Adds Nemo Curator K8s example

docs/user-guide/CPUvsGPU.rst

@@ -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.

docs/user-guide/KubernetesCurator.rst

@@ -0,0 +1,386 @@
+.. _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
+------------------------
+
+The environment to run the provided scripts in this example does not need the full
+``nemo_curator`` package, so you can create a virtual environment with just the
+required packages as follows:
+
+.. 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/my_dataset to /my_dataset within the PVC.
+    # Change foobar to the directory or file you wish to upload.
+    ( cd $LOCAL_WORKSPACE; tar cf - my_dataset | 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
+
+(Opt #1) 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/my_dataset \
+        --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/my_dataset
+    #                  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!
+
+
+(Opt #2) 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/my_dataset \
+        --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:
+
+.. code-block:: bash
+
+    # 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