Modernizing the open-source community Noah-MP land surface model (version 5.0) with enhanced modularity, interoperability, and applicability

He, Cenlin; Valayamkunnath, Prasanth; Barlage, Michael; Chen, Fei; Gochis, David; Cabell, Ryan; Schneider, Tim; Rasmussen, Roy; Niu, Guo-Yue; Yang, Zong-Liang; Niyogi, Dev; Ek, Michael

doi:https://doi.org/10.5194/egusphere-2023-675

Preprints

https://doi.org/10.5194/egusphere-2023-675

Preprints

12 Apr 2023

| 12 Apr 2023

Modernizing the open-source community Noah-MP land surface model (version 5.0) with enhanced modularity, interoperability, and applicability

Cenlin He, Prasanth Valayamkunnath, Michael Barlage, Fei Chen, David Gochis, Ryan Cabell, Tim Schneider, Roy Rasmussen, Guo-Yue Niu, Zong-Liang Yang, Dev Niyogi, and Michael Ek

Abstract. The widely-used open-source community Noah-MP land surface model (LSM) is designed for applications ranging from uncoupled land-surface and ecohydrological process studies to coupled numerical weather prediction and decadal global/regional climate simulations. It has been used in many coupled community weather/climate/hydrology models. In this study, we modernize/refactor the Noah-MP LSM by adopting modern Fortran code and data structures and standards, which substantially enhances the model modularity, interoperability, and applicability. The modernized Noah-MP is released as the version 5.0 (v5.0), which has five key features: (1) enhanced modularization and interoperability by re-organizing model physics into individual process-level Fortran module files, (2) enhanced data structure with new hierarchical data types and optimized variable declaration and initialization structures, (3) enhanced code structure and calling workflow by leveraging the new data structure and modularization, (4) enhanced (descriptive and self-explanatory) model variable naming standard, and (5) enhanced driver and interface structures to couple with host weather/climate/hydrology models. In addition, we create a comprehensive technical documentation of the Noah-MP v5.0 and a set of model benchmark and reference datasets. The Noah-MP v5.0 will be coupled to various weather/climate/hydrology models in the future. Overall, the modernized Noah-MP will allow a more efficient and convenient process for future model developments and applications.

Received: 05 Apr 2023 – Discussion started: 12 Apr 2023

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Journal article(s) based on this preprint

08 Sep 2023

Modernizing the open-source community Noah with multi-parameterization options (Noah-MP) land surface model (version 5.0) with enhanced modularity, interoperability, and applicability

Cenlin He, Prasanth Valayamkunnath, Michael Barlage, Fei Chen, David Gochis, Ryan Cabell, Tim Schneider, Roy Rasmussen, Guo-Yue Niu, Zong-Liang Yang, Dev Niyogi, and Michael Ek

Geosci. Model Dev., 16, 5131–5151, https://doi.org/10.5194/gmd-16-5131-2023,https://doi.org/10.5194/gmd-16-5131-2023, 2023

Short summary

Cenlin He, Prasanth Valayamkunnath, Michael Barlage, Fei Chen, David Gochis, Ryan Cabell, Tim Schneider, Roy Rasmussen, Guo-Yue Niu, Zong-Liang Yang, Dev Niyogi, and Michael Ek

Interactive discussion

Status: closed

CEC1:
'Comment on egusphere-2023-675', Juan Antonio Añel, 05 May 2023

Dear authors,

Unfortunately, after checking your manuscript, it has come to our attention that it does not comply with our "Code and Data Policy".
https://www.geoscientific-model-development.net/policies/code_and_data_policy.html

You have archived your code on GitHub. However, GitHub is not a suitable repository for scientific publication. GitHub itself instructs authors to use other alternatives for long-term archival and publishing, such as Zenodo. Therefore, please, publish your code in one of the appropriate repositories, and reply to this comment with the relevant information (link and DOI) as soon as possible, as it should be available for the Discussions stage.

I have to highlight that if you do not fix this problem as soon as possible, we will have to reject your manuscript for publication in our journal. I should note that, actually, your manuscript should not have been accepted in Discussions, given this lack of compliance with our policy. Therefore, the current situation with your manuscript is irregular.

Also, you must include in a potentially reviewed version of your manuscript the modified 'Code and Data Availability' section, the DOI of the code. Also, in the GitHub repositories, there are no licenses listed for both NOAH-MP and HRLDAS/Noah-MP. If you do not include a license, despite what you state in the README file, the code is not "open-source"; it continues to be your property. Therefore, when uploading the model's code to Zenodo, you could want to choose a free software/open-source (FLOSS) license. We recommend the GPLv3. You only need to include the file 'https://www.gnu.org/licenses/gpl-3.0.txt' as LICENSE.txt with your code. Also, you can choose other options that Zenodo provides: GPLv2, Apache License, MIT License, etc.

Regarding the data, I agree that 8 TB is a sensible amount of data to store, and given the nature of this manuscript, we can understand the limitations that this represents to data sharing. However, we would expect that you can issue a DOI for the data relevant to your manuscript. It would be good if you provided better information about where it is stored (HPC infrastructure, servers, physical location, internal path in the file system, etc.)

Juan A. Añel
Geosci. Model Dev. Exec. Editor

Citation: https://doi.org/10.5194/egusphere-2023-675-CEC1
- AC1:
  'Reply on CEC1', Cenlin He, 06 May 2023
  
  Dear Dr. Añel,
  Thank you for the important notes. We have fixed all the issues following your suggestions. Specifially,
  1. We have applied DOI for both Noah-MP and HRLDAS model code GitHub repositories through Zenodo. We have also included the doi information in the two GitHub pages. The doi for Noah-MP code is: https://doi.org/10.5281/zenodo.7901855, and the doi for HRLDAS code is: https://doi.org/10.5281/zenodo.7901867
  2. We have added LICENSE.txt in both model code GitHub repositories. The Noah-MP GitHub repository: https://github.com/NCAR/noahmp, and the HRLDAS GitHub repository: https://github.com/NCAR/hrldas
  3. We have made corresponding changes to our "Code and data availability" section in the manuscript to reflect the new doi and updated GitHub pages. Please see the attached revised manuscript with track-change.
  4. We have also added more details about the 8.8-TB data archival, including the data storage system and path as follows (please also see the revised "Code and data availability" section in the attached manuscript): "The benchmark datasets are stored in the NCAR high-performance supercomputer (HPC) campaign storage file system (data path: /glade/campaign/ral/hap/cenlinhe/NoahMP_benchmark/, see details about the storage system at https://arc.ucar.edu/knowledge_base/70549621) and can be provided by the corresponding author upon request, due to the extremely large data size (8.8 TB)."
  Hope that our revision satisfies the journal requirement and please let me know if you found any further issues.
  Thank you
  Cenlin He
  
  Citation: https://doi.org/10.5194/egusphere-2023-675-AC1
  - CEC2: 'Reply on AC1', Juan Antonio Añel, 10 May 2023
    
    Dear authors,
    Many thanks for your quick reply. It solves all the issues regarding code and data for this version of your manuscript.
    Regards,
    Juan A. Añel
    Geosci. Model Dev. Executive Editor
    
    Citation: https://doi.org/10.5194/egusphere-2023-675-CEC2
RC1:
'Comment on egusphere-2023-675', Anonymous Referee #1, 22 May 2023

This manuscript describes the modernization and refactoring of the widely-used state-of-art Noah-MP LSM, which was released as Noah-MP v5.0. The mordent Fortran code and data structures and standards are adopted in the refactoring. Five key features, including re-organized model physics inro individual process-level Fortran module files, enhanced data structure, enhanced code structure, self-explanatory variable naming standard, and enhanced interface structure to couple with the host models are introduced. It is introduced that the latest released Noah-MP has been coupled with NCAR/HRLDAS system. Some benchmark simulation results over the CONUS are presented. The work of coupling the Noah-MP v5.0 with the latest NASA/LIS system and the WRF-Hydro/NWM system is on-going. In the future, it is also plan to couple to other weather and climate models.

The original code of the model is length single Fortran file. One has to read through the whole file and locate places interested. The refactoring procedures provide a modernized and interoperated model system, with which users could easily understand, modify or utilize in wide applications. As an open-sourced model, the simulation results should be reproducible with given forcing datasets. It is a substantial contribution to modelling science within the scope of Geoscientific Model Development. The manuscript is logical clearly, concisely, and well-structurally interpreted. In addition, model refactoring is a burdensome but less productive task. Not much people have willingness to do this work. This manuscript describes the refactoring conception and processes of the widely-used land surface model. For this kind fundamental work, encourage and circulate should be deserved. I think it is acceptable with minor revisions.

The manuscript detailed describes the model structures, and what have been done with the model coupling to HRLDAS. My only concern is about the future plans. It is stated that the Noah-MP v5,0 will be coupled with more host models. It is encouraging. However, every model has its discrepancies. What are the advantages and disadvantages of this model? how about the future plans for model developments and applications? What is the next step in next several years to promote the advantages and makeup the weakness?

Citation: https://doi.org/10.5194/egusphere-2023-675-RC1
- AC2: 'Response to Reviewer #1 comments', Cenlin He, 15 Jul 2023
  
  Dear Reviewer,
  Thank you for your comments. We have provided a detailed response and revision in the attached file.
  
  Citation: https://doi.org/10.5194/egusphere-2023-675-AC2
RC2:
'Comment on egusphere-2023-675', Anonymous Referee #2, 25 Jun 2023

This paper describes the refactored version of the NoahMP land surface model. As the authors acknowledge, work described here is a software exercise and I do not find much utility in this manuscript, particularly given that a technical report (He et al. 2023) has already been developed. In my opinion, while the software exercise mentioned here sounds like a good step, it doesn’t rise to the level of a paper for a number of reasons, listed below:

MAJOR COMMENTS
From what I can make out based on the description and the expertise of the authors, I think they missed a major opportunity in this refactorization exercise, as there is no mention or adherence to any formal software engineering principles. In many places (e.g. line 92), the mention of ‘modern Fortran code standard’ has been highlighted. Is there a formal standard that you are referring to? Be specific.

Page 3: The five key features mentioned seem quite interrelated and qualitative. What does enhanced data structure, enhanced code structure, optimized variable declaration etc mean? What formal software engineering principles were followed? Did this effort involve software engineers? How do you know if this new version is ‘enhanced’? Did you solicit the input of the community in designing this new framework?

Section 3: Other than separating the code into different modules, has the calling structure changed? From a debugging point of view, having the source code in different modules is no different from having them in a single file. For example, are there explicit code locations of extensibility defined in the new structure?

One of the major impediments to using land surface models is the specification of input datasets. How does the new structure provide an improvement in this regard?

Finally, this refactorization (despite the wide use of Noah-MP) seems like an insular effort. Did you solicit the requirements of different communities that use NoahMP (NWP, Hydrology, Data Assimilation, Crop modelers, etc.)? Did you ensure that this new infrastructure is actually more efficient for including in systems like NWM, WRF, LIS, etc.?

MINOR COMMENTS

Line 26 and 28: The modularization, interoperability mentions are repeated. Additionally, it is mentioned again in the text, and in Conclusions. Please reduce the redundancy of such descriptions.

Line 46: ‘Moden LSMs have been …. As indispensable components …’

Page 2, last para: This is an impressive set of references of the use of NoahMP. I still think it could use some improvements; Liu et al. 2017 is not provided. There are several use of NoahMP for data assimilation than mentioned here, please include them.

Line 97: This is not a ‘study’, rather a description of the software reorganization of the code.

Page 4, paragraph beginning on line 140: I suggest rewriting this para to improve the readability. In this para, there are four sentences that begin with the style of ‘Noah-MP does this’.

Line 263: What is the point of describing new physics that is NOT included in the community release? Is it listing different physics options being worked on? Please explain the significance or remove this para.

Section 4: What is the definition of flux, state, and parameters?

Figure 11: 2m temperature is an input to the model. Why is that being benchmarked?

Citation: https://doi.org/10.5194/egusphere-2023-675-RC2
- AC3: 'Response to Reviewer #2 comments', Cenlin He, 15 Jul 2023
  
  Dear Reviewer,
  Thank you for your comments. We have provided a detailed point-by-point response and revision in the attached file.
  
  Citation: https://doi.org/10.5194/egusphere-2023-675-AC3

Interactive discussion

Status: closed

CEC1:
'Comment on egusphere-2023-675', Juan Antonio Añel, 05 May 2023

Dear authors,

Unfortunately, after checking your manuscript, it has come to our attention that it does not comply with our "Code and Data Policy".
https://www.geoscientific-model-development.net/policies/code_and_data_policy.html

You have archived your code on GitHub. However, GitHub is not a suitable repository for scientific publication. GitHub itself instructs authors to use other alternatives for long-term archival and publishing, such as Zenodo. Therefore, please, publish your code in one of the appropriate repositories, and reply to this comment with the relevant information (link and DOI) as soon as possible, as it should be available for the Discussions stage.

I have to highlight that if you do not fix this problem as soon as possible, we will have to reject your manuscript for publication in our journal. I should note that, actually, your manuscript should not have been accepted in Discussions, given this lack of compliance with our policy. Therefore, the current situation with your manuscript is irregular.

Also, you must include in a potentially reviewed version of your manuscript the modified 'Code and Data Availability' section, the DOI of the code. Also, in the GitHub repositories, there are no licenses listed for both NOAH-MP and HRLDAS/Noah-MP. If you do not include a license, despite what you state in the README file, the code is not "open-source"; it continues to be your property. Therefore, when uploading the model's code to Zenodo, you could want to choose a free software/open-source (FLOSS) license. We recommend the GPLv3. You only need to include the file 'https://www.gnu.org/licenses/gpl-3.0.txt' as LICENSE.txt with your code. Also, you can choose other options that Zenodo provides: GPLv2, Apache License, MIT License, etc.

Regarding the data, I agree that 8 TB is a sensible amount of data to store, and given the nature of this manuscript, we can understand the limitations that this represents to data sharing. However, we would expect that you can issue a DOI for the data relevant to your manuscript. It would be good if you provided better information about where it is stored (HPC infrastructure, servers, physical location, internal path in the file system, etc.)

Juan A. Añel
Geosci. Model Dev. Exec. Editor

Citation: https://doi.org/10.5194/egusphere-2023-675-CEC1
- AC1:
  'Reply on CEC1', Cenlin He, 06 May 2023
  
  Dear Dr. Añel,
  Thank you for the important notes. We have fixed all the issues following your suggestions. Specifially,
  1. We have applied DOI for both Noah-MP and HRLDAS model code GitHub repositories through Zenodo. We have also included the doi information in the two GitHub pages. The doi for Noah-MP code is: https://doi.org/10.5281/zenodo.7901855, and the doi for HRLDAS code is: https://doi.org/10.5281/zenodo.7901867
  2. We have added LICENSE.txt in both model code GitHub repositories. The Noah-MP GitHub repository: https://github.com/NCAR/noahmp, and the HRLDAS GitHub repository: https://github.com/NCAR/hrldas
  3. We have made corresponding changes to our "Code and data availability" section in the manuscript to reflect the new doi and updated GitHub pages. Please see the attached revised manuscript with track-change.
  4. We have also added more details about the 8.8-TB data archival, including the data storage system and path as follows (please also see the revised "Code and data availability" section in the attached manuscript): "The benchmark datasets are stored in the NCAR high-performance supercomputer (HPC) campaign storage file system (data path: /glade/campaign/ral/hap/cenlinhe/NoahMP_benchmark/, see details about the storage system at https://arc.ucar.edu/knowledge_base/70549621) and can be provided by the corresponding author upon request, due to the extremely large data size (8.8 TB)."
  Hope that our revision satisfies the journal requirement and please let me know if you found any further issues.
  Thank you
  Cenlin He
  
  Citation: https://doi.org/10.5194/egusphere-2023-675-AC1
  - CEC2: 'Reply on AC1', Juan Antonio Añel, 10 May 2023
    
    Dear authors,
    Many thanks for your quick reply. It solves all the issues regarding code and data for this version of your manuscript.
    Regards,
    Juan A. Añel
    Geosci. Model Dev. Executive Editor
    
    Citation: https://doi.org/10.5194/egusphere-2023-675-CEC2
RC1:
'Comment on egusphere-2023-675', Anonymous Referee #1, 22 May 2023

This manuscript describes the modernization and refactoring of the widely-used state-of-art Noah-MP LSM, which was released as Noah-MP v5.0. The mordent Fortran code and data structures and standards are adopted in the refactoring. Five key features, including re-organized model physics inro individual process-level Fortran module files, enhanced data structure, enhanced code structure, self-explanatory variable naming standard, and enhanced interface structure to couple with the host models are introduced. It is introduced that the latest released Noah-MP has been coupled with NCAR/HRLDAS system. Some benchmark simulation results over the CONUS are presented. The work of coupling the Noah-MP v5.0 with the latest NASA/LIS system and the WRF-Hydro/NWM system is on-going. In the future, it is also plan to couple to other weather and climate models.

The original code of the model is length single Fortran file. One has to read through the whole file and locate places interested. The refactoring procedures provide a modernized and interoperated model system, with which users could easily understand, modify or utilize in wide applications. As an open-sourced model, the simulation results should be reproducible with given forcing datasets. It is a substantial contribution to modelling science within the scope of Geoscientific Model Development. The manuscript is logical clearly, concisely, and well-structurally interpreted. In addition, model refactoring is a burdensome but less productive task. Not much people have willingness to do this work. This manuscript describes the refactoring conception and processes of the widely-used land surface model. For this kind fundamental work, encourage and circulate should be deserved. I think it is acceptable with minor revisions.

The manuscript detailed describes the model structures, and what have been done with the model coupling to HRLDAS. My only concern is about the future plans. It is stated that the Noah-MP v5,0 will be coupled with more host models. It is encouraging. However, every model has its discrepancies. What are the advantages and disadvantages of this model? how about the future plans for model developments and applications? What is the next step in next several years to promote the advantages and makeup the weakness?

Citation: https://doi.org/10.5194/egusphere-2023-675-RC1
- AC2: 'Response to Reviewer #1 comments', Cenlin He, 15 Jul 2023
  
  Dear Reviewer,
  Thank you for your comments. We have provided a detailed response and revision in the attached file.
  
  Citation: https://doi.org/10.5194/egusphere-2023-675-AC2
RC2:
'Comment on egusphere-2023-675', Anonymous Referee #2, 25 Jun 2023

This paper describes the refactored version of the NoahMP land surface model. As the authors acknowledge, work described here is a software exercise and I do not find much utility in this manuscript, particularly given that a technical report (He et al. 2023) has already been developed. In my opinion, while the software exercise mentioned here sounds like a good step, it doesn’t rise to the level of a paper for a number of reasons, listed below:

MAJOR COMMENTS
From what I can make out based on the description and the expertise of the authors, I think they missed a major opportunity in this refactorization exercise, as there is no mention or adherence to any formal software engineering principles. In many places (e.g. line 92), the mention of ‘modern Fortran code standard’ has been highlighted. Is there a formal standard that you are referring to? Be specific.

Page 3: The five key features mentioned seem quite interrelated and qualitative. What does enhanced data structure, enhanced code structure, optimized variable declaration etc mean? What formal software engineering principles were followed? Did this effort involve software engineers? How do you know if this new version is ‘enhanced’? Did you solicit the input of the community in designing this new framework?

Section 3: Other than separating the code into different modules, has the calling structure changed? From a debugging point of view, having the source code in different modules is no different from having them in a single file. For example, are there explicit code locations of extensibility defined in the new structure?

One of the major impediments to using land surface models is the specification of input datasets. How does the new structure provide an improvement in this regard?

Finally, this refactorization (despite the wide use of Noah-MP) seems like an insular effort. Did you solicit the requirements of different communities that use NoahMP (NWP, Hydrology, Data Assimilation, Crop modelers, etc.)? Did you ensure that this new infrastructure is actually more efficient for including in systems like NWM, WRF, LIS, etc.?

MINOR COMMENTS

Line 26 and 28: The modularization, interoperability mentions are repeated. Additionally, it is mentioned again in the text, and in Conclusions. Please reduce the redundancy of such descriptions.

Line 46: ‘Moden LSMs have been …. As indispensable components …’

Page 2, last para: This is an impressive set of references of the use of NoahMP. I still think it could use some improvements; Liu et al. 2017 is not provided. There are several use of NoahMP for data assimilation than mentioned here, please include them.

Line 97: This is not a ‘study’, rather a description of the software reorganization of the code.

Page 4, paragraph beginning on line 140: I suggest rewriting this para to improve the readability. In this para, there are four sentences that begin with the style of ‘Noah-MP does this’.

Line 263: What is the point of describing new physics that is NOT included in the community release? Is it listing different physics options being worked on? Please explain the significance or remove this para.

Section 4: What is the definition of flux, state, and parameters?

Figure 11: 2m temperature is an input to the model. Why is that being benchmarked?

Citation: https://doi.org/10.5194/egusphere-2023-675-RC2
- AC3: 'Response to Reviewer #2 comments', Cenlin He, 15 Jul 2023
  
  Dear Reviewer,
  Thank you for your comments. We have provided a detailed point-by-point response and revision in the attached file.
  
  Citation: https://doi.org/10.5194/egusphere-2023-675-AC3

Peer review completion

AR: Author's response | RR: Referee report | ED: Editor decision | EF: Editorial file upload

AR by Cenlin He on behalf of the Authors (15 Jul 2023) Author's response Author's tracked changes Manuscript

ED: Referee Nomination & Report Request started (18 Jul 2023) by Jatin Kala

RR by Anonymous Referee #1 (25 Jul 2023)

ED: Publish as is (04 Aug 2023) by Jatin Kala

AR by Cenlin He on behalf of the Authors (04 Aug 2023)

Journal article(s) based on this preprint

08 Sep 2023

Modernizing the open-source community Noah with multi-parameterization options (Noah-MP) land surface model (version 5.0) with enhanced modularity, interoperability, and applicability

Cenlin He, Prasanth Valayamkunnath, Michael Barlage, Fei Chen, David Gochis, Ryan Cabell, Tim Schneider, Roy Rasmussen, Guo-Yue Niu, Zong-Liang Yang, Dev Niyogi, and Michael Ek

Geosci. Model Dev., 16, 5131–5151, https://doi.org/10.5194/gmd-16-5131-2023,https://doi.org/10.5194/gmd-16-5131-2023, 2023

Short summary

Cenlin He, Prasanth Valayamkunnath, Michael Barlage, Fei Chen, David Gochis, Ryan Cabell, Tim Schneider, Roy Rasmussen, Guo-Yue Niu, Zong-Liang Yang, Dev Niyogi, and Michael Ek

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The requested preprint has a corresponding peer-reviewed final revised paper. You are encouraged to refer to the final revised version.

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Short summary

Noah-MP is one of the most widely-used community land surface models in the world, which is designed for applications ranging from uncoupled land-surface and ecohydrological process studies to coupled numerical weather prediction and decadal climate simulations. To facilitate model developments and applications, we modernize Noah-MP by adopting modern Fortran code and data structures and standards, which substantially enhances the model modularity, interoperability, and applicability.


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Modernizing the open-source community Noah-MP land surface model (version 5.0) with enhanced modularity, interoperability, and applicability

Journal article(s) based on this preprint

Interactive discussion

Interactive discussion

Peer review completion

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Journal article(s) based on this preprint

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