Zimo Xiao

CyberGIS;UIUC

 Recent Activity

ABSTRACT:

Dear CUAHSI community members,

We are pleased to announce a new quarterly release of the CyberGIS-Jupyter for Water (CJW) platform at https://go.illinois.edu/cybergis-jupyter-water. This release includes several new capabilities and features summarized as follows.

Transition to CyberGIS-Compute V2:
CyberGIS-Compute V2 is a new development phase of the CyberGIS-Compute framework that was initially released (denoted as V1) one year ago through CJW 2020-Q4. Compared with V1, V2 includes several major enhancements: 1) a new workflow for model contribution to facilitate adding new hydrologic models by community developers; 2) a GUI in the notebook environment to simplify and guide users through the job submission process; 3) transparent and bi-directional data transfers between CJW and high-performance computing (HPC) resources using Globus by default, and 4) detailed tracking of usage and metrics. It is worth noting that due to the upgraded architecture in V2, existing models implemented in V1 would need to be migrated. For a smooth transition and backward compatibility, services in V1 will remain available in parallel to those in V2, and all the old notebooks that use V1 remain functional.

SUMMA Model Migrated to CyberGIS-Compute V2:
We have migrated the SUMMA model to CyberGIS-Compute V2, and end users can now benefit from the new features mentioned above in SUMMA modeling work. Please refer to the example notebook below for details. In addition, the implementation of SUMMA in CyberGIS-Compute V2 is accessible on a Github repo (https://github.com/cybergis/cybergis-compute-v2-summa), which can serve as a real-world example to model developers who may want to contribute their models for sharing with the community. A “HelloWorld” implementation is also available serving as a model-agnostic example (https://github.com/cybergis/cybergis-compute-mpi-helloworld).

New Modules and Kernel Customization:
Upon user requests, two new easybuild-based modules have been added to the CJW toolbox and are now ready to use: NCL (https://www.ncl.ucar.edu/) for scientific data analysis and visualization (e.g., NetCDF, GRID, HDF); and CDO (https://code.mpimet.mpg.de/projects/cdo) for manipulation of climate and Numerical Weather Prediction (NWP) data. Furthermore, for advanced users who may want to customize the provided software environment and kernels, an example notebook (see below) is available for users to walk through the basics on how to install new libraries on top of existing environments or set up a Conda environment from scratch.

New UI Elements on CJW:
CJW has further customized the Jupyter Notebook user interface to include a virtual Announcement Board (in the header area) for timely communicating with users on upcoming events including downtimes and new releases, and a Bug Report button (at the upper-right corner) that opens an issue tracker page in a publicly accessible Github repo for quick bug reporting.

Please refer to the following resources for details and examples:
Run ensemble SUMMA 3.0 model with CyberGIS-Compute V2
https://www.hydroshare.org/resource/deac1b0b5b46415aaedb886b9dc16f45/

Customize Software Environment on CJW
https://www.hydroshare.org/resource/461a8a853d8e42a8ae170c68c4cfa8f1/

Implementation of SUMMA model using CyberGIS-Compute V2
https://github.com/cybergis/cybergis-compute-v2-summa

Implementation of HelloWorld model using CyberGIS-Compute V2
https://github.com/cybergis/cybergis-compute-mpi-helloworld

See Release Notes on HydroShare
https://www.hydroshare.org/resource/2086b241b16b453d827db847e8640475/

Please let us know if you have any questions or run into any problems (help@cybergis.org). Any feedback would be greatly appreciated.

Best regards,
CyberGIS-Hydro team

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ABSTRACT:

This notebook demonstrates how to configure ensemble runs for SUMMA 3.0 model and submit to a High-Performance Computing (HPC) resource for parallel execution though the CyberGIS-Compute V2 service. The content is intended for end users who want to use the SUMMA model in CJW environment. For developers who may want to contribute new models to CyberGIS-Compute, the implementation of SUMMA on Github (https://github.com/cybergis/cybergis-compute-v2-summa) can serve as an example.

Some steps in this notebook require user interaction. "Run cell by cell" is recommended. "Run All" may not work as expected.

How to run the notebook:
1) Click on the OpenWith button in the upper-right corner;
2) Select "CyberGIS-Jupyter for Water";
3) Open the notebook and follow instructions;

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Composite Resource Composite Resource
Run ensemble SUMMA 3.0 model on HPC using CyberGIS-Compute V2
Created: Dec. 7, 2021, 9 p.m.
Authors:

ABSTRACT:

This notebook demonstrates how to configure ensemble runs for SUMMA 3.0 model and submit to a High-Performance Computing (HPC) resource for parallel execution though the CyberGIS-Compute V2 service. The content is intended for end users who want to use the SUMMA model in CJW environment. For developers who may want to contribute new models to CyberGIS-Compute, the implementation of SUMMA on Github (https://github.com/cybergis/cybergis-compute-v2-summa) can serve as an example.

Some steps in this notebook require user interaction. "Run cell by cell" is recommended. "Run All" may not work as expected.

How to run the notebook:
1) Click on the OpenWith button in the upper-right corner;
2) Select "CyberGIS-Jupyter for Water";
3) Open the notebook and follow instructions;

Show More
Collection Resource Collection Resource
CyberGIS-Jupyter for Water (CJW) 2021-Q4 Release Notes
Created: Dec. 7, 2021, 9:11 p.m.
Authors:

ABSTRACT:

Dear CUAHSI community members,

We are pleased to announce a new quarterly release of the CyberGIS-Jupyter for Water (CJW) platform at https://go.illinois.edu/cybergis-jupyter-water. This release includes several new capabilities and features summarized as follows.

Transition to CyberGIS-Compute V2:
CyberGIS-Compute V2 is a new development phase of the CyberGIS-Compute framework that was initially released (denoted as V1) one year ago through CJW 2020-Q4. Compared with V1, V2 includes several major enhancements: 1) a new workflow for model contribution to facilitate adding new hydrologic models by community developers; 2) a GUI in the notebook environment to simplify and guide users through the job submission process; 3) transparent and bi-directional data transfers between CJW and high-performance computing (HPC) resources using Globus by default, and 4) detailed tracking of usage and metrics. It is worth noting that due to the upgraded architecture in V2, existing models implemented in V1 would need to be migrated. For a smooth transition and backward compatibility, services in V1 will remain available in parallel to those in V2, and all the old notebooks that use V1 remain functional.

SUMMA Model Migrated to CyberGIS-Compute V2:
We have migrated the SUMMA model to CyberGIS-Compute V2, and end users can now benefit from the new features mentioned above in SUMMA modeling work. Please refer to the example notebook below for details. In addition, the implementation of SUMMA in CyberGIS-Compute V2 is accessible on a Github repo (https://github.com/cybergis/cybergis-compute-v2-summa), which can serve as a real-world example to model developers who may want to contribute their models for sharing with the community. A “HelloWorld” implementation is also available serving as a model-agnostic example (https://github.com/cybergis/cybergis-compute-mpi-helloworld).

New Modules and Kernel Customization:
Upon user requests, two new easybuild-based modules have been added to the CJW toolbox and are now ready to use: NCL (https://www.ncl.ucar.edu/) for scientific data analysis and visualization (e.g., NetCDF, GRID, HDF); and CDO (https://code.mpimet.mpg.de/projects/cdo) for manipulation of climate and Numerical Weather Prediction (NWP) data. Furthermore, for advanced users who may want to customize the provided software environment and kernels, an example notebook (see below) is available for users to walk through the basics on how to install new libraries on top of existing environments or set up a Conda environment from scratch.

New UI Elements on CJW:
CJW has further customized the Jupyter Notebook user interface to include a virtual Announcement Board (in the header area) for timely communicating with users on upcoming events including downtimes and new releases, and a Bug Report button (at the upper-right corner) that opens an issue tracker page in a publicly accessible Github repo for quick bug reporting.

Please refer to the following resources for details and examples:
Run ensemble SUMMA 3.0 model with CyberGIS-Compute V2
https://www.hydroshare.org/resource/deac1b0b5b46415aaedb886b9dc16f45/

Customize Software Environment on CJW
https://www.hydroshare.org/resource/461a8a853d8e42a8ae170c68c4cfa8f1/

Implementation of SUMMA model using CyberGIS-Compute V2
https://github.com/cybergis/cybergis-compute-v2-summa

Implementation of HelloWorld model using CyberGIS-Compute V2
https://github.com/cybergis/cybergis-compute-mpi-helloworld

See Release Notes on HydroShare
https://www.hydroshare.org/resource/2086b241b16b453d827db847e8640475/

Please let us know if you have any questions or run into any problems (help@cybergis.org). Any feedback would be greatly appreciated.

Best regards,
CyberGIS-Hydro team

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