CHIMERE with OpenACC annotations CHIMERE/acc

CHIMERE with OpenACC annotations CHIMERE/acc#

Description#

This is the plugin to run the CTM CHIMERE. Please see further details on the CTM itself here.

YAML arguments#

The following arguments are used to configure the plugin. pyCIF will return an exception at the initialization if mandatory arguments are not specified, or if any argument does not fit accepted values or type:

Mandatory arguments#

direxec : str, mandatory

Path to CHIMERE sources and/or executables. For executables, fwdchimere.e, tlchimere.e and achimere.e should be in ${path}/src, ${path}/src_tl and ${path}/src_ad respective sub-folders.

nphour_ref : int, mandatory

Number of physical steps per hour. 6 is well tested for regional cases.

ichemstep : int, mandatory

Number of chemical refined iterations, i.e., refined time steps relative to physical time steps. Down to 1/4 degree resolution, phys=6 and step=1 is fine; For finer grids (5-10 kms), take at least step=4; For grids of 2-5 kms, try step=6 or more.

ideepconv : 0 or 1 or 2, mandatory

Computation of the deep convection.

  • 0: No deep convection

  • 1: Select deep convection automatically according to resolution, deep conv fluxes from Tiedtke

  • 2: Select deep convection automatically according to resolution, deep conv fluxes from meteorological data

nivout : int, mandatory

Number of vertical layers in output files.

nlevemis : int, mandatory

Number of levels for emissions. Applies to AEMISSION files.

Optional arguments#

autoflush : bool, optional, default False

Cleans big temporary files when the simulation is done. Triggers the function flushrun of the model if available

ensrf_restart_file : str, optional

Use in EnSRF mode to point at relevant restart file

ensrf_datei : str, optional

New start date to use in EnSRF

ensrf_same_restart : bool, optional

Use in EnSRF mode to check if same restart

dir_sources : str, optional, default “”

Path to CHIMERE sources. Overwrites direxec if specified.

periods : str, optional, default “1D”

Length of sub-simulations periods. Use Pandas frequency strings

ihoursu : int, optional, default 0

Number of spin-up hours.

useemisb : bool, optional, default False

Include biogenic emissions, i.e. the file BEMISSIONS.nc

dumpnctype : “double” or “float”, optional, default “float”

Precision for the output NetCDF files. Do not impact the values in mod.txt

  • “double”: double precision: needed if precise post-processing of output files

  • “float”: float precision: save some disk space

nc4type : bool, optional, default True

Use NetCDF4 or not (NetCDF3 classic)

dumpncoutput : bool, optional, default True

Dump outputs into a NetCDF file.

dumpncpar : bool, optional, default False

Dump parameters into a NetCDF file.

usechemistry : 0 or 1, optional, default 0

Use chemistry.

useemissions : 0 or 1, optional, default 1

Use emisions.

usetransmix : 0 or 1, optional, default 1

Use transport and mixing.

usewetdepos : 0 or 1, optional, default 0

Use wet deposition.

usedepos : 0 or 1, optional, default 0

Use dry deposition.

nsavedepos : int, optional, default 4

Save deposition in NetCDF file every … hours.

nitgs : 1 or 2, optional, default 1

Number of Gauss-Seidel iterations in the TWOSTEP solver.

  • 1: for model testing, and when using the adjoint

  • 2: for better accuracy

nitgssu : 1 or 2, optional, default 1

Same during spin-up

  • 1: for model testing, and when using the adjoint

  • 2: for better accuracy

useabsclipconc : 0 or 1, optional, default 0

Clip small (in absolute value) concentrations when = 1; clip small (including all negative) concentrations when = 0. Warning: the clipping is done in twostep, not only when writing the output writing; thus, clipping must be used with care as it can alter the mass conservationsee CHIMERE doc for more information on the use of clipconc

clipconc : float, optional, default 1

Clipping concentration (in molecule/cm3)

ntyperate : int, optional, default 50

Max number of reaction types

nvegtype : int, optional, default 16

Number of vegetation types

nlduse : int, optional, default 9

Max number of landuse classes

nparammax : int, optional, default 30

Max number of output parameters

hpulse : int, optional, default 0

Hour of emission pulse. All emissions before this hour from the beginning of the simulations are ignored, and all transport/chemistry computations are skipped.To be used when computing response functions from a given hour

auto-recompile : bool, optional, default False

Auto-compile executables before running if executables not available

force-recompile : bool, optional, default False

Force compilation even if executables available

optimization-mode : “PROD” or “DEBUG”, optional, default “PROD”

Optimization option

  • “PROD”: production mode; all optimizations are activated

  • “DEBUG”: check-all and traceback are activated, hence slowing down the execution

compile-clean : bool, optional, default True

Cleaning repositories before compiling; slows the compilation but prevent side-effects from re-compiling.Can be switched of for minor modifications in the code

monitor : bool, optional, default False

Sets NVCOMPILER_ACC_TIME=1, allowing GPU basic profiling

gpu-mode : “gpu” or “multicore” or “seq”, optional, default “gpu”

Compiling option for NVIDIA

  • “gpu”: Full GPU optimization

  • “multicore”: NVIDIA ACC optimization for CPUs

  • “seq”: Disabling all parallelization

compiler : “nvfortran” or “gfortran”, optional, default “nvfortran”

Compiler used for Fortran ACC

  • “nvfortran”: NVIDIA Fortran compiler

  • “gfortran”: gfortran compiler

compile-only : list, optional, default [‘A’, ‘L’, ‘D’]

Compile only part of the available CHIMERE modes (tangent-linear, forward and adjoint)

force-compile-stderr : bool, optional, default False

Force printing stderr from compiling (even when executable correctly generated after compiling)

nlevemis_bio : int, optional, default 1

Number of vertical levels in biogenic emissions (BEMISSIONS.nc)

nproc : int, optional

Force using a given number of processors. By default, CIMERE GPU uses all available processors

ignore_input_dates : bool, optional, default False

Forces CHIMERE to by-pass the checks on the consistency of dates in AEMISSIONS, BEMISSIONS, BOUN_CONCS, INI_COCNS and METEO; useful to use input files from another periodwithout duplicating them only for the dates.

useRAMonly : bool, optional, default False

Force relying on the RAM only, instead of TMP files, to save forward simulations necessary for the adjoint. This trades I/O burden with TMP files with RAM burden

Warning

This option can use a LOT of RAM. Please test the option on a simple case and compare with a case using TMP files. Depending on your cluster and your test case, choose the fastest one.

force_clean_run : bool, optional, default False

Clean run subdirectory just after running to limit disk space usage

stopORmore : list, optional, default []

To avoid running simulations for which the simulated concentrations are smaller than a given thresholdfor a set of species; please provide a list of tuples (species,threshold) (species is from ACTIVE_SPECIES and treshold in XXUNITXX

pre-computed-meteo : bool, optional, default True

Simplified METEO mapper when the meteo is already computed. Set to False if using diagmet transform

keep_log_stderr : bool, optional, default False

Redirect the standard error from chimere.e to prof.log (particularly useful for checking time in ACC)

Requirements#

The current plugin requires the present plugins to run properly:

Requirement name

Requirement type

Explicit definition

Any valid

Default name

Default version

domain

Domain

False

False

CHIMERE

std

chemistry

Chemistry

False

False

CHIMERE

gasJtab

flux

DataStream

True

False

CHIMERE

AEMISSIONS

bioflux

DataStream

True

False

CHIMERE

AEMISSIONS

meteo

DataStream

True

False

CHIMERE

std

latcond

DataStream

True

False

CHIMERE

icbc

topcond

DataStream

True

False

CHIMERE

icbc

inicond

DataStream

True

False

CHIMERE

icbc

YAML template#

Please find below a template for a YAML configuration:

 1model:
 2  plugin:
 3    name: CHIMERE
 4    version: acc
 5    type: model
 6
 7  # Mandatory arguments
 8  direxec: XXXXX  # str
 9  nphour_ref: XXXXX  # int
10  ichemstep: XXXXX  # int
11  ideepconv: XXXXX  # 0|1|2
12  nivout: XXXXX  # int
13  nlevemis: XXXXX  # int
14
15  # Optional arguments
16  autoflush: XXXXX  # bool
17  ensrf_restart_file: XXXXX  # str
18  ensrf_datei: XXXXX  # str
19  ensrf_same_restart: XXXXX  # bool
20  dir_sources: XXXXX  # str
21  periods: XXXXX  # str
22  ihoursu: XXXXX  # int
23  useemisb: XXXXX  # bool
24  dumpnctype: XXXXX  # double|float
25  nc4type: XXXXX  # bool
26  dumpncoutput: XXXXX  # bool
27  dumpncpar: XXXXX  # bool
28  usechemistry: XXXXX  # 0|1
29  useemissions: XXXXX  # 0|1
30  usetransmix: XXXXX  # 0|1
31  usewetdepos: XXXXX  # 0|1
32  usedepos: XXXXX  # 0|1
33  nsavedepos: XXXXX  # int
34  nitgs: XXXXX  # 1|2
35  nitgssu: XXXXX  # 1|2
36  useabsclipconc: XXXXX  # 0|1
37  clipconc: XXXXX  # float
38  ntyperate: XXXXX  # int
39  nvegtype: XXXXX  # int
40  nlduse: XXXXX  # int
41  nparammax: XXXXX  # int
42  hpulse: XXXXX  # int
43  auto-recompile: XXXXX  # bool
44  force-recompile: XXXXX  # bool
45  optimization-mode: XXXXX  # PROD|DEBUG
46  compile-clean: XXXXX  # bool
47  monitor: XXXXX  # bool
48  gpu-mode: XXXXX  # gpu|multicore|seq
49  compiler: XXXXX  # nvfortran|gfortran
50  compile-only: XXXXX  # list
51  force-compile-stderr: XXXXX  # bool
52  nlevemis_bio: XXXXX  # int
53  nproc: XXXXX  # int
54  ignore_input_dates: XXXXX  # bool
55  useRAMonly: XXXXX  # bool
56  force_clean_run: XXXXX  # bool
57  stopORmore: XXXXX  # list
58  pre-computed-meteo: XXXXX  # bool
59  keep_log_stderr: XXXXX  # bool

See also

API reference (functions & code)