mismatch between forecast recdevs in modified par file vs forecast

[iantaylor-NOAA]

Working through the Debugging.R script shared by @JuanMatiasBraccini at https://drive.google.com/drive/folders/1oUEPHeFbU9gf33REEZuIvR5Mq_DAS2_E (private, but shared with @nathanvaughan-NOAA and me), I modified the base.dir to work for my computer and ran with DO='cod' and DO='gummy' and replicated the finding that the cod model worked and the gummy shark model didn't. The failure seems to be caused by the files in \Outputs\gummy_S1\1\gummy_OM_OM\ not working currently with SS3 due to a mismatch between forecast recdevs in modified par file vs the forecast file.

The ss3.par file has

# Fcast_recruitments:
0.00000000000 0.00000000000 0.00000000000 0.00000000000 0.00000000000

whereas the model has 2023 as both the ending year of the model and the last year of the main devs and forecast file has 1 #_Nforecastyrs, so there should only be one forecast recruitment parameter in the par file for it to run successfully. Trying to figure out when and where the wrong number is being set is too confusing for me, given my limited understanding of the package.

@JuanMatiasBraccini, sorry, I was clearly too optimistic about what it would take to update this package to work with recent versions of SS3.

@nathanvaughan-NOAA, if you have time to look at this at any point, or have debugging tips, please let me know how I can help.

[nathanvaughan-NOAA]

Thanks for all the work @iantaylor-NOAA I'm bouncing between meetings but did a quick check rerunning SS in the gummy_EM folder and it got rid of the 5 years of devs in the par file. Could that have just been a bad file from an old run? SSMSE shouldn't be changing any of the files in those folders so it makes sense that the bad par would crash SS. All the files in the EM and OM folders need to be exactly as there come out of a finished SS estimation run. Let us know if you know where the 5 years came from @JuanMatiasBraccini

[iantaylor-NOAA]

@nathanvaughan-NOAA, thank you for looking at this during a busy week/month.
I'm sorry I missed seeing that the original input files had the mismatch with the ss3.par. Because the original models weren't relying on ss3.par they ran fine so I didn't catch the source of the 5 forecast recdevs as coming from there.
However, when I modify the Fcast_recruitments line in gummy_OM and gummy_EM (and confirm that they can run from the .par file), then run_SSMSE() now successfully runs SS3 in Outputs\gummy_S1\1\gummy_OM_OM and produces a Report.sso file. But I get "Error: names do not match previous names." and Outputs\gummy_S1\1\gummy_EM_EM_init only contains input files.

[nathanvaughan-NOAA]

Thanks @iantaylor-NOAA that looks like more of a real error and makes sense given that naming changes are the primary issue between versions.

[JuanMatiasBraccini]

OFFICIAL Hi guys, Apologies for the silence but I had a surfing accident last Thursday and was off work till today... Thanks for looking into this, the 5 years in ss3.par$Fcast_recruitments come from my SS assessment where I forecast for 5 years by default. The wrapping functions I created for updating the OM and EM modified the forecast.ss$#_Nforecastyrs (set to 1) but did not modify ss3.par$Fcast_recruitments. I've now updated these wrapping functions to make sure the forecast.ss$#_Nforecastyrs=1 and ss3.par$Fcast_recruitments=1 in both the OM and EM. After implementing this, I generated the same error that Ian raised 'Iteration 1 failed in directory D:/SSMSE/Gummy shark/Outputs/S1. Error: names do not match previous names. Please delete folders with failed runs before running summary functions'. Cheers Matias Dr Matias Braccini | Principal Research Scientist Aquatic Science and Assessment Fisheries and Sustainability Department of Primary Industries and Regional Development 39 Northside Drive | Hillarys WA 6025 t +61 (0)8 9203 0211 | w dpird.wa.gov.au Adjunct Research Fellow School of Molecular and Life Sciences Curtin University IUCN Species Survival Commission (SSC) Shark Specialist Group From: Nathan Vaughan ***@***.***> Sent: Thursday, 13 August 2026 12:58 AM To: nmfs-ost/SSMSE ***@***.***> Cc: Matias Braccini ***@***.***>; Mention ***@***.***> Subject: [EXT] - Re: [nmfs-ost/SSMSE] mismatch between forecast recdevs in modified par file vs forecast (Issue #239) CAUTION: This email originated from outside of DPIRD. Do not click links or open attachments unless you recognise the sender and know the content is safe. [https://avatars.githubusercontent.com/u/53061482?s=20&v=4]nathanvaughan-NOAA left a comment (nmfs-ost/SSMSE#239)<#239 (comment)> Thanks @iantaylor-NOAA<https://github.com/iantaylor-NOAA> that looks like more of a real error and makes sense given that naming changes are the primary issue between versions. - Reply to this email directly, view it on GitHub<#239?email_source=notifications&email_token=AEAKRGS7TJAA4YCQJ6DQRLT5JSOZ3A5CNFSNUABFM5UWIORPF5TWS5BNNB2WEL2JONZXKZKDN5WW2ZLOOQXTKMRWHE4DKMJVGIY2M4TFMFZW63VHNVSW45DJN5XKKZLWMVXHJLDGN5XXIZLSL5RWY2LDNM#issuecomment-5269851521>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AEAKRGW6MBCHSV2YTCZVKO35JSOZ3AVCNFSNUABFKJSXA33TNF2G64TZHMYTSNZQGY4TQMBRHNEXG43VMU5TKMJSGU2DEOBXHAZKC5QC>. Triage notifications, keep track of coding agent tasks and review pull requests on the go with GitHub Mobile for iOS<https://github.com/notifications/mobile/ios/AEAKRGXLBREE3GVZPYWOPZD5JSOZ3A5CNFSNUABFM5UWIORPF5TWS5BNNB2WEL2JONZXKZKDN5WW2ZLOOQXTKMRWHE4DKMJVGIY2M4TFMFZW63VHNVSW45DJN5XKKZLWMVXHJKTGN5XXIZLSL5UW64Y> and Android<https://github.com/notifications/mobile/android/AEAKRGQUWWGYUQL7QZ34YGD5JSOZ3A5CNFSNUABFM5UWIORPF5TWS5BNNB2WEL2JONZXKZKDN5WW2ZLOOQXTKMRWHE4DKMJVGIY2M4TFMFZW63VHNVSW45DJN5XKKZLWMVXHJLTGN5XXIZLSL5QW4ZDSN5UWI>. Download it today! You are receiving this because you were mentioned.Message ID: ***@***.******@***.***>> [Facebook]<https://www.facebook.com/DPIRDWA> [x] <https://x.com/dpirdbroadacre> [Linkedin] <https://www.linkedin.com/company/dpirdwa> [Instagram] <https://www.instagram.com/dpirdwa/> [Dept of Primary Industries and Regional Development] [Protect, Grow, Innovate] [Artwork: "Kangaroos going to the Waterhole" by Willarra Barker.] DPIRD acknowledges the Traditional Custodians of Country, the Aboriginal people of the many lands that we work on and their language groups throughout Western Australia and recognise their continuing connection to the land and waters. We respect their continuing culture and the contribution they make to the life of our regions and we pay our respects to their Elders past, present and emerging. Artwork: "Kangaroos going to the Waterhole" by Willarra Barker. DISCLAIMER: The information contained in this email (including attachments) is intended only for the use of the person(s) to whom it is addressed as it may be confidential and contain legally privileged information. If you are not the intended recipient you are hereby notified that any perusal, use, distribution, copying or disclosure is strictly prohibited. If you have received this email in error, please immediately advise us by return email and delete the email document. This email and any attachments to it are also subject to copyright and any unauthorised reproduction, adaptation or transmission is prohibited. This notice should not be removed.