Re: Sardine SS3 version update - 3.24 to 3.30
Richard Methot - NOAA Federal
Stock Assessment Research Scientist (ST)
Northwest Fisheries Science Center
NOAA Fisheries | U.S. Department of Commerce
Office: (425) 666-9893
Mobile: (301) 830-2454
Dear all,
I work at Ifremer in France, and I am currently updating the Stock Synthesis (SS3) model for the Bay of Biscay sardine stock (Sardine 27.8abd), which is currently running on version 3.24.
While upgrading to a newer version, I encountered a few difficulties, and several questions came up.
To perform the transition, I used a conversion executable that I had downloaded from the Stock Synthesis VLAB, where it was uploaded by Richard Methot in 2019.
However, the User Manual for version 3.30.24 states that SS_trans executables are available for transitions from versions 3.30.01 to 3.30.17, and that the executable required to convert a model from version 3.24 to a version later than 3.30.17 is available from a GitHub repository.
Unfortunately, I was unable to locate it. Could you please let me know where I can download this executable, or provide the link to the relevant GitHub repository?
I also have a few additional questions about the update process. Some of these issues may be related to the conversion executable I used, but I thought it would still be helpful to ask my questions in case they point to other aspects of the version update process.
I) To provide some context: the Bay of Biscay sardine model includes several fleets: a commercial fleet, a biomass index survey, and a DEPM (Daily Egg Production Method), which is an index of spawning biomass expressed in biomass units. We have weight-at-age data for the commercial fleet and for the biomass index, but not for the DEPM. In version 3.30, it is necessary to enter weight-at-age data for all fleets: “There must be an entry for fecundity […], and weight-at-age for each fleet (even if these vectors are identical in some cases)”. What would you recommend entering when weight-at-age data are not available for all fleets (in biomass unit)?
II) Due to the nature of the DEPM index, its units should be linked to spawning biomass. In recent versions of SS3, this can be achieved by setting the fleet unit to 30 in the table #_CPUE_and_surveyabundance_observations.
In version 3.24, however, the closest equivalent seems to be setting the size selectivity parameter (see Chapter 8.3.3, Abundance Indices, section Data format – Special Surveys in the 3.24 User Manual), but we do not have any length data.
What would you recommend as the best way to represent a spawning biomass index in both versions 3.24 and 3.30?
III) Finally, we use maturity-at-age data read from the wtatage.ss file. In version 3.24, setting the Maturity_option to 5 indicates that this file should be read (see Chapter 9.3.12, Empirical Weight-at-Age, in the 3.24 User Manual).
However, after upgrading to version 3.30, the control.ss file still has Maturity_option set to 5, whereas the 3.30 User Manual states that option 5 means "disable".
Could you clarify what "disable" means in this context? Also, is option 4 ("read a fecundity × maturity-at-age vector for all ages") the equivalent of option 5 in version 3.24?
If you've made it this far, thank you! I know this is quite a long list of questions, but I would greatly appreciate any advice you may have.
Thank you in advance for your time and help.
Best regards,
Klervi Verbrugghe – engineer at Pêcheurs de Bretagne and Ifremer
Elizabeth Perl - NOAA Affiliate
Massimiliano Cardinale
Dear
If there are issues with the translator, translating this model manually as alternative should not be so hard, I can assist as well along Rick, if needed.
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From: 'Richard Methot - NOAA Federal' via SS3 - Forum <ss3-...@googlegroups.com>
Sent: Saturday, 18 July 2026 02:21
To: Klervi VERBRUGGHE <klervi.v...@pecheursdebretagne.eu>
Cc: nmfs.stock...@noaa.gov; ss3-...@googlegroups.com
Subject: [SS3] Re: Sardine SS3 version update - 3.24 to 3.30
CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and know the content is safe.
I'll take a look at your questions next week, but it has been several years since anyone has used the 3.24 translator. You will have a few manual changes to make after you run it, but it does take care of most of the data file changes. I have no cumulative list of the additional changes to guide you.
The links you seek were all in the VLAB message I sent. Here they are again:
We are thankful for the services that VLAB provided the SS3 project for many years. Over a year ago, The SS3 team completed migration of SS3's development, archiving, and communication to github. With this notice, we will soon terminate this Forum at VLAB and the SS3 development and collaboration sites at VLAB. If you have not already done so, please continue to engage with SS3 at:
Richard D. Methot Jr.
Stock Assessment Research Scientist (ST)
Northwest Fisheries Science Center
NOAA Fisheries | U.S. Department of Commerce
Office: (425) 666-9893
Mobile: (301) 830-2454
On Fri, Jul 17, 2026 at 9:01 AM Klervi VERBRUGGHE <klervi.v...@pecheursdebretagne.eu> wrote:
Dear all,
I work at Ifremer in France, and I am currently updating the Stock Synthesis (SS3) model for the Bay of Biscay sardine stock (Sardine 27.8abd), which is currently running on version 3.24.
While upgrading to a newer version, I encountered a few difficulties, and several questions came up.
To perform the transition, I used a conversion executable that I had downloaded from the Stock Synthesis VLAB, where it was uploaded by Richard Methot in 2019.
However, the User Manual for version 3.30.24 states that SS_trans executables are available for transitions from versions 3.30.01 to 3.30.17, and that the executable required to convert a model from version 3.24 to a version later than 3.30.17 is available from a GitHub repository.
Unfortunately, I was unable to locate it. Could you please let me know where I can download this executable, or provide the link to the relevant GitHub repository?
I also have a few additional questions about the update process. Some of these issues may be related to the conversion executable I used, but I thought it would still be helpful to ask my questions in case they point to other aspects of the version update process.
I) To provide some context: the Bay of Biscay sardine model includes several fleets: a commercial fleet, a biomass index survey, and a DEPM (Daily Egg Production Method), which is an index of spawning biomass expressed in biomass units. We have weight-at-age data for the commercial fleet and for the biomass index, but not for the DEPM. In version 3.30, it is necessary to enter weight-at-age data for all fleets: “There must be an entry for fecundity […], and weight-at-age for each fleet (even if these vectors are identical in some cases)”. What would you recommend entering when weight-at-age data are not available for all fleets (in biomass unit)?
II) Due to the nature of the DEPM index, its units should be linked to spawning biomass. In recent versions of SS3, this can be achieved by setting the fleet unit to 30 in the table #_CPUE_and_surveyabundance_observations.
In version 3.24, however, the closest equivalent seems to be setting the size selectivity parameter (see Chapter 8.3.3, Abundance Indices, section Data format – Special Surveys in the 3.24 User Manual), but we do not have any length data.
What would you recommend as the best way to represent a spawning biomass index in both versions 3.24 and 3.30?
III) Finally, we use maturity-at-age data read from the wtatage.ss file. In version 3.24, setting the Maturity_option to 5 indicates that this file should be read (see Chapter 9.3.12, Empirical Weight-at-Age, in the 3.24 User Manual).
However, after upgrading to version 3.30, the control.ss file still has Maturity_option set to 5, whereas the 3.30 User Manual states that option 5 means "disable".
Could you clarify what "disable" means in this context? Also, is option 4 ("read a fecundity × maturity-at-age vector for all ages") the equivalent of option 5 in version 3.24?
If you've made it this far, thank you! I know this is quite a long list of questions, but I would greatly appreciate any advice you may have.
Thank you in advance for your time and help.
Best regards,
Klervi Verbrugghe – engineer at Pêcheurs de Bretagne and Ifremer
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