Binata Roy

University of Virginia

 Recent Activity

ABSTRACT:

This HydroShare resource has the results of performance tests that are computational_time.csv, size.csv, and complexity.csv.
Using Jupyter notebook, we created four performance plots in the manuscript of "Comparing Approaches to Achieve Reproducible Computational Modeling for Hydrological and Environmental Systems" in Environmental Modeling and Software.

Figure 9. The total scores of complexity on reproducible approaches for developer and user work
Figure 10 Comparison of the size for reproducible artifacts in five local reproducible approaches
Figure 11 Comparison of computational time in five local reproducible approaches
Figure 12 Comparison of computational time in six remote reproducible approaches

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ABSTRACT:

This is a collection resource for "Comparing Approaches to Achieve Reproducible Computational Modeling for Hydrological and Environmental Systems" manuscript in Environmental Modeling and Software.

HS-1: Collection Resource for Comparing Approaches to Achieve Reproducible Computational Modeling for Hydrological and Environmental Systems

For SUMMA simulation, we created two SUMMA model instances.
HS-2. Model Instance for the Impact of Stomatal Resistance Parameterizations on ET of SUMMA Model in Aspen stand at Reynolds Mountain East
HS-3. Model Instance for the Impact of Lateral Flow Parameterizations on Runoff of SUMMA Model at Reynolds Mountain East

For SUMMA simulation, we created a SUMMA model program
HS-4: Remote Approach-11: Using HPC Cluster (Rivanna: HPC at University of Virginia) for the reproducibility of SUMMA modeling

There are five HS resources for reproducible approaches.
HS-5. A Virtual Box image that includes five local approaches:
- Approach-1 Compiling the core model software
- Approach-2 Containerizing the core model software only with Docker
- Approach-3 Containerizing all software with Docker
- Approach-4 Containerizing all software with Singularity
- Approach-5 Containerizing all software and modeling workflows with Sciunit
HS-6. Approach-6 Using CUAHSI JupyterHub
HS-7. Approach-7 Using CyberGIS-Jupyter for water
HS-8. Approach-8 Using Sciunit in CUAHSI JupyterHub
HS-9. Approach-9 Using Sciunit in CyberGIS-Jupyter for water

Lastly, we created a notebook for performance tests using the different reproducible approaches.
HS-10. Jupyter notebook for performance test using the different reproducible approaches

In addition, there are three GitHub repositories for reproducible approaches in related resources in the reference section.
Git-1. Approach-10 Using Binder
Git-2. Description of Approach-3 to show how to create Docker environments
Git-3. Description of Approach-4 and 11 to show how to use a Singularity image in HPC

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ABSTRACT:

This HydroShare resource provides five local approaches using Virtual Box image.
First, users need to install Virtual Box (https://www.virtualbox.org/wiki/Downloads) at first.
Then import this "research.ova" to create a SUMMA and pySUMMA computational environment in Virtual Box.

After creating "research.ova" image on Virtual Box, users need to move to the "/home/hydro/project/Performance_Test" folder to start SUMMA run.
Then, users can follow the "instruction.txt" in each approach foler.
The password of this "research.ova" image is "hydro."

This Virtual Box image five local approaches:
- Approach-1 Compiling the core model software
- Approach-2 Containerizing the core model software only with Docker
- Approach-3 Containerizing all software with Docker
- Approach-4 Containerizing all software with Singularity
- Approach-5 Containerizing all software and modeling workflows with Sciunit

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ABSTRACT:

This HydroShare resource provides the Jupyter Notebooks for the reproducibility of SUMMA modeling using Sciunit in CUAHSI JupyterHub in the manuscript of "Comparing Approaches to Achieve Reproducible Computational Modeling for Hydrological and Environmental Systems" in Environmental Modeling and Software.

To find out the instructions on how to run Jupyter Notebooks, please refer to the README file which is provided in this resource.

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ABSTRACT:

This HydroShare resource provides the Jupyter Notebooks for the reproducibility of SUMMA modeling using Sciunit in CyberGIS-Jupyter for water in the manuscript of "Comparing Approaches to Achieve Reproducible Computational Modeling for Hydrological and Environmental Systems" in Environmental Modeling and Software.

To find out the instructions on how to run Jupyter Notebooks, please refer to the README file which is provided in this resource.

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Model Program Resource Model Program Resource

ABSTRACT:

This HydroShare resource provides a Singularity image for Remote Approach 11: Using an HPC Cluster in the manuscript of "Comparing Approaches to Achieve Reproducible Computational Modeling for Hydrological and Environmental Systems" in Environmental Modeling and Software.

For more detailed information, please see this GitHub
https://github.com/DavidChoi76/Using_Singularity_in_Local_Approach_4_and_HPC_Cluster_Approach_11_for_the_reproducibility_of_SUMMA

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Composite Resource Composite Resource

ABSTRACT:

This HydroShare resource provides the Jupyter Notebooks for the reproducibility of SUMMA modeling using CyberGIS-Jupyter for water in the manuscript of "Comparing Approaches to Achieve Reproducible Computational Modeling for Hydrological and Environmental Systems" in Environmental Modeling and Software.

To find out the instructions on how to run Jupyter Notebooks, please refer to the README file which is provided in this resource.

Show More
Composite Resource Composite Resource

ABSTRACT:

This HydroShare resource provides the Jupyter Notebooks for the reproducibility of SUMMA modeling using CUAHSI JupyterHub in the manuscript of "Comparing Approaches to Achieve Reproducible Computational Modeling for Hydrological and Environmental Systems" in Environmental Modeling and Software.

To find out the instructions on how to run Jupyter Notebooks, please refer to the README file which is provided in this resource.

Show More
Composite Resource Composite Resource

ABSTRACT:

This HydroShare resource provides the Jupyter Notebooks for the reproducibility of SUMMA modeling using Sciunit in CyberGIS-Jupyter for water in the manuscript of "Comparing Approaches to Achieve Reproducible Computational Modeling for Hydrological and Environmental Systems" in Environmental Modeling and Software.

To find out the instructions on how to run Jupyter Notebooks, please refer to the README file which is provided in this resource.

Show More
Composite Resource Composite Resource

ABSTRACT:

This HydroShare resource provides the Jupyter Notebooks for the reproducibility of SUMMA modeling using Sciunit in CUAHSI JupyterHub in the manuscript of "Comparing Approaches to Achieve Reproducible Computational Modeling for Hydrological and Environmental Systems" in Environmental Modeling and Software.

To find out the instructions on how to run Jupyter Notebooks, please refer to the README file which is provided in this resource.

Show More
Composite Resource Composite Resource

ABSTRACT:

This HydroShare resource provides five local approaches using Virtual Box image.
First, users need to install Virtual Box (https://www.virtualbox.org/wiki/Downloads) at first.
Then import this "research.ova" to create a SUMMA and pySUMMA computational environment in Virtual Box.

After creating "research.ova" image on Virtual Box, users need to move to the "/home/hydro/project/Performance_Test" folder to start SUMMA run.
Then, users can follow the "instruction.txt" in each approach foler.
The password of this "research.ova" image is "hydro."

This Virtual Box image five local approaches:
- Approach-1 Compiling the core model software
- Approach-2 Containerizing the core model software only with Docker
- Approach-3 Containerizing all software with Docker
- Approach-4 Containerizing all software with Singularity
- Approach-5 Containerizing all software and modeling workflows with Sciunit

Show More
Collection Resource Collection Resource

ABSTRACT:

This is a collection resource for "Comparing Approaches to Achieve Reproducible Computational Modeling for Hydrological and Environmental Systems" manuscript in Environmental Modeling and Software.

HS-1: Collection Resource for Comparing Approaches to Achieve Reproducible Computational Modeling for Hydrological and Environmental Systems

For SUMMA simulation, we created two SUMMA model instances.
HS-2. Model Instance for the Impact of Stomatal Resistance Parameterizations on ET of SUMMA Model in Aspen stand at Reynolds Mountain East
HS-3. Model Instance for the Impact of Lateral Flow Parameterizations on Runoff of SUMMA Model at Reynolds Mountain East

For SUMMA simulation, we created a SUMMA model program
HS-4: Remote Approach-11: Using HPC Cluster (Rivanna: HPC at University of Virginia) for the reproducibility of SUMMA modeling

There are five HS resources for reproducible approaches.
HS-5. A Virtual Box image that includes five local approaches:
- Approach-1 Compiling the core model software
- Approach-2 Containerizing the core model software only with Docker
- Approach-3 Containerizing all software with Docker
- Approach-4 Containerizing all software with Singularity
- Approach-5 Containerizing all software and modeling workflows with Sciunit
HS-6. Approach-6 Using CUAHSI JupyterHub
HS-7. Approach-7 Using CyberGIS-Jupyter for water
HS-8. Approach-8 Using Sciunit in CUAHSI JupyterHub
HS-9. Approach-9 Using Sciunit in CyberGIS-Jupyter for water

Lastly, we created a notebook for performance tests using the different reproducible approaches.
HS-10. Jupyter notebook for performance test using the different reproducible approaches

In addition, there are three GitHub repositories for reproducible approaches in related resources in the reference section.
Git-1. Approach-10 Using Binder
Git-2. Description of Approach-3 to show how to create Docker environments
Git-3. Description of Approach-4 and 11 to show how to use a Singularity image in HPC

Show More
Composite Resource Composite Resource

ABSTRACT:

This HydroShare resource has the results of performance tests that are computational_time.csv, size.csv, and complexity.csv.
Using Jupyter notebook, we created four performance plots in the manuscript of "Comparing Approaches to Achieve Reproducible Computational Modeling for Hydrological and Environmental Systems" in Environmental Modeling and Software.

Figure 9. The total scores of complexity on reproducible approaches for developer and user work
Figure 10 Comparison of the size for reproducible artifacts in five local reproducible approaches
Figure 11 Comparison of computational time in five local reproducible approaches
Figure 12 Comparison of computational time in six remote reproducible approaches

Show More