Version 4 (modified by acc, 4 years ago) (diff) |
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Name and subject of the action
Last edition: Wikinfo(changed_ts)? by Wikinfo(changed_by)?
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Summary
Action | ENHANCE-10_acc_fix_traqsr |
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PI(S) | acc |
Digest | Reduce use of 3D allocatable arrays in RGB light penetration schemes |
Dependencies | If any |
Branch | source:/NEMO/branches/{YEAR}/dev_r{REV}_{ACTION_NAME} |
Previewer(s) | Names |
Reviewer(s) | Names |
Ticket | #XXXX |
Description
The current implementation of RGB light penetration in traqsr (either varying or constant chlorophyll) uses 6, domain-sized 3D, temporary arrays which can be reduced to a few 2D arrays. The impact of the current implementation is most evident at lower processor counts where the impact of the extra 3D arrays can cause cache-misses and memory band-width issues. In an extreme case traqsr can switch from consuming 2% of run-time to 68% (comparing ORCA025 running on 200 cores vs 48 cores).
A simple redesign of the algorithm should remove this behaviour.
Implementation
The current code is structured thus:
CASE( np_RGB , np_RGBc ) !== R-G-B fluxes ==! ! ALLOCATE( zekb(jpi,jpj) , zekg(jpi,jpj) , zekr (jpi,jpj) , & & ze0 (jpi,jpj,jpk) , ze1 (jpi,jpj,jpk) , ze2 (jpi,jpj,jpk) , & & ze3 (jpi,jpj,jpk) , zea (jpi,jpj,jpk) , zchl3d(jpi,jpj,jpk) ) ! ! code to set zchl3d(:,:,1:nskr+1) ! (the chlorophyll value projected from the surface values) ! zcoef = ( 1. - rn_abs ) / 3._wp !* surface equi-partition in R-G-B DO_2D_00_00 ze0(ji,jj,1) = rn_abs * qsr(ji,jj) ze1(ji,jj,1) = zcoef * qsr(ji,jj) ze2(ji,jj,1) = zcoef * qsr(ji,jj) ze3(ji,jj,1) = zcoef * qsr(ji,jj) zea(ji,jj,1) = qsr(ji,jj) END_2D ! DO jk = 2, nksr+1 !* interior equi-partition in R-G-B depending of vertical profile of Chl DO_2D_00_00 zchl = MIN( 10. , MAX( 0.03, zchl3d(ji,jj,jk) ) ) irgb = NINT( 41 + 20.*LOG10(zchl) + 1.e-15 ) zekb(ji,jj) = rkrgb(1,irgb) zekg(ji,jj) = rkrgb(2,irgb) zekr(ji,jj) = rkrgb(3,irgb) END_2D DO_2D_00_00 zc0 = ze0(ji,jj,jk-1) * EXP( - e3t(ji,jj,jk-1,Kmm) * xsi0r ) zc1 = ze1(ji,jj,jk-1) * EXP( - e3t(ji,jj,jk-1,Kmm) * zekb(ji,jj) ) zc2 = ze2(ji,jj,jk-1) * EXP( - e3t(ji,jj,jk-1,Kmm) * zekg(ji,jj) ) zc3 = ze3(ji,jj,jk-1) * EXP( - e3t(ji,jj,jk-1,Kmm) * zekr(ji,jj) ) ze0(ji,jj,jk) = zc0 ze1(ji,jj,jk) = zc1 ze2(ji,jj,jk) = zc2 ze3(ji,jj,jk) = zc3 zea(ji,jj,jk) = ( zc0 + zc1 + zc2 + zc3 ) * wmask(ji,jj,jk) END_2D END DO ! DO_3D_00_00( 1, nksr ) qsr_hc(ji,jj,jk) = r1_rho0_rcp * ( zea(ji,jj,jk) - zea(ji,jj,jk+1) ) END_3D ! DEALLOCATE( zekb , zekg , zekr , ze0 , ze1 , ze2 , ze3 , zea , zchl3d ) !
Where most of the temporary, full-depth arrays are not necessary because only two vertical levels are required at any one time. In fact even the zea array is unnecessary since the zchl3d array could be repurposed once its value has been used.
Option 1: Minmum memory usage
By rearranging the loop order and placing the vertical loop innermost then the code can be greatly simplified to an equivalent using minimal temporary storage. A couple of other changes seem sensible too, namely:
- rename the zchl3d array to ztmp3d (since it is now used for two purposes)
- only allocate ztmp3d to nksr+1; values below this are not used and nksr + 1 is likely << jpk
- calculate and store the attenuation coefficient look-up table index as soon as the sub-surface chlorophyll value is known. This keeps all LOG operations in one loop.
CASE( np_RGB , np_RGBc ) !== R-G-B fluxes ==! ! ALLOCATE( ztmp3d(jpi,jpj,nksr + 1) ) ! ! code to set ztmp3d(:,:,1:nskr+1) ! including the following changes after IF( nqsr == np_RGBc ) THEN !* Variable Chlorophyll . DO_3D_00_00( 1, nksr + 1 ) . . no change until after zCze = 1.12 * (zchl)**0.803 ! ! NB. make sure zchl value is such that: zchl = MIN( 10. , MAX( 0.03, zchl ) ) zchl = MIN( 10. , MAX( 0.03, zCze * ( zCb + zCmax * EXP( -( (zpsi - zpsimax) / zdelpsi )**2 ) ) ) ) ! Convert chlorophyll value to attenuation coefficient look-up table index ztmp3d(ji,jj,jk) = 41 + 20.*LOG10(zchl) + 1.e-15 END_3D ELSE !* constant chrlorophyll zchl = 0.05 ! NB. make sure constant value is such that: zchl = MIN( 10. , MAX( 0.03, zchl ) ) ! Convert chlorophyll value to attenuation coefficient look-up table index zlui = 41 + 20.*LOG10(zchl) + 1.e-15 DO jk = 1, nksr + 1 ztmp3d(:,:,jk) = zlui END DO ENDIF ! ! zcoef = ( 1. - rn_abs ) / 3._wp !* surface equi-partition in R-G-B ! store the surface SW radiation; re-purpose the surface ztmp3d array ! since the surface attenuation coefficient is not used ztmp3d(:,:,1) = qsr(:,:) ! !* interior equi-partition in R-G-B depending of vertical profile of Chl DO_2D_00_00 zc0 = rn_abs * qsr(ji,jj) zc1 = zcoef * qsr(ji,jj) zc2 = zc1 zc3 = zc1 zc4 = e3t(ji,jj,1,Kmm) DO jk = 2, nksr+1 irgb = NINT( ztmp3d(ji,jj,jk) ) zc0 = zc0 * EXP( - zc4 * xsi0r ) zc1 = zc1 * EXP( - zc4 * rkrgb(1,irgb) ) zc2 = zc2 * EXP( - zc4 * rkrgb(2,irgb) ) zc3 = zc3 * EXP( - zc4 * rkrgb(3,irgb) ) zc4 = e3t(ji,jj,jk,Kmm) ! store the SW radiation penetrating to this location ! re-purpose the ztmp3d array since the attenuation coefficient ! at this point will not be needed again ztmp3d(ji,jj,jk) = ( zc0 + zc1 + zc2 + zc3 ) * wmask(ji,jj,jk) END DO END_2D ! DO_3D_00_00( 1, nksr ) qsr_hc(ji,jj,jk) = r1_rho0_rcp * ( ztmp3d(ji,jj,jk) - ztmp3d(ji,jj,jk+1) ) END_3D ! DEALLOCATE( ztmp3d )
This is code and memory efficient but may perform poorly due to non-contiguous access to the array elements (see performance section below).
Option 2: Low memory use (retain loop order).
A compromise solution, which reduces memory use and should perform better is to remove all unnecessary full-depth arrays but maintain loop order by keeping a few 2D arrays.
CASE( np_RGB , np_RGBc ) !== R-G-B fluxes ==! ! ALLOCATE( ze0 (jpi,jpj) , ze1 (jpi,jpj) , & & ze2 (jpi,jpj) , ze3 (jpi,jpj) , & & ztmp3d(jpi,jpj,nksr + 1) ) ! ! code to set ztmp3d(:,:,1:nskr+1) ! including the following changes after IF( nqsr == np_RGBc ) THEN !* Variable Chlorophyll . DO_3D_00_00( 1, nksr + 1 ) . . no change until after zCze = 1.12 * (zchl)**0.803 ! ! NB. make sure zchl value is such that: zchl = MIN( 10. , MAX( 0.03, zchl ) ) zchl = MIN( 10. , MAX( 0.03, zCze * ( zCb + zCmax * EXP( -( (zpsi - zpsimax) / zdelpsi )**2 ) ) ) ) ! Convert chlorophyll value to attenuation coefficient look-up table index ztmp3d(ji,jj,jk) = 41 + 20.*LOG10(zchl) + 1.e-15 END_3D ELSE !* constant chlorophyll zchl = 0.05 ! NB. make sure constant value is such that: zchl = MIN( 10. , MAX( 0.03, zchl ) ) ! Convert chlorophyll value to attenuation coefficient look-up table index zlui = 41 + 20.*LOG10(zchl) + 1.e-15 DO jk = 1, nksr + 1 ztmp3d(:,:,jk) = zlui END DO ENDIF ! zcoef = ( 1. - rn_abs ) / 3._wp !* surface equi-partition in R-G-B DO_2D_00_00 ze0(ji,jj) = rn_abs * qsr(ji,jj) ze1(ji,jj) = zcoef * qsr(ji,jj) ze2(ji,jj) = zcoef * qsr(ji,jj) ze3(ji,jj) = zcoef * qsr(ji,jj) ! store the surface SW radiation; re-use the surface ztmp3d array ! since the surface attenuation coefficient is not used ztmp3d(ji,jj,1) = qsr(ji,jj) END_2D ! !* interior equi-partition in R-G-B depending of vertical profile of Chl DO_3D_00_00( 2, nksr+1 ) irgb = NINT( ztmp3d(ji,jj,jk) ) ze3t = e3t(ji,jj,jk-1,Kmm) ze0(ji,jj) = ze0(ji,jj) * EXP( - ze3t * xsi0r ) ze1(ji,jj) = ze1(ji,jj) * EXP( - ze3t * rkrgb(1,irgb) ) ze2(ji,jj) = ze2(ji,jj) * EXP( - ze3t * rkrgb(2,irgb) ) ze3(ji,jj) = ze3(ji,jj) * EXP( - ze3t * rkrgb(3,irgb) ) ! store the SW radiation penetrating to this location ! re-use the ztmp3d array since the attenuation coefficient ! at this point will not be needed again ztmp3d(ji,jj,jk) = ( ze0(ji,jj) + ze1(ji,jj) + ze2(ji,jj) + ze3(ji,jj) ) * wmask(ji,jj,jk) END_3D ! DO_3D_00_00( 1, nksr ) qsr_hc(ji,jj,jk) = r1_rho0_rcp * ( ztmp3d(ji,jj,jk) - ztmp3d(ji,jj,jk+1) ) END_3D ! DEALLOCATE( ze0 , ze1 , ze2 , ze3 , ztmp3d )
Performance and evaluation
Both these options produce identical results to the original code (based on an ORCA2_ICE_PISCES test using SETTE (which includes variable surface chlorophyll inputs). ln_timing was activated and the CPU time (averaged across all processors) spent in tra_qsr used as a simple measure of performance. Unfortunately, variations in runtime between successive tests (even with the same code) on the NOC cluster were almost as great as any difference arising from algorithmic differences. Each test was repeated 6 times with the following results:
code option | ||||||
original code | 0.34 | 0.34 | 0.35 | 0.35 | 0.34 | 0.34 |
minimum memory option | 0.36 | 0.36 | 0.37 | 0.36 | 0.36 | 0.37 |
low memory option | 0.35 | 0.35 | 0.35 | 0.36 | 0.36 | 0.35 |
from which the tentative conclusion is that the minimum memory option does perform consistently worst but the low memory option appears to be a suitable replacement to the original code. More stringent tests are require to confirm this.
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Attachments (13)
- traqsr_lomem.F90 (21.4 KB) - added by acc 4 years ago.
- traqsr_trunk.F90 (21.3 KB) - added by acc 4 years ago.
- traqsr_minmem.F90 (21.0 KB) - added by acc 4 years ago.
- percent_cpu_qsr.png (91.6 KB) - added by acc 4 years ago.
- rankqsr.png (83.8 KB) - added by acc 4 years ago.
- rankqsr.2.png (83.8 KB) - added by acc 4 years ago.
- percent_cpu_qsr.2.png (91.6 KB) - added by acc 4 years ago.
- rankqsr.3.png (77.8 KB) - added by acc 4 years ago.
- percent_cpu_qsr.3.png (91.3 KB) - added by acc 4 years ago.
- traqsr_lomem_v2.F90 (21.5 KB) - added by acc 4 years ago.
- rankqsr.4.png (75.5 KB) - added by acc 4 years ago.
- percent_cpu_qsr.4.png (88.2 KB) - added by acc 4 years ago.
- eORCA025_traqsr.png (98.0 KB) - added by acc 4 years ago.
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