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Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
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============================== |
============================== |
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o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO |
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Option to use mdsio_read_whalos.F/mdsio_write_whalos.F, |
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rather than mdsio_readvector.F/mdsio_writevector.F, within |
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adread_adwrite.F to read/write adjoint-related tapes to disk. |
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o eesup and pkg/mdsio: ALLOW_WHIO |
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Option to write/read 2D fields to files including tiles halos. |
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The main purpose is for adjoint related "tape I/O". |
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The secondary purpose is for debugging phases. |
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A word on those rather specifically intended purposes. |
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The code was meant to be stripped down to the bare minimum. |
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Typically, there is a unique and basic mapping to the global |
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buffer (tile by tile, then proc by proc, then level by level), and |
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byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not |
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meant to generate user friendly outputs of various shapes and forms. |
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Rather it is intended, for the knowledgeabale developers, |
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to be largely independent of the many mdsio options, to allow |
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outputs of tiles+halos in debugging phases and in adjoint runs, |
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and to allow some flexibility in tuning (adoint) I/O depending on each |
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file system behavior. With regard to tuning, most of the potential knobs |
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(to leave files open, to allocate the I/O indep. of usesinglecpuio, |
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to specify directories, to specify the typical size of I/O calls, etc.) |
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are not yet included, and will be added if they prove useful. |
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o pkg/seaice: |
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fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F |
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o pkg/seaice: |
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new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty |
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code (seaice_budget_ice_if.F) which enable to recover old standard |
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code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined. |
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temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F. |
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o model/src (rStar): |
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use simple average (not area weighted) of rStarFac at U,V point when using |
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vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection) |
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update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20. |
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checkpoint62k (2010/09/17) |
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o adjoint |
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* changed verification/global_ocean.cs32x15 ; adjoint now tests |
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Adams-Bashforth 3 + NLFS + RSTAR |
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* some more modifs required for ECCO-GODAE v4 |
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o pkg/seaice |
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add SEAICE_AGE_VOL option to use volume instead of area for |
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integrating SEAICE_AGE |
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o model/src: |
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first check-in of sigma & hybrid-sigma coordinate code ; also includes |
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non-linear free-surface parts ; but pressure-gradient not yet coded. |
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o pkg/ptracers: |
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option for ptracer to convert Salt Relax into additional EmP. |
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tested in exp. global_ocean.90x40x15.dwnslp (update output) |
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checkpoint62j (2010/08/25) |
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o pkg/ggl90: |
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other minor changes: remove 3-D temp array gTKE (+ add argument myIter) |
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o pkg/dic: car_flux.F, phos_flux.F |
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- reduce number of exp-calls in order to improve performance |
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- clean up a little (replace fields by their macros, etc., fix |
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typo in CPP-flag) |
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o pkg/ggl90: minor changes |
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- GGL90diffKrS was removed --> always use GGL90diffKr |
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- GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV |
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- hack of mxlMaxFlag=2 --> ensure mixing between first and second level |
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(commented out for now) |
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- change in max/min operations to ensure that smoothing is ok |
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- smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr) |
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- always use diffKrNrT as background profile (i.e. never use diffKr field) |
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o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj) |
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o pkg/dic: |
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- model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better |
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vectorization |
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- small bug fix in insol for the unlikely case of a cartesian grid |
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- towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F |
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+ now vectorize, which also removes adjoint recomputations; |
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+ replace integer maksp1 by _RL maskp1 |
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+ replace a**x by exp(x*log(a)) in phos_flux.F for speed |
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checkpoint62i (2010/07/21) |
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o pkg/flt: |
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- with OBCS: stop floats which enter the OB region |
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o model/src: |
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- use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones) |
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for implicit vertical advection. |
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o pkg/seaice: |
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- account for melting in seaice age evolution. |
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- remove double counting of seaice ridging effect on seaice age. |
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checkpoint62h (2010/06/18) |
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o pkg/exch2: |
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- remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1). |
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o tools/genmake2 |
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- remove "-pdefault" option: redundant with the use of "packages.conf"; |
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- remove file pkg/pkg_default : set the default as a pkg group |
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("default_pkg_list") defined in pkg/pkg_groups; |
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- fix for case pkg/pkg_depend is missing (was hanging before); |
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- add option "-pgroups" to specify a different pkg_groups than the default. |
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o verification/adjustment.cs-32x32x1: |
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add a "minimal" set-up test (code_min & input_min) which only compiles |
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eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc. |
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o tools/genmake2 |
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- extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg])) |
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- fix details of checking for mnc & profile pkg when NetCDF is unavailable. |
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o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these |
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files are nearly the same anyway. |
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Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04: |
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- redefinition of tau(i,i) (by a factor of ustar) |
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- 1./exf(Const/T) -> exf(-Const/T) (big change in the results) |
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- replace rhonil by rhoConstFresh in computation of evap (bug fix) |
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- replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results) |
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- replace |
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rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh ) |
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shn = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j) |
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by |
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shn = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh ) |
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(changes results) |
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-> exf_bulkformulae v1.22, |
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update verification experiments lab_sea, offline_exf_seaice, seaice_obcs |
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(lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13, |
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output.txt 1.63 |
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offline_exf_seaice: output.seaicetd.txt 1.7 |
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seaice_obcs: output.txt 1.10) |
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Step 2: do the actual merge and remove exf_bulk_largeyeager04.F |
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-> exf_bulkformulae v1.23, |
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unfortunately requires updating lab_sea.salt_plume (6 matching digits), |
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and global_ocean.cs32x15.icedyn (only 11 matching digits) |
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Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice. |
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o adjoint of exch-1: |
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- pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list) |
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(note: was already like this when using EXCH-2) and remove flow dir |
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and hand-written AD version of high-level EXCH S/R (pkg/autodiff); |
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- provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow); |
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- update pkg/exch2 diff list. |
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checkpoint62g (2010/05/19) |
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o eesupp/src (exch-1): |
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- split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F) |
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and remove argument "simulationMode"; same thing for all exch_*rx_cube.F |
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(renamed to exch1_*rx_cube.F). |
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- change accordingly exch_*_rx.template and AD version in pkg/autodiff |
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to call new exch1 S/R ; update Makefile and .cvsignore. |
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- replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove |
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exch2_xy_rx later) |
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Note: after updating your code, need to run "make clean" in eesupp/src |
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o test experiment bottom_ctrl_5x5: |
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new output_adm.txt with fewer grdchk & less monitor output. |
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o model/src: |
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remove the call to ini_cori in initialise_varia.F (just keep the usual one |
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in initialise_fixed.F). More consistent with coriolis & horizontal grid |
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beeing treated in the same way (ini_grid is not called a 2nd time). |
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o pkg/exf: |
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- rewrite exf_bulk_largeyeager04.F for better vectorization, changes |
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global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated |
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- fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now) |
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- cosmetic changes to exf_bulkformulae.F to make it look more like |
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exf_bulk_largeyeager04.F |
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o eesupp/src (exch-1): |
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- Fix AD EXCH code for 2-D domain special cases (Nx=1 or Ny=1). |
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- Separate buffer filling and MPI sending: allow EXCH-1 to work for local |
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array (non-shared) when using MPI+MTH. Also reduces number of BARRIER |
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(even without using MPI). |
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- Message mode: move RecvAck setting (indicator of buffer being ready) |
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from send_put to recv_get S/R (was useless before, but not sure if |
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it's much more useful now); |
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- Switch the order of sync: MPI-proc 1rst and then threads; |
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- take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead. |
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- fix AD code for communication mode ='get' (but not used). |
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o model/src: |
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initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does |
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not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp). |
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o utils/matlab/rdmnc.m: adapt to be able to use the generic matlab netcdf API |
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o pkg/ctrl: require a specific set of control variables and exf-flags for |
o pkg/ctrl: require a specific set of control variables and exf-flags for |
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adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied) |
adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied) |
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o model/src: |
o model/src: |
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