#2285 closed Task (fixed)
Optimization of the communications in BDY
Reported by: | girrmann | Owned by: | girrmann |
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Priority: | low | Milestone: | IMMERSE 2019 |
Component: | BDY | Version: | trunk |
Severity: | minor | Keywords: | |
Cc: |
Description (last modified by girrmann)
Summary
Action | HPC-13_IRRMANN_BDY_optimization |
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PI(S) | Gaston Irrmann, Sebastien Masson |
Digest | Optimization of the communications in BDY |
Dependencies | |
Branch | NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization |
Previewer(s) | |
Reviewer(s) | |
Wiki | wiki:2019WP/... |
Abstract
Reduce MPI communications as much as possible in BDY routines, do some cleaning as well...
Description
Take each BDY routine and check if communications can be removed
Implementation
- Step 0 : Improve corner treatment in neumann (bdy_nmn) and bdy_ssh, this first modifications change the results.
- Step 1 : Extend local BDY to the full local domain : change change bdy definition in bdyini.F90 and add CYCLE instruction in the routines to avoid out of bounds access. Does not change the result.
- Step 2 : Remove unneeded communications once bdy is extended over the full local domain. Does not change the result.
Commit History (42)
Changeset | Author | Time | ChangeLog |
---|---|---|---|
11525 | smasson | 2019-09-10T16:18:42+02:00 | dev_r10984_HPC-13 : merge with trunk@,11524 see #2285 |
11512 | smasson | 2019-09-09T12:05:20+02:00 | dev_r10984_HPC-13 : merge with trunk@11511, see #2285 |
11398 | smasson | 2019-08-02T18:43:29+02:00 | dev_r10984_HPC-13 : add nammpp parameter ln_listonly, see #2285 |
11391 | smasson | 2019-08-02T11:03:40+02:00 | dev_r10984_HPC-13 : flowri compiling without key_iomput, see #2285 |
11389 | smasson | 2019-08-02T09:51:41+02:00 | dev_r10984_HPC-13 : add timing of each time step, see #2285 |
11373 | smasson | 2019-07-30T17:33:23+02:00 | dev_r10984_HPC-13 : timing working with more than 9999 cores, see #2285 |
11364 | smasson | 2019-07-29T16:54:28+02:00 | dev_r10984_HPC-13 : update BENCH to be more robust, see #2285 |
11359 | smasson | 2019-07-26T18:29:57+02:00 | dev_r10984_HPC-13 : add new machine and update BENCH scripts, see #2285 |
11358 | smasson | 2019-07-26T16:10:19+02:00 | dev_r10984_HPC-13 : supress output files with nn_stock and nn_write = -1, see #2285 |
11353 | smasson | 2019-07-25T16:55:58+02:00 | dev_r10984_HPC-13 : merge with trunk@11352, see #2285 |
11320 | smasson | 2019-07-22T14:52:29+02:00 | dev_r10984_HPC-13 : add missing if(lwp) in [11317], see #2307 and #2285 |
11319 | girrmann | 2019-07-22T12:27:25+02:00 | dev_r10984_HPC-13 : bugfix for ENT scheme, see #2285 |
11317 | smasson | 2019-07-22T10:32:59+02:00 | dev_r10984_HPC-13 : improve error handling, see #2307 and #2285 |
11268 | smasson | 2019-07-15T15:20:49+02:00 | dev_r10984_HPC-13 : introduce a logical to force vertical interpolation if the number of vertical levels in bdy dta == jpk, see #2285 |
11267 | smasson | 2019-07-15T12:58:45+02:00 | dev_r10984_HPC-13 : cleanup the use of freqh as REAL in fldread (done old commit [4144]), see #2285 |
11265 | smasson | 2019-07-12T16:02:06+02:00 | dev_r10984_HPC-13 : bugfix for AGRIF, see #2285 |
11263 | smasson | 2019-07-12T12:47:53+02:00 | dev_r10984_HPC-13 : merge with trunk@11242, see #2285 |
11262 | girrmann | 2019-07-12T11:40:17+02:00 | dev_r10984_HPC-13 : small modification of lbc_lnk, see #2285 |
11261 | girrmann | 2019-07-12T10:28:39+02:00 | dev_r10984_HPC-13 : bugfix, see #2285 |
11258 | smasson | 2019-07-11T18:21:02+02:00 | dev_r10984_HPC-13 : minor bugfix and cleaning, see #2285 |
11245 | girrmann | 2019-07-10T17:27:04+02:00 | |
11241 | girrmann | 2019-07-10T11:46:48+02:00 | dev_r10984_HPC-13 : regroup communications in dyn_spg_ts, does not change the result, see #2285 |
11240 | girrmann | 2019-07-10T11:08:58+02:00 | dev_r10984_HPC-13 : remove a communication in dyn_spg_ts, see #2285 |
11234 | girrmann | 2019-07-09T18:09:16+02:00 | dev_r10984_HPC-13 : cleaning of dyn_spg_ts routine, does not change the results, see #2285 |
11224 | smasson | 2019-07-08T11:19:12+02:00 | dev_r10984_HPC-13 : bugfix to work will all configurations, see #2285 |
11223 | smasson | 2019-07-05T20:53:14+02:00 | dev_r10984_HPC-13 : cleaning of rewriting of bdydta, see #2285 |
11210 | girrmann | 2019-07-03T12:08:42+02:00 | dev_r10984_HPC-13 : remove some communications in bdy treatment in case nn_hls > 1, see #2285 |
11195 | girrmann | 2019-06-28T12:59:32+02:00 | dev_r10984_HPC-13 : update of trc_bdy following [11191], merge of lbc_lnk and lbc_bdy_lnk in a single lbc_lnk routine, see #2285 |
11194 | smasson | 2019-06-27T16:51:16+02:00 | dev_r10984_HPC-13 : reorganization of lbclnk, part 1: bugfix following [11192], see #2285 |
11193 | smasson | 2019-06-27T12:47:43+02:00 | dev_r10984_HPC-13 : reorganization of lbclnk, part 1: missing delete of lbc_lnk_generic.h90 in [11192], see #2285 |
11192 | smasson | 2019-06-27T12:40:32+02:00 | dev_r10984_HPC-13 : reorganization of lbclnk, part 1: simpler mpp_lnk_generic.h90 supress lbc_lnk_generic.h90, see #2285 |
11191 | girrmann | 2019-06-27T10:14:39+02:00 | dev_r10984_HPC-13 : bdy treatment can now handel a rim 0 and a rim 1, results are unchanged when only rim 1 is provided, see #2288 and #2285 |
11183 | girrmann | 2019-06-26T16:09:28+02:00 | dev_r10984_HPC-13 : improvement of neumann boundary condition, changes the results, see #2285 |
11149 | girrmann | 2019-06-20T12:48:17+02:00 | dev_r10984_HPC-13 : minor modification of flather, the change in results is due to the non associativity of addition, see #2285 |
11074 | girrmann | 2019-06-04T17:46:46+02:00 | dev_r10984_HPC-13 : bug fix and cleaning of flather, see #2287 and #2285 |
11071 | girrmann | 2019-06-04T14:58:06+02:00 | dev_r10984_HPC-13 : step 2, remove unneeded communications, see #2285 |
11067 | girrmann | 2019-05-29T11:34:32+02:00 | dev_r10984_HPC-13 : new implementation of lbc_bdy_lnk in prevision of step 2, regroup communications, see #2285 |
11059 | girrmann | 2019-05-27T13:05:25+02:00 | dev_r10984_HPC-13 : simplify bdyini.F90 following extension of bdy detection, see #2285 |
11056 | girrmann | 2019-05-24T15:52:26+02:00 | |
11049 | girrmann | 2019-05-24T10:22:47+02:00 | dev_r10984_HPC-13 : CYCLE instruction is not systematic anymore, computation is done on the halo whenever possible and overwritten by lbc_bdy instruction, see #2285 |
11044 | girrmann | 2019-05-23T17:13:38+02:00 | |
11024 | girrmann | 2019-05-21T16:07:24+02:00 | dev_r10984_HPC-13 : imrpove bdy treatment ssh and neumann, see #2285 |
Change History (59)
comment:1 Changed 5 years ago by girrmann
comment:2 Changed 5 years ago by girrmann
- Status changed from new to assigned
improve bdy treatment ssh and neumann, see [11024]
Warning : this modification changes the results
comment:3 Changed 5 years ago by girrmann
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Warning [11044] changes the result
comment:6 Changed 5 years ago by girrmann
- Description modified (diff)
comment:7 Changed 5 years ago by girrmann
dev_r10984_HPC-13 : Step 1, boundary is now detected all over the local domain, this does not change the result. Improve bdy treatment for bdy_rnf in bdytra.F90, this changes the result when keyword runoff is specified in namelist, see #2285
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comment:23 follow-up: ↓ 36 Changed 4 years ago by smasson
[11223] do not change the results
but nb_jpk_bdy has been removed from the namelist (it is now directly defined from the variable dimensions in the netcdf file)
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comment:34 Changed 4 years ago by smasson
drg_init subroutine was already existing zdfdrg.F90.
AGRIF was lost with these 2 subroutines having the same name and was no more able to compile zdfdrg.
I don't understand how dynspg_ts was able to compile as if was including a private subroutine called drg_init and was using the module zdfdrg that was aslo including a public subroutine called drg_init...
Bugfix was simple, I just changed the name of drg_init in dynspg_ts.
comment:35 Changed 4 years ago by smasson
Results of the sette tests (old version: NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization@11263) performed on CURIE (without the compilation option -xCORE-AVX512 and with nn_sponge_len = 1 in agrif_oce.F90 (see bellow).
The failed tests are exactly the same as NEMO/trunk@11258
run.stat files of this branch are exactly the same as the ones of NEMO/trunk@11258 except for AMM12 and SPITZ12, which is expected because of the changes we made in BDY (see previous comments of this ticket.
cfgs/AGRIF_DEMO_ST/LONG/run.stat same as trunk@11258 cfgs/AMM12_ST/LONG/run.stat same as trunk@11258 cfgs/AMM12_ST/LONG/run.stat /ccc/scratch/cont005/ra0542/massons/rev11258_trunk/cfgs/AMM12_ST/LONG/run.stat differ: byte 194, line 2 cfgs/GYRE_PISCES_ST/LONG/run.stat same as trunk@11258 cfgs/ORCA2_ICE_PISCES_ST/LONG/run.stat same as trunk@11258 cfgs/ORCA2_SAS_ICE_ST/LONG/run.stat same as trunk@11258 cfgs/SPITZ12_ST/LONG/run.stat same as trunk@11258 cfgs/SPITZ12_ST/LONG/run.stat /ccc/scratch/cont005/ra0542/massons/rev11258_trunk/cfgs/SPITZ12_ST/LONG/run.stat differ: byte 47, line 1 tests/LOCK_EXCHANGE_ST/LONG/run.stat same as trunk@11258 tests/OVERFLOW_ST/LONG/run.stat same as trunk@11258 tests/VORTEX_ST/LONG/run.stat same as trunk@11258
-bash-4.2$ ./sette_rpt.sh svn /ccc/scratch/cont005/ra0542/massons/dev_bdylast/sette/../.svn SETTE validation report : utils @ r10779 ( last change @ r11263 ) !!---------------1st pass------------------!! !----restart----! WGYRE_PISCES_ST run.stat restartability passed : 20190712 WGYRE_PISCES_ST tracer.stat restartability passed : 20190712 WORCA2_ICE_PISCES_ST run.stat restartability passed : 20190712 WORCA2_ICE_PISCES_ST tracer.stat restartability FAILED : 20190712 WORCA2_OFF_PISCES_ST tracer.stat restartability passed : 20190712 WAMM12_ST run.stat restartability passed : 20190712 WORCA2_SAS_ICE_ST run.stat restartability FAILED : 20190712 WAGRIF_DEMO_ST run.stat restartability passed : 20190712 WSPITZ12_ST run.stat restartability passed : 20190712 WISOMIP_ST directory is MISSING : 20190712 WOVERFLOW_ST run.stat restartability passed : 20190712 WLOCK_EXCHANGE_ST run.stat restartability passed : 20190712 WVORTEX_ST run.stat restartability passed : 20190712 WICE_AGRIF_ST directory is MISSING : 20190712 !----repro----! WGYRE_PISCES_ST run.stat reproducibility passed : 20190712 WGYRE_PISCES_ST tracer.stat reproducibility passed : 20190712 WORCA2_ICE_PISCES_ST run.stat reproducibility passed : 20190712 WORCA2_ICE_PISCES_ST tracer.stat reproducibility passed : 20190712 WORCA2_OFF_PISCES_ST tracer.stat reproducibility passed : 20190712 WAMM12_ST run.stat reproducibility passed : 20190712 WORCA2_SAS_ICE_ST run.stat reproducibility passed : 20190712 WORCA2_ICE_OBS_ST directory is MISSING : 20190712 WAGRIF_DEMO_ST run.stat reproducibility passed : 20190712 WSPITZ12_ST run.stat reproducibility passed : 20190712 WISOMIP_ST directory is MISSING : 20190712 WVORTEX_ST run.stat reproducibility passed : 20190712 WICE_AGRIF_ST directory is MISSING : 20190712 !----agrif check----! ORCA2 AGRIF vs ORCA2 NOAGRIF run.stat unchanged - passed : 20190712 20190712 !!---------------2nd pass------------------!!
comment:36 in reply to: ↑ 23 Changed 4 years ago by jamesharle
Replying to smasson:
[11223] do not change the results
but nb_jpk_bdy has been removed from the namelist (it is now directly defined from the variable dimensions in the netcdf file)
The original (and possibly a little lazy) reason for putting nb_jpk_bdy in the namelist was that I was often running a 75 level hybrid sigma/zps run using a 75 z-level run for my lateral boundary conditions - with the re-write you now have:
IF( ipkb /= ipk ) THEN
do interpolation
at line 738 in fldread.F90. So in many of my simulations the interpolation of the lateral boundary conditions, whilst needed, will be skipped.
comment:37 Changed 4 years ago by smasson
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[11268] was done in response to the comment of jamesharle a few lines above.
We did agree to use a logical (ln_zinterp) instead of the old variable nb_jpk_bdy, which name/use was not really explicit.
ln_zinterp has been added to nambdy_dta instead of nambdy as it is part of each bdy data definition.
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Results of sette tests for
NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization@11325
X64_IRENE
without the compilation option -xCORE-AVX512 and with nn_sponge_len = 1 in agrif_oce.F90
same */*_ST/*/run.stat files as in NEMO/trunk@11258 except for AMM12 and SPITZ12 which is expected
same */*_ST/*/run.stat files as in NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization@11319
/ccc/scratch/cont005/ra0542/massons/rev11325_dev_bdy/sette/../.svn SETTE validation report : utils @ r10779 ( last change @ r11325 ) !!---------------1st pass------------------!! !----restart----! WGYRE_PISCES_ST run.stat restartability passed : 20190723 WGYRE_PISCES_ST tracer.stat restartability passed : 20190723 WORCA2_ICE_PISCES_ST run.stat restartability passed : 20190723 WORCA2_ICE_PISCES_ST tracer.stat restartability FAILED : 20190723 WORCA2_OFF_PISCES_ST tracer.stat restartability passed : 20190723 WAMM12_ST run.stat restartability passed : 20190723 WORCA2_SAS_ICE_ST run.stat restartability FAILED : 20190723 WAGRIF_DEMO_ST run.stat restartability passed : 20190723 WSPITZ12_ST run.stat restartability passed : 20190723 WISOMIP_ST run.stat restartability passed : 20190723 WOVERFLOW_ST run.stat restartability passed : 20190723 WLOCK_EXCHANGE_ST incomplete test WLOCK_EXCHANGE_ST ocean.output is MISSING : 20190723 WVORTEX_ST run.stat restartability passed : 20190723 WICE_AGRIF_ST run.stat restartability passed : 20190723 !----repro----! WGYRE_PISCES_ST run.stat reproducibility passed : 20190723 WGYRE_PISCES_ST tracer.stat reproducibility passed : 20190723 WORCA2_ICE_PISCES_ST run.stat reproducibility passed : 20190723 WORCA2_ICE_PISCES_ST tracer.stat reproducibility passed : 20190723 WORCA2_OFF_PISCES_ST tracer.stat reproducibility passed : 20190723 WAMM12_ST run.stat reproducibility passed : 20190723 WORCA2_SAS_ICE_ST run.stat reproducibility passed : 20190723 WORCA2_ICE_OBS_ST directory is MISSING : 20190723 WAGRIF_DEMO_ST run.stat reproducibility passed : 20190723 WSPITZ12_ST run.stat reproducibility passed : 20190723 WISOMIP_ST run.stat reproducibility passed : 20190723 WVORTEX_ST run.stat reproducibility passed : 20190723 WICE_AGRIF_ST run.stat reproducibility passed : 20190723 !----agrif check----! ORCA2 AGRIF vs ORCA2 NOAGRIF run.stat unchanged - passed : 20190723 20190723
comment:45 Changed 4 years ago by smasson
small bugfixes in [11352]
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small bugfixes in [11356]
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Results of the sette tests (old version: NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization@11263) performed on CURIE (without the compilation option -xCORE-AVX512 and with nn_sponge_len = 1 in agrif_oce.F90 (see bellow).
The failed tests are exactly the same as NEMO/trunk@11258
/ccc/scratch/cont005/ra0542/massons/rev11530_dev_bdy/sette/../.svn SETTE validation report : utils @ r10779 ( last change @ r11530 ) !!---------------1st pass------------------!! !----restart----! WGYRE_PISCES_ST run.stat restartability passed : 20190911 WGYRE_PISCES_ST tracer.stat restartability passed : 20190911 WORCA2_ICE_PISCES_ST run.stat restartability passed : 20190911 WORCA2_ICE_PISCES_ST tracer.stat restartability FAILED : 20190911 WORCA2_OFF_PISCES_ST tracer.stat restartability passed : 20190911 WAMM12_ST run.stat restartability passed : 20190911 WORCA2_SAS_ICE_ST run.stat restartability FAILED : 20190911 WAGRIF_DEMO_ST run.stat restartability passed : 20190911 WSPITZ12_ST run.stat restartability passed : 20190911 WISOMIP_ST run.stat restartability passed : 20190911 WOVERFLOW_ST run.stat restartability passed : 20190911 WLOCK_EXCHANGE_ST run.stat restartability passed : 20190911 WVORTEX_ST run.stat restartability passed : 20190911 WICE_AGRIF_ST run.stat restartability passed : 20190911 !----repro----! WGYRE_PISCES_ST run.stat reproducibility passed : 20190911 WGYRE_PISCES_ST tracer.stat reproducibility passed : 20190911 WORCA2_ICE_PISCES_ST run.stat reproducibility passed : 20190911 WORCA2_ICE_PISCES_ST tracer.stat reproducibility passed : 20190911 WORCA2_OFF_PISCES_ST tracer.stat reproducibility passed : 20190911 WAMM12_ST run.stat reproducibility passed : 20190911 WORCA2_SAS_ICE_ST run.stat reproducibility passed : 20190911 WORCA2_ICE_OBS_ST run.stat reproducibility passed : 20190911 WAGRIF_DEMO_ST run.stat reproducibility passed : 20190911 WSPITZ12_ST run.stat reproducibility passed : 20190911 WISOMIP_ST run.stat reproducibility passed : 20190911 WVORTEX_ST run.stat reproducibility passed : 20190911 WICE_AGRIF_ST run.stat reproducibility passed : 20190911 !----agrif check----! ORCA2 AGRIF vs ORCA2 NOAGRIF run.stat unchanged - passed : 20190911 20190911
with the debug option:
Note that in this case: ORCA2 AGRIF vs ORCA2 NOAGRIF run.stat changed
/ccc/scratch/cont005/ra0542/massons/rev11530_dev_bdy_debug/sette/../.svn SETTE validation report : utils @ r10779 ( last change @ r11530 ) !!---------------1st pass------------------!! !----restart----! WGYRE_PISCES_ST run.stat restartability passed : 20190911 WGYRE_PISCES_ST tracer.stat restartability passed : 20190911 WORCA2_ICE_PISCES_ST run.stat restartability passed : 20190911 WORCA2_ICE_PISCES_ST tracer.stat restartability FAILED : 20190911 WORCA2_OFF_PISCES_ST tracer.stat restartability passed : 20190911 WAMM12_ST run.stat restartability passed : 20190911 WORCA2_SAS_ICE_ST run.stat restartability FAILED : 20190911 WAGRIF_DEMO_ST run.stat restartability passed : 20190911 WSPITZ12_ST run.stat restartability passed : 20190911 WISOMIP_ST run.stat restartability passed : 20190911 WOVERFLOW_ST run.stat restartability passed : 20190911 WLOCK_EXCHANGE_ST run.stat restartability passed : 20190911 WVORTEX_ST run.stat restartability passed : 20190911 WICE_AGRIF_ST run.stat restartability passed : 20190911 !----repro----! WGYRE_PISCES_ST run.stat reproducibility passed : 20190911 WGYRE_PISCES_ST tracer.stat reproducibility passed : 20190911 WORCA2_ICE_PISCES_ST run.stat reproducibility passed : 20190911 WORCA2_ICE_PISCES_ST tracer.stat reproducibility passed : 20190911 WORCA2_OFF_PISCES_ST tracer.stat reproducibility passed : 20190911 WAMM12_ST run.stat reproducibility passed : 20190911 WORCA2_SAS_ICE_ST run.stat reproducibility passed : 20190911 WORCA2_ICE_OBS_ST run.stat reproducibility passed : 20190911 WAGRIF_DEMO_ST run.stat reproducibility passed : 20190911 WSPITZ12_ST run.stat reproducibility passed : 20190911 WISOMIP_ST run.stat reproducibility passed : 20190911 WVORTEX_ST run.stat reproducibility passed : 20190911 WICE_AGRIF_ST run.stat reproducibility passed : 20190911 !----agrif check----! ORCA2 AGRIF vs ORCA2 NOAGRIF run.stat changed - FAILED : 20190911 20190911
comment:58 Changed 4 years ago by smasson
- Resolution set to fixed
- Status changed from assigned to closed
comment:59 Changed 4 years ago by smasson
- branch_review changed from pending to passed
- wp_comment changed from Unspecified to done
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