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Ticket Resolution Summary Owner Reporter
#2597 duplicate cleaning/upgrade of MPI interface systeam smasson
Description

Context

1) Review, simplification and cleaning of the MPI interface is needed 2) There is a few bugs:

  • potential bug with the corners if nn_hls > 1 (or 2?) with point-to-point communication
  • collective communications is not working with BDY (as BDY has its own exchanges)

3) There is other things to further improve:

  • do not send/receive if send/receive only land points (depend on nn_hls)
  • send/receive only the oce values (checking mask, depend on nn_hls)
  • keep in memory the send/receive buffers (if they are not too big for ex < jpi*jpj) from one call to another -> for point-to-point put the mpi_waitall at the beginning of next call
  • make sure the north pole folding does not need east-west comm. done if nogather = F. to be done if nogather = T... so we could place it where we want (no need to wait for east-west comm).
  • if north pole folding: force the last row of MPI-subdomains to have jpj much smaller (the smallest value?) so they go faster and other don't wait for them
#2595 fixed Swap DO_2D and DO_3D* macro arguments to a more natural i-j-k ordering systeam acc
Description

Context

The arguments to the current DO_LOOP macros have to specified in an order that can cause confusion. Currently, it is j-loop limits followed by i-loop limits followed (in the 3D cases) by k-loop limits. The order was chosen for the original 2D macros to reflect the nested order of the loops but should be changed to a more natural ordering.

Analysis

This is relatively simple to achieve. This perl script will locate and swap the entries: 

#!/bin/bash
#
DOSTRS=( DO_2D DO_3D )
#
# build a list of files that need to be changed
#
listfile=tmplistfile$$.txt
for iunit in ${DOSTRS[@]}
do
  grep -l $iunit `find ./ -name '*.[fFh]90'` >>  $listfile
done
allfiles=`cat $listfile | grep -v substitute | sort -u`
echo $allfiles
#
if [ -f $listfile ] ; then rm $listfile; fi
for f in  $allfiles
do
 echo "Working on " $f
 n=0
 for n in `seq 0 1 $(( ${#DOSTRS[*]} - 1 ))`
 do
   perl -ni -e 'unless ( m@^\s*'${DOSTRS[$n]}'@) { print  } else { $line= $_ ; $line=~s@(^\s*'${DOSTRS[$n]}'.*\()([^\,]*),([^\,]*),([^\,]*),(\s*[^\,\s\)]*)(.*)@\1\4,\5,\2,\3\6@ ; print $line }' $f
 done
done

And the changes to do_loop_substitute.h90 are straight-forward:

  • src/OCE/do_loop_substitute.h90

     
    11#if defined show_comments 
    22! These comments are not intended to be retained during preprocessing; i.e. do not define "show_comments" 
    33!!---------------------------------------------------------------------- 
    4 !! NEMO/OCE 4.0 , NEMO Consortium (2018) 
     4!! NEMO/OCE 4.x , NEMO Consortium (2020) 
    55!! Software governed by the CeCILL license (see ./LICENSE) 
    66!!---------------------------------------------------------------------- 
    77! This header file contains preprocessor definitions and macros used in the do-loop substitutions introduced 
    … …  
    2424! Lower limits of 1, 2 or fs_2 
    2525! Upper limits of jpi, jpim1 or fs_jpim1 (for ji) or jpj, jpjm1 or fs_jpjm1 (for jj) 
    2626! 
    27 ! The macro naming convention takes the form: DO_2D( B, T, L, R) where: 
     27! The macro naming convention takes the form: DO_2D( L, R, B, T) where: 
     28!   L is the Left   offset from the PE's inner domain; 
     29!   R is the Right  offset from the PE's inner domain 
    2830!   B is the Bottom offset from the PE's inner domain; 
    2931!   T is the Top    offset from the PE's inner domain; 
    30 !   L is the Left   offset from the PE's inner domain; 
    31 !   R is the Right  offset from the PE's inner domain 
    3232! 
    3333! So, given an inner domain of 2,jpim1 and 2,jpjm1, a typical example would replace: 
    3434! 
    … …  
    4141! 
    4242! with: 
    4343! 
    44 !   DO_2D( 0, 1, 1, 0 ) 
     44!   DO_2D( 1, 0, 0, 1 ) 
    4545!      . 
    4646!      . 
    4747!   END_2D 
    … …  
    5858! 
    5959#endif 
    6060 
    61 #define DO_2D(B, T, L, R) DO jj = ntsj-(B), ntej+(T)   ;   DO ji = ntsi-(L), ntei+(R) 
     61#define DO_2D(L, R, B, T) DO jj = ntsj-(B), ntej+(T)   ;   DO ji = ntsi-(L), ntei+(R) 
    6262#define A1Di(H) ntsi-H:ntei+H 
    6363#define A1Dj(H) ntsj-H:ntej+H 
    6464#define A2D(H) A1Di(H),A1Dj(H) 
    … …  
    6969#define JPTS  : 
    7070#define KJPT  : 
    7171 
    72 #define DO_3D(B, T, L, R, ks, ke) DO jk = ks, ke   ;   DO_2D(B, T, L, R) 
     72#define DO_3D(L, R, B, T, ks, ke) DO jk = ks, ke   ;   DO_2D(L, R, B, T) 
    7373 
    74 #define DO_3DS(B, T, L, R, ks, ke, ki) DO jk = ks, ke, ki   ;   DO_2D(B, T, L, R) 
     74#define DO_3DS(L, R, B, T, ks, ke, ki) DO jk = ks, ke, ki   ;   DO_2D(L, R, B, T) 
    7575 
    7676#define END_2D   END DO   ;   END DO 
    7777#define END_3D   END DO   ;   END DO   ;   END DO 

Additionally, because the majority of loop pairs have matching offset limits , only these modules are actually altered by this change: 

M       src/ABL/ablmod.F90
M       src/ICE/icedyn_adv_pra.F90
M       src/ICE/icedyn_adv_umx.F90
M       src/OCE/DIA/diaptr.F90
M       src/OCE/DOM/dommsk.F90
M       src/OCE/DYN/dynldf_iso.F90
M       src/OCE/DYN/dynspg_ts.F90
M       src/OCE/ISF/isftbl.F90
M       src/OCE/SBC/geo2ocean.F90
M       src/OCE/SBC/sbcice_cice.F90
M       src/OCE/TRA/traadv_qck.F90
M       src/OCE/TRA/trabbl.F90
M       src/OCE/TRA/traldf_lap_blp.F90
M       src/OCE/TRA/traldf_triad.F90
M       src/OCE/TRA/tranpc.F90
M       src/OCE/TRA/traqsr.F90
M       src/OCE/TRA/trasbc.F90
M       src/OCE/ZDF/zdfosm.F90
M       src/OCE/do_loop_substitute.h90
M       src/TOP/TRP/trcsbc.F90
M       src/TOP/trcbc.F90

Recommendation

Make this change. Confirm before and after SETTE results match and commit asap ...

#2594 fixed Misplaced boundary conditions on avm with AGRIF systeam jchanut
Description

Context

AGRIF boundary condition on avm (with tke or gls schemes)

Analysis

The boundary condition on vertical viscosity (needed with schemes that do use vertical shear) is applied on avm_k, after avm has been updated by avm_k. Hence it does really overwrite the current value of avm as seen in outputs. However, this has no impact on the results.

Fix

Call Agrif_avm before setting avm=avm_k so that correct boundary value is found in outputs

...

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