HSDS (Highly Scalable Data Service) - REST-based service for HDF5 data

Introduction

HSDS is a web service that implements a REST-based web service for HDF5 data stores. Data can be stored in either a POSIX files system, or using object-based storage such as AWS S3, Azure Blob Storage, or MinIO <min.io>. HSDS can be run a single machine using Docker or on a cluster using Kubernetes (or AKS on Microsoft Azure).

In addition, HSDS can be run in serverless mode with AWS Lambda or h5pyd local mode.

Quick Start

Make sure you have Python 3, Pip, and git installed, then:

1. Clone this repo: $ git clone https://github.com/HDFGroup/hsds
2. Go to the hsds directory: $ cd hsds
3. Run install: $ python setup.py install OR install from pypi: $ pip install hsds
4. Setup password file: $ cp admin/config/passwd.default admin/config/passwd.txt
5. Create a directory the server will use to store data, and then set the ROOT_DIR environment variable to point to it: $ mkdir ~/hsds_data; export ROOT_DIR="${HOME}/hsds_data"
6. Create the hsds test bucket: $ mkdir $ROOT_DIR/hsdstest
7. Start server: $ ./runall.sh --no-docker
8. In a new shell, set the environment variable HSDS_ENDPOINT to the string displayed. E.g.: $ export HSDS_ENDPOINT=http+unix://%2Ftmp%2Fhs%2Fsn_1.sock
9. Set environment variables for the admin account: $ export ADMIN_USERNAME=admin and $ export ADMIN_PASSWORD=admin (adjust for any changes made to the passwd.txt file)
10. Run the test suite: $ python testall.py
11. (Optional) Post install setup (test data, home folders, cli tools, etc): docs/post_install.md
12. (Optional) Install the h5pyd package for an h5py compatible api and tool suite: https://github.com/HDFGroup/h5pyd

To shut down the server, and the server was started with the --no-docker option, just control-C.

If using docker, run: $ ./stopall.sh

Note: passwords can (and should for production use) be modified by changing values in hsds/admin/config/password.txt and rebuilding the docker image. Alternatively, an external identity provider such as Azure Active Directory or KeyCloak can be used. See: docs/azure_ad_setup.md for Azure AD setup instructions or docs/keycloak_setup.md for KeyCloak.

Detailed Install Instructions

On AWS

For complete instructions to install on a single Azure VM with Docker:

• See: docs/docker_install_aws.md

For complete instructions to install on AWS Kubernetes Service (EKS):

• See: docs/kubernetes_install_aws.md

For complete instructions to install on AWS Lambda:

• See: docs/aws_lambda_setup.md.

On Azure

For complete instructions to install on a single Azure VM with Docker:

• See: docs/docker_install_azure.md

For complete instructions to install on Azure Kubernetes Service (AKS):

• See: docs/kubernetes_install_azure.md

On Prem (POSIX-based storage)

For complete instructions to install on a desktop or local server:

• See: docs/docker_install_posix.md

On DCOS (BETA)

For complete instructions to install on DCOS:

• See: docs/docker_install_dcos.md

General Install Topics

Setting up docker:

• See docs/setup_docker.md

Post install setup and testing:

• See docs/post_install.md

Authorization, ACLs, and Role Based Access Control (RBAC):

• See docs/authorization.md

Running serverless with h5pyd:

• See https://github.com/HDFGroup/h5pyd/blob/master/README.rst

Writing Client Applications

As a REST service, clients be developed using almost any programming language. The test programs under: hsds/test/integ illustrate some of the methods for performing different operations using Python and HSDS REST API (using the requests package).

The related project: https://github.com/HDFGroup/h5pyd provides a (mostly) h5py-compatible interface to the server for Python clients.

For C/C++ clients, the HDF REST VOL is a HDF5 library plugin that enables the HDF5 API to read and write data using HSDS. See: https://github.com/HDFGroup/vol-rest. Note: requires v1.12.0 or greater version of the HDF5 library.

Uninstalling

HSDS only modifies the storage location that it is configured to use, so to uninstall just remove source files, Docker images, and S3 bucket/Azure Container/directory files.

Reporting bugs (and general feedback)

Create new issues at http://github.com/HDFGroup/hsds/issues for any problems you find.

For general questions/feedback, please use the HSDS forum: https://forum.hdfgroup.org/c/hsds.

License

HSDS is licensed under an APACHE 2.0 license. See LICENSE in this directory.

Integration with JupyterHub

The HDF Group provides access to an HSDS instance that is integrated with JupyterLab: HDF Lab. HDF Lab is a hosted Jupyter environment with these features:

• Connection to a HSDS instance
• Dedicated Xeon core per user
• 10 GB Posix Disk
• 200 GB S3 storage for HDF data
• Sample programs and data files

Sign up for HDF Lab here: https://www.hdfgroup.org/hdfkitalab/.

Azure Marketplace

VM Offer for Azure Marketplace. HSDS for Azure Marketplace provides an easy way to setup a Azure instance with HSDS. See: https://azuremarketplace.microsoft.com/en-us/marketplace/apps/thehdfgroup1616725197741.hsdsazurevm?tab=Overview for more information.

Websites

• Main website: https://www.hdfgroup.org/solutions/highly-scalable-data-service-hsds/
• Source code: https://github.com/HDFGroup/hsds
• Forum: https://forum.hdfgroup.org/c/hsds
• Documentation: http://h5serv.readthedocs.org (For REST API)

Other useful resources

HDF Group Blog Posts

• Web Caching: https://www.hdfgroup.org/2022/10/improve-hdf5-performance-using-caching/
• HSDS Streaming: https://www.hdfgroup.org/2022/08/hsds-streaming/
• Cloud Storage Options for HDF5: https://www.hdfgroup.org/2022/08/cloud-storage-options-for-hdf5/
• HSDS Docker Images: https://www.hdfgroup.org/2022/07/hsds-docker-images/
• HSDS Container Types: https://www.hdfgroup.org/2022/07/deep-dive-hsds-container-types/
• Using Multiprocessing in Python: https://www.hdfgroup.org/2022/06/speed-up-cloud-access-using-multiprocessing/
• Biosimulations - case study with HSDS and Vega: https://www.hdfgroup.org/2022/02/biosimulations-a-platform-for-sharing-and-reusing-biological-simulations/
• HSDS for Microsoft Azure: https://www.hdfgroup.org/2021/08/hsds-for-azure/
• New Features in HSDS v0.6: https://www.hdfgroup.org/2020/10/new-features-in-hsds-version-0-6/
• HSDS Security: https://hdfgroup.org/wp/2015/12/serve-protect-web-security-hdf5
• HDF for the Web: HDF Server: https://www.hdfgroup.org/2015/04/hdf5-for-the-web-hdf-server/

External Blogs and Articles

• A RESTful Meeting Between MATLAB and HDF Server: https://www.mathworks.com/matlabcentral/fileexchange/59072-a-restful-meeting-between-matlab-and-hdf-server-web-based-hdf5-access-using-matlab
• AWS Big Data Blog: https://aws.amazon.com/blogs/big-data/power-from-wind-open-data-on-aws/

Slide Decks

• HSDS v0.7 New Features, EUHUG 2022: https://www.hdfgroup.org/wp-content/uploads/2022/05/HSDS_New_Feautres_7.0.pdf
• HSDS Serverless, EUHUG 2021: https://www.hdfgroup.org/wp-content/uploads/2021/07/ServerlessHSDS.pdf
• HSDS REST, HUG 2020: https://www.hdfgroup.org/wp-content/uploads/2020/10/HSDS_Rest_Service_HDF5_Readey.pdf
• HSDS with Jupyter, ESIP 2018: https://www.slideshare.net/HDFEOS/hdf-kita-lab-jupyterlab-hdf-service
• HDF Data Services, SciPy17: http://s3.amazonaws.com/hdfgroup/docs/hdf_data_services_scipy2017.pdf

Videos

• HSDS Webinar: https://www.youtube.com/watch?v=9b5TO7drqqE
• HSDS Overview, Allotrope Connect Day: https://www.youtube.com/watch?v=nRHXEkhlfZ0
• The Use of HSDS on SlideRule, HUG 2020: https://www.youtube.com/watch?v=i-KIoGqdEMg
• HDF Data Services, SciPy 2017: https://www.youtube.com/watch?v=EmnCz1Hg-VM
• RESTful HDF, SciPy 2015: https://www.youtube.com/watch?v=JSFZ3i3WcjQ

Papers

• restfulSE: A semantically rich interface for cloud-scale genomics with Bioconductor: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6392152
• RESTful HDF5 White Paper: https://www.hdfgroup.org/pubs/papers/RESTful_HDF5.pdf