another segmentation fault

[jaco...@gmail.com]

I am trying to run the latest version from git. I am getting a segmentation fault. I put a bunch of fprints in and have narrowed the problem down, but I cant figure out the issue.

I have log.txt (verbose 6) but it is too big to post here. Below is a paste of the last few lines with my fprints.

Any help would be great.

Thanks

Call physics
Entering transportBM
Entering tracerForcingBM and doing temperature ID 877
Entering tracerForcingBM and doing salinity ID 878
Entering Saturation_Check
Leaving tracerForcingBM
Leaving tracerForcingBM
JMK: Call dealing with boundaries
JMK: DEBUG - Entering boundaries function...
JMK: DEBUG - Passed boundaries function.
JMK: DEBUG - Ice on status: 0
JMK: DEBUG - Copying water column tracers...
JMK: DEBUG - Finished copying water column tracers.
JMK: DEBUG - Copying sediment tracers...
JMK: DEBUG - Finished copying sediment tracers.
JMK: DEBUG - Calling vertgeom...
JMK: DEBUG - Finished vertgeom.
JMK: DEBUG - Calling sedprops...
JMK: DEBUG - Finished sedprops.
JMK: DEBUG - Calling Check_Contam_Totals...
JMK: DEBUG - Finished Check_Contam_Totals.
JMK: DEBUG - Flushing stdout and stderr...
JMK: DEBUG - Finished flushing stdout and stderr.
JMK: DEBUG - Updating time step: t = 11145600.000000, dt = 43200.000000
JMK: DEBUG - Finished updating time step. New t = 11188800.000000
JMK: DEBUG - Updating step counter: nt = 258
JMK: DEBUG - Finished updating step counter. New nt = 259
JMK: DEBUG - Checking delete_to_halt_run file...
JMK: DEBUG - Found delete_to_halt_run file.
JMK: DEBUG - Exiting runNextTimeStep. Halt status: 0, Updated time: 11188800.000000, Updated nt: 259
JMK: DEBUG - Entering runNextTimeStep. Current time: 11188800.000000, tstop: 157680000.000000, nt: 259, halt: 0
Call checking time
checking the time
Activity patterns determined
t = 129.5, hd.t = 130.5, TofY: 129, % Done: 7.095890
JMK: DEBUG - Checking before copying new water column tracers: bm->nbox=53, bm->wcnz=6, bm->ntracer=880
JMK: DEBUG - Finished copying new water column tracers.
JMK: DEBUG - Checking before copying new sediment tracers: bm->nbox=53, bm->sednz=1, bm->ntracer=880
JMK: DEBUG - Finished copying new sediment tracers.
Segmentation fault
Atlantis run completed at þri 18.feb 2025, 11:53:41 GMT
Total runtime: 00:08:50

[Fulton, Beth (Environment, Hobart)]

G’day

 

Anyway you can put the log file or run prms anywhere I can get them to take a look?

 

Its failing after the memcopy so most likely when it goes into your Effort routines (based on time of year and what comes after the memcopy). Is it the effort displacement code kicking in and causing troubles (it is untried in the way you’re using it)?

 

Beth

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[jaco...@gmail.com]

here are the links to those files, Beth. If anyone else would like access I can grant it. 

This should not have do to with effort as it occurs during the first year, and I do not force effort until the 52nd year.

out.txt

log.txt