[MITgcm-devel] LAYERS update
Jean-Michel Campin
jmc at ocean.mit.edu
Tue Jun 2 10:04:32 EDT 2015
Hi Ryan,
I am cc the mitgcm-devel list so that everyone knowns.
I will suggest the folowing plan:
1) if you can send me a tar file with all new files + all
modified files, I will run the Adjoint testreport (both using
TAF and OpenAD). Should not be a ploblem, but sometimes there are
some tricky behaviour (e.g., the order of included header files matters)
that are better to check.
2) will let you know (soon after (1)) if it's good and you will
check-in your changes ; if you have some problems checking-in
code into the CVS repos, I could do it for you (but it's better
if you can do it yourself).
3) could wait until next week to add the verification test
(a: I will have more time next week ; b: we will be sure by that time
that the few special WE testreport tests are OK).
Because pkg/layers is not supposed to modified the model solution,
we could think of turning it on in an alredy compiled experiment,
just adding a new run-test (input.layers, results/output.layers.txt).
Can discuss this off the list.
Cheers,
Jean-Michel
On Mon, Jun 01, 2015 at 10:52:39PM -0400, Ryan Abernathey wrote:
> Jean-Michel,
>
> I am resurrecting our old email thread.
>
> After six months (sorry!!! ;) I have finally managed to get my layers code
> up to date with the latest cvs. I have verified that all the verification
> testreports pass according to your instructions above, including most
> importantly the cfc_example, which is the only one with layers enabled. (I
> would be happy to send you my testreport summary.txt if you want to
> confirm.)
>
> Below is a list of the modified files. The reason that I modified things
> like gad, thermodynamics, etc, is to be able to save the necessary flux
> fields to reconstruct the theta and salt budgets from within layers. There
> may be a more efficient way to do this (e.g. by coordinating better with
> diagnostics), but what I have now works ok. Most importantly, it can all be
> turned off with the compile-time flag LAYERS_THERMODYNAMICS.
>
> There is also a significant bug fix in layers_fluxcalc involving the way
> interpolation works with partial cells.
>
> As part of my ongoing work with this, I would like to create a
> layers_example verification experiment. And I will continue making updates
> to the layers_thermodynamics stuff.
>
> Let me know if I should check this in directly, or if you would like to
> look at the changes first yourself (e.g. test with the adjoint, with I
> can't do.)
>
> Thanks again for your help!
>
> Cheers,
> Ryan
>
>
>
> Here are all my locally modified files that I would like to check in.
> Repository revision: 1.15
> /u/gcmpack/MITgcm/model/src/diags_oceanic_surf_flux.F,v
> Repository revision: 1.34 /u/gcmpack/MITgcm/model/src/impldiff.F,v
> Repository revision: 1.157 /u/gcmpack/MITgcm/model/src/thermodynamics.F,v
> Repository revision: 1.75
> /u/gcmpack/MITgcm/pkg/generic_advdiff/gad_advection.F,v
> Repository revision: 1.72
> /u/gcmpack/MITgcm/pkg/generic_advdiff/gad_calc_rhs.F,v
> Repository revision: 1.22
> /u/gcmpack/MITgcm/pkg/generic_advdiff/gad_implicit_r.F,v
> Repository revision: 1.13
> /u/gcmpack/MITgcm/pkg/generic_advdiff/gad_som_advect.F,v
> Repository revision: 1.14 /u/gcmpack/MITgcm/pkg/layers/LAYERS.h,v
> Repository revision: 1.6 /u/gcmpack/MITgcm/pkg/layers/LAYERS_OPTIONS.h,v
> Repository revision: 1.26 /u/gcmpack/MITgcm/pkg/layers/layers_calc.F,v
> Repository revision: 1.7 /u/gcmpack/MITgcm/pkg/layers/layers_check.F,v
> Repository revision: 1.8
> /u/gcmpack/MITgcm/pkg/layers/layers_diagnostics_init.F,v
> Repository revision: 1.12
> /u/gcmpack/MITgcm/pkg/layers/layers_fluxcalc.F,v
> Repository revision: 1.10
> /u/gcmpack/MITgcm/pkg/layers/layers_init_fixed.F,v
> Repository revision: 1.8
> /u/gcmpack/MITgcm/pkg/layers/layers_init_varia.F,v
> Repository revision: 1.1 /u/gcmpack/MITgcm/pkg/layers/layers_mnc_init.F,v
> Repository revision: 1.12 /u/gcmpack/MITgcm/pkg/layers/layers_output.F,v
> Repository revision: 1.9
> /u/gcmpack/MITgcm/pkg/layers/layers_readparms.F,v
> Repository revision: 1.2 /u/gcmpack/MITgcm/pkg/layers/layers_save.F,v
> Repository revision: 1.3
> /u/gcmpack/MITgcm/pkg/layers/layers_thermodynamics.F,v
>
>
>
>
>
>
> On Sun, Jan 18, 2015 at 1:49 PM, Jean-Michel Campin <jmc at ocean.mit.edu>
> wrote:
>
> > Hi Ryan,
> >
> > This sounds good.
> >
> > Thanks,
> > Jean-Michel
> >
> > On Sun, Jan 18, 2015 at 01:12:42PM -0500, Ryan Abernathey wrote:
> > > Thanks so much for spending time helping me on this. I really appreciate
> > it.
> > >
> > >
> > > > Now, we need to find a way that work for you. Since the total number
> > > > of files that you have modified is not so large (10 to 20 ?) and it's
> > only
> > > > in
> > > > few pkgs, you could try to cvs update them locally (especially if it
> > works
> > > > without
> > > > conflict) and put them back in a freshly downloaded version
> > (up-to-date)
> > > > of MITgcm.
> > > >
> > > > Would this work ?
> > > >
> > >
> > > I think I understand what you are suggesting.
> > > 1. Make a copy my working code directory (65c with modifications)
> > > 2. Update each file individually, i.e. for each file: cvs update <file>
> > > 3. Check out a new fresh copy of MITgcm (latest release)
> > > 4. Copy each of the udpated files (from 2) to this new source tree
> > > 5. Build from the new source tree and run my tests to make sure the code
> > > still works properly
> > > 6. Run the testreports using the new code
> > > 7. Once everything works, commit the changes
> > >
> > > I can do this.
> > >
> > > Not directly related to this, but just as a reminder: To be able to
> > > > check-in,
> > > > you will have to do it from a version of the code that has be
> > downloaded
> > > > not with "cvsanon".
> > > >
> > >
> > > Yes, I am always accessing with my rpa at mitgcm.org account.
> > >
> > >
> > > >
> > > > Cheers,
> > > > Jean-Michel
> > > >
> > > > On Sat, Jan 17, 2015 at 07:29:35PM -0500, Ryan Abernathey wrote:
> > > > > Yes, fortunately I still have a clean version of my working code
> > based on
> > > > > 65c. (I made a backup before trying to update.) Attached is that file
> > > > from
> > > > > my pre-update folder. Keep in mind it is only a single example out of
> > > > many.
> > > > >
> > > > > Here is a full list of all the files with merge conflicts. Nearly
> > all (I
> > > > > haven't checked every single one) of these conflicts are due to the
> > > > header
> > > > > in the first three lines.
> > > > >
> > > > > File: devel_HOWTO.sgml Status: File had conflicts on merge
> > > > > File: tag-index Status: Unresolved Conflict
> > > > > File: PARAMS.h Status: Unresolved Conflict
> > > > > File: apply_forcing.F Status: Unresolved Conflict
> > > > > File: calc_gw.F Status: Unresolved Conflict
> > > > > File: calc_viscosity.F Status: Unresolved Conflict
> > > > > File: config_check.F Status: Unresolved Conflict
> > > > > File: config_summary.F Status: Unresolved Conflict
> > > > > File: do_atmospheric_phys.F Status: Unresolved Conflict
> > > > > File: do_oceanic_phys.F Status: Unresolved Conflict
> > > > > File: do_the_model_io.F Status: Unresolved Conflict
> > > > > File: dynamics.F Status: Unresolved Conflict
> > > > > File: forward_step.F Status: Unresolved Conflict
> > > > > File: ini_forcing.F Status: Unresolved Conflict
> > > > > File: ini_parms.F Status: Unresolved Conflict
> > > > > File: initialise_varia.F Status: Unresolved Conflict
> > > > > File: load_fields_driver.F Status: Unresolved Conflict
> > > > > File: main_do_loop.F Status: Unresolved Conflict
> > > > > File: packages_boot.F Status: Unresolved Conflict
> > > > > File: packages_check.F Status: Unresolved Conflict
> > > > > File: packages_init_fixed.F Status: Unresolved Conflict
> > > > > File: packages_init_variables.F Status: Unresolved Conflict
> > > > > File: packages_write_pickup.F Status: Unresolved Conflict
> > > > > File: salt_integrate.F Status: Unresolved Conflict
> > > > > File: set_defaults.F Status: Unresolved Conflict
> > > > > File: set_parms.F Status: Unresolved Conflict
> > > > > File: temp_integrate.F Status: Unresolved Conflict
> > > > > File: the_main_loop.F Status: Unresolved Conflict
> > > > > File: the_model_main.F Status: Unresolved Conflict
> > > > > File: timestep.F Status: Unresolved Conflict
> > > > > File: write_grid.F Status: Unresolved Conflict
> > > > > File: atm_phys_driver.F Status: Unresolved Conflict
> > > > > File: atm_phys_init_fixed.F Status: Unresolved Conflict
> > > > > File: atm_phys_init_varia.F Status: Unresolved Conflict
> > > > > File: atm_phys_read_pickup.F Status: Unresolved Conflict
> > > > > File: atm_phys_write_pickup.F Status: Unresolved Conflict
> > > > > File: radiation_mod.F90 Status: Unresolved Conflict
> > > > > File: AUTODIFF.h Status: Unresolved Conflict
> > > > > File: AUTODIFF_OPTIONS.h Status: Unresolved Conflict
> > > > > File: addummy_in_stepping.F Status: Unresolved Conflict
> > > > > File: autodiff_check.F Status: Unresolved Conflict
> > > > > File: autodiff_inadmode_set_ad.F Status: Unresolved Conflict
> > > > > File: autodiff_inadmode_unset_ad.F Status: Unresolved Conflict
> > > > > File: autodiff_restore.F Status: Unresolved Conflict
> > > > > File: autodiff_store.F Status: Unresolved Conflict
> > > > > File: generate_tag.F Status: Unresolved Conflict
> > > > > File: COST_OPTIONS.h Status: Unresolved Conflict
> > > > > File: cost_final.F Status: Unresolved Conflict
> > > > > File: cost_init_varia.F Status: Unresolved Conflict
> > > > > File: CTRL_GENARR.h Status: Unresolved Conflict
> > > > > File: CTRL_OPTIONS.h Status: Unresolved Conflict
> > > > > File: CTRL_SIZE.h Status: Unresolved Conflict
> > > > > File: ctrl.h Status: Unresolved Conflict
> > > > > File: ctrl_check.F Status: Unresolved Conflict
> > > > > File: ctrl_dummy.h Status: Unresolved Conflict
> > > > > File: ctrl_get_gen.F Status: Unresolved Conflict
> > > > > File: ctrl_getobcse.F Status: Unresolved Conflict
> > > > > File: ctrl_getobcsn.F Status: Unresolved Conflict
> > > > > File: ctrl_getobcss.F Status: Unresolved Conflict
> > > > > File: ctrl_getobcsw.F Status: Unresolved Conflict
> > > > > File: ctrl_getrec.F Status: Unresolved Conflict
> > > > > File: ctrl_init.F Status: Unresolved Conflict
> > > > > File: ctrl_init_obcs_variables.F Status: Unresolved Conflict
> > > > > File: ctrl_init_variables.F Status: Unresolved Conflict
> > > > > File: ctrl_init_wet.F Status: Unresolved Conflict
> > > > > File: ctrl_map_gentim2d.F Status: Unresolved Conflict
> > > > > File: ctrl_map_ini.F Status: Unresolved Conflict
> > > > > File: ctrl_map_ini_ecco.F Status: Unresolved Conflict
> > > > > File: ctrl_map_ini_gen.F Status: Unresolved Conflict
> > > > > File: ctrl_map_ini_genarr.F Status: Unresolved Conflict
> > > > > File: ctrl_mask_set_xz.F Status: Unresolved Conflict
> > > > > File: ctrl_mask_set_yz.F Status: Unresolved Conflict
> > > > > File: ctrl_pack.F Status: Unresolved Conflict
> > > > > File: ctrl_readparms.F Status: Unresolved Conflict
> > > > > File: ctrl_set_pack_xz.F Status: Unresolved Conflict
> > > > > File: ctrl_set_pack_yz.F Status: Unresolved Conflict
> > > > > File: ctrl_set_unpack_xz.F Status: Unresolved Conflict
> > > > > File: ctrl_set_unpack_yz.F Status: Unresolved Conflict
> > > > > File: ctrl_summary.F Status: Unresolved Conflict
> > > > > File: ctrl_unpack.F Status: Unresolved Conflict
> > > > > File: ctrl_weights.h Status: Unresolved Conflict
> > > > > File: DIAGNOSTICS_CALC.h Status: Unresolved Conflict
> > > > > File: diag_calc_psivel.F Status: Unresolved Conflict
> > > > > File: diag_cg2d.F Status: Unresolved Conflict
> > > > > File: diagnostics_calc_phivel.F Status: Unresolved Conflict
> > > > > File: diagnostics_readparms.F Status: Unresolved Conflict
> > > > > File: diagnostics_set_calc.F Status: Unresolved Conflict
> > > > > File: DIC_LOAD.h Status: Unresolved Conflict
> > > > > File: DIC_OPTIONS.h Status: Unresolved Conflict
> > > > > File: DIC_VARS.h Status: Unresolved Conflict
> > > > > File: bio_export.F Status: Unresolved Conflict
> > > > > File: dic_biotic_forcing.F Status: Unresolved Conflict
> > > > > File: dic_cost.F Status: Unresolved Conflict
> > > > > File: dic_fields_load.F Status: Unresolved Conflict
> > > > > File: dic_ini_atmos.F Status: Unresolved Conflict
> > > > > File: dic_ini_forcing.F Status: Unresolved Conflict
> > > > > File: dic_readparms.F Status: Unresolved Conflict
> > > > > File: dic_set_control.F Status: Unresolved Conflict
> > > > > File: dic_surfforcing.F Status: Unresolved Conflict
> > > > > File: dic_surfforcing_init.F Status: Unresolved Conflict
> > > > > File: cost_argo_salt.F Status: Unresolved Conflict
> > > > > File: cost_argo_theta.F Status: Unresolved Conflict
> > > > > File: cost_atlantic.F Status: Unresolved Conflict
> > > > > File: cost_averagesfields.F Status: Unresolved Conflict
> > > > > File: cost_averagesgeneric.F Status: Unresolved Conflict
> > > > > File: cost_averagesinit.F Status: Unresolved Conflict
> > > > > File: cost_bottomdrag.F Status: Unresolved Conflict
> > > > > File: cost_bp.F Status: Unresolved Conflict
> > > > > File: cost_bp_read.F Status: Unresolved Conflict
> > > > > File: cost_ctds.F Status: Unresolved Conflict
> > > > > File: cost_ctdsclim.F Status: Unresolved Conflict
> > > > > File: cost_ctdt.F Status: Unresolved Conflict
> > > > > File: cost_ctdtclim.F Status: Unresolved Conflict
> > > > > File: cost_curmtr.F Status: Unresolved Conflict
> > > > > File: cost_diffkr.F Status: Unresolved Conflict
> > > > > File: cost_drift.F Status: Unresolved Conflict
> > > > > File: cost_drifter.F Status: Unresolved Conflict
> > > > > File: cost_driftw.F Status: Unresolved Conflict
> > > > > File: cost_etan0.F Status: Unresolved Conflict
> > > > > File: cost_forcing.F Status: Unresolved Conflict
> > > > > File: cost_gen_transport.F Status: Unresolved Conflict
> > > > > File: cost_gencost_all.F Status: Unresolved Conflict
> > > > > File: cost_gencost_assignperiod.F Status: Unresolved Conflict
> > > > > File: cost_gencost_boxmean.F Status: Unresolved Conflict
> > > > > File: cost_gencost_customize.F Status: Unresolved Conflict
> > > > > File: cost_gencost_seaicev4.F Status: Unresolved Conflict
> > > > > File: cost_gencost_sshv4.F Status: Unresolved Conflict
> > > > > File: cost_gencost_sstv4.F Status: Unresolved Conflict
> > > > > File: cost_generic.F Status: Unresolved Conflict
> > > > > File: cost_geoid.F Status: Unresolved Conflict
> > > > > File: cost_hyd.F Status: Unresolved Conflict
> > > > > File: cost_ies.F Status: Unresolved Conflict
> > > > > File: cost_ies_read.F Status: Unresolved Conflict
> > > > > File: cost_internal_params.F Status: Unresolved Conflict
> > > > > File: cost_kapgm.F Status: Unresolved Conflict
> > > > > File: cost_kapredi.F Status: Unresolved Conflict
> > > > > File: cost_mean_heatflux.F Status: Unresolved Conflict
> > > > > File: cost_mean_saltflux.F Status: Unresolved Conflict
> > > > > File: cost_obcs.F Status: Unresolved Conflict
> > > > > File: cost_obcs_ageos.F Status: Unresolved Conflict
> > > > > File: cost_obcse.F Status: Unresolved Conflict
> > > > > File: cost_obcsn.F Status: Unresolved Conflict
> > > > > File: cost_obcss.F Status: Unresolved Conflict
> > > > > File: cost_obcsvol.F Status: Unresolved Conflict
> > > > > File: cost_obcsw.F Status: Unresolved Conflict
> > > > > File: cost_readargos.F Status: Unresolved Conflict
> > > > > File: cost_readargot.F Status: Unresolved Conflict
> > > > > File: cost_readers.F Status: Unresolved Conflict
> > > > > File: cost_readgeoid.F Status: Unresolved Conflict
> > > > > File: cost_readgfo.F Status: Unresolved Conflict
> > > > > File: cost_readscatxfields.F Status: Unresolved Conflict
> > > > > File: cost_readscatyfields.F Status: Unresolved Conflict
> > > > > File: cost_readtopex.F Status: Unresolved Conflict
> > > > > File: cost_readtopexmean.F Status: Unresolved Conflict
> > > > > File: cost_salt.F Status: Unresolved Conflict
> > > > > File: cost_salt0.F Status: Unresolved Conflict
> > > > > File: cost_salt_ini_fin.F Status: Unresolved Conflict
> > > > > File: cost_scat.F Status: Unresolved Conflict
> > > > > File: cost_sigmar.F Status: Unresolved Conflict
> > > > > File: cost_ssh.F Status: Unresolved Conflict
> > > > > File: cost_ssh_mean.F Status: Unresolved Conflict
> > > > > File: cost_ssh_new.F Status: Unresolved Conflict
> > > > > File: cost_sshv4.F Status: Unresolved Conflict
> > > > > File: cost_tau_eddy.F Status: Unresolved Conflict
> > > > > File: cost_theta.F Status: Unresolved Conflict
> > > > > File: cost_theta0.F Status: Unresolved Conflict
> > > > > File: cost_theta_ini_fin.F Status: Unresolved Conflict
> > > > > File: cost_trans_merid.F Status: Unresolved Conflict
> > > > > File: cost_trans_zonal.F Status: Unresolved Conflict
> > > > > File: cost_usercost_all.F Status: Unresolved Conflict
> > > > > File: cost_uvel0.F Status: Unresolved Conflict
> > > > > File: cost_vvel0.F Status: Unresolved Conflict
> > > > > File: cost_xbt.F Status: Unresolved Conflict
> > > > > File: ecco.h Status: Unresolved Conflict
> > > > > File: ecco_ad_check_lev1_dir.h Status: Unresolved Conflict
> > > > > File: ecco_ad_check_lev2_dir.h Status: Unresolved Conflict
> > > > > File: ecco_ad_check_lev3_dir.h Status: Unresolved Conflict
> > > > > File: ecco_ad_check_lev4_dir.h Status: Unresolved Conflict
> > > > > File: ecco_check.F Status: Unresolved Conflict
> > > > > File: ecco_cost.h Status: Unresolved Conflict
> > > > > File: ecco_cost_driver.F Status: Unresolved Conflict
> > > > > File: ecco_cost_final.F Status: Unresolved Conflict
> > > > > File: ecco_cost_init_barfiles.F Status: Unresolved Conflict
> > > > > File: ecco_cost_init_fixed.F Status: Unresolved Conflict
> > > > > File: ecco_cost_init_varia.F Status: Unresolved Conflict
> > > > > File: ecco_cost_summary.F Status: Unresolved Conflict
> > > > > File: ecco_cost_weights.F Status: Unresolved Conflict
> > > > > File: ecco_phys.F Status: Unresolved Conflict
> > > > > File: ecco_readparms.F Status: Unresolved Conflict
> > > > > File: ecco_summary.F Status: Unresolved Conflict
> > > > > File: exf_bulkformulae.F Status: Unresolved Conflict
> > > > > File: exf_getclim.F Status: Unresolved Conflict
> > > > > File: exf_getffields.F Status: Unresolved Conflict
> > > > > File: exf_getforcing.F Status: Unresolved Conflict
> > > > > File: exf_getsurfacefluxes.F Status: Unresolved Conflict
> > > > > File: exf_mapfields.F Status: Unresolved Conflict
> > > > > File: exf_radiation.F Status: Unresolved Conflict
> > > > > File: exf_wind.F Status: Unresolved Conflict
> > > > > File: gchem_forcing_sep.F Status: Unresolved Conflict
> > > > > File: gad_calc_rhs.F Status: Unresolved Conflict
> > > > > File: gmredi_calc_eigs.F Status: Unresolved Conflict
> > > > > File: gmredi_calc_psi_b.F Status: Unresolved Conflict
> > > > > File: gmredi_calc_tensor.F Status: Unresolved Conflict
> > > > > File: gmredi_diagnostics_init.F Status: Unresolved Conflict
> > > > > File: gmredi_do_exch.F Status: Unresolved Conflict
> > > > > File: gmredi_k3d.F Status: Unresolved Conflict
> > > > > File: gmredi_rtransport.F Status: Unresolved Conflict
> > > > > File: gmredi_slope_limit.F Status: Unresolved Conflict
> > > > > File: gmredi_slope_psi.F Status: Unresolved Conflict
> > > > > File: gmredi_xtransport.F Status: Unresolved Conflict
> > > > > File: gmredi_ytransport.F Status: Unresolved Conflict
> > > > > File: grdchk_get_obcs_mask.F Status: Unresolved Conflict
> > > > > File: grdchk_get_position.F Status: Unresolved Conflict
> > > > > File: grdchk_getadxx.F Status: Unresolved Conflict
> > > > > File: grdchk_getxx.F Status: Unresolved Conflict
> > > > > File: grdchk_init.F Status: Unresolved Conflict
> > > > > File: grdchk_loc.F Status: Unresolved Conflict
> > > > > File: grdchk_setxx.F Status: Unresolved Conflict
> > > > > File: grdchk_summary.F Status: Unresolved Conflict
> > > > > File: kl10_calc.F Status: Unresolved Conflict
> > > > > File: kl10_calc_diff.F Status: Unresolved Conflict
> > > > > File: kpp_calc.F Status: Unresolved Conflict
> > > > > File: kpp_do_exch.F Status: Unresolved Conflict
> > > > > File: kpp_forcing_surf.F Status: Unresolved Conflict
> > > > > File: kpp_routines.F Status: Unresolved Conflict
> > > > > File: kpp_transport_ptr.F Status: Unresolved Conflict
> > > > > File: mom_calc_hfacz.F Status: Unresolved Conflict
> > > > > File: mom_u_bottomdrag.F Status: Unresolved Conflict
> > > > > File: mom_v_bottomdrag.F Status: Unresolved Conflict
> > > > > File: mom_fluxform.F Status: Unresolved Conflict
> > > > > File: mom_vecinv.F Status: Unresolved Conflict
> > > > > File: my82_calc.F Status: Unresolved Conflict
> > > > > File: OBCS_GRID.h Status: Unresolved Conflict
> > > > > File: OBCS_OPTIONS.h Status: Unresolved Conflict
> > > > > File: OBCS_PARAMS.h Status: Unresolved Conflict
> > > > > File: obcs_ad_check_lev1_dir.h Status: Unresolved Conflict
> > > > > File: obcs_calc_stevens.F Status: Unresolved Conflict
> > > > > File: obcs_diag_balance.F Status: Unresolved Conflict
> > > > > File: obcs_init_fixed.F Status: Unresolved Conflict
> > > > > File: obcs_prescribe_read.F Status: Unresolved Conflict
> > > > > File: obcs_readparms.F Status: Unresolved Conflict
> > > > > File: obcs_sponge.F Status: Unresolved Conflict
> > > > > File: externalDummies.F Status: Unresolved Conflict
> > > > > File: the_model_main.F Status: Unresolved Conflict
> > > > > File: pp81_calc.F Status: Unresolved Conflict
> > > > > File: pp81_calc_diff.F Status: Unresolved Conflict
> > > > > File: cost_profiles.F Status: Unresolved Conflict
> > > > > File: profiles_inloop.F Status: Unresolved Conflict
> > > > > File: profiles_readparms.F Status: Unresolved Conflict
> > > > > File: profiles_readvector.F Status: Unresolved Conflict
> > > > > File: ptracers_ad_dump.F Status: Unresolved Conflict
> > > > > File: ptracers_convect.F Status: Unresolved Conflict
> > > > > File: ptracers_debug.F Status: Unresolved Conflict
> > > > > File: ptracers_integrate.F Status: Unresolved Conflict
> > > > > File: ptracers_monitor_ad.F Status: Unresolved Conflict
> > > > > File: ptracers_readparms.F Status: Unresolved Conflict
> > > > > File: ptracers_switch_onoff.F Status: Unresolved Conflict
> > > > > File: rbcs_add_tendency.F Status: Unresolved Conflict
> > > > > File: salt_plume_calc_depth.F Status: Unresolved Conflict
> > > > > File: SEAICE.h Status: Unresolved Conflict
> > > > > File: SEAICE_OPTIONS.h Status: Unresolved Conflict
> > > > > File: SEAICE_PARAMS.h Status: Unresolved Conflict
> > > > > File: SEAICE_SIZE.h Status: Unresolved Conflict
> > > > > File: advect.F Status: Unresolved Conflict
> > > > > File: cost_ice_test.F Status: Unresolved Conflict
> > > > > File: dynsolver.F Status: Unresolved Conflict
> > > > > File: lsr.F Status: Unresolved Conflict
> > > > > File: seaice_ad_dump.F Status: Unresolved Conflict
> > > > > File: seaice_advdiff.F Status: Unresolved Conflict
> > > > > File: seaice_advection.F Status: Unresolved Conflict
> > > > > File: seaice_calc_ice_strength.F Status: Unresolved Conflict
> > > > > File: seaice_calc_lhs.F Status: Unresolved Conflict
> > > > > File: seaice_calc_residual.F Status: Unresolved Conflict
> > > > > File: seaice_calc_strainrates.F Status: Unresolved Conflict
> > > > > File: seaice_calc_viscosities.F Status: Unresolved Conflict
> > > > > File: seaice_check.F Status: Unresolved Conflict
> > > > > File: seaice_cost_areasst.F Status: Unresolved Conflict
> > > > > File: seaice_cost_concentration.F Status: Unresolved Conflict
> > > > > File: seaice_cost_driver.F Status: Unresolved Conflict
> > > > > File: seaice_cost_final.F Status: Unresolved Conflict
> > > > > File: seaice_cost_sss.F Status: Unresolved Conflict
> > > > > File: seaice_cost_sst.F Status: Unresolved Conflict
> > > > > File: seaice_cost_weights.F Status: Unresolved Conflict
> > > > > File: seaice_ctrl_map_ini.F Status: Unresolved Conflict
> > > > > File: seaice_diagnostics_init.F Status: Unresolved Conflict
> > > > > File: seaice_diagnostics_state.F Status: Unresolved Conflict
> > > > > File: seaice_diffusion.F Status: Unresolved Conflict
> > > > > File: seaice_do_ridging.F Status: Unresolved Conflict
> > > > > File: seaice_dynsolver.F Status: Unresolved Conflict
> > > > > File: seaice_evp.F Status: Unresolved Conflict
> > > > > File: seaice_freedrift.F Status: Unresolved Conflict
> > > > > File: seaice_growth.F Status: Unresolved Conflict
> > > > > File: seaice_init_varia.F Status: Unresolved Conflict
> > > > > File: seaice_itd_pickup.F Status: Unresolved Conflict
> > > > > File: seaice_itd_redist.F Status: Unresolved Conflict
> > > > > File: seaice_itd_sum.F Status: Unresolved Conflict
> > > > > File: seaice_jfnk.F Status: Unresolved Conflict
> > > > > File: seaice_lsr.F Status: Unresolved Conflict
> > > > > File: seaice_map_thsice.F Status: Unresolved Conflict
> > > > > File: seaice_model.F Status: Unresolved Conflict
> > > > > File: seaice_monitor_ad.F Status: Unresolved Conflict
> > > > > File: seaice_oceandrag_coeffs.F Status: Unresolved Conflict
> > > > > File: seaice_preconditioner.F Status: Unresolved Conflict
> > > > > File: seaice_prepare_ridging.F Status: Unresolved Conflict
> > > > > File: seaice_readparms.F Status: Unresolved Conflict
> > > > > File: seaice_reg_ridge.F Status: Unresolved Conflict
> > > > > File: seaice_solve4temp.F Status: Unresolved Conflict
> > > > > File: seaice_summary.F Status: Unresolved Conflict
> > > > > File: SHELFICE.h Status: Unresolved Conflict
> > > > > File: shelfice_cost_final.F Status: Unresolved Conflict
> > > > > File: shelfice_cost_shifwflx.F Status: Unresolved Conflict
> > > > > File: shelfice_init_fixed.F Status: Unresolved Conflict
> > > > > File: shelfice_init_varia.F Status: Unresolved Conflict
> > > > > File: shelfice_readparms.F Status: Unresolved Conflict
> > > > > File: shelfice_thermodynamics.F Status: Unresolved Conflict
> > > > > File: shelfice_u_drag.F Status: Unresolved Conflict
> > > > > File: shelfice_update_masks.F Status: Unresolved Conflict
> > > > > File: shelfice_v_drag.F Status: Unresolved Conflict
> > > > > File: smooth_correl2dw.F Status: Unresolved Conflict
> > > > > File: smooth_diff2d.F Status: Unresolved Conflict
> > > > > File: smooth_diff3d.F Status: Unresolved Conflict
> > > > > File: STREAMICE.h Status: Unresolved Conflict
> > > > > File: adstreamice_cg_solve.F Status: Unresolved Conflict
> > > > > File: streamice.flow Status: Unresolved Conflict
> > > > > File: streamice_adv_flux_fl_x.F Status: Unresolved Conflict
> > > > > File: streamice_adv_flux_fl_y.F Status: Unresolved Conflict
> > > > > File: streamice_adv_front.F Status: Unresolved Conflict
> > > > > File: streamice_advect_2dtracer.F Status: Unresolved Conflict
> > > > > File: streamice_advect_thickness.F Status: Unresolved Conflict
> > > > > File: streamice_cg_solve.F Status: Unresolved Conflict
> > > > > File: streamice_cg_solve_petsc.F Status: Unresolved Conflict
> > > > > File: streamice_cg_wrapper.F Status: Unresolved Conflict
> > > > > File: streamice_check.F Status: Unresolved Conflict
> > > > > File: streamice_cost_surf_accum.F Status: Unresolved Conflict
> > > > > File: streamice_fields_load.F Status: Unresolved Conflict
> > > > > File: streamice_init_fixed.F Status: Unresolved Conflict
> > > > > File: streamice_init_varia.F Status: Unresolved Conflict
> > > > > File: streamice_readparms.F Status: Unresolved Conflict
> > > > > File: streamice_upd_ffrac_uncoupled.F Status: Unresolved Conflict
> > > > > File: streamice_vel_solve.F Status: Unresolved Conflict
> > > > > File: streamice_velmask_upd.F Status: Unresolved Conflict
> > > > > File: streamice_visc_beta_hybrid.F Status: Unresolved Conflict
> > > > > File: do_tst_2+2 Status: Unresolved Conflict
> > > > > File: linux_amd64_gfortran Status: Unresolved Conflict
> > > > > File: linux_amd64_ifort+mpi_ice_nas Status: Unresolved Conflict
> > > > > File: aces_test_all Status: Unresolved Conflict
> > > > > File: aces_test_pgi_mpi Status: Unresolved Conflict
> > > > > File: test_aces_adm_mpi Status: Unresolved Conflict
> > > > > File: test_aces_gnu_mp2 Status: Unresolved Conflict
> > > > > File: test_aces_gnu_mpi Status: Unresolved Conflict
> > > > > File: test_aces_ifc_adm Status: Unresolved Conflict
> > > > > File: test_aces_ifc_mpi Status: Unresolved Conflict
> > > > > File: test_aces_op64_mpi Status: Unresolved Conflict
> > > > > File: test_aces_op64_tuv Status: Unresolved Conflict
> > > > > File: test_aces_path_mpi Status: Unresolved Conflict
> > > > > File: test_aces_path_mth Status: Unresolved Conflict
> > > > > File: test_aces_pgi_mpi Status: Unresolved Conflict
> > > > > File: test_aces_pgi_oad Status: Unresolved Conflict
> > > > > File: def_API_msk.m Status: Unresolved Conflict
> > > > > File: line_sep.m Status: Unresolved Conflict
> > > > > File: sep_API_basins.m Status: Unresolved Conflict
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > On Sat, Jan 17, 2015 at 6:46 PM, Jean-Michel Campin <
> > jmc at ocean.mit.edu>
> > > > > wrote:
> > > > >
> > > > > > Hi Ryan,
> > > > > >
> > > > > > This is strange.
> > > > > > Did you keep a version of all your MITgcm code before doing this
> > > > > > "cvs update" ?
> > > > > > If yes, you coud send me, e.g. this (non updated)
> > > > > > pkg/streamice/streamice_velmask_upd.F file
> > > > > > so that I could check.
> > > > > >
> > > > > > Cheers,
> > > > > > Jean-Michel
> > > > > >
> > > > > > On Sat, Jan 17, 2015 at 05:09:40PM -0500, Ryan Abernathey wrote:
> > > > > > > Jean-Michel,
> > > > > > >
> > > > > > > I am embarrassed that I don't understand better how to work with
> > > > MITgcm
> > > > > > > cvs. Unfortunately I am confused and I have to ask for your
> > advice.
> > > > > > >
> > > > > > > I am trying to bring my modified source code branch up to date. I
> > > > > > followed
> > > > > > > the advice of the documentation (
> > > > http://mitgcm.org/public/using_cvs.html
> > > > > > )
> > > > > > > and used the command cvs update -d -P -A.
> > > > > > >
> > > > > > > But this resulted in a huge number of messages reporting
> > conflicts in
> > > > > > files
> > > > > > > that I did not touch, for example:
> > > > > > > RCS file:
> > /u/gcmpack/MITgcm/pkg/streamice/streamice_velmask_upd.F,v
> > > > > > > retrieving revision 1.7
> > > > > > > retrieving revision 1.8
> > > > > > > Merging differences between 1.7 and 1.8 into
> > streamice_velmask_upd.F
> > > > > > > rcsmerge: warning: conflicts during merge
> > > > > > > It looks like this conflict is just in the header:
> > > > > > > <<<<<<< streamice_velmask_upd.F
> > > > > > > C $Header:
> > /u/gcmpack/MITgcm/pkg/streamice/streamice_velmask_upd.F,v
> > > > 1.7
> > > > > > > 2014/04/30 12:18:32 dgoldberg Exp $
> > > > > > > C $Name: checkpoint65c $
> > > > > > > =======
> > > > > > > C $Header:
> > /u/gcmpack/MITgcm/pkg/streamice/streamice_velmask_upd.F,v
> > > > 1.8
> > > > > > > 2014/09/09 23:09:21 jmc Exp $
> > > > > > > C $Name: $
> > > > > > > >>>>>>> 1.8
> > > > > > >
> > > > > > > Ironically, all my changes in layers merged without conflict.
> > > > > > >
> > > > > > > It would be extremely tedious to merge all of these conflicts by
> > > > hand,
> > > > > > > since there are literally hundreds of such files.
> > > > > > >
> > > > > > > Perhaps you can advise me on a more efficient approach to
> > bringing my
> > > > > > code
> > > > > > > up to date.
> > > > > > >
> > > > > > > Thanks,
> > > > > > > Ryan
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > > On Fri, Jan 16, 2015 at 4:22 PM, Jean-Michel Campin <
> > > > jmc at ocean.mit.edu>
> > > > > > > wrote:
> > > > > > >
> > > > > > > > Hi Ryan,
> > > > > > > >
> > > > > > > > few things:
> > > > > > > > 1) might be goo to start to bring your code & modification
> > > > > > > > up to date, from c65c to now. You will need to do that
> > anyway.
> > > > > > > > If you need some help, let me know.
> > > > > > > > 2) about testreport:
> > > > > > > > a) there is a little bit of documentation about testreport
> > and
> > > > > > > > the verification experiments in the HOWTO document.
> > > > > > > > b) > cd verification
> > > > > > > > > testreport -h
> > > > > > > > can be useful
> > > > > > > > c) I recommand to specify an optfile.
> > > > > > > > d) On baudelaire (now ssh to baudelaire is limited from
> > within
> > > > MIT,
> > > > > > > > so I ssh to ocean first and then to baudelaire), the
> > "reference"
> > > > > > > > testreport would be:
> > > > > > > > > testreport -of ../tools/build_options/linux_amd64_gfortran
> > > > -devel
> > > > > > > > -match 13
> > > > > > > > 3) there might be more things (TAF, OpenAD .. ) to check
> > > > (depending on
> > > > > > > > changes in
> > > > > > > > pkg/generic_advdiff), so may be, before you check-in your
> > > > changes,
> > > > > > > > you could send me the modified pkg/generic_advdiff source
> > code
> > > > > > > > so that I can test TAF & OpenAD.
> > > > > > > >
> > > > > > > > Cheers,
> > > > > > > > Jean-Michel
> > > > > > > >
> > > > > > > > On Fri, Jan 16, 2015 at 03:51:33PM -0500, Ryan Abernathey
> > wrote:
> > > > > > > > > Hi Jean-Michel,
> > > > > > > > >
> > > > > > > > > I have a rather big layers update that I would like to check
> > in.
> > > > > > This is
> > > > > > > > > basically a fully working water-mass-transformation
> > framework.
> > > > Below
> > > > > > is a
> > > > > > > > > list of all the modified files. These modification were
> > branched
> > > > off
> > > > > > > > > checkpoint 65c, and I haven't updated since.
> > > > > > > > >
> > > > > > > > > I thought I would check with you before I do the check-in.
> > Do you
> > > > > > > > > anticipate any problems? I can give you more info on the
> > > > > > modifications if
> > > > > > > > > you like.
> > > > > > > > >
> > > > > > > > > I don't really understand how the testreport system works,
> > but I
> > > > > > would be
> > > > > > > > > happy to try to test this before checking in. (If you give me
> > > > some
> > > > > > > > guidance
> > > > > > > > > on how to do that.)
> > > > > > > > >
> > > > > > > > > Cheers,
> > > > > > > > > Ryan
> > > > > > > > >
> > > > > > > > > MITgcm65c]$ cvs -q diff --brief
> > > > > > > > > Enter passphrase for key '/glade/u/home/rpa/.ssh/id_rsa':
> > > > > > > > > ? utils/python/MITgcmutils/MITgcmutils.egg-info
> > > > > > > > > ? utils/python/MITgcmutils/build
> > > > > > > > > ? utils/python/MITgcmutils/dist
> > > > > > > > > Index: pkg/generic_advdiff/gad_advection.F
> > > > > > > > >
> > > > ===================================================================
> > > > > > > > > RCS file:
> > /u/gcmpack/MITgcm/pkg/generic_advdiff/gad_advection.F,v
> > > > > > > > > retrieving revision 1.75
> > > > > > > > > diff --brief -r1.75 gad_advection.F
> > > > > > > > > Files /tmp/cvsOG3CoZ and gad_advection.F differ
> > > > > > > > > Index: pkg/generic_advdiff/gad_calc_rhs.F
> > > > > > > > >
> > > > ===================================================================
> > > > > > > > > RCS file:
> > /u/gcmpack/MITgcm/pkg/generic_advdiff/gad_calc_rhs.F,v
> > > > > > > > > retrieving revision 1.70
> > > > > > > > > diff --brief -r1.70 gad_calc_rhs.F
> > > > > > > > > Files /tmp/cvsfrua4J and gad_calc_rhs.F differ
> > > > > > > > > Index: pkg/generic_advdiff/gad_implicit_r.F
> > > > > > > > >
> > > > ===================================================================
> > > > > > > > > RCS file:
> > > > /u/gcmpack/MITgcm/pkg/generic_advdiff/gad_implicit_r.F,v
> > > > > > > > > retrieving revision 1.22
> > > > > > > > > diff --brief -r1.22 gad_implicit_r.F
> > > > > > > > > Files /tmp/cvsq9DY0u and gad_implicit_r.F differ
> > > > > > > > > Index: pkg/generic_advdiff/gad_som_advect.F
> > > > > > > > >
> > > > ===================================================================
> > > > > > > > > RCS file:
> > > > /u/gcmpack/MITgcm/pkg/generic_advdiff/gad_som_advect.F,v
> > > > > > > > > retrieving revision 1.13
> > > > > > > > > diff --brief -r1.13 gad_som_advect.F
> > > > > > > > > Files /tmp/cvszaR31f and gad_som_advect.F differ
> > > > > > > > > Index: pkg/layers/LAYERS.h
> > > > > > > > >
> > > > ===================================================================
> > > > > > > > > RCS file: /u/gcmpack/MITgcm/pkg/layers/LAYERS.h,v
> > > > > > > > > retrieving revision 1.14
> > > > > > > > > diff --brief -r1.14 LAYERS.h
> > > > > > > > > Files /tmp/cvs6jCrN3 and LAYERS.h differ
> > > > > > > > > Index: pkg/layers/layers_calc.F
> > > > > > > > >
> > > > ===================================================================
> > > > > > > > > RCS file: /u/gcmpack/MITgcm/pkg/layers/layers_calc.F,v
> > > > > > > > > retrieving revision 1.23
> > > > > > > > > diff --brief -r1.23 layers_calc.F
> > > > > > > > > Files /tmp/cvsnr5BAR and layers_calc.F differ
> > > > > > > > > Index: pkg/layers/layers_check.F
> > > > > > > > >
> > > > ===================================================================
> > > > > > > > > RCS file: /u/gcmpack/MITgcm/pkg/layers/layers_check.F,v
> > > > > > > > > retrieving revision 1.7
> > > > > > > > > diff --brief -r1.7 layers_check.F
> > > > > > > > > Files /tmp/cvsu3uypF and layers_check.F differ
> > > > > > > > > Index: pkg/layers/layers_diagnostics_init.F
> > > > > > > > >
> > > > ===================================================================
> > > > > > > > > RCS file:
> > > > /u/gcmpack/MITgcm/pkg/layers/layers_diagnostics_init.F,v
> > > > > > > > > retrieving revision 1.6
> > > > > > > > > diff --brief -r1.6 layers_diagnostics_init.F
> > > > > > > > > Files /tmp/cvsxzjdft and layers_diagnostics_init.F differ
> > > > > > > > > Index: pkg/layers/layers_fluxcalc.F
> > > > > > > > >
> > > > ===================================================================
> > > > > > > > > RCS file: /u/gcmpack/MITgcm/pkg/layers/layers_fluxcalc.F,v
> > > > > > > > > retrieving revision 1.10
> > > > > > > > > diff --brief -r1.10 layers_fluxcalc.F
> > > > > > > > > Files /tmp/cvs4s8N6g and layers_fluxcalc.F differ
> > > > > > > > > Index: pkg/layers/layers_init_fixed.F
> > > > > > > > >
> > > > ===================================================================
> > > > > > > > > RCS file: /u/gcmpack/MITgcm/pkg/layers/layers_init_fixed.F,v
> > > > > > > > > retrieving revision 1.10
> > > > > > > > > diff --brief -r1.10 layers_init_fixed.F
> > > > > > > > > Files /tmp/cvsjlWM14 and layers_init_fixed.F differ
> > > > > > > > > Index: pkg/layers/layers_init_varia.F
> > > > > > > > >
> > > > ===================================================================
> > > > > > > > > RCS file: /u/gcmpack/MITgcm/pkg/layers/layers_init_varia.F,v
> > > > > > > > > retrieving revision 1.8
> > > > > > > > > diff --brief -r1.8 layers_init_varia.F
> > > > > > > > > Files /tmp/cvsyJXtXS and layers_init_varia.F differ
> > > > > > > > > Index: pkg/layers/layers_mnc_init.F
> > > > > > > > >
> > > > ===================================================================
> > > > > > > > > RCS file: /u/gcmpack/MITgcm/pkg/layers/layers_mnc_init.F,v
> > > > > > > > > retrieving revision 1.1
> > > > > > > > > diff --brief -r1.1 layers_mnc_init.F
> > > > > > > > > Files /tmp/cvsHIZPTG and layers_mnc_init.F differ
> > > > > > > > > Index: pkg/layers/layers_output.F
> > > > > > > > >
> > > > ===================================================================
> > > > > > > > > RCS file: /u/gcmpack/MITgcm/pkg/layers/layers_output.F,v
> > > > > > > > > retrieving revision 1.12
> > > > > > > > > diff --brief -r1.12 layers_output.F
> > > > > > > > > Files /tmp/cvsk1ilSu and layers_output.F differ
> > > > > > > > > Index: pkg/layers/layers_readparms.F
> > > > > > > > >
> > > > ===================================================================
> > > > > > > > > RCS file: /u/gcmpack/MITgcm/pkg/layers/layers_readparms.F,v
> > > > > > > > > retrieving revision 1.9
> > > > > > > > > diff --brief -r1.9 layers_readparms.F
> > > > > > > > > Files /tmp/cvsRSByRi and layers_readparms.F differ
> > > > > > > > > Index: pkg/layers/layers_save.F
> > > > > > > > >
> > > > ===================================================================
> > > > > > > > > RCS file: /u/gcmpack/MITgcm/pkg/layers/layers_save.F,v
> > > > > > > > > retrieving revision 1.2
> > > > > > > > > diff --brief -r1.2 layers_save.F
> > > > > > > > > Files /tmp/cvsQq3ER6 and layers_save.F differ
> > > > > > > > > Index: pkg/layers/layers_thermodynamics.F
> > > > > > > > >
> > > > ===================================================================
> > > > > > > > > RCS file:
> > /u/gcmpack/MITgcm/pkg/layers/layers_thermodynamics.F,v
> > > > > > > > > retrieving revision 1.3
> > > > > > > > > diff --brief -r1.3 layers_thermodynamics.F
> > > > > > > > > Files /tmp/cvsDXxtSU and layers_thermodynamics.F differ
> > > > > > > >
> > > > > >
> > > >
> > > >
> > > >
> >
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