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[K8s]: Adds a helper script to create a dask cluster on k8s and includes
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instructions for how to a Curator workload on k8s
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@terrykong
terrykong committed Apr 22, 2024
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8 changes: 8 additions & 0 deletions docs/user-guide/CPUvsGPU.rst
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Expand Up @@ -96,3 +96,11 @@ Every SLURM cluster is different, so make sure you understand how your SLURM clu

Our Python examples are designed to work such that they can be run locally on their own, or easily substituted into the ``start-slurm.sh`` to run on multiple nodes.
You can adapt your scripts easily too by simply following the pattern of adding ``get_client`` with ``add_distributed_args``.

-----------------------------------------
Dask with K8s
-----------------------------------------

We also provide an example guide for how to get started with NeMo Curator on a Kubernetes cluster.

Please visit :ref:`curator_kubernetes` for more information.
382 changes: 382 additions & 0 deletions docs/user-guide/KubernetesCurator.rst
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.. _curator_kubernetes:

======================================
Running NeMo Curator on Kubernetes
======================================
The following example demonstrates how to run the NeMo Curator with NVIDIA GPUs on a Kubernetes cluster,
with PersistentVolumeClaims as the storage option.

.. note::
This project will download and install additional third-party open source software projects. Review the license terms of these open source projects before use.

Prerequisuites
--------------
* Kubernetes cluster
* `GPU operator <https://docs.nvidia.com/datacenter/cloud-native/gpu-operator/latest/getting-started.html>`__
* `Dask Operator <https://kubernetes.dask.org/en/latest/operator_installation.html>`__
* `kubectl <https://kubernetes.io/docs/tasks/tools>`__: the Kubernetes Cluster CLI
* Please reach out to your Kubernetes cluster admin for how to setup your ``kubectl`` KUBECONFIG
* `ReadWriteMany <https://kubernetes.io/docs/concepts/storage/persistent-volumes/#access-modes>`__ `StorageClass <https://kubernetes.io/docs/concepts/storage/storage-classes/>`__ (setup by Kubernetes cluster admin)

Storage
-------
To run NeMo Curator, we need to setup storage to upload and store the input
files, as well as any processed outputs.

Here is an example of how to create a dynamic PV from a StorageClass setup
by your cluster admin. Replace ``STORAGE_CLASS=<...>`` with the name of
your StorageClass.

This example requests ``150Gi`` of space. Adjust that number for your
workloads and be aware that not all storage provisioners support volume
resizing.

.. code-block:: bash
STORAGE_CLASS=<...>
PVC_NAME=nemo-workspace
kubectl apply -f - <<EOF
apiVersion: v1
kind: PersistentVolumeClaim
metadata:
name: ${PVC_NAME}
spec:
accessModes:
- ReadWriteMany
storageClassName: ${STORAGE_CLASS}
resources:
requests:
# Requesting enough storage for a few experiments
storage: 150Gi
EOF
.. note::
The storage class must support ``ReadWriteMany`` because multiple Pods
may need to access the PVC to concurrently read and write.
Setup PVC Busybox Helper Pod
############################
Inspecting the PVC and copying to and from it is facilitated with a busybox container.
Some examples below assume you have this Pod running to copy to and from the PVC.
.. code-block:: bash
PVC_NAME=nemo-workspace
MOUNT_PATH=/nemo-workspace
kubectl create -f - <<EOF
apiVersion: v1
kind: Pod
metadata:
name: nemo-workspace-busybox
spec:
containers:
- name: busybox
image: busybox
command: ["sleep", "infinity"]
volumeMounts:
- name: workspace
mountPath: ${MOUNT_PATH}
volumes:
- name: workspace
persistentVolumeClaim:
claimName: ${PVC_NAME}
EOF
Feel free to delete this container if no longer needed, but it should use very little
resources when idle.
.. code-block:: bash
kubectl delete pod nemo-workspace-busybox
Setup Docker Secrets
--------------------
A Kubernetes Secret needs to be created on the k8s cluster to authenticate with the NGC
private registry. If not done already, get an NGC key from ngc.nvidia.com. Create a
secret key on the k8s cluster with (replace ``<NGC KEY HERE>`` with your NGC secret
key. Note that if you have any special characters in your key you might need to wrap
the key in single quotes (``'``) so it can be parsed correctly by k8s)::
kubectl create secret docker-registry ngc-registry --docker-server=nvcr.io --docker-username=\$oauthtoken --docker-password=<NGC KEY HERE>
Setup Python Environment
------------------------
Setup a virtual environment:
.. code-block:: bash
python3 -m venv venv
source venv/bin/activate
pip install 'dask_kubernetes>=2024.4.1'
Upload Data to PVC
------------------
To copy into the ``nemo-workspace`` PVC, we will do so with ``kubectl exec``. You may also
use ``kubectl cp``, but ``exec`` has fewer surprises regarding compressed files:
.. code-block:: bash
# Replace <...> with a path on your local machine
LOCAL_WORKSPACE=<...>
# This copies $LOCAL_WORKSPACE/big_english to /big_english within the PVC.
# Change foobar to the directory or file you wish to upload.
( cd $LOCAL_WORKSPACE; tar cf - big_english | kubectl exec -i nemo-workspace-busybox -- tar xf - -C /nemo-workspace )
.. note::
See :ref:`data-curator-download` for an example of how to download local data that can be uploaded to the PVC
with the above instruction.
Create a Dask Cluster
---------------------
Use the ``create_dask_cluster.py`` to create a CPU or GPU dask cluster.
.. note::
If you are creating another Dask cluster with the same ``--name <name>``, first delete it via::
kubectl delete daskcluster <name>
.. code-block:: bash
# Creates a CPU Dask cluster with 1 worker
python create_dask_cluster.py \
--name rapids-dask \
--n_workers 1 \
--image nvcr.io/nvidian/bignlp-train:nemofw-nightly \
--image_pull_secret ngc-registry \
--pvcs nemo-workspace:/nemo-workspace
#╭───────────────────── Creating KubeCluster 'rapids-dask' ─────────────────────╮
#│ │
#│ DaskCluster Running │
#│ Scheduler Pod Running │
#│ Scheduler Service Created │
#│ Default Worker Group Created │
#│ │
#│ ⠧ Getting dashboard URL │
#╰──────────────────────────────────────────────────────────────────────────────╯
#cluster = KubeCluster(rapids-dask, 'tcp://localhost:61757', workers=2, threads=510, memory=3.94 TiB)
# Creates a GPU Dask cluster with 2 workers with 1 GPU each
python create_dask_cluster.py \
--name rapids-dask \
--n_workers 2 \
--n_gpus_per_worker 1 \
--image nvcr.io/nvidian/bignlp-train:nemofw-nightly \
--image_pull_secret ngc-registry \
--pvcs nemo-workspace:/nemo-workspace
After creating a cluster, you should be able to proceed after confirming the scheduler and the workers are all ``Running``:
.. code-block:: bash
# Set DASK_CLUSTER_NAME to the value of --name
DASK_CLUSTER_NAME=rapids-dask
kubectl get pods -l "dask.org/cluster-name=$DASK_CLUSTER_NAME"
# NAME READY STATUS RESTARTS AGE
# rapids-dask-default-worker-587238cf2c-7d685f4d75-k6rnq 1/1 Running 0 57m
# rapids-dask-default-worker-f8ff963886-5577fff76b-qmvcd 1/1 Running 3 (52m ago) 57m
# rapids-dask-scheduler-654799869d-9bw4z 1/1 Running 0 57m
.. tab-set::
.. tab-item:: Running Existing Module
Here is an example of running the existing `gpu_exact_dedup` Curator module. The arguments and script name
will need to be changed according to the module you wish to run:
.. code-block:: bash
# Set DASK_CLUSTER_NAME to the value of --name
DASK_CLUSTER_NAME=rapids-dask
SCHEDULER_POD=$(kubectl get pods -l "dask.org/cluster-name=$DASK_CLUSTER_NAME,dask.org/component=scheduler" -o name)
# Starts an interactive shell session in the scheduler pod
kubectl exec -it $SCHEDULER_POD -- bash
########################
# Inside SCHEDULER_POD #
########################
# Run the following inside the interactive shell to launch script in the background and
# tee the logs to the /nemo-workspace PVC that was mounted in for persistence.
# The command line flags will need to be replaced with whatever the module script accepts.
# Recall that the PVC is mounted at /nemo-workspace, so any outputs should be written
# to somewhere under /nemo-workspace.
mkdir -p /nemo-workspace/curator/{output,log,profile}
# Write logs to script.log and to a log file with a date suffix
LOGS="/nemo-workspace/curator/script.log /nemo-workspace/curator/script.log.$(date +%y_%m_%d-%H-%M-%S)"
(
echo "Writing to: $LOGS"
gpu_exact_dedup \
--input-data-dirs /nemo-workspace/big_english \
--output-dir /nemo-workspace/curator/output \
--hash-method md5 \
--log-dir /nemo-workspace/curator/log \
--num-files -1 \
--files-per-partition 1 \
--profile-path /nemo-workspace/curator/profile \
--log-frequency 250 \
--scheduler-address localhost:8786 \
2>&1
echo "Finished!"
) | tee $LOGS &
# At this point, feel free to disconnect the shell via Ctrl+D or simply
exit
At this point you can tail the logs and look for ``Finished!`` in ``/nemo-workspace/curator/script.log``:
.. code-block:: bash
# Command will follow the logs of the running module (Press ctrl+C to close)
kubectl exec -it $SCHEDULER_POD -- tail -f /nemo-workspace/curator/script.log
# Writing to: /nemo-workspace/curator/script.log /nemo-workspace/curator/script.log.24_03_27-15-52-31
# Computing hashes for /nemo-workspace/big_english
# adlr_id _hashes
# 0 cc-2023-14-0397113620 91b77eae49c10a65d485ac8ca18d6c43
# 1 cc-2023-14-0397113621 a266f0794cc8ffbd431823e6930e4f80
# 2 cc-2023-14-0397113622 baee533e2eddae764de2cd6faaa1286c
# 3 cc-2023-14-0397113623 87dd52a468448b99078f97e76f528eab
# 4 cc-2023-14-0397113624 a17664daf4f24be58e0e3a3dcf81124a
# Finished!
.. tab-item:: Running Custom Module
In this example, we'll demonstrate how to run a NeMo Curator module that you have defined locally.
Since your curator module may depend on version of the Curator that differs from what is in the
container, we will need to build a custom image with your code installed:
.. code-block:: bash
# Clone your repo. This example uses the official repo
git clone https://github.com/NVIDIA/NeMo-Curator.git NeMo-Curator-dev
# Checkout specific ref. This example uses a commit in the main branch
git -C NeMo-Curator-dev checkout fc167a6edffd38a55c333742972a5a25b901cb26
# Example NeMo base image. Change it according to your requirements
BASE_IMAGE=nvcr.io/nvidian/bignlp-train:nemofw-nightly
docker build -t nemo-curator-custom ./NeMo-Curator-dev -f - <<EOF
FROM ${BASE_IMAGE}
COPY ./ /NeMo-Curator-dev/
RUN pip install -e /NeMo-Curator-dev
EOF
# Then push this image to your registry: Change <private-registry>/<image>:<tag> accordingly
docker tag nemo-curator-custom <private-registry>/<image>:<tag>
docker push <private-registry>/<image>:<tag>
.. note::
When using a custom image, you will likely need to create a different secret unless you pushed to a public registry:
.. code-block:: bash
# Fill in <private-registry>/<username>/<password>
kubectl create secret docker-registry my-private-registry --docker-server=<private-registry> --docker-username=<username> --docker-password=<password>
And with this new secret, you create your new dask cluster:
.. code-block:: bash
# Fill in <private-registry>/<username>/<password>
python create_dask_cluster.py \
--name rapids-dask \
--n_workers 2 \
--n_gpus_per_worker 1 \
--image <private-registry>/<image>:<tag> \
--image_pull_secret my-private-registry \
--pvcs nemo-workspace:/nemo-workspace
After the Dask cluster is deployed, you can proceed to run your module. In this example we'll use
the ``NeMo-Curator/nemo_curator/scripts/find_exact_duplicates.py`` module, but you can find other templates
in `NeMo-Curator/examples <https://github.com/NVIDIA/NeMo-Curator/tree/main/examples>`__:
.. code-block:: bash
# Set DASK_CLUSTER_NAME to the value of --name
DASK_CLUSTER_NAME=rapids-dask
SCHEDULER_POD=$(kubectl get pods -l "dask.org/cluster-name=$DASK_CLUSTER_NAME,dask.org/component=scheduler" -o name)
# Starts an interactive shell session in the scheduler pod
kubectl exec -it $SCHEDULER_POD -- bash
########################
# Inside SCHEDULER_POD #
########################
# Run the following inside the interactive shell to launch script in the background and
# tee the logs to the /nemo-workspace PVC that was mounted in for persistence.
# The command line flags will need to be replaced with whatever the module script accepts.
# Recall that the PVC is mounted at /nemo-workspace, so any outputs should be written
# to somewhere under /nemo-workspace.
mkdir -p /nemo-workspace/curator/{output,log,profile}
# Append logs to script.log and write to a log file with a date suffix
LOGS="/nemo-workspace/curator/script.log /nemo-workspace/curator/script.log.$(date +%y_%m_%d-%H-%M-%S)"
(
echo "Writing to: $LOGS"
# Recall that /NeMo-Curator-dev was copied and installed in the Dockerfile above
python3 -u /NeMo-Curator-dev/nemo_curator/scripts/find_exact_duplicates.py \
--input-data-dirs /nemo-workspace/big_english \
--output-dir /nemo-workspace/curator/output \
--hash-method md5 \
--log-dir /nemo-workspace/curator/log \
--files-per-partition 1 \
--profile-path /nemo-workspace/curator/profile \
--log-frequency 250 \
--scheduler-address localhost:8786 \
2>&1
echo "Finished!"
) | tee $LOGS &
# At this point, feel free to disconnect the shell via Ctrl+D or simply
exit
At this point you can tail the logs and look for ``Finished!`` in ``/nemo-workspace/curator/script.log``:
.. code-block:: bash
# Command will follow the logs of the running module (Press ctrl+C to close)
kubectl exec -it $SCHEDULER_POD -- tail -f /nemo-workspace/curator/script.log
# Writing to: /nemo-workspace/curator/script.log /nemo-workspace/curator/script.log.24_03_27-20-52-07
# Reading 2 files
# /NeMo-Curator-dev/nemo_curator/modules/exact_dedup.py:157: UserWarning: Output path f/nemo-workspace/curator/output/_exact_duplicates.parquet already exists and will be overwritten
# warnings.warn(
# Finished!
Deleting Cluster
----------------
After you have finished using the created dask cluster, you can delete it to release the resources::
# Where <name> is the flag passed to create_dask_cluster.py. Example: `--name <name>`
kubectl delete daskcluster <name>
Download Data from PVC
----------------------
To download data from your PVC, you can use the ``nemo-workspace-busybox`` Pod created earlier:
.. code-block:: bash
# Replace <...> with a path on your local machine
LOCAL_WORKSPACE=<...>
# Tar will fail if LOCAL_WORKSPACE doesn't exist
mkdir -p $LOCAL_WORKSPACE
# Copy file in PVC at /nemo-workspace/foobar.txt to local file-system at $LOCAL_WORKSPACE/nemo-workspace/foobar.txt
kubectl exec nemo-workspace-busybox -- tar cf - /nemo-workspace/foobar.txt | tar xf - -C $LOCAL_WORKSPACE
# Copy directory in PVC /nemo-workspace/fizzbuzz to local file-system at $LOCAL_WORKSPACE/fizzbuzz
kubectl exec nemo-workspace-busybox -- tar cf - /nemo-workspace/fizzbuzz | tar xf - -C $LOCAL_WORKSPACE
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