still stuck on first timestep

[Tom Ihde]

Hello again, Atlantis modelers, 

Thanks for the replies and suggestions.  

We have not fixed the problem yet, and are still stuck on the first timestep, which partially loads but fails here:

In Eat for group ZL, cohort 0 in box4-1. Amount of FPL eaten is infinite 

• We do have all the detritus groups in the model pPrey
• within pPrey all the values are correct for this specific interaction (our jellyfish "ZL" are eating an infinite amount of our shad "FPL"), which is set as "0"
• Additional info:
• FPL is the first group listed in pPrey
• The only thing different about ZL (which is read in the middle of the model) is that it is the first invertebrate group in the water column that is not age-structured (CEP is also a water column invert that successfully read in before ZL, but CEP has 2 life stages)

Any ideas, please? 

Thank you, 

-Tom

On Tue, Jan 14, 2025 at 4:02 AM Cecilie Hansen <cecil...@gmail.com> wrote:

Hi tom,

i've seen this before (snow crab eating infinite amounts of polar bear) - i'm trying to recollect what i did to get rid of it. will get back to you!

best,

cecilie

mandag 13. januar 2025 kl. 19:47:41 UTC+1 skrev hemnalini.morzarialuna:

Tom, 

something i know the recent versions of code use that might not have been present in older code versions is that you have to include Detritus in sediment as prey. So the last three prey items (columns) of each predator diets should be as follows,   

DL_s

DR_s

DC_s

On Sat, Jan 11, 2025 at 2:47 PM Tom Ihde <thomas...@gmail.com> wrote:

Folks, 

I'm happy to share that the Chesapeake Atlantis Model is almost running  again...almost!  

We have been updating the code from v2,000-something to v6665 with a LOT of help from Andy Beet (thank you, Andy!), and the model is now on the first timestep.  

However, there have been so many changes, I no longer even know where to begin looking for why things are crashing, and this is complicated, in my view, by being at the first timestep, where the model still has not fully loaded.  I've got verbose output on, but don't even know where to start looking  (the log from just before the first timestep began is seen below). 

In Eat for group ZL, cohort 0 in box4-1. Amount of FPL eaten is infinite

Needless to say, I have never seen this error before, but am hoping that it is familiar to some of you, and you might be able to give me some guidance to get past this.  Note, FPL is the first group in the groups.csv, so I am expecting this problem will extend to all biological groups.  

TIA, 

-Tom

Thomas F. Ihde, PhD
Research Assistant Professor
Morgan State University
Patuxent Environmental & Aquatic Research Laboratory (PEARL)
Cell: 443.975.3736
Office: 443.885.5932
https://www.linkedin.com/in/Tom-F-Ihde
Thoma...@morgan.edu  |  Thomas...@gmail.com

[Fulton, Beth (Environment, Hobart)]

G’day

 

Send me the updated prm you’re using and I can try to track what’s happening. Best bet is to spell out each term of the appropriate equation and see how it is getting an infinite answer. There will be a param-config mess up but without seeing what is derailed it is hard to say what (could be ZL_sn?).

 

Beth

 

From: <atlantis-eco...@googlegroups.com> on behalf of Tom Ihde <thomas...@gmail.com>
Date: Thursday 23 January 2025 at 6:20 am
To: Atlantis ecosystem model <atlantis-eco...@googlegroups.com>
Subject: still stuck on first timestep

 

Hello again, Atlantis modelers, 

Thanks for the replies and suggestions.  

We have not fixed the problem yet, and are still stuck on the first timestep, which partially loads but fails here:

 

In Eat for group ZL, cohort 0 in box4-1. Amount of FPL eaten is infinite 

·  We do have all the detritus groups in the model pPrey

·  within pPrey all the values are correct for this specific interaction (our jellyfish "ZL" are eating an infinite amount of our shad "FPL"), which is set as "0"

·  Additional info:

o FPL is the first group listed in pPrey

o The only thing different about ZL (which is read in the middle of the model) is that it is the first invertebrate group in the water column that is not age-structured (CEP is also a water column invert that successfully read in before ZL, but CEP has 2 life stages)

--
You received this message because you are subscribed to the Google Groups "Atlantis ecosystem model" group.
To unsubscribe from this group and stop receiving emails from it, send an email to atlantis-ecosystem...@googlegroups.com.
To view this discussion, visit https://groups.google.com/d/msgid/atlantis-ecosystem-model/CAOLWZ6GYsMfhe6NBw32FWABha9QmxOvdRsh9EpFhWoc_nVin4A%40mail.gmail.com.

[Tom Ihde]

Problem resolved. Beth figured out what we were doing wrong. 

CAM2 is now running again, after only 8 years of downtime! 

In case anyone else ever encounters this issue, this was the solution:

G’day

 

You need to make sure all predators (including ZL) have KUP > 0. That should sort it 😊. [Basically you said they couldn’t eat anything < 0cm in length with KLP which is fine, but you also said they couldn’t eat anything > 0 which is what you also said was KUP value]. If you set KUP to non-zero value (like 0.1) then all good.

 

Cheers

 

Beth

Thank you, Beth! 

Cheers, 

-Tom