Stuck at "Bootstrap Iteration: 1" (Alternatives to VPA/ASAP for bootstrap file generation)

[efletcherPIFSC]

@JonBrodziak

AGEPRO binaries from a525a7b and f8bca42 (used in AGEPRO-GUI 4.3.6) does not allow me to use the Example1 Bootstrap file on test case agepro model input files: Using Example1.BSN bootstrap file for a test case AGEPRO mode lead to the calculation engine stuck at "Bootstrap Iteration; 1".

Using the Example1 bootstrap file with the input file works without issue. Example 2, 3, 4 worked fine.

Documentation about bootstrap files is limited to VPA/ADAPT/ASAP program. Although I used the example bootstrap file on test input files on previous versions, I do not know what changes were made to AGEPRO to cause this issue, or if this was the intended method.

To put it short, for a new AGEPRO model case, what is needed to have a "vaild" bootstrap file to run?

Which raises another issue the programs creation of bootstrap files: VPA(Virtual Population Analysis) and ASAP(Age Structured Assessment Program). This is a documentation holdover that can updated with NOAA FIT/FIMS R-based packages.

Screenshots

Issue

Documentation

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[efletcherPIFSC]

It the CRAN package boot a viable alternative?

boot::boot() manual page
https://cran.r-project.org/web/packages/boot/refman/boot.html#boot

[JonBrodziak]

OK, I will check the Example1 bootstrap file with the 4.25 executable and respond to this issue. Jon

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On Thu, Feb 5, 2026 at 11:01 AM Eric Fletcher ***@***.***> wrote: *efletcherPIFSC* created an issue (noaa-pifsc/AGEPRO#16) <#16> @JonBrodziak <https://github.com/JonBrodziak> AGEPRO binaries from a525a7b <a525a7b> and f8bca42 <f8bca42> (used in AGEPRO-GUI 4.3.6) does not allow me to use the Example1 Bootstrap file on test case agepro model input files: Using Example1.BSN bootstrap file for a test case AGEPRO mode lead to the calculation engine stuck at "Bootstrap Iteration; 1". Using the Example1 bootstrap file with the input file works without issue. Example 2, 3, 4 worked fine. Documentation about bootstrap files is limited to VPA/ADAPT/ASAP program. Although I used the example bootstrap file on test input files on previous versions, I do not know what changes were made to AGEPRO to cause this issue, or if this was the intended method. To put it short, for a new AGEPRO model case, what is needed to have a "vaild" bootstrap file to run? Which raises another issue the programs creation of bootstrap files: *VPA*(Virtual Population Analysis) and *ASAP*(Age Structured Assessment Program). This is a documentation holdover that can updated with NOAA FIT/FIMS R-based packages. Screenshots Issue Screenshot.2026-02-05.104131.png (view on web) <https://github.com/user-attachments/assets/c05ec2ee-9aaa-4969-8b50-426b6d5fe238> Documentation Screenshot.2026-02-05.103537.png (view on web) <https://github.com/user-attachments/assets/28286ce4-7808-46b5-bb62-7c82c7d29ccc> . — Reply to this email directly, view it on GitHub <#16>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACVXIZQOLUHKEU6DR4ALNSL4KOVTTAVCNFSM6AAAAACUETYNR6VHI2DSMVQWIX3LMV43ASLTON2WKOZTHEYDGNJXGQ3TSMI> . You are receiving this because you were mentioned.Message ID: ***@***.***>

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------------------------------ Jon Brodziak Mathematical Statistician Pacific Islands Fisheries Science Center NOAA Fisheries | U.S. Department of Commerce Office: (808) 725-5617 www.fisheries.noaa.gov | PIFSC Stock Assessment <https://pifscstockassessments.github.io/>

[efletcherPIFSC]

@JonBrodziak The Input File's random number seed is an important value can be the key difference between a successful bootstrapping fun and one that's hanging up described in this issue.

For example I created a new AGEPRO model input file and copy and pasted every value in Example1, except for the SEED value (which defaults to 0). I saved as "test2.INP", used "Example1.BSN" and got stuck on "Bootstrap Iteration :1". Note that quitting out out if that program (will return an *.out file with 0KB).

I created another new AGEPRO input case model and copied all the values from "Example1.INP" including the random seed value, to "test3.INP", used "Example1.BSN" and it ran without this issue.

[efletcherPIFSC]

@JonBrodziak The issue is primary how AGEPRO-GUI is sending Input Model's with Random Number Seed value 0 to the calculation engine. This can be patched on the AGEPRO-GUI side by reassigning the 0 Random Number Seed Value to a pseudorandom number before launched to the calculation engine.

Sending a AGEPRO model with the bootstrap file with the correct dimensions, and with a non-zero random number seed GENERAL parameter works.

[JonBrodziak]

Setting the random seed in linear congruential random number generator can lead to a degenerative state of all zero's. This is what is happening with AGEPRO. The random seed is X0 and the formula for calculating the next random integer X(n+1) from the current integer X(n) is X(n+1) = (a*X(n) + c) mod M. If X(0) = 0 then X(1) = (a**0 + c) mod M = 0. So the random sequence degenerates into 0, 0, 0, 0, .... That's what is happening with the seed = 0.

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On Fri, Feb 13, 2026 at 2:16 PM Eric Fletcher ***@***.***> wrote: *efletcherPIFSC* left a comment (noaa-pifsc/AGEPRO#16) <#16 (comment)> @JonBrodziak <https://github.com/JonBrodziak> The issue is primary how AGEPRO-GUI is sending Input Model's with *Random Number Seed* value 0 to the calculation engine. This can be patched on the AGEPRO-GUI side by *reassigning* the 0 Random Number Seed Value to a *pseudorandom* number before launched to the calculation engine. Sending a AGEPRO model with the bootstrap file with the correct dimensions, and with a non-zero random number seed GENERAL parameter works. — Reply to this email directly, view it on GitHub <#16 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACVXIZUVV4RFVUWK4IAPLWL4LZSLZAVCNFSM6AAAAACUETYNR6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTSMBQGIZDMNZWGU> . You are receiving this because you were mentioned.Message ID: ***@***.***>

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------------------------------ Jon Brodziak Mathematical Statistician Pacific Islands Fisheries Science Center NOAA Fisheries | U.S. Department of Commerce Office: (808) 725-5617 www.fisheries.noaa.gov | PIFSC Stock Assessment <https://pifscstockassessments.github.io/>

[efletcherPIFSC]

@JonBrodziak I will make make adjustments to AGEPRO-GUI (and ageproR) to ensure that AGEPRO Input files will not save the random number seed to 0.

For documentation purposes, the Random Number Seed value 0 is an invalid value.