PySpark on YARN in self-contained environments

pyspark-on-yarn-self-contained.md

PySpark on YARN in self-contained environments

Author: https://github.com/seanorama

Note: This was tested on HDP 3.1. It may not work with other Spark/YARN distributions.

Reference:

• https://community.cloudera.com/t5/Community-Articles/Using-VirtualEnv-with-PySpark/ta-p/245905
• https://community.cloudera.com/t5/Community-Articles/Running-PySpark-with-Conda-Env/ta-p/247551
• https://stackoverflow.com/questions/48770263/bundling-python3-packages-for-pyspark-results-in-missing-imports
• https://stackoverflow.com/questions/53524696/livy-no-yarn-application-is-found-with-tag-livy-batch-10-hg3po7kp-in-120-seconds
• https://conda.github.io/conda-pack/spark.html
• https://spark.apache.org/docs/latest/running-on-yarn.html#spark-properties
• https://spark.apache.org/docs/latest/configuration.html
• https://livy.incubator.apache.org/docs/latest/rest-api.html
• https://github.com/apache/zeppelin/blob/master/docs/interpreter/livy.md#configuration

Why

By default, pyspark jobs will use the Python from the local system of each YARN NodeManager host. Which means:

• If a different version of Python is needed, it must be installed and maintain on all of the hosts
• If additional modules (i.e. from pip) are needed they must be installed and maintained on all of the hosts

This presents a lot of overhead and introduces many risks. Also, the Spark developers typically do not have direct access to YARN NodeManager hosts.

Further, it is a good practice to manage dependencies from the development side, which is only possible if all Python dependencies are "self-contained".

Overview

There are 2 methods to have self-contained environments:

• a) Use an archive (i.e. tar.gz) of a Python environment (virtualenv or conda):
  • Benefits:
    • Faster load time than an empty 'virtualenv' since the packages are already present.
    • Uses the YARN Shared cache: https://hadoop.apache.org/docs/stable/hadoop-yarn/hadoop-yarn-site/SharedCache.html
      • During 1st use of the environment, it will be cached. Future uses will load very fast.
    • Not tied to the Python driver of the NodeManager machines, meaning any Python version can be used and nothing ever has to be done on the NodeManagers.
    • Completely self-contained. No external dependencies.
  • Caveats:
    • Can't install additional packages at run-time.
• b) Use python.pyspark.virtualenv which creates a new virtualenv at Spark runtime:
  • Benefits:
    • Install packages at runtime.
  • Caveats:
    • Not entirely self-contained since it depends on the interpreter being available on all YARN NodeManager hosts (i.e. at /usr/bin/python3 or wherever you place it). Which also makes it harder to change versions.
    • Very SLOW as every job will require downloading and building the pip packages.
    • Depends on public internet access, or a local network pypi/conda repo.

---

How to: Use an archive (i.e. tar.gz) of a Python environment (virtualenv or conda):

Overview:

1. Create an environment with virtualenv or conda
2. Archive the environment to a .tar.gz or .zip.
3. Upload the archive to HDFS
4. Tell Spark (via spark-submit, pyspark, livy, zeppelin) to use this environment
5. Repeat for each different virtualenv that is required or when the virtualenv needs updating

(Optional) Create a shared HDFS path for storing the environment(s):

Only necessary if sharing the environment and if a location doesn't already exist.

sudo -u hdfs -i

## if kerberos
keytab=/etc/security/keytabs/hdfs.headless.keytab
kinit -kt ${keytab} $(klist -kt ${keytab}| awk '{print $NF}'|tail -1)
## endif

hdfs dfs -mkdir -p /share/python-envs
hdfs dfs -chmod -R 775 /share

## replace the group with a user group that will be managing the archives
hdfs dfs -chown -R hdfs:hadoop /share

exit

---

Create archive using Python virtualenv and tar

1. Install python3 and python-virtualenv on a host with same Operating System and CPU architecture as the cluster, such as an edge host:
   • Can be in your home-directory without root/sudo access
     • downloading python manually
     • using pyenv or similar application
   • Or system-wide:

sudo yum install python3 python-virtualenv

2. Create the archive:

## Create requirements for `pip`
tee requirements.txt > /dev/null << EOF
arrow
jupyter
numpy
pandas
scikit-learn
EOF

## The name of the environment
env="python3-venv"

## Create the environment
python3 -m venv ${env} --copies
source ${env}/bin/activate
pip install -U pip
pip install -r requirements.txt
deactivate

## Archive the environment
cd ${env}
tar -hzcf ../${env}.tar.gz *
cd ..

Or create archive using conda and conda-pack

1. Install Anaconda or Conda on a host with same Operating System and CPU architecture as the cluster, such as an edge host:

   • Can be in your home-directory without root/sudo access
     • Anaconda: https://www.anaconda.com/distribution/
     • Miniconda: https://docs.conda.io/en/latest/miniconda.html
   • Or system-wide with yum or apt:
     • https://docs.conda.io/projects/conda/en/latest/user-guide/install/rpm-debian.html

2. Create the archive:

## Create requirements for `conda`
tee requirements.txt > /dev/null << EOF
arrow
jupyter
numpy
pandas
scikit-learn
EOF

## The name of the environment
env="python3-venv"

## Create the environment
conda create -y -n ${env} python=3.7 ## May give a file-system error. If so, simply run again. This is due to conda not being initialized
conda activate ${env}
conda install -y -n ${env} -f requirements.txt
conda install -y -n ${env} -c conda-forge conda-pack

## Archive the environment
conda pack -f -n ${env} -o ${env}.tar.gz

conda deactivate

Use the archive: Same steps for a virtualenv or for conda:

3. Put to HDFS:
   • You may need to kinit 1st. Can do this as your own user.

hdfs dfs -put -f ${env}.tar.gz /share/python-envs/
hdfs dfs -chmod 0664 /share/python-envs/${env}.tar.gz

4. Test it:

## Create test script
tee test.py > /dev/null << EOF
from pyspark import SparkConf
from pyspark import SparkContext

conf = SparkConf()
conf.setAppName('pyspark-test')
sc = SparkContext(conf=conf)

import numpy
print("Hello World!")
sc.parallelize(range(1,10)).map(lambda x : numpy.__version__).collect()
EOF

## Submit to Spark
deactivate
conda deactivate

## Note: `--archives` can be used instead of `--conf spark.yarn.dist.archives`. I prefer to see the full conf statement.
spark-submit \
--conf spark.yarn.appMasterEnv.PYSPARK_PYTHON=./environment/bin/python \
--conf spark.yarn.dist.archives=hdfs:///share/python-envs/${env}.tar.gz#environment \
--master yarn \
--deploy-mode cluster \
test.py

## Check the logs: Update the `id` to the id of your job from above.
id=application_GetTheIdFromOutputOfCommandAbove
yarn logs -applicationId ${id} | grep "Hello World"

5. Update Zeppelin %livy2.pyspark

• Note: This only works with YARN cluster deploy mode. It is the default in HDP3.
• In Zeppelin: click "top right" menu -> Interpreters -> Add to the livy2 interpreter:

livy.spark.yarn.appMasterEnv.PYSPARK_PYTHON=./environment/bin/python
livy.spark.yarn.dist.archives=hdfs:///share/python-envs/python3-venv.tar.gz#environment

• Test from a notebook:

%livy2.pyspark
import numpy
print("Hello World!")
sc.parallelize(range(1,10)).map(lambda x : numpy.__version__).collect()

---

Howto create a virtualenv at run-time

1. Install python3 and python-virtualenv

   • For this method it must be done on all hosts in the cluster.
   • See the archives instructions for more details of how to install.

2. Example using pyspark shell:

PYSPARK_PYTHON=/bin/python3 \
pyspark \
--conf spark.pyspark.virtualenv.enabled=true \
--conf spark.pyspark.virtualenv.type=native \
--conf spark.pyspark.virtualenv.bin.path=/usr/bin/virtualenv \
--conf spark.pyspark.virtualenv.python_version=3.6 \
--master yarn \
--deploy-mode client

## then, in the shell, install packages:
sc.install_packages(["numpy"])

3. Example using spark-submit.
   • Note the addition of a requirements file.
     • This is optional, you could use the same sc.install_packages file instead inside test.py.
     • If using from HDFS, make sure to upload it ;)
     • You can use it with pyspark above, but the file then must be on the localhost that you are executing pyspark from.

spark-submit \
--conf spark.yarn.appMasterEnv.PYSPARK_PYTHON=/usr/bin/python3 \
--conf spark.pyspark.virtualenv.enabled=true \
--conf spark.pyspark.virtualenv.type=native \
--conf spark.pyspark.virtualenv.bin.path=/usr/bin/virtualenv \
--conf spark.pyspark.virtualenv.python_version=3.6 \
--conf spark.pyspark.virtualenv.requirements=hdfs:///share/python-envs/python3-venv.requirements.txt \
--master yarn \
--deploy-mode cluster \
test.py

4. Update Zeppelin %livy2.pyspark

   • In Zeppelin: click "top right" menu -> Interpreters -> Add to the livy2 interpreter:

livy.spark.yarn.appMasterEnv.PYSPARK_PYTHON=/usr/bin/python3
livy.spark.pyspark.virtualenv.enabled=true
livy.spark.pyspark.virtualenv.type=virtualenv
livy.spark.pyspark.virtualenv.bin.path=/usr/bin/virtualenv
livy.spark.pyspark.virtualenv.python_version=3.7
livy.spark.pyspark.virtualenv.requirements=hdfs:///share/python-envs/python3-venv.requirements.txt ## this is optional

java.io.IOException: Cannot run program "./venv/bin/python": error=13, Permission denied

java.io.IOException: Cannot run program "./venv/bin/python": error=13, Permission denied

need to tar replace soft link with real file,and finally working for me

tar -hzcf ../python-3.6.tar.gz *

or use conda-pack
https://conda.github.io/conda-pack/spark.html

Updated with a -h on tar. And yeah, you could use Conda instead.

what about spark2-submit --deploy-mode cluster --conf spark.pyspark.virtualenv.enabled=true --conf spark.pyspark.virtualenv.type=conda --conf spark.pyspark.virtualenv.requirements=/usr/local/airflow/requirements.txt --conf spark.pyspark.virtualenv.bin.path=/opt/miniconda365/bin/conda /usr/local/airflow/test_virtual.py

spark.pyspark.virtualenv.type=conda doesn't seem to work

Does this need python3 on hadoop nodes?
I am getting the below Error. Can you please help me with this?
venv/bin/python: error while loading shared libraries: libpython3.6m.so.1.0: cannot open shared object file: No such file or directory

Does this need python3 on hadoop nodes?
I am getting the below Error. Can you please help me with this?
venv/bin/python: error while loading shared libraries: libpython3.6m.so.1.0: cannot open shared object file: No such file or directory

meet the same error, but resolve by conda-pack