This blog post serves as a checklist for all the little loose ends that I need to tie up before launching the new model runs.

  • Set up header file and compile ROMS on klone (x11ab)
    • Define AVERAGES and undefine PERFECT_RESTART
    • Use new fennel.h with 50% particle burial and corrected carbon burial

  • Get latest version of ROMS
    • Delete older varinfo files on local pc/perigee/apogee
    • Git pull latest version of ROMS on klone
    • Recompile ROMS after git pull

  • Increase nudging to climatology
    • Create nudgcoef.nc file for all biogeochemistry variables
    • Update nudgcoef.nc file name in BLANK.in (to nudgcoef_tracer100.nc)
    • Copy nudgecoef_tracer100.nc file into LO_data on apogee

  • Set up dot in folder
    • Copy Parker’s cas7_t1_x11ab folder to LO_user and rename as cas7_newtraps_x11ab
    • Use newest BLANK.in version with shifted tides
    • Use MPDATA advection scheme for bio tracers in bio_Fennel.in
    • Adjust forcing list (atm00, ocnG00, tide00, trapsN00)
    • Ensure make_dot_in.py is compatible with 320 cores for tiling
    • Make sure make_dot_in is set up for daily averages with continuation
    • Make another copy called cas7_newtrapsnoN_x11ab
      • Specify trapsN01 forcing

  • Generate new river/WWTP forcing using updated TRAPS for October 2012 - December 2017 on apogee
    • Final code edits to eliminate any remaining bugs
    • Adjust forcing code to discharge zero NO3 and NH4 from WWTPs
    • Generate one set of forcing with DIN in WWTP effluent (trapsN00)
    • Generate another set of forcing with zero DIN in WWTP effluent (trapsN01)
    • Check that forcing is correct

  • Make an adjusted driver_roms4 script in LO_user/driver
    • Set up file to look for atmospheric, tidal, and ocean forcing in Parker’s apogee account (dat1/parker/LO_output/forcing/cas7)
    • But look for river/WWTP forcing in Aurora’s apogee account

  • SCP files in LO_data/grids/cas7 into klone?

  • Launch model run
    • Email Parker before-hand to get final confirmation of resources
    • Check with Jilian about resources
    • Use start type “newcontinuation”
    • Use 10 ckpt-g2 slices for each test condition
    • Save output on dat1 in apogee

  • Set up crontab so I receive email updates of model progress every few hours

  • Generate script to calculate bit-reproducibility after one day of run time