hung up at the start of the model run

[Tom Ihde]

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

Calculate_Turbid_Effects
Doing Ecology_Calculate_Total_Abundance
Call migration of invertebrates
Dealing with invertebrate movement
Call ecology
processing box 1
Light levels are assessed
Oxygen levels are assessed
Rugosity level assessed
Doing Box_Bio_Process
Time: 0.000000e+00 Doing adaptive timestep for box: 1, layer 3 (Water Column)
Water_Column_Box
Water_Column_Box
Doing vertebrate reproduction
Doing Get_Settlers for FPL
Doing Get_Settlers for FPO
Doing Get_Settlers for FPS
Doing Get_Settlers for FVD
Doing Get_Settlers for FVV
Doing Get_Settlers for FVS
Doing Get_Settlers for FVB
Doing Get_Settlers for FVT
Doing Get_Settlers for FVO
Doing Get_Settlers for FMM
Doing Get_Settlers for FMWARNING: Time: 0.000000e+00, box: 1, layer: 0 had to reset DIN in sediment to minpool as was = 0
WARNING: group SG is nutrient limited in box 1, layer 0, DIN (NO + NH) = 1.000000e-16, Si = 0.000000e+00, Fe = 0.000000e+00, P = 0.000000e+00
N
Doing Get_Settlers for FBP
Doing Get_Settlers for FDD
Doing Get_Settlers for FDE
Doing Get_Settlers for FDS
Doing Get_Settlers for FDM
Doing Get_Settlers for FDP
Doing Get_Settlers for FDC
Doing Get_Settlers for FDF
Doing Get_Settlers for SHB
Doing Get_Settlers for SHD
Doing Get_Settlers for SHC
Doing Get_Settlers for SSK
Doing Get_Settlers for SB
Doing Get_Settlers for PIN
Doing Get_Settlers for REP
Time: 0.000000e+00 Doing adaptive timestep for box: 1, layer 2 (Water Column)
Water_Column_Box
Water_Column_Box
Doing vertebrate reproduction
Doing Get_Settlers for FPL
Doing Get_Settlers for FPO
Doing Get_Settlers for FPS
Doing Get_Settlers for FVD
Doing Get_Settlers for FVV
Doing Get_Settlers for FVS
Doing Get_Settlers for FVB
Doing Get_Settlers for FVT
Doing Get_Settlers for FVO
Doing Get_Settlers for FMM
Doing Get_Settlers for FMN
Doing Get_Settlers for FBP
Doing Get_Settlers for FDD
Doing Get_Settlers for FDE
Doing Get_Settlers for FDS
Doing Get_Settlers for FDM
Doing Get_Settlers for FDP
Doing Get_Settlers for FDC
Doing Get_Settlers for FDF
Doing Get_Settlers for SHB
Doing Get_Settlers for SHD
Doing Get_Settlers for SHC
Doing Get_Settlers for SSK
Doing Get_Settlers for SB
Doing Get_Settlers for PIN
Doing Get_Settlers for REP
Time: 0.000000e+00 Doing adaptive timestep for box: 1, layer 1 (Water Column)
Water_Column_Box
Doing vertebrate reproduction
Doing Get_Settlers for FPL
Doing Get_Settlers for FPO
Doing Get_Settlers for FPS
Doing Get_Settlers for FVD
Doing Get_Settlers for FVV
Doing Get_Settlers for FVS
Doing Get_Settlers for FVB
Doing Get_Settlers for FVT
Doing Get_Settlers for FVO
Doing Get_Settlers for FMM
Doing Get_Settlers for FMN
Doing Get_Settlers for FBP
Doing Get_Settlers for FDD
Doing Get_Settlers for FDE
Doing Get_Settlers for FDS
Doing Get_Settlers for FDM
Doing Get_Settlers for FDP
Doing Get_Settlers for FDC
Doing Get_Settlers for FDF
Doing Get_Settlers for SHB
Doing Get_Settlers for SHD
Doing Get_Settlers for SHC
Doing Get_Settlers for SSK
Doing Get_Settlers for SB
Doing Get_Settlers for PIN
Doing Get_Settlers for REP
Time: 0.000000e+00 Doing adaptive timestep for box: 1, layer 0 (Water Column)
Epibenthic_Box
Water_Column_Box
Sediment_Box
Doing vertebrate reproduction
Doing Get_Settlers for FPL
Doing Get_Settlers for FPO
Doing Get_Settlers for FPS
Doing Get_Settlers for FVD
Doing Get_Settlers for FVV
Doing Get_Settlers for FVS
Doing Get_Settlers for FVB
Doing Get_Settlers for FVT
Doing Get_Settlers for FVO
Doing Get_Settlers for FMM
Doing Get_Settlers for FMN
Doing Get_Settlers for FBP
Doing Get_Settlers for FDD
Doing Get_Settlers for FDE
Doing Get_Settlers for FDS
Doing Get_Settlers for FDM
Doing Get_Settlers for FDP
Doing Get_Settlers for FDC
Doing Get_Settlers for FDF
Doing Get_Settlers for SHB
Doing Get_Settlers for SHD
Doing Get_Settlers for SHC
Doing Get_Settlers for SSK
Doing Get_Settlers for SB
Doing Get_Settlers for PIN
Doing Get_Settlers for REP
processing box 2
Light levels are assessed
Oxygen levels are assessed
Rugosity level assessed
Doing Box_Bio_Process
Time: 0.000000e+00 Doing adaptive timestep for box: 2, layer 3 (Water Column)
Water_Column_Box
Water_Column_Box
Doing vertebrate reproduction
Doing Get_Settlers for FPL
Doing Get_Settlers for FPO
Doing Get_Settlers for FPS
Doing Get_Settlers for FVD
Doing Get_Settlers for FVV
Doing Get_Settlers for FVS
Doing Get_Settlers for FVB
Doing Get_Settlers for FVT
Doing Get_Settlers for FVO
Doing Get_Settlers for FMM
Doing Get_Settlers for FMN
Doing Get_Settlers for FBP
Doing Get_Settlers for FDD
Doing Get_Settlers for FDE
Doing Get_Settlers for FDS
Doing Get_Settlers for FDM
Doing Get_Settlers for FDP
Doing Get_Settlers for FDC
Doing Get_Settlers for FDF
Doing Get_Settlers for SHB
Doing Get_Settlers for SHD
Doing Get_Settlers for SHC
Doing Get_Settlers for SSK
Doing Get_Settlers for SB
Doing Get_Settlers for PIN
Doing Get_Settlers for REP
Time: 0.000000e+00 Doing adaptive timestep for box: 2, layer 2 (Water Column)
Water_Column_Box
Water_Column_Box
Doing vertebrate reproduction
Doing Get_Settlers for FPL
Doing Get_Settlers for FPO
Doing Get_SeWARNING: Time: 0.000000e+00, box: 2, layer: 0 had to reset DIN in sediment to minpool as was = 0
WARNING: group SG is nutrient limited in box 2, layer 0, DIN (NO + NH) = 1.000000e-16, Si = 0.000000e+00, Fe = 0.000000e+00, P = 0.000000e+00
ttlers for FPS
Doing Get_Settlers for FVD
Doing Get_Settlers for FVV
Doing Get_Settlers for FVS
Doing Get_Settlers for FVB
Doing Get_Settlers for FVT
Doing Get_Settlers for FVO
Doing Get_Settlers for FMM
Doing Get_Settlers for FMN
Doing Get_Settlers for FBP
Doing Get_Settlers for FDD
Doing Get_Settlers for FDE
Doing Get_Settlers for FDS
Doing Get_Settlers for FDM
Doing Get_Settlers for FDP
Doing Get_Settlers for FDC
Doing Get_Settlers for FDF
Doing Get_Settlers for SHB
Doing Get_Settlers for SHD
Doing Get_Settlers for SHC
Doing Get_Settlers for SSK
Doing Get_Settlers for SB
Doing Get_Settlers for PIN
Doing Get_Settlers for REP
Time: 0.000000e+00 Doing adaptive timestep for box: 2, layer 1 (Water Column)
Water_Column_Box
Water_Column_Box
Doing vertebrate reproduction
Doing Get_Settlers for FPL
Doing Get_Settlers for FPO
Doing Get_Settlers for FPS
Doing Get_Settlers for FVD
Doing Get_Settlers for FVV
Doing Get_Settlers for FVS
Doing Get_Settlers for FVB
Doing Get_Settlers for FVT
Doing Get_Settlers for FVO
Doing Get_Settlers for FMM
Doing Get_Settlers for FMN
Doing Get_Settlers for FBP
Doing Get_Settlers for FDD
Doing Get_Settlers for FDE
Doing Get_Settlers for FDS
Doing Get_Settlers for FDM
Doing Get_Settlers for FDP
Doing Get_Settlers for FDC
Doing Get_Settlers for FDF
Doing Get_Settlers for SHB
Doing Get_Settlers for SHD
Doing Get_Settlers for SHC
Doing Get_Settlers for SSK
Doing Get_Settlers for SB
Doing Get_Settlers for PIN
Doing Get_Settlers for REP
Time: 0.000000e+00 Doing adaptive timestep for box: 2, layer 0 (Water Column)
Epibenthic_Box
Water_Column_Box
Sediment_Box
Epibenthic_Box
Water_Column_Box
Sediment_Box
Epibenthic_Box
Water_Column_Box
Sediment_Box
Doing vertebrate reproduction
Doing Get_Settlers for FPL
Doing Get_Settlers for FPO
Doing Get_Settlers for FPS
Doing Get_Settlers for FVD
Doing Get_Settlers for FVV
Doing Get_Settlers for FVS
Doing Get_Settlers for FVB
Doing Get_Settlers for FVT
Doing Get_Settlers for FVO
Doing Get_Settlers for FMM
Doing Get_Settlers for FMN
Doing Get_Settlers for FBP
Doing Get_Settlers for FDD
Doing Get_Settlers for FDE
Doing Get_Settlers for FDS
Doing Get_Settlers for FDM
Doing Get_Settlers for FDP
Doing Get_Settlers for FDC
Doing Get_Settlers for FDF
Doing Get_Settlers for SHB
Doing Get_Settlers for SHD
Doing Get_Settlers for SHC
Doing Get_Settlers for SSK
Doing Get_Settlers for SB
Doing Get_Settlers for PIN
Doing Get_Settlers for REP
processing box 3
Light levels are assessed
Oxygen levels are assessed
Rugosity level assessed
Doing Box_Bio_Process
Time: 0.000000e+00 Doing adaptive timestep for box: 3, layer 3 (Water Column)
Water_Column_Box
Water_Column_Box
Doing vertebrate reproduction
Doing Get_Settlers for FPL
Doing Get_Settlers for FPO
Doing Get_Settlers for FPS
Doing Get_Settlers for FVD
Doing Get_Settlers for FVV
Doing Get_Settlers for FVS
Doing Get_Settlers for FVB
Doing Get_Settlers for FVT
Doing Get_Settlers for FVO
Doing Get_Settlers for FMM
Doing Get_Settlers for FMN
Doing Get_Settlers for FBP
Doing Get_Settlers for FDD
Doing Get_Settlers for FDE
Doing Get_Settlers for FDS
Doing Get_Settlers for FDM
Doing Get_Settlers for FDP
Doing Get_Settlers for FDC
Doing Get_Settlers for FDF
Doing Get_Settlers for SHB
Doing Get_Settlers for SHD
Doing Get_Settlers for SHC
Doing Get_Settlers for SSK
Doing Get_Settlers for SB
Doing Get_Settlers for PIN
Doing Get_Settlers for REP
Time: 0.000000e+00 Doing adaptive timestep for box: 3, layer 2 (Water Column)
Water_Column_Box
Water_Column_Box
Doing vertebrate reproduction
Doing Get_Settlers for FPL
Doing Get_Settlers for FPO
Doing Get_Settlers for FPS
Doing Get_Settlers for FVD
Doing Get_Settlers for FVV
Doing Get_Settlers for FVS
Doing Get_Settlers for FVB
Doing Get_Settlers for FVT
Doing Get_Settlers for FVO
Doing Get_Settlers for FMM
Doing Get_Settlers for FMN
Doing Get_Settlers for FBP
Doing Get_Settlers for FDD
Doing Get_Settlers for FDE
Doing Get_Settlers for FDS
Doing Get_Settlers for FDM
Doing Get_Settlers for FDP
Doing Get_Settlers for FDC
Doing Get_Settlers for FDF
Doing Get_Settlers for SHB
Doing Get_Settlers for SHD
Doing WARNING: Time: 0.000000e+00, box: 3, layer: 0 had to reset DIN in sediment to minpool as was = 0
WARNING: group SG is nutrient limited in box 3, layer 0, DIN (NO + NH) = 1.000000e-16, Si = 0.000000e+00, Fe = 0.000000e+00, P = 0.000000e+00




Get_Settlers for SHC
Doing Get_Settlers for SSK
Doing Get_Settlers for SB
Doing Get_Settlers for PIN
Doing Get_Settlers for REP
Time: 0.000000e+00 Doing adaptive timestep for box: 3, layer 1 (Water Column)
Water_Column_Box
Water_Column_Box
Doing vertebrate reproduction
Doing Get_Settlers for FPL
Doing Get_Settlers for FPO
Doing Get_Settlers for FPS
Doing Get_Settlers for FVD
Doing Get_Settlers for FVV
Doing Get_Settlers for FVS
Doing Get_Settlers for FVB
Doing Get_Settlers for FVT
Doing Get_Settlers for FVO
Doing Get_Settlers for FMM
Doing Get_Settlers for FMN
Doing Get_Settlers for FBP
Doing Get_Settlers for FDD
Doing Get_Settlers for FDE
Doing Get_Settlers for FDS
Doing Get_Settlers for FDM
Doing Get_Settlers for FDP
Doing Get_Settlers for FDC
Doing Get_Settlers for FDF
Doing Get_Settlers for SHB
Doing Get_Settlers for SHD
Doing Get_Settlers for SHC
Doing Get_Settlers for SSK
Doing Get_Settlers for SB
Doing Get_Settlers for PIN
Doing Get_Settlers for REP
Time: 0.000000e+00 Doing adaptive timestep for box: 3, layer 0 (Water Column)
Epibenthic_Box
Water_Column_Box
Sediment_Box
Doing vertebrate reproduction
Doing Get_Settlers for FPL
Doing Get_Settlers for FPO
Doing Get_Settlers for FPS
Doing Get_Settlers for FVD
Doing Get_Settlers for FVV
Doing Get_Settlers for FVS
Doing Get_Settlers for FVB
Doing Get_Settlers for FVT
Doing Get_Settlers for FVO
Doing Get_Settlers for FMM
Doing Get_Settlers for FMN
Doing Get_Settlers for FBP
Doing Get_Settlers for FDD
Doing Get_Settlers for FDE
Doing Get_Settlers for FDS
Doing Get_Settlers for FDM
Doing Get_Settlers for FDP
Doing Get_Settlers for FDC
Doing Get_Settlers for FDF
Doing Get_Settlers for SHB
Doing Get_Settlers for SHD
Doing Get_Settlers for SHC
Doing Get_Settlers for SSK
Doing Get_Settlers for SB
Doing Get_Settlers for PIN
Doing Get_Settlers for REP
processing box 4
Light levels are assessed
Oxygen levels are assessed
Rugosity level assessed
Doing Box_Bio_Process
Time: 0.000000e+00 Doing adaptive timestep for box: 4, layer 1 (Water Column)
Water_Column_Box
In Eat for group ZL, cohort 0 in box4-1. Amount of FPL eaten is infinite

Atlantis ecosystem model <atlantis-eco...@googlegroups.com>

[Lovindeer, Raisha]

Hi Tom,

I've never gotten this error before, but it seems like maybe you should check your pprey matrix. That output seems to imply that zooplankton is trying to eat fish, which is a red flag. Maybe check that your pPREYZL row has 0s for all the other groups except those it's feeding on...

That's all I can think of at the moment. 

Raisha

---

From: atlantis-eco...@googlegroups.com <atlantis-eco...@googlegroups.com> on behalf of Tom Ihde <thomas...@gmail.com>
Sent: Saturday, January 11, 2025 2:47:30 PM
To: Atlantis ecosystem model
Subject: hung up at the start of the model run

 

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[Hem Nalini Morzaria Luna - NOAA Affiliate]

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

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Hem Nalini Morzaria-Luna (how to pronounce), Ph.D. | Marine ecologist

Long Live the Kings| NOAA - Affiliate | Pronouns: she/her

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[Cecilie Hansen]

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