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Commit 034254e4 authored by Oriol Tintó Prims's avatar Oriol Tintó Prims
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Change file structure.

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2 merge requests!2Split prepare_rundir.sh into three different stages for the whole experiment,...,!1Cast checkpoint time to integer, add 10 minutes to the simulation to guarantee...
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conf/jobs.yaml → conf/jobs_real-from-dwd-ana.yaml
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...@@ -57,42 +57,42 @@ JOBS: ...@@ -57,42 +57,42 @@ JOBS:
# EXECUTABLE: /my_python_env/python3 # EXECUTABLE: /my_python_env/python3
BUILD_ICON: BUILD_ICON:
FILE: templates/build_icon.sh FILE: templates/common/build_icon.sh
WALLCLOCK: 04:00 WALLCLOCK: 04:00
PROCESSORS: 16 PROCESSORS: 16
BUILD_PYTHON_ENVIRONMENT: BUILD_PYTHON_ENVIRONMENT:
FILE: templates/build_python_environment.sh FILE: templates/common/build_python_environment.sh
# Right now we rely on spack for building icon and having a python interpreter, so we need this dependency: # Right now we rely on spack for building icon and having a python interpreter, so we need this dependency:
DEPENDENCIES: BUILD_ICON DEPENDENCIES: BUILD_ICON
WALLCLOCK: 01:00 WALLCLOCK: 01:00
PROCESSORS: 16 PROCESSORS: 16
PREPARE_EXPERIMENT: PREPARE_EXPERIMENT:
FILE: templates/prepare_experiment.sh FILE: templates/common/prepare_experiment.sh
DEPENDENCIES: BUILD_ICON DEPENDENCIES: BUILD_ICON
RUNNING: once RUNNING: once
WALLCLOCK: 01:00 WALLCLOCK: 01:00
PREPARE_DATE: PREPARE_DATE:
FILE: templates/prepare_date.sh FILE: templates/common/prepare_date.sh
RUNNING: date RUNNING: date
WALLCLOCK: 01:00 WALLCLOCK: 01:00
PREPARE_MEMBER: PREPARE_MEMBER:
FILE: templates/prepare_member.sh FILE: templates/common/prepare_member.sh
DEPENDENCIES: PREPARE_EXPERIMENT PREPARE_DATE DEPENDENCIES: PREPARE_EXPERIMENT PREPARE_DATE
RUNNING: member RUNNING: member
WALLCLOCK: 01:00 WALLCLOCK: 01:00
PREPARE_CHUNK: PREPARE_CHUNK:
FILE: templates/prepare_chunk.sh FILE: templates/common/prepare_chunk.sh
DEPENDENCIES: PREPARE_MEMBER RUN_ICON-1 DEPENDENCIES: PREPARE_MEMBER RUN_ICON-1
WALLCLOCK: 00:05 WALLCLOCK: 00:05
RUNNING: chunk RUNNING: chunk
RUN_ICON: RUN_ICON:
FILE: templates/run_icon.sh FILE: templates/common/run_icon.sh
DEPENDENCIES: PREPARE_CHUNK DEPENDENCIES: PREPARE_CHUNK
WALLCLOCK: 04:00 WALLCLOCK: 04:00
RUNNING: chunk RUNNING: chunk
...@@ -101,7 +101,7 @@ JOBS: ...@@ -101,7 +101,7 @@ JOBS:
CUSTOM_DIRECTIVES: [ "#SBATCH --exclusive", "export OMPI_MCA_btl_tcp_if_include=10.0.0.0/8"] CUSTOM_DIRECTIVES: [ "#SBATCH --exclusive", "export OMPI_MCA_btl_tcp_if_include=10.0.0.0/8"]
COMPRESS: COMPRESS:
FILE: templates/compress.py FILE: templates/common/compress.py
DEPENDENCIES: RUN_ICON BUILD_PYTHON_ENVIRONMENT COMPRESS-1 DEPENDENCIES: RUN_ICON BUILD_PYTHON_ENVIRONMENT COMPRESS-1
RUNNING: chunk RUNNING: chunk
TYPE: python TYPE: python
...@@ -110,7 +110,7 @@ JOBS: ...@@ -110,7 +110,7 @@ JOBS:
MEMORY: 16384 MEMORY: 16384
TRANSFER: TRANSFER:
FILE: templates/transfer.sh FILE: templates/common/transfer.sh
DEPENDENCIES: COMPRESS DEPENDENCIES: COMPRESS
# Since this is running locally, can simply leave a long wallclock. # Since this is running locally, can simply leave a long wallclock.
WALLCLOCK: 24:00 WALLCLOCK: 24:00
...@@ -118,7 +118,7 @@ JOBS: ...@@ -118,7 +118,7 @@ JOBS:
PLATFORM: LOCAL PLATFORM: LOCAL
CLEAN: CLEAN:
FILE: templates/clean.sh FILE: templates/common/clean.sh
DEPENDENCIES: TRANSFER DEPENDENCIES: TRANSFER
WALLCLOCK: 00:10 WALLCLOCK: 00:10
RUNNING: member RUNNING: member
......
conf/proj.yaml → conf/proj_real-from-dwd-ana.yaml
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...@@ -15,24 +15,24 @@ python_environment: ...@@ -15,24 +15,24 @@ python_environment:
- git+https://gitlab.physik.uni-muenchen.de/Oriol.Tinto/otils.git - git+https://gitlab.physik.uni-muenchen.de/Oriol.Tinto/otils.git
simulation: simulation:
BGRID_GLOBAL: icon_grid_0012_R02B04_G.nc dynamics_grid_filename: icon_grid_0016_R02B06_G.nc
RGRID_GLOBAL: icon_grid_0011_R02B03_R.nc radiation_grid_filename: icon_grid_0015_R02B05_R.nc
BGRID: icon_grid_0016_R02B06_G.nc external_parameters_filename: icon_extpar_0016_R02B06_G_20131206.nc
RGRID: icon_grid_0015_R02B05_R.nc
BEXTPAR: icon_extpar_0016_R02B06_G_20131206.nc
BGRID_NEST: icon_grid_nest_G_DOM01.nc
RGRID_NEST: icon_grid_nest_R_DOM01.nc
BGRID_NEST_LATBC: icon_grid_nest_G_DOM01_latbc.nc
# List of output files
OUTPUT_FILES: "init_DOM01_ML_*.nc latbc_DOM01_ML_*.nc"
FILES_TO_CLEAN: "*.nc"
# List of output file names that will be copied (Wildcards * allowed)
output_file_names: "init_DOM01_ML_*.nc latbc_DOM01_ML_*.nc"
files_to_clean: "*.nc"
data_management: data_management:
# Where do we put the output files afterwards?
local_folder: /scratch/o/Oriol.Tinto/tmp/ local_folder: /scratch/o/Oriol.Tinto/tmp/
initial_conditions: initial_conditions:
# Where are we getting our initial data from?
parent_folder: /archive/meteo/external-models/dwd/icon/oper/icon_oper_eps_gridded-global_rolling/ parent_folder: /archive/meteo/external-models/dwd/icon/oper/icon_oper_eps_gridded-global_rolling/
member: 1 member: 1
\ No newline at end of file
namelist:
# Path to the namelist
master_path: "%PROJDIR%/namelists/icon_master_real-from-dwd-ana.namelist"
atmosphere_path: "%PROJDIR%/namelists/icon_atmosphere_real-from-dwd-ana.namelist"
\ No newline at end of file
templates/build_icon.sh → templates/common/build_icon.sh
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templates/clean.sh → templates/common/clean.sh
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templates/compress.py → templates/common/compress.py
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templates/common/prepare_chunk.sh 0 → 100644
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#!/bin/bash -l
# Get some variables provided by autosubmit.
WORKDIR=%HPCROOTDIR%
dynamics_grid_filename=%simulation.dynamics_grid_filename%
radiation_grid_filename=%simulation.radiation_grid_filename%
external_parameters_filename=%simulation.external_parameters_filename%
STARTDATE=%SDATE%
# Example of date format "2018-06-01T00:00:00Z"
START_YEAR=%Chunk_START_YEAR%
START_MONTH=%Chunk_START_MONTH%
START_DAY=%Chunk_START_DAY%
START_HOUR=%Chunk_START_HOUR%
END_YEAR=%Chunk_END_YEAR%
END_MONTH=%Chunk_END_MONTH%
END_DAY=%Chunk_END_DAY%
END_HOUR=%Chunk_END_HOUR%
Chunk_START_DATE="${START_YEAR}-${START_MONTH}-${START_DAY}T${START_HOUR}:00:00Z"
Chunk_END_DATE="${END_YEAR}-${END_MONTH}-${END_DAY}T${END_HOUR}:00:00Z"
# Convert dates to Unix timestamps
t1_unix=$(date -d "$Chunk_START_DATE" +%s)
t2_unix=$(date -d "$Chunk_END_DATE" +%s)
# Compute difference in seconds
checkpoint_time=$(((t2_unix - t1_unix)))
# Compute number of steps
dtime=180
# Extend chunk 10 minutes to ensure checkpoint creation at the proper time
# TODO: Works but it is a bit ugly.
Chunk_END_DATE="${END_YEAR}-${END_MONTH}-${END_DAY}T${END_HOUR}:10:00Z"
MEMBER=%MEMBER%
CHUNK=%CHUNK%
# If the chunk is not the first one, start from a restart file.
if [[ "${CHUNK}" -eq "1" ]]; then
is_restart=.false.
else
is_restart=.true.
fi
# Define rundir
RUNDIR=${WORKDIR}/${STARTDATE}/${MEMBER}
cd ${RUNDIR} || exit
# Get AN and FG file names from file that was saved during prepare_rundir
AN_FILE=$( cat an_file.txt )
FG_FILE=$( cat fg_file.txt )
templates/prepare_date.sh → templates/common/prepare_date.sh
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templates/prepare_member.sh → templates/common/prepare_member.sh
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templates/run_icon.sh → templates/common/run_icon.sh
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templates/transfer.sh → templates/common/transfer.sh
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templates/prepare_chunk.sh deleted 100644 → 0
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#!/bin/bash -l
# Get some variables provided by autosubmit.
WORKDIR=%HPCROOTDIR%
ICON_VERSION=%ICON_VERSION%
BGRID_GLOBAL=%simulation.BGRID_GLOBAL%
RGRID_GLOBAL=%simulation.RGRID_GLOBAL%
BGRID=%simulation.BGRID%
RGRID=%simulation.RGRID%
BEXTPAR=%simulation.BEXTPAR%
STARTDATE=%SDATE%
# Example of date format "2018-06-01T00:00:00Z"
START_YEAR=%Chunk_START_YEAR%
START_MONTH=%Chunk_START_MONTH%
START_DAY=%Chunk_START_DAY%
START_HOUR=%Chunk_START_HOUR%
END_YEAR=%Chunk_END_YEAR%
END_MONTH=%Chunk_END_MONTH%
END_DAY=%Chunk_END_DAY%
END_HOUR=%Chunk_END_HOUR%
Chunk_START_DATE="${START_YEAR}-${START_MONTH}-${START_DAY}T${START_HOUR}:00:00Z"
Chunk_END_DATE="${END_YEAR}-${END_MONTH}-${END_DAY}T${END_HOUR}:00:00Z"
# Convert dates to Unix timestamps
t1_unix=$(date -d "$Chunk_START_DATE" +%s)
t2_unix=$(date -d "$Chunk_END_DATE" +%s)
# Compute difference in seconds
checkpoint_time=$(((t2_unix - t1_unix)))
# Compute number of steps
dtime=180
nsteps=$((checkpoint_time / ${dtime}))
# Extend chunk 10 minutes to ensure checkpoint creation at the proper time
# TODO: Works but it is a bit ugly.
Chunk_END_DATE="${END_YEAR}-${END_MONTH}-${END_DAY}T${END_HOUR}:10:00Z"
MEMBER=%MEMBER%
CHUNK=%CHUNK%
# If the chunk is not the first one, start from a restart file.
if [[ "${CHUNK}" -eq "1" ]]; then
is_restart=.false.
else
is_restart=.true.
fi
# Define rundir
RUNDIR=${WORKDIR}/${STARTDATE}/${MEMBER}
cd ${RUNDIR}
# Get AN and FG file names from file that was saved during prepare_rundir
AN_FILE=$( cat an_file.txt )
FG_FILE=$( cat fg_file.txt )
# cat >icon_master.namelist <<EOF
# &master_nml
# lrestart = ${is_restart}
# lrestart_write_last = .true.
# /
# &master_model_nml
# model_type = 1 ! atmospheric model
# model_name = "ATMO" ! name of this model component
# model_namelist_filename = "icon_atmosphere.namelist"
# /
# &master_time_control_nml
# calendar = "proleptic gregorian"
# experimentStartDate = '${Chunk_START_DATE}'
# experimentStopDate = '${Chunk_END_DATE}'
# /
# EOF
# cat >icon_atmosphere.namelist <<EOF
# &run_nml
# ltestcase = .TRUE. ! idealized testcase runs
# dtime = 300 ! time step of 300 seconds
# output = 'nml' ! use output nameslists
# msg_level = 15
# nsteps = ${nsteps}
# num_lev = 31
# lvert_nest = .false.
# ldynamics = .true.
# ltransport = .true.
# ntracer = 5
# iforcing = 3
# /
# &time_nml
# dt_restart = ${checkpoint_time}
# /
# &io_nml
# dt_checkpoint = ${checkpoint_time}
# /
# &grid_nml
# dynamics_grid_filename = '$BGRID_GLOBAL'
# radiation_grid_filename = '$RGRID_GLOBAL'
# dynamics_parent_grid_id = 0
# lredgrid_phys = .true.
# /
# &nh_testcase_nml
# nh_test_name = 'APE_nwp' ! testcase selection
# ape_sst_case = 'sst_qobs'
# /
# &nonhydrostatic_nml
# damp_height = 18000
# rayleigh_coeff = 0.75
# /
# &nwp_phy_nml
# inwp_surface = 0
# /
# &parallel_nml
# nproma = 16
# /
# ! the following two output files are used to initialize the next run
# &output_nml
# file_interval = 'PT3600S'
# output_start = '${Chunk_START_DATE}'
# output_end = '${Chunk_END_DATE}'
# output_filename = "init-test"
# output_interval = 'PT3600S'
# include_last = .true.
# mode = 1
# taxis_tunit = 1
# ml_varlist = 'group:dwd_fg_atm_vars', 'group:dwd_fg_sfc_vars'
# remap = 1
# reg_lon_def = -30.,0.5,30.
# reg_lat_def = 90.,-0.5, -90.
# /
# &output_nml
# steps_per_file = 1
# output_start = '${Chunk_START_DATE}'
# output_end = '${Chunk_START_DATE}'
# output_filename = "init-test-ext"
# include_last = .true.
# output_interval = 'PT3600S'
# ml_varlist = 'depth_lk', 'emis_rad', 'fr_lake', 'fr_land', 'topography_c', 'soiltyp', 'sso_stdh', 'sso_theta', 'sso_gamma', 'sso_sigma'
# /
# EOF
# TODO: The namelist shouldn't be hardcoded into the template files.
cat > icon_atmosphere.namelist << EOF
&run_nml
ltestcase = .false.
dtime = ${dtime}
output = 'nml'
msg_level = 15
num_lev = 90
lvert_nest = .false.
ldynamics = .true.
ltransport = .true.
ntracer = 5
iforcing = 3
/
&time_nml
dt_restart = ${checkpoint_time}
/
&io_nml
dt_checkpoint = ${checkpoint_time}
/
&nwp_phy_nml
lupatmo_phy = .FALSE.
/
&grid_nml
dynamics_parent_grid_id = 0
dynamics_grid_filename = '$BGRID'
radiation_grid_filename = '$RGRID'
lredgrid_phys = .true.
/
&extpar_nml
itopo = 1
extpar_filename = '$BEXTPAR'
/
&initicon_nml
init_mode = 1,
dwdfg_filename = '$FG_FILE'
dwdana_filename = '$AN_FILE'
lconsistency_checks = .false.
ana_varnames_map_file = 'ana_varnames_map_file.txt'
/
! settings from operational setup for vertical coordinate
&sleve_nml
min_lay_thckn = 20.
max_lay_thckn = 400.
htop_thcknlimit = 14000.
top_height = 75000.
stretch_fac = 0.9
decay_scale_1 = 4000.
decay_scale_2 = 2500.
decay_exp = 1.2
flat_height = 16000.
/
&nonhydrostatic_nml
damp_height = 22000.
rayleigh_coeff = 1
/
&parallel_nml
nproma = 16
/
! LATBC files, these files will be used as input for the next example.
&output_nml
file_interval = 'PT3600S'
output_start = '${Chunk_START_DATE}'
output_end = '${Chunk_END_DATE}'
output_filename = "latbc"
output_interval = 'PT3600S'
include_last = .true.
ml_varlist = 'u', 'v', 'w', 'theta_v', 'rho', 'qv', 'qc', 'qi', 'qr', 'qs', 'z_ifc'
/
! First Guess file
&output_nml
file_interval = 'PT3600S'
output_start = '${Chunk_START_DATE}'
output_end = '${Chunk_END_DATE}'
output_filename = "init"
output_interval = 'PT3600S'
include_last = .true.
ml_varlist = 'group:dwd_fg_atm_vars', 'group:dwd_fg_sfc_vars'
/
EOF
cat > icon_master.namelist << EOF
&master_nml
lrestart = ${is_restart}
lrestart_write_last = .true.
/
&master_model_nml
model_type = 1 ! atmospheric model
model_name = "ATMO" ! name of this model component
model_namelist_filename = "icon_atmosphere.namelist"
/
&master_time_control_nml
calendar = "proleptic gregorian"
experimentStartDate = '${Chunk_START_DATE}'
experimentStopDate = '${Chunk_END_DATE}'
/
EOF
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