Memory Allocation Issue in Atlantis Model Version 6698

[Kévin Cazelles]

Hi all,

While working with Atlantis model version 6698, I encountered an issue related to memory allocation for BITAC_sp used in the harvest module. Specifically, at line 1166 of the atManageSetup.c file, the following allocation is used:

bm->BiTAC_sp = (double ****) alloc4d(2, bm->K_num_tot_sp, totalreg_id + 1, 6);

However, the way BiTAC_sp is utilized throughout the code is consistent with the following allocation instead:

bm->BiTAC_sp = (double ****) alloc4d(2, totalreg_id + 1, bm->K_num_tot_sp, 6);

This misallocation caused a segmentation fault in my use case. It’s possible that this issue has been addressed in newer versions of Atlantis, but unfortunately, I do not have access to those versions to confirm.

I wanted to bring this to the attention of the community in case others have encountered a similar problem or if it might still exist in current versions.

Kevin Cazelles

[Isaac Kaplan - NOAA Federal]

Hi Kevin,

  In v6718,  I can confirm that I have the same as the first line you noted: 

bm->BiTAC_sp = (double ****) alloc4d(2, bm->K_num_tot_sp, totalreg_id + 1, 6);

 I suspect that most use cases just get lucky and allocate more than necessary. At least I can confirm that I have encountered segmentation faults before, when I forget to think about whether other  "K_num" vector size parameters match what I intend. 

A quick look at a Run.prm file from Puget Sound , for instance, shows:  (no fishery management actually active though) 

K_num_tot_sp    79      # 73 for puget sound including detritus.  total number of biological groups in the model

K_num_reg         2    # Maximum number of management zonings used in the model

I think other western North American models have something similar. 

Others have more expertise here but I suspect you have made a good catch. 

Isaac

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Isaac Kaplan

Northwest Fisheries Science Center
National Marine Fisheries Service, NOAA
Conservation Biology Division, Room 205 South
2725 Montlake Blvd. E., Seattle WA 98112

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