Install on Azure Synpase Analytics

This tutorial will guide you through the process of installing Sedona on Azure Synapse Analytics when Data Exfiltration Protection (DEP) is enabled or when you have no internet connection from the Spark pools due to other networking constraints.

Before you begin¶

This tutorial focuses on getting you up and running with Sedona 1.6.1 on Spark 3.4 Python 3.10

If you want to run newer version, you will need to dive into the detailed build and diagnose process detailed in the lower part of this document.

Strong recommendations¶

Start with a clean Spark pool with no other packages installed to avoid package conflicts.
Apache Spark pool -> Apache Spark configuration: Use default configuration

Sedona 1.6.1 on Spark 3.4 Python 3.10¶

Step1: Download packages (9)¶

Caution: Precise versions are critical, latest is not always greatest here.

From Maven

From PyPi

Step 2: Upload packages to Synapse Workspace¶

https://learn.microsoft.com/en-us/azure/synapse-analytics/spark/apache-spark-manage-workspace-packages

Step 3: Add packages to Spark Pool¶

This tutorial used the second method on this page: If you are updating from the Synapse Studio

https://learn.microsoft.com/en-us/azure/synapse-analytics/spark/apache-spark-manage-pool-packages#manage-packages-from-synapse-studio-or-azure-portal

Step 4: Notebook¶

Start your notebook with:

from sedona.spark import SedonaContext

config = SedonaContext.builder() \
    .config('spark.jars.packages',
            'org.apache.sedona:sedona-spark-shaded-3.4_2.12-1.6.1,'
            'org.datasyslab:geotools-wrapper-1.6.1-28.2') \
    .config("spark.serializer","org.apache.spark.serializer.KryoSerializer") \
    .config("spark.kryo.registrator", "org.apache.sedona.core.serde.SedonaKryoRegistrator") \
    .config("spark.sql.extensions", "org.apache.sedona.viz.sql.SedonaVizExtensions,org.apache.sedona.sql.SedonaSqlExtensions") \
    .getOrCreate()

sedona = SedonaContext.create(config)

Run a test

sedona.sql("SELECT ST_GeomFromEWKT('SRID=4269;POINT(40.7128 -74.0060)')").show()

If you see the output of the point, then the installation is successful. Are you are all done with the setup.

Packages for Sedona 1.6.0 on Spark 3.4 Python 10¶

spark-xml_2.12-0.17.0.jar
sedona-spark-shaded-3.4_2.12-1.6.0.jar

click_plugins-1.1.1-py2.py3-none-any.whl
affine-2.4.0-py3-none-any.whl
apache_sedona-1.6.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
cligj-0.7.2-py3-none-any.whl
rasterio-1.3.10-cp310-cp310-manylinux2014_x86_64.whl
shapely-2.0.4-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
snuggs-1.4.7-py3-none-any.whl
geotools-wrapper-1.6.0-28.2.jar

Background: How to identify packages for other/future versions of Spark and/or Sedona¶

Warning: this process is going to require some tenacious technical skills and troubleshooting.

Broad steps: build a linux VM from the same image as the deployed Spark Pool, configure for Synapse, install Sedona packages, identify required packages over and above baseline Synapse config.

This is the process for Sedona 1.6.1 on Spark 3.4 Python 3.10. (The same process was used for Sedona 1.6.0)

Important settings if using Hyper-V

Enable Secure Boot: Microsoft UEFI Certificate authority
Cores 2
Disable Dynamic Memory (fix at 8Gb), forgetting this setting causes havoc.

Step 4: patch the VM¶

Connect the VM. Note: it will take longer to first boot than you'd expect

sudo dnf upgrade

Step 5: optional but strongly recommended - install ssh-server (for best copy and paste experience)¶

sudo tdnf install -y openssh-server

Enable root and password auth

sudo vi /etc/ssh/sshd_config
-   PasswordAuthentication yes
-   PermitRootLogin yes

Start ssh-server

sudo systemctl enable --now sshd.service

Identify the ip of the VM (I'm using Hyper-V on windows 10 desktop)

Get-VMNetworkAdapter -VMName "Synapse Spark 3.4 Python 3.10 Sedona 1.6.1" | Select-Object -ExpandProperty IPAddresses

Step 6: install Miniconda¶

cd /tmp
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
chmod +x Miniconda3-latest-Linux-x86_64.sh
./Miniconda3-latest-Linux-x86_64.sh

Step 7: install compilers¶

sudo tdnf -y install gcc g++

Step 8: create baseline synapse virtual env¶

Download the virtual env spec

wget -O Synapse-Python310-CPU.yml https://raw.githubusercontent.com/microsoft/synapse-spark-runtime/refs/heads/main/Synapse/spark3.4/Synapse-Python310-CPU.yml source

conda env create -f Synapse-Python310-CPU.yml -n synapse

if you get errors due to fsspec_wrapper then remove fsspec_wrapper==0.1.13=py_3 from the yml and run again

if you get further but different errors from pip after making the above change, ignore them you can still proceed

Step 9: install sedona python packages¶

conda activate synapse
echo "apache-sedona==1.6.1" > requirements.txt
pip install -r requirements.txt > pip-output.txt

Step 10: identify Python packages to download¶

grep Downloading pip-output.txt

This will be the list of packages you need to locate and download from PyPi

Example output

Downloading apache_sedona-1.6.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (177 kB)
Downloading shapely-2.0.6-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (2.5 MB)
Downloading rasterio-1.4.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (22.2 MB)
Downloading affine-2.4.0-py3-none-any.whl (15 kB)
Downloading cligj-0.7.2-py3-none-any.whl (7.1 kB)
Downloading click_plugins-1.1.1-py2.py3-none-any.whl (7.5 kB)

Step 11: identify package conflicts in your deployed Azure Synapse Spark Pool (the real one, not the VM)¶

upload packages to workspace
add packages to your (clean!) Spark pool

Pay careful attention to errors reported back from Synpase and troubleshoot to resolve conflicts.

Note: We didn't have issues with Sedona 1.6.0 on Spark 3.4, but Sedona 1.6.1 and supporting packages had a conflict around numpy which requires us to download a specific version and add it to the packages list. numpy was not listed in the output of the grep.