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=Overview=
=Overview= <!--T:1-->


<!--T:2-->
[https://rapids.ai/ RAPIDS] is a suite of open source software libraries from NVIDIA mainly for executing data science and analytics pipelines in Python on GPUs. It relies on NVIDIA CUDA primitives for low level compute optimization and provides users with friendly Python APIs, similar to those in Pandas, Scikit-learn, etc.
[https://rapids.ai/ RAPIDS] is a suite of open source software libraries from NVIDIA mainly for executing data science and analytics pipelines in Python on GPUs. It relies on NVIDIA CUDA primitives for low level compute optimization and provides users with friendly Python APIs, similar to those in Pandas, Scikit-learn, etc.


<!--T:3-->
Since RAPIDS is available as Conda packages which require having [[Anaconda/en|Anaconda]] for the installation, however Anaconda is not advised to use on the Compute Canada clusters. Instead, a container solution of using [[Singularity|Singularity]] is recommended. As RAPIDS is also available as Docker container images from NVIDIA, a Singularity image for RAPIDS can be built based from a Docker image.
Since RAPIDS is available as Conda packages which require having [[Anaconda/en|Anaconda]] for the installation, however Anaconda is not advised to use on the Compute Canada clusters. Instead, a container solution of using [[Singularity|Singularity]] is recommended. As RAPIDS is also available as Docker container images from NVIDIA, a Singularity image for RAPIDS can be built based from a Docker image.


<!--T:4-->
This page provides the instructions for working with RAPIDS on Compute Canada clusters based from a Singularity container.
This page provides the instructions for working with RAPIDS on Compute Canada clusters based from a Singularity container.


=Build a Singularity image for RAPIDS=
=Build a Singularity image for RAPIDS= <!--T:5-->


To build a Singularity image for RAPIDS the first thing to do is to find and select a Docker image for RAPIDS from NVIDIA.
To build a Singularity image for RAPIDS the first thing to do is to find and select a Docker image for RAPIDS from NVIDIA.
   
   
==Find a Docker image for RAPIDS==
==Find a Docker image for RAPIDS== <!--T:6-->
   
   
There are three types of RAPIDS Docker images, i.e. ''base'', ''runtime'', and ''devel'' types, and they are available at two major sites. For each type of Docker images, multiple images are provided with different combinations of RAPIDS versions and CUDA versions either on Ubuntu or on CentOS. You can find the Docker pull command of a selected image via the '''Tags''' tab on each given site:   
There are three types of RAPIDS Docker images, i.e. ''base'', ''runtime'', and ''devel'' types, and they are available at two major sites. For each type of Docker images, multiple images are provided with different combinations of RAPIDS versions and CUDA versions either on Ubuntu or on CentOS. You can find the Docker pull command of a selected image via the '''Tags''' tab on each given site:   


<!--T:7-->
* [https://ngc.nvidia.com/catalog/containers/nvidia:rapidsai:rapidsai NVIDIA GPU Cloud (NGC)]: this site provides two types of RAPIDS images, i.e. ''base'' type and ''runtime'' type.   
* [https://ngc.nvidia.com/catalog/containers/nvidia:rapidsai:rapidsai NVIDIA GPU Cloud (NGC)]: this site provides two types of RAPIDS images, i.e. ''base'' type and ''runtime'' type.   
** ''base'' - contains a RAPIDS environment ready to use. Use this type of image if you want to submit a job to the Slurm scheduler.
** ''base'' - contains a RAPIDS environment ready to use. Use this type of image if you want to submit a job to the Slurm scheduler.
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** ''devel'' - contains the full RAPIDS source tree, the compiler toolchain, the debugging tools, the headers and the static libraries for RAPIDS development. Use this type of image if you want to implement any customized operations with low-level access to cuda-based processes.
** ''devel'' - contains the full RAPIDS source tree, the compiler toolchain, the debugging tools, the headers and the static libraries for RAPIDS development. Use this type of image if you want to implement any customized operations with low-level access to cuda-based processes.


==Build a RAPIDS Singularity image==
==Build a RAPIDS Singularity image== <!--T:8-->


<!--T:9-->
For example, if a docker pull command for a selected image is given as:  
For example, if a docker pull command for a selected image is given as:  


<!--T:10-->
<source lang="console">docker pull nvcr.io/nvidia/rapidsai/rapidsai:cuda11.0-runtime-centos7</source>  
<source lang="console">docker pull nvcr.io/nvidia/rapidsai/rapidsai:cuda11.0-runtime-centos7</source>  
   
   
Line 34: Line 40:
<source lang="console">[name@server ~]$ singularity build rapids.sif docker://nvcr.io/nvidia/rapidsai/rapidsai:cuda11.0-runtime-centos7</source>
<source lang="console">[name@server ~]$ singularity build rapids.sif docker://nvcr.io/nvidia/rapidsai/rapidsai:cuda11.0-runtime-centos7</source>


<!--T:11-->
It usually takes half to one hour to complete the image building process. Since the image size is relatively large, you need to have enough memory and disk spaces on the server for building such an image.
It usually takes half to one hour to complete the image building process. Since the image size is relatively large, you need to have enough memory and disk spaces on the server for building such an image.


=Work on Clusters with a RAPIDS Singularity image=
=Work on Clusters with a RAPIDS Singularity image= <!--T:12-->
Once you have a Singularity image for RAPIDS located on Compute Canada clusters, you can work interactively by requesting an interactive session on a GPU node or submit a batch job to the Slurm queue if you have your RAPIDS code ready.
Once you have a Singularity image for RAPIDS located on Compute Canada clusters, you can work interactively by requesting an interactive session on a GPU node or submit a batch job to the Slurm queue if you have your RAPIDS code ready.
==Explore the contents in RAPIDS==
==Explore the contents in RAPIDS==


<!--T:13-->
If simply exploring the contents without doing any computations, you can use following commands to access the container shell of the Singularity image, e.g. called ''rapids.sif''  on any node without requesting any GPUs.
If simply exploring the contents without doing any computations, you can use following commands to access the container shell of the Singularity image, e.g. called ''rapids.sif''  on any node without requesting any GPUs.


   
   
<!--T:14-->
Load the Singularity module first:
Load the Singularity module first:
<source lang="console">[name@server ~]$ module load singularity</source>
<source lang="console">[name@server ~]$ module load singularity</source>


   
   
<!--T:15-->
Then access the container shell:
Then access the container shell:
<source lang="console">[name@server ~]$ singularity shell rapids.sif</source>
<source lang="console">[name@server ~]$ singularity shell rapids.sif</source>


<!--T:16-->
The shell prompt is then changed to:
The shell prompt is then changed to:
   
   
Line 55: Line 66:
</source>
</source>


<!--T:17-->
Inside the singularity shell initiate Conda and activate RAPIDS environment:
Inside the singularity shell initiate Conda and activate RAPIDS environment:
   
   
Line 61: Line 73:
</source>
</source>


<!--T:18-->
The shell prompt in the rapids env is then changed to:
The shell prompt in the rapids env is then changed to:
   
   
Line 66: Line 79:
</source>
</source>


<!--T:19-->
Then you can list available packages in the rapids env:
Then you can list available packages in the rapids env:
   
   
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</source>
</source>


<!--T:20-->
To deactivate rapids env and exit from the container:
To deactivate rapids env and exit from the container:
   
   
Line 77: Line 92:
</source>
</source>


<!--T:21-->
You are then back to the host shell.
You are then back to the host shell.


==Work interactively on a GPU node==
==Work interactively on a GPU node== <!--T:22-->


<!--T:23-->
If a Singularity image was built based on a ''runtime'' or a ''devel'' type of Docker image, it includes a Jupyter Notebook server and can be used to explore RAPIDS interactively on a compute node with GPU.
If a Singularity image was built based on a ''runtime'' or a ''devel'' type of Docker image, it includes a Jupyter Notebook server and can be used to explore RAPIDS interactively on a compute node with GPU.


<!--T:24-->
To request an interactive session on a compute node with a single GPU, e.g. a T4 type of GPU on Graham:
To request an interactive session on a compute node with a single GPU, e.g. a T4 type of GPU on Graham:
<source lang="console">[name@gra-login ~]$ salloc --ntasks=1 --cpus-per-task=2 --mem=10G --gres=gpu:t4:1 --time=1:0:0 --account=def-someuser</source>
<source lang="console">[name@gra-login ~]$ salloc --ntasks=1 --cpus-per-task=2 --mem=10G --gres=gpu:t4:1 --time=1:0:0 --account=def-someuser</source>


<!--T:25-->
Once the requested resource is granted, start RAPIDS shell on the GPU node:
Once the requested resource is granted, start RAPIDS shell on the GPU node:


<!--T:26-->
<source lang="console">[name@gra#### ~]$ module load singularity
<source lang="console">[name@gra#### ~]$ module load singularity
[name@gra#### ~]$ singularity shell --nv -B /home -B /project -B /scratch  rapids.sif
[name@gra#### ~]$ singularity shell --nv -B /home -B /project -B /scratch  rapids.sif
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Where '''--nv''' option is to bind mount the GPU driver on the host to the container, so the GPU device can be accessed from inside of the singularity container, and '''-B''' option is to bind mount any file system that you would like to access in the container.
Where '''--nv''' option is to bind mount the GPU driver on the host to the container, so the GPU device can be accessed from inside of the singularity container, and '''-B''' option is to bind mount any file system that you would like to access in the container.


<!--T:27-->
After the shell prompt changes to '''Singularity>''', you can check the GPU stats in the container to make sure the GPU device is accessible:
After the shell prompt changes to '''Singularity>''', you can check the GPU stats in the container to make sure the GPU device is accessible:
<source lang="console">Singularity> nvidia-smi</source>
<source lang="console">Singularity> nvidia-smi</source>


<!--T:28-->
Then to initiate Conda and activate rapids env:
Then to initiate Conda and activate rapids env:
<source lang="console">Singularity> source /opt/conda/etc/profile.d/conda.sh
<source lang="console">Singularity> source /opt/conda/etc/profile.d/conda.sh
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</source>
</source>


<!--T:29-->
After the shell prompt changes to '''(rapids) Singularity>''', you can launch the Jupyter Notebook server in the rapids env with following command, and the URL of the Notebook server is displayed after it starts successfully::
After the shell prompt changes to '''(rapids) Singularity>''', you can launch the Jupyter Notebook server in the rapids env with following command, and the URL of the Notebook server is displayed after it starts successfully::
<source lang="console">(rapids) Singularity> jupyter-lab --ip $(hostname -f) --no-browser
<source lang="console">(rapids) Singularity> jupyter-lab --ip $(hostname -f) --no-browser
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[C 22:28:20.244 LabApp]
[C 22:28:20.244 LabApp]


     To access the notebook, open this file in a browser:
     <!--T:30-->
To access the notebook, open this file in a browser:
         file:///home/jhqin/.local/share/jupyter/runtime/nbserver-76967-open.html
         file:///home/jhqin/.local/share/jupyter/runtime/nbserver-76967-open.html
     Or copy and paste one of these URLs:
     Or copy and paste one of these URLs:
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As there is no direct Internet connection on a compute node on Graham, you would need to setup an SSH tunnel with port forwarding between your local computer and the GPU node. See [[Jupyter#Connecting_to_Jupyter_Notebook|detailed instructions for connecting to Jupyter Notebook]].
As there is no direct Internet connection on a compute node on Graham, you would need to setup an SSH tunnel with port forwarding between your local computer and the GPU node. See [[Jupyter#Connecting_to_Jupyter_Notebook|detailed instructions for connecting to Jupyter Notebook]].


==Submit a RAPIDS job to Slurm scheduler==
==Submit a RAPIDS job to Slurm scheduler== <!--T:31-->
Once you have your RAPIDS code ready and would like to submit a job execution request to the Slurm scheduler, you need to prepare two script files, i.e. a job submission script and a job execution script.
Once you have your RAPIDS code ready and would like to submit a job execution request to the Slurm scheduler, you need to prepare two script files, i.e. a job submission script and a job execution script.


<!--T:32-->
Here is an example of a job submission script, e.g. ''submit.sh'':
Here is an example of a job submission script, e.g. ''submit.sh'':
{{File
{{File
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#SBATCH --account=def-someuser
#SBATCH --account=def-someuser


<!--T:33-->
module load singularity
module load singularity


<!--T:34-->
singularity run --nv -B /home -B /scratch rapids.sif /path/to/run_script.sh
singularity run --nv -B /home -B /scratch rapids.sif /path/to/run_script.sh
}}
}}
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nvidia-smi  
nvidia-smi  


<!--T:35-->
python /path/to/my_rapids_code.py  
python /path/to/my_rapids_code.py  
}}
}}


=Helpful Links=
=Helpful Links= <!--T:36-->


<!--T:37-->
* [https://docs.rapids.ai/ RAPIDS Docs]: a collection of all the documentation for RAPIDS, how to stay connected and report issues.
* [https://docs.rapids.ai/ RAPIDS Docs]: a collection of all the documentation for RAPIDS, how to stay connected and report issues.
* [https://github.com/rapidsai/notebooks RAPIDS Notebooks]: a collection of example notebooks on GitHub for getting started quickly.
* [https://github.com/rapidsai/notebooks RAPIDS Notebooks]: a collection of example notebooks on GitHub for getting started quickly.

Revision as of 22:06, 22 January 2021

Other languages:

Overview

RAPIDS is a suite of open source software libraries from NVIDIA mainly for executing data science and analytics pipelines in Python on GPUs. It relies on NVIDIA CUDA primitives for low level compute optimization and provides users with friendly Python APIs, similar to those in Pandas, Scikit-learn, etc.

Since RAPIDS is available as Conda packages which require having Anaconda for the installation, however Anaconda is not advised to use on the Compute Canada clusters. Instead, a container solution of using Singularity is recommended. As RAPIDS is also available as Docker container images from NVIDIA, a Singularity image for RAPIDS can be built based from a Docker image.

This page provides the instructions for working with RAPIDS on Compute Canada clusters based from a Singularity container.

Build a Singularity image for RAPIDS

To build a Singularity image for RAPIDS the first thing to do is to find and select a Docker image for RAPIDS from NVIDIA.

Find a Docker image for RAPIDS

There are three types of RAPIDS Docker images, i.e. base, runtime, and devel types, and they are available at two major sites. For each type of Docker images, multiple images are provided with different combinations of RAPIDS versions and CUDA versions either on Ubuntu or on CentOS. You can find the Docker pull command of a selected image via the Tags tab on each given site:

  • NVIDIA GPU Cloud (NGC): this site provides two types of RAPIDS images, i.e. base type and runtime type.
    • base - contains a RAPIDS environment ready to use. Use this type of image if you want to submit a job to the Slurm scheduler.
    • runtime - extends the base image by adding a Jupyter notebook server and example notebooks. Use this type of image if you want to interactively work with RAPIDS through notebooks and examples.
  • Docker Hub: this site provides RAPIDS images in devel type.
    • devel - contains the full RAPIDS source tree, the compiler toolchain, the debugging tools, the headers and the static libraries for RAPIDS development. Use this type of image if you want to implement any customized operations with low-level access to cuda-based processes.

Build a RAPIDS Singularity image

For example, if a docker pull command for a selected image is given as: 

docker pull nvcr.io/nvidia/rapidsai/rapidsai:cuda11.0-runtime-centos7

On a computer that has Singularity supported, you can build a Singularity image, e.g. called rapids.sif, with following command based on the given pull tag: 

[name@server ~]$ singularity build rapids.sif docker://nvcr.io/nvidia/rapidsai/rapidsai:cuda11.0-runtime-centos7

It usually takes half to one hour to complete the image building process. Since the image size is relatively large, you need to have enough memory and disk spaces on the server for building such an image.

Work on Clusters with a RAPIDS Singularity image

Once you have a Singularity image for RAPIDS located on Compute Canada clusters, you can work interactively by requesting an interactive session on a GPU node or submit a batch job to the Slurm queue if you have your RAPIDS code ready.

Explore the contents in RAPIDS

If simply exploring the contents without doing any computations, you can use following commands to access the container shell of the Singularity image, e.g. called rapids.sif on any node without requesting any GPUs.


Load the Singularity module first: 

[name@server ~]$ module load singularity


Then access the container shell: 

[name@server ~]$ singularity shell rapids.sif

The shell prompt is then changed to: 

Singularity>

Inside the singularity shell initiate Conda and activate RAPIDS environment: 

Singularity> source /opt/conda/etc/profile.d/conda.sh
Singularity> conda activate rapids

The shell prompt in the rapids env is then changed to: 

(rapids) Singularity>

Then you can list available packages in the rapids env: 

(rapids) Singularity> conda list

To deactivate rapids env and exit from the container: 

(rapids) Singularity> conda deactivate
Singularity> exit

You are then back to the host shell.

Work interactively on a GPU node

If a Singularity image was built based on a runtime or a devel type of Docker image, it includes a Jupyter Notebook server and can be used to explore RAPIDS interactively on a compute node with GPU.

To request an interactive session on a compute node with a single GPU, e.g. a T4 type of GPU on Graham: 

[name@gra-login ~]$ salloc --ntasks=1 --cpus-per-task=2 --mem=10G --gres=gpu:t4:1 --time=1:0:0 --account=def-someuser

Once the requested resource is granted, start RAPIDS shell on the GPU node: 

[name@gra#### ~]$ module load singularity
[name@gra#### ~]$ singularity shell --nv -B /home -B /project -B /scratch  rapids.sif

Where --nv option is to bind mount the GPU driver on the host to the container, so the GPU device can be accessed from inside of the singularity container, and -B option is to bind mount any file system that you would like to access in the container.

After the shell prompt changes to Singularity>, you can check the GPU stats in the container to make sure the GPU device is accessible: 

Singularity> nvidia-smi

Then to initiate Conda and activate rapids env: 

Singularity> source /opt/conda/etc/profile.d/conda.sh
Singularity> conda activate rapids

After the shell prompt changes to (rapids) Singularity>, you can launch the Jupyter Notebook server in the rapids env with following command, and the URL of the Notebook server is displayed after it starts successfully:: 

(rapids) Singularity> jupyter-lab --ip $(hostname -f) --no-browser
[I 22:28:20.215 LabApp] JupyterLab extension loaded from /opt/conda/envs/rapids/lib/python3.7/site-packages/jupyterlab
[I 22:28:20.215 LabApp] JupyterLab application directory is /opt/conda/envs/rapids/share/jupyter/lab
[I 22:28:20.221 LabApp] Serving notebooks from local directory: /scratch/jhqin/RAPIDS_Demo
[I 22:28:20.221 LabApp] Jupyter Notebook 6.1.3 is running at:
[I 22:28:20.221 LabApp] http://gra1160.graham.sharcnet:8888/?token=5d4b75bf2ec3481fab1b625656a322afc96775440b7bb8c4
[I 22:28:20.221 LabApp]  or http://127.0.0.1:8888/?token=5d4b75bf2ec3481fab1b625656a322afc96775440b7bb8c4
[I 22:28:20.222 LabApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
[C 22:28:20.244 LabApp]

    To access the notebook, open this file in a browser:
        file:///home/jhqin/.local/share/jupyter/runtime/nbserver-76967-open.html
    Or copy and paste one of these URLs:
        http://gra1160.graham.sharcnet:8888/?token=5d4b75bf2ec3481fab1b625656a322afc96775440b7bb8c4
     or http://127.0.0.1:8888/?token=5d4b75bf2ec3481fab1b625656a322afc96775440b7bb8c4

Where the URL for the notebook server in above example is: 

http://gra1160.graham.sharcnet:8888/?token=5d4b75bf2ec3481fab1b625656a322afc96775440b7bb8c4

As there is no direct Internet connection on a compute node on Graham, you would need to setup an SSH tunnel with port forwarding between your local computer and the GPU node. See detailed instructions for connecting to Jupyter Notebook.

Submit a RAPIDS job to Slurm scheduler

Once you have your RAPIDS code ready and would like to submit a job execution request to the Slurm scheduler, you need to prepare two script files, i.e. a job submission script and a job execution script.

Here is an example of a job submission script, e.g. submit.sh:

File : submit.sh

#!/bin/bash
#SBATCH --ntasks=1
#SBATCH --gres=gpu:t4:1
#SBATCH --cpus-per-task=2
#SBATCH --mem=10G
#SBATCH --time=dd:hh:mm
#SBATCH --account=def-someuser

module load singularity

singularity run --nv -B /home -B /scratch rapids.sif /path/to/run_script.sh


Here is an example of a job execution script, e.g. run_script.sh, which you would like to run in the container to start the execution of the python code that has been programed with RAPIDS:

File : run_script.sh

#!/bin/bash
source /opt/conda/etc/profile.d/conda.sh
conda activate rapids
nvidia-smi 

python /path/to/my_rapids_code.py


Helpful Links

  • RAPIDS Docs: a collection of all the documentation for RAPIDS, how to stay connected and report issues.
  • RAPIDS Notebooks: a collection of example notebooks on GitHub for getting started quickly.
  • RAPIDS on Medium: a collection of use cases and blogs for RAPIDS applications.
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