo "## Installing networkx"
pip install networkx[default]

echo "#### Testing"
echo "networkx"
python -c "import networkx as nx; print(nx.__version__); G = nx.Graph(); G.add_node(1); print(list(G.nodes))"

echo "#### Done"

Make sure to check the slurm output file for any error messages.

If you need additional extra packages

for pyyaml, lxml and pydot, you can just add pip install pyyaml lxml pydot to the batch file after line 40
for gdal, you can load the corresponding module (module load GDAL/3.2.1-foss-2020b)
for pygraphviz, this package needs Graphviz which is not yet installed system-wide

SHARK

Make sure that you have a clean module environment
You can either copy the commands or safe them in a shell script and execute them
You can run the instructions on the login nodes
Adjust the path (line 6) as needed

#!/bin/bash
module purge
module load system/python/3.10.2

# Set the path as needed
venv_path='/path/to/nx_venv'

############################
# Commands below should work
# without modifications
############################

# Create virtual environment
python -m venv $venv_path

# Source the virtual environment
source $venv_path/bin/activate

# Some prerequisites
# Update pip and setuptools and install wheel
pip install --upgrade pip
pip install --upgrade setuptools
pip install wheel

# Install networkx with default packages
pip install networkx[default]

# Test it
python -c "import networkx as nx; print(nx.__version__); G = nx.Graph(); G.add_node(1); print(list(G.nodes))"

If you need additional extra packages

for pyyaml, lxml and pydot, you can just add pip install pyyaml lxml pydot to the batch file after line 27
for gdal, you can try using an existing module module load library/gdal/3.0.4/gcc-8.3.1
for pygraphviz, you need to install Graphviz