HOTSSea v1: a NEMO-based physical Hindcast of the Salish Sea (1980–2018) supporting ecosystem model development

Oldford, Greig; Jarníková, Tereza; Christensen, Villy; Dunphy, Michael

doi:https://doi.org/10.5194/gmd-18-211-2025

Articles | Volume 18, issue 2

https://doi.org/10.5194/gmd-18-211-2025

© Author(s) 2025. This work is distributed under
the Creative Commons Attribution 4.0 License.

https://doi.org/10.5194/gmd-18-211-2025

© Author(s) 2025. This work is distributed under
the Creative Commons Attribution 4.0 License.

Articles | Volume 18, issue 2

Model description paper

|

20 Jan 2025

Model description paper |

| 20 Jan 2025

HOTSSea v1: a NEMO-based physical Hindcast of the Salish Sea (1980–2018) supporting ecosystem model development

Greig Oldford, Tereza Jarníková, Villy Christensen, and Michael Dunphy

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Final revised paper (published on 20 Jan 2025)
Supplement to the final revised paper
Preprint (discussion started on 22 May 2024)

Interactive discussion

Status: closed

CEC1:
'Comment on gmd-2024-58', Juan Antonio Añel, 14 Jun 2024

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
For your work you use the NEMO and HOTSSea models, and our policy request that all the source code used for a submitted manuscript must be published in a long-term trusted repository at the time of submission. However, in the Code and Data Policy section of your manuscript you do not provide such repositories. Therefore, please, you must publish the full NEMO and HoTSSea code that you use (not only configuration files) in one of the appropriate repositories, and reply to this comment with the relevant information (link and DOI) as soon as possible, as we can not accept manuscripts in Discussions that do not comply with our policy. In this regard I note that the current situation with your manuscript is irregular. Also, please, remember to include the relevant primary input/output data necessary to perform simulations.
Note that if you do not fix this problem, we will have to reject your manuscript for publication in our journal.
Also, you must include in a potentially reviewed version of your manuscript the modified 'Code and Data Availability' section, the DOI of the code (and another DOI for the dataset if necessary).
Juan A. Añel

Geosci. Model Dev. Executive Editor

Citation: https://doi.org/10.5194/gmd-2024-58-CEC1
- AC1:
  'Reply on CEC1', Greig Oldford, 24 Jun 2024
  
  Thank you for pointing this out. All code and data will be provided in accordance with the GMD data policy.
  
  Citation: https://doi.org/10.5194/gmd-2024-58-AC1
  - CEC2: 'Reply on AC1', Juan Antonio Añel, 25 Jun 2024
    
    Dear authors,
    Thanks for your reply; unfortunately, you did not address the issue mentioned in my previous comment. To avoid misunderstandings, you must publish it now. I commented on this and asked for the code and data eleven days ago. I do not see a reason why you could not have published the code in such a time frame. Your manuscript should not be under Discussion because of this lack of compliance with our policy.
    
    Therefore, I urge you to address this issue immediately and reply to this comment with the links and DOIs of the repositories containing the code and data. If you do not address it, we must stop the Discussion and review process and reject your manuscript. We must use wisely the time of reviewers, editors, and other colleagues who could be reviewing the paper in Discussions, and we can not allow that they invest their time just to come out with having to reject your manuscript later because of lack of compliance.
    Regards,
    Juan A. Añel
    Geosci. Model Dev. Executive Editor
    
    Citation: https://doi.org/10.5194/gmd-2024-58-CEC2
    
    AC3: 'Reply on CEC2', Greig Oldford, 25 Jun 2024
    
    Hello,
    Please understand that it is our intention to comply with your data and code policy.
    I am sorry for any misunderstanding or miscommunication. Our lead author was at a conference and then travelling for one week, as per our co-author's email sent June 14 (editorial@copernicus.org). Did you receive this email?
    We sent an email with the updated DOI's yesterday because we could not see a way to edit the Assets uploaded in your system through the preprint submission system. Did you receive this email with the updated links to the data and code?
    I will post below the updated DOI's and attach them to this response. Please advise on the proper way to make these modifications.
    We created a new Github code repo and therefore have new Zenodo DOI's and links to provide, which are shown below.
    ################
    Data sets:
    Forcings 1: HRDPS
    https://zenodo.org/doi/10.5281/zenodo.12193923
    Forcings 2: RDRS
    https://zenodo.org/doi/10.5281/zenodo.12206290
    Forcings 3: ERA5, CIOPS, Runoff, etc
    https://zenodo.org/doi/10.5281/zenodo.12312768
    Note - due to storage limits, three Zenodo archives were required
    
    ################
    Model code and software:
    HOTSSea_v1_NEMOandSupportCode
    https://doi.org/10.5281/zenodo.12520931
    which archives the following github repo:
    https://github.com/goldford/HOTSSea_v1_NEMOandSupportCode/tree/main
    with files specifically requested by the reviewer and editor here (NEMO sources):
    https://github.com/goldford/HOTSSea_v1_NEMOandSupportCode/tree/main/serverside/NEMO
    
    ################
    Interactive computing environment:
    HOTSSea_v1_NEMOandSupportCode
    https://doi.org/10.5281/zenodo.12520931
    which archives the following github repo:
    https://github.com/goldford/HOTSSea_v1_NEMOandSupportCode/tree/main
    with python notebooks found here:
    https://github.com/goldford/HOTSSea_v1_NEMOandSupportCode/tree/main/desktop/code
    Note - this is in the same repo as the model code and software
    Please advise on how best to update the data and code in the online manuscript submission. Originally, there was a section in the preprint submission section that we filled out, but I don't see a way to access this again.
    
    Citation: https://doi.org/10.5194/gmd-2024-58-AC3
  - EC1: 'Reply on AC1', Vassilios Vervatis, 25 Jun 2024
    
    Dear authors,
    Thank you for your reply. Starting the review and discussion process of your ms., more than a month ago, I have given you instructions to upload your NEMO code in a zenodo repository. I recommend you address this issue immediately.
    Regards,
    Vassilios Vervatis
    GMD Topical Editor
    
    Citation: https://doi.org/10.5194/gmd-2024-58-EC1
    
    AC2: 'Reply on EC1', Greig Oldford, 25 Jun 2024
    
    Hello,
    Please understand that it is our intention to comply with your data and code policy.
    I am sorry for any misunderstanding or miscommunication. Our lead author was at a conference and then travelling for one week, as per our co-author's email sent June 14 (editorial@copernicus.org). Did you receive this email?
    We sent an email with the updated DOI's yesterday because we could not see a way to edit the Assets uploaded in your system through the preprint submission system. Did you receive this email with the updated links to the data and code?
    I will post below the updated DOI's and attach them to this response. Please advise on the proper way to make these modifications.
    We created a new Github code repo and therefore have new Zenodo DOI's and links to provide, which are shown below.
    ################
    Data sets:
    Forcings 1: HRDPS
    https://zenodo.org/doi/10.5281/zenodo.12193923
    Forcings 2: RDRS
    https://zenodo.org/doi/10.5281/zenodo.12206290
    Forcings 3: ERA5, CIOPS, Runoff, etc
    https://zenodo.org/doi/10.5281/zenodo.12312768
    Note - due to storage limits, three Zenodo archives were required
    
    ################
    Model code and software:
    HOTSSea_v1_NEMOandSupportCode
    https://doi.org/10.5281/zenodo.12520931
    which archives the following github repo:
    https://github.com/goldford/HOTSSea_v1_NEMOandSupportCode/tree/main
    with files specifically requested by the reviewer and editor here (NEMO sources):
    https://github.com/goldford/HOTSSea_v1_NEMOandSupportCode/tree/main/serverside/NEMO
    
    ################
    Interactive computing environment:
    HOTSSea_v1_NEMOandSupportCode
    https://doi.org/10.5281/zenodo.12520931
    which archives the following github repo:
    https://github.com/goldford/HOTSSea_v1_NEMOandSupportCode/tree/main
    with python notebooks found here:
    https://github.com/goldford/HOTSSea_v1_NEMOandSupportCode/tree/main/desktop/code
    Note - this is in the same repo as the model code and software
    Please advise on how best to update the data and code in the online manuscript submission. Originally, there was a section in the preprint submission section that we filled out, but I don't see a way to access this again.
    
    Citation: https://doi.org/10.5194/gmd-2024-58-AC2
    
    EC2: 'Reply on AC2', Vassilios Vervatis, 26 Jun 2024
    
    Dear authors,
    Thank you for the reply.
    Please make sure in your repositories, within the NEMO tree directory "serverside/NEMO/Software/NEMO36OPP/NEMOGCM/CONFIG/SalishSea1500/", the WORK/ and MY_SRC/ directories contain properly the *.F90 modules (as it is now, they are empty files), in order for other researchers to be able to compile the code and reproduce simulations.
    Regards,
    Vassilios Vervatis
    GMD Topical Editor
    
    Citation: https://doi.org/10.5194/gmd-2024-58-EC2
    
    AC4: 'Reply on EC2', Greig Oldford, 26 Jun 2024
    
    Apologies that the symlinks from the unix machine were not carried over during the compression and download/upload process to github and zenodo.
    
    An update has now been pushed to https://github.com/goldford/HOTSSea_v1_NEMOandSupportCode archived at 10.5281/zenodo.12520930
    
    To clarify for readers or anyone wishing to repeat the simulation, what happens in the build stage is the procedure generates 'symlinks' to reference the code we used for the simulation and puts these in CONFIG/SalishSea1500/WORK, overriding some files with symlinks to MY SRC files which were found here in our previous release: "serverside/NEMO/Software/NEMO36OPP/NEMOGCM/CONFIG/SHARED/MY_SRC"
    The SalishSea1500/WORK folder in "serverside/NEMO/Software/NEMO36OPP/NEMOGCM/CONFIG/SalishSea1500/" on our machine therefore contains a few hundred symlinks to the source code found in other folders. These links were generated at build time and contain fully qualified paths that are specific to our machine. The SalishSea1500/MY_SRC folder on our machine is actually a symlink to the /MY_SRC folder in "serverside/NEMO/Software/NEMO36OPP/NEMOGCM/CONFIG/SHARED/". So, the symlinks as-is will not work on another machine unless the folder structure is identical.
    
    For transparency, and since the symlinks are fully qualified and given that downloading symlinks to / from unix, Windows, and git is often problematic (resulting in empty files), we have now modified the code originally uploaded to support this manuscript so that the actual files linked to are now in the /MY_SRC and /WORK folders in "serverside/NEMO/Software/NEMO36OPP/NEMOGCM/CONFIG/SalishSea1500/".
    
    Just to make it clear, following our setup, to re-run our simulation one would need to download, install, and configure the NEMO v3.6 software for their machine (ours is unix CentOS) and run the build procedure on their machine which will regenerate symlinks with paths specific to their machine.
    
    Citation: https://doi.org/10.5194/gmd-2024-58-AC4
    
    CEC3: 'Reply on AC4', Juan Antonio Añel, 27 Jun 2024
    
    Dear authors,
    Thanks for addressing these issues.
    I would like to ask you to stop adding links to GitHub repositories to your replies . GitHub is not a valid repository for scientific publication, and mentioning GitHub and Zenodo repositories only introduces unnecessary noise in this discussion, and misleads potential readers. Therefore, for the Discussion and publication of your manuscript, please, avoid making reference to git repositories and any other storage systems that do serve the purpose of assuring the long-term accessibility and replicability of your work.
    Thanks,
    Juan A. Añel
    Geosci. Model Dev. Executive Editor
    
    Citation: https://doi.org/10.5194/gmd-2024-58-CEC3
RC1:
'Comment on gmd-2024-58', Anonymous Referee #1, 11 Jul 2024

Dear Editor and Authors,
Please find attached my review of the manuscript titled "HOTSSea v1: a NEMO-based physical Hindcast of the Salish Sea (1980 – 2018) supporting ecosystem model development" (GMD-2024-58) by Oldford et al. (2024).
The manuscript presents a valuable contribution to the field of regional ocean modeling by developing a 38-year hindcast model of the Salish Sea, a region with limited observational data. The model demonstrates skill in reproducing observed temperature variability and trends, particularly after applying a temperature bias correction. However, several limitations, including the exclusion of Puget Sound, persistent salinity biases, and depth-dependent temperature biases, require further attention and revision.

Please see the pdf for a fuller expansion of the review.

Citation: https://doi.org/10.5194/gmd-2024-58-RC1
- RC2:
  'Reply on RC1', Anonymous Referee #1, 11 Jul 2024
  
  I realise I also forget in the review issues with the initial condition and flushing time for the spin up. Given it is from a different historic period and the flushing time is of the order 3 years it would seem the 1 year spin up period is in appropriate and may cause issues the authors report in the early years of the hindcast.
  
  Citation: https://doi.org/10.5194/gmd-2024-58-RC2
  - AC6: 'Reply on RC2', Greig Oldford, 26 Aug 2024
    
    We thank the anonymous referee for their helpful and insightful feedback. We are processing the feedback and will provide our response as soon as possible.
    
    Citation: https://doi.org/10.5194/gmd-2024-58-AC6
  - AC7: 'Reply on RC2', Greig Oldford, 03 Oct 2024
    
    Thank you to the anonymous referee #1 for the feedback. We have now revised the manuscript to address the issues that were raised. We have attached our detailed response to your review here. We have been instructed not to post the revised manuscript here as supplement. Also note we added your previous additional comment (re: spin-up) to this response.
    
    Citation: https://doi.org/10.5194/gmd-2024-58-AC7
RC3:
'Comment on gmd-2024-58', Anonymous Referee #2, 21 Aug 2024

Please find attached my review of the manuscript "HOTSSea v1: a NEMO-based physical Hindcast of the Salish Sea (1980 – 2018) supporting ecosystem model development" (GMD-2024-58) by Oldford et al. (2024).
A 38-year hindcast of the region presents an extremely valuable resource for analyzing the Salish Sea's dynamic connections to large-scale climate indices and assessing the region's vulnerability to climate change. The evaluation is thorough and clear, with a well-conceived step-wise approach to model forcing assessment, and the effectiveness of the temperature bias correction is impressive. With some revisions, this research will be well-suited for publication in GMD. Specifically, the authors should address the limitations of conducting evaluations by comparing their results to another model (SalishSeaCast) and justify their decision not to perform evaluations in Puget Sound or implement a salinity bias correction. Additionally, a more in-depth discussion of the applicability of HOTSSea to ecosystem modeling would benefit the paper, as I am not yet convinced that a 1.5 km resolution is sufficient for salmon research.
The PDF includes more detailed explanations of my general comments, as well as smaller line-by-line comments.

Citation: https://doi.org/10.5194/gmd-2024-58-RC3
- AC5: 'Reply on RC3', Greig Oldford, 26 Aug 2024
  
  The authors wish to extend their gratitude to the anonymous referee for their helpful and insightful feedback. We are now processing these and will post our response as soon as possible.
  
  Citation: https://doi.org/10.5194/gmd-2024-58-AC5
- AC8: 'Reply on RC3', Greig Oldford, 03 Oct 2024
  
  Thank you to the anonymous referee #2 for their detailed and helpful feedback. We have now revised our manuscript to address the issues you mentioned. Please see our more detailed response attached.
  
  Citation: https://doi.org/10.5194/gmd-2024-58-AC8

Peer review completion

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

AR by Greig Oldford on behalf of the Authors (04 Oct 2024) Author's response Manuscript

EF by Sarah Buchmann (08 Oct 2024) Supplement

ED: Referee Nomination & Report Request started (08 Oct 2024) by Vassilios Vervatis

RR by Anonymous Referee #1 (31 Oct 2024)

RR by Anonymous Referee #2 (31 Oct 2024)

EF by Anna Mirena Feist-Polner (29 Oct 2024) Author's tracked changes

ED: Publish subject to minor revisions (review by editor) (01 Nov 2024) by Vassilios Vervatis

AR by Greig Oldford on behalf of the Authors (10 Nov 2024) Author's response Author's tracked changes Manuscript

ED: Publish as is (14 Nov 2024) by Vassilios Vervatis

AR by Greig Oldford on behalf of the Authors (14 Nov 2024) Author's response Manuscript

Short summary

We developed a 3D ocean model called the Hindcast of the Salish Sea (HOTSSea v1) that recreates physical conditions throughout the Salish Sea from 1980 to 2018. It was not clear that acceptable accuracy could be achieved because of computational and data limitations, but the model's predictions agreed well with observations. When we used the model to examine ocean temperature trends in areas that lack observations, it indicated that some seasons and areas are warming faster than others.

HOTSSea v1: a NEMO-based physical Hindcast of the Salish Sea (1980–2018) supporting ecosystem model development

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Interactive discussion

Peer review completion

Suggestions for revision or reasons for rejection