Glacier Energy and Mass Balance (GEMB): a model of firn processes for cryosphere research

Gardner, Alex S.; Schlegel, Nicole-Jeanne; Larour, Eric

doi:https://doi.org/10.5194/gmd-16-2277-2023

Articles | Volume 16, issue 8

https://doi.org/10.5194/gmd-16-2277-2023

© Author(s) 2023. This work is distributed under
the Creative Commons Attribution 4.0 License.

https://doi.org/10.5194/gmd-16-2277-2023

© Author(s) 2023. This work is distributed under
the Creative Commons Attribution 4.0 License.

Articles | Volume 16, issue 8

Model description paper

|

27 Apr 2023

Model description paper |

| 27 Apr 2023

Glacier Energy and Mass Balance (GEMB): a model of firn processes for cryosphere research

Alex S. Gardner, Nicole-Jeanne Schlegel, and Eric Larour

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Final revised paper (published on 27 Apr 2023)
Preprint (discussion started on 16 Aug 2022)

Interactive discussion

Status: closed

CC1: 'Comment on egusphere-2022-674', Juan Antonio Añel, 24 Aug 2022

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 NASA servers. However, NASA is not a suitable repository for long-term archival and scientific publications. You must use one of the long-term archival and publishing alternatives listed in our policy. 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. Also, you must include the modified 'Code and Data Availability' section in a potential reviewed version of your manuscript, with the DOI of the code.

Please, be aware that failing to comply promptly with this request could result in rejecting your manuscript for publication.

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

Citation: https://doi.org/10.5194/egusphere-2022-674-CC1
CEC1:
'Comment on egusphere-2022-674', Juan Antonio Añel, 24 Aug 2022

Dear authors,

(re-posting this comment, now as Chief Editor, not as a community comment)

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 NASA servers. However, NASA is not a suitable repository for long-term archival and scientific publications. You must use one of the long-term archival and publishing alternatives listed in our policy. 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. Also, you must include the modified 'Code and Data Availability' section in a potential reviewed version of your manuscript, with the DOI of the code.

Please, be aware that failing to comply promptly with this request could result in rejecting your manuscript for publication.

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

Citation: https://doi.org/10.5194/egusphere-2022-674-CEC1
- AC1:
  'Reply on CEC1', Alex Gardner, 24 Aug 2022
  
  Dear Juan,
  Thank you for taking the time to provide us with feedback on our paper. The link (https://issm.jpl.nasa.gov/) in question is the project page for NASA's Ice-sheet and Sea-level System Model (ISSM), of which GEMB is the surface mass and energy balance module. ISSM has been open source since 2011 and is a complex multi-istitutional model that is fully open source but under Caltech copywrite. Moving the model outside of it's current location would be a major undertaking and may not even be possible. ISSM meets all of the GMD "Archive standards" for "Third-party archives" and the reviewers have open access to the code. Hopefully this alleviates some of your concerns even though we are not able to relocate the model.
  
  Sincerely,
  Alex
  
  Citation: https://doi.org/10.5194/egusphere-2022-674-AC1
  - AC2: 'Reply on AC1', Alex Gardner, 24 Aug 2022
    
    Hi Juan,
    
    Looking at past ISSM papers in GMD they have included statments similar to this:
    
    Code Availability: GEMB is a module implemented inside of ISSM. The code can be downloaded, compiled, and executed following the instructions available on the ISSM website: https://issm.jpl.nasa.gov/download (last access: June 1, 2022). The public SVN repository for the ISSM code can also be found directly at https://issm.ess.uci.edu/svn/issm/issm/trunk (Larour et al., 2022), and can be downloaded using username “anon” and password “anon”. The version of the code for this study, corresponding to ISSM release 4.19, is SVN version tag number 27035.
    Larour, E., Morlighem, M., and Seroussi, H.: Ice-Sheet and Sea-Level System Model, svn repository, available at: https: //issm.ess.uci.edu/svn/issm/issm/trunk (last access: June 1, 2022), 2022.
    
    We will make sure to include this in the next round of revisions.
    
    Sincerely,
    Alex
    
    Citation: https://doi.org/10.5194/egusphere-2022-674-AC2
    
    CEC2: 'Reply on AC2', Juan Antonio Añel, 24 Aug 2022
    
    Dear authors,
    Thanks for the quick reply. Unfortunately, we can not accept your explanation of the potential complexity or impossibility of sharing the code outside Caltech servers. This, at best, sounds like an apology for not undergoing the effort to share the code in a valid repository. What technical complexity explains why it can not be deposited in an external repository? That is, we need the technical details about what makes it impossible to assess if such motivation is acceptable.
    Also, you mention a previous paper with the same code published in our journal. Thanks for pointing it out. Could you provide the details of the paper to consult it? It could be a long process for us to look at the entire database of published papers looking for the one with such a Code Availability section.
    Regards,
    Juan A. Añel
    Geosci. Model Dev. Executive Editor
    
    Citation: https://doi.org/10.5194/egusphere-2022-674-CEC2
    
    EC1: 'Reply on CEC2', Andrew Wickert, 25 Aug 2022
    
    Dear Juan and Authors,
    First, thanks to Juan for catching this; I had not realized that the NASA repository was not in compliance with GMD standards.
    Second -- and not to sidetrack the current request regarding the other paper, which seems valuable in its own right: Would another possibility be for the source code to GEMB to be made fully available (e.g., on GitHub)? This is not a situation that I have encountered before, but I believe that GMD allows open-source code in closed-source frameworks to (e.g., with Matlab). In this case, perhaps an open-source code in a not-GMD-standard open-source framework would do?
    I hope that we can find a smooth solution, and I also do wonder if there could be long-term benefit (likely beyond the scope of this submission) in ISSM moving into a more mainstream open-source access and archiving framework.
    Best wishes,
    Andy Wickert
    
    Citation: https://doi.org/10.5194/egusphere-2022-674-EC1
    
    CC2: 'Reply on EC1', Nicole-Jeanne Schlegel, 26 Aug 2022
    
    Dear editors,
    Thank you for your discussion on this topic. While we and the ISSM work for a solution to your concerns so our publications can move forward, I think it is important to specifically and officially clarify in this discussion that the public version of ISSM is not archived on a NASA server. To be more precise, as Dr. Gardner pointed out earlier in comment AC2, ISSM is archived on an open-source svn server at the University of California, Irvine (UCI), at https://issm.ess.uci.edu, and has been since 2011. The confusion may be that the ISSM homepage itself and other ISSM helpful model documentation is archived on a NASA server (https://issm.jpl.nasa.gov).
    We realize that the UCI server in question may still not be in compliance with your open-source policy (?), and in that case, we will continue to work towards a solution that is acceptable to GMD.
    Thank you, Nicole Schlegel
    
    Citation: https://doi.org/10.5194/egusphere-2022-674-CC2
    
    CEC3: 'Reply on CC2', Juan Antonio Añel, 26 Aug 2022
    
    Dear authors and Andy,
    GitHub is not valid. Indeed, storing code on Github is by far the problem that accumulates the most violations of code publication policies in scientific research, or at least in our journal. You have to understand that GitHub is a product of a company (Microsoft) that could decide to terminate its service at any point and delete all the material stored there. Our policy (and policies should be read before submitting manuscripts) states it clearly, and what is more, GitHub says on its web page that it is not a service that can be used for long-term archival:
    
    "Project or institution websites and online revision control sites such as GitHub11, GitLab12 or Bitbucket13 are made for code development but unsuitable for archiving frozen code versions."
    
    https://www.geoscientific-model-development.net/policies/code_and_data_policy.html#item3
    
    To qualify as a suitable long-term archival for scientific publication, a repository needs to be funded for the next 10-20 years at the minimum and regulated by bylaws that show the commitment for perdurance along time. Again, our policy provides a list of suitable ones.
    
    In your case, if moving the code to GitHub is easier from the technical point of view, I recommend moving it there and then using the Zenodo-GitHub integration (functionality provided by GitHub) to store a copy in Zenodo. Zenodo is one of the acceptable repositories. I hope this helps.
    
    Again, please, give me the details about which is the paper you have mentioned before. We need to check it to maintain coherence for all the submitted and published manuscripts.
    
    Regards,
    Juan
    Juan A. Añel
    Geosci. Model Dev. Executive Editor
    
    Citation: https://doi.org/10.5194/egusphere-2022-674-CEC3
    
    AC3: 'Reply on CEC3', Alex Gardner, 26 Aug 2022
    
    Dear Editors,
    We are working to archive a static copy of the current version of ISSM on an acceptable third party server. The latest maintained model will remain in UCI servers for the time being so we will still encourage readers to look there if they're interested in the latest version of ISSM.
    
    Given that the code is publicaly accessable for the reviewers to inspect, I wonder if we can start the review process while we archive a static copy of the code on a third party server.
    
    For reference here is the list of 11 publications of ISSM already published in GMD. We note that our software has long-term support and has been hosted at UCI for the past 14 years and is publicaly accesable.
    Bulthuis, K., & Larour, E. (2022). Implementation of a Gaussian Markov random field sampler for forward uncertainty quantification in the Ice-sheet and Sea-level System Model v4.19. Geoscientific Model Development, 15(3), 1195–1217. https://doi.org/10.5194/gmd-15-1195-2022
    
    dos Santos, T. D., Morlighem, M., & Seroussi, H. (2021). Assessment of numerical schemes for transient, finite-element ice flow models using ISSM v4.18. Geoscientific Model Development, 14(5), 2545–2573. https://doi.org/10.5194/gmd-14-2545-2021
    
    Larour, E., Caron, L., Morlighem, M., Adhikari, S., Frederikse, T., Schlegel, N.-J., et al. (2020). ISSM-SLPS: geodetically compliant Sea-Level Projection System for the Ice-sheet and Sea-level System Model v4.17. Geoscientific Model Development, 13(10), 4925–4941. https://doi.org/10.5194/gmd-13-4925-2020
    
    Rückamp, M., Humbert, A., Kleiner, T., Morlighem, M., & Seroussi, H. (2020). Extended enthalpy formulations in the Ice-sheet and Sea-level System Model (ISSM) version 4.17: discontinuous conductivity and anisotropic streamline upwind Petrov–Galerkin (SUPG) method. Geoscientific Model Development, 13(9), 4491–4501. https://doi.org/10.5194/gmd-13-4491-2020
    
    dos Santos, T. D., Morlighem, M., Seroussi, H., Devloo, P. R. B., & Simões, J. C. (2019). Implementation and performance of adaptive mesh refinement in the Ice Sheet System Model (ISSM v4.14). Geoscientific Model Development, 12(1), 215–232. https://doi.org/10.5194/gmd-12-215-2019
    
    Cuzzone, J. K., Morlighem, M., Larour, E., Schlegel, N., & Seroussi, H. (2018). Implementation of higher-order vertical finite elements in ISSM v4.13 for improved ice sheet flow modeling over paleoclimate timescales. Geoscientific Model Development, 11(5), 1683–1694. https://doi.org/10.5194/gmd-11-1683-2018
    
    Larour, E., Cheng, D., Perez, G., Quinn, J., Morlighem, M., Duong, B., et al. (2017). A JavaScript API for the Ice Sheet System Model (ISSM) 4.11: towards an online interactive model for the cryosphere community. Geoscientific Model Development, 10(12), 4393–4403. https://doi.org/10.5194/gmd-10-4393-2017
    
    Habbal, F., Larour, E., Morlighem, M., Seroussi, H., Borstad, C. P., & Rignot, E. (2017). Optimal numerical solvers for transient simulations of ice flow using the Ice Sheet System Model (ISSM versions 4.2.5 and 4.11). Geoscientific Model Development, 10(1), 155–168. https://doi.org/10.5194/gmd-10-155-2017
    
    Larour, E., Utke, J., Bovin, A., Morlighem, M., & Perez, G. (2016). An approach to computing discrete adjoints for MPI-parallelized models applied to Ice Sheet System Model 4.11. Geoscientific Model Development, 9(11), 3907–3918. https://doi.org/10.5194/gmd-9-3907-2016
    
    Adhikari, S., Ivins, E. R., & Larour, E. (2016). ISSM-SESAW v1.0: mesh-based computation of gravitationally consistent sea-level and geodetic signatures caused by cryosphere and climate driven mass change. Geoscientific Model Development, 9(3), 1087–1109. https://doi.org/10.5194/gmd-9-1087-2016
    
    Le Morzadec, K., Tarasov, L., Morlighem, M., & Seroussi, H. (2015). A new sub-grid surface mass balance and flux model for continental-scale ice sheet modelling: testing and last glacial cycle. Geoscientific Model Development, 8(10), 3199–3213. https://doi.org/10.5194/gmd-8-3199-2015
    
    Citation: https://doi.org/10.5194/egusphere-2022-674-AC3
    
    CC3: 'Reply on AC3', Nicole-Jeanne Schlegel, 26 Aug 2022
    
    Dear editors,
    The frozen version of the source code for ISSM v4.21 has been archived at https://doi.org/10.5281/zenodo.7026445 . This should satisfy the archiving requirement. We will update our code availability statement accordingly.
    We have many ISSM publications in GMD, as Dr. Gardner has listed in his latest post. You can also access a full list of publications at: https://issm.jpl.nasa.gov/publications/ .
    Thank you for your guidance in this matter,
    Nicole Schlegel
    
    Citation: https://doi.org/10.5194/egusphere-2022-674-CC3
    
    CEC4: 'Reply on CC3', Juan Antonio Añel, 29 Aug 2022
    
    Dear authors,
    Many thanks for your reply and for storing the code in Zenodo. We can consider the problem solved.
    
    Regarding your previous question about beginning the review process as the code is available to reviewers, our policy mandates that a paper can not even be published in Discussions if it does not comply with the code and data availability statements. Therefore, the fact that your manuscript is already in Discussions was an oversight by our side, so there was no point in inviting reviewers. However, now that the issue with the ISSM code has been fixed, we can proceed with it.
    Regards,
    Juan A., Añel
    Geosci. Model Dev. Executive Editor
    
    Citation: https://doi.org/10.5194/egusphere-2022-674-CEC4
    
    AC4: 'Reply on CEC4', Alex Gardner, 29 Aug 2022
    
    Dear Editors,
    Thank you both for your patience. Glad we could get this sorted.
    Sincerely,
    Alex Garnder and coauthors
    
    Citation: https://doi.org/10.5194/egusphere-2022-674-AC4
    
    EC2: 'Reply on CEC3', Andrew Wickert, 29 Aug 2022
    
    Dear Juan,
    Indeed, I intended to note the Zenodo integration of GitHub for storage there, with GitHub being a good tool for updating and re-archiving (at Zenodo) should a need for updates arise in the review process, as they often do. My apologies for the lack of precision; I was responding in the midst of an international move.
    Andy
    
    Citation: https://doi.org/10.5194/egusphere-2022-674-EC2
    
    AC5: 'Reply on EC2', Alex Gardner, 14 Nov 2022
    
    The comment was uploaded in the form of a supplement: https://egusphere.copernicus.org/preprints/2022/egusphere-2022-674/egusphere-2022-674-AC5-supplement.pdf
    
    Citation: https://doi.org/10.5194/egusphere-2022-674-AC5
    
    AC8: 'Reply on AC5', Alex Gardner, 14 Nov 2022
    
    apologies for submitting reply to reviewer in wrong location
    
    Citation: https://doi.org/10.5194/egusphere-2022-674-AC8
RC1:
'Comment on egusphere-2022-674', Anonymous Referee #1, 15 Oct 2022

Please see attached pdf.

Citation: https://doi.org/10.5194/egusphere-2022-674-RC1
- AC6: 'Reply on RC1', Alex Gardner, 14 Nov 2022
  
  The comment was uploaded in the form of a supplement: https://egusphere.copernicus.org/preprints/2022/egusphere-2022-674/egusphere-2022-674-AC6-supplement.pdf
  
  Citation: https://doi.org/10.5194/egusphere-2022-674-AC6
RC2:
'Comment on egusphere-2022-674', Anonymous Referee #2, 19 Oct 2022

Please see the attached supplement.

Citation: https://doi.org/10.5194/egusphere-2022-674-RC2
- AC7: 'Reply on RC2', Alex Gardner, 14 Nov 2022
  
  The comment was uploaded in the form of a supplement: https://egusphere.copernicus.org/preprints/2022/egusphere-2022-674/egusphere-2022-674-AC7-supplement.pdf
  
  Citation: https://doi.org/10.5194/egusphere-2022-674-AC7

Peer review completion

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

AR by Alex Gardner on behalf of the Authors (30 Dec 2022) Author's response Author's tracked changes Manuscript

ED: Referee Nomination & Report Request started (04 Jan 2023) by Andrew Wickert

RR by Anonymous Referee #1 (20 Jan 2023)

RR by Anonymous Referee #2 (10 Feb 2023)

ED: Publish subject to minor revisions (review by editor) (10 Feb 2023) by Andrew Wickert

AR by Alex Gardner on behalf of the Authors (10 Feb 2023) Author's response Author's tracked changes Manuscript

ED: Publish as is (20 Mar 2023) by Andrew Wickert

AR by Alex Gardner on behalf of the Authors (28 Mar 2023) Manuscript

Short summary

This is the first description of the open-source Glacier Energy and Mass Balance (GEMB) model. GEMB models the ice sheet and glacier surface–atmospheric energy and mass exchange, as well as the firn state. The model is evaluated against the current state of the art and in situ observations and is shown to perform well.

Glacier Energy and Mass Balance (GEMB): a model of firn processes for cryosphere research

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Interactive discussion

Peer review completion

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