Commit ef5de84c authored by Peters, Wouter's avatar Peters, Wouter
Browse files

Merge branch 'master' into 'master'

We changed the master project to once again run the random observation...

See merge request ctdas/CTDAS!12
parents 2a19664b 32449638
......@@ -56,7 +56,7 @@ class CO2GriddedDaSystem(DaSystem):
'regtype']
for k, v in self.iteritems():
for k, v in self.items():
if v == 'True' : self[k] = True
if v == 'False': self[k] = False
......
......@@ -145,7 +145,7 @@ class CO2GriddedStateVector(StateVector):
dof += np.sum(s) ** 2 / sum(s ** 2)
try:
C = np.linalg.cholesky(matrix)
except np.linalg.linalg.LinAlgError, err:
except np.linalg.linalg.LinAlgError as err:
logging.error('Cholesky decomposition has failed ')
logging.error('For a matrix of dimensions: %d' % matrix.shape[0])
logging.debug(err)
......
......@@ -89,7 +89,7 @@ class CO2GriddedStateVector(StateVector):
if 'pco2' in file or 'cov_ocean' in file:
cov_ocn = f.get_variable('CORMAT')
parnr = range(9805,9835)
parnr = list(range(9805,9835))
cov = cov_ocn
elif 'tropic' in file:
cov = f.get_variable('covariance')
......@@ -157,7 +157,7 @@ class CO2GriddedStateVector(StateVector):
dof += np.sum(s) ** 2 / sum(s ** 2)
try:
C = np.linalg.cholesky(matrix)
except np.linalg.linalg.LinAlgError, err:
except np.linalg.linalg.LinAlgError as err:
logging.error('Cholesky decomposition has failed ')
logging.error('For a matrix of dimensions: %d' % matrix.shape[0])
logging.debug(err)
......
......@@ -13,31 +13,28 @@
!!! Info for the CarbonTracker data assimilation system
datadir : /store/empa/em05/parsenov/
datadir : /Storage/CO2/carbontracker/input/ctdas_2016/
! For ObsPack
obspack.input.id : obspack
obspack.input.dir : ${datadir}
!/obspack !/${obspack.input.id}
obs.sites.rc : ${obspack.input.dir}/summary/sites_weights_ctdas.rc
obspack.input.id : obspack_co2_1_GLOBALVIEWplus_v2.1_2016-09-02
obspack.input.dir : ${datadir}/obspacks/${obspack.input.id}
obs.sites.rc : ${obspack.input.dir}/summary/sites_weights_Dec2016.rc
! Using a second ObsPack (from 1 January 2016)
!obspack.input.id2 : obspack_co2_1_NRT_v3.0_2016-06-06
!obspack.input.dir2 : ${datadir}/obspacks/${obspack.input.id2}
!obs.sites.rc2 : ${obspack.input.dir2}/summary/sites_weights_Dec2016.rc
!ocn.covariance : ${datadir}/oceans/oif/cov_ocean.2000.01.nc
!deltaco2.prefix : oif_p3_era40.dpco2
ocn.covariance : ${datadir}/oceans/oif/cov_ocean.2000.01.nc
deltaco2.prefix : oif_p3_era40.dpco2
!bio.cov.dir : ${datadir}/covariances/gridded_NH/
!bio.cov.prefix : cov_ecoregion
bio.cov.dir : ${datadir}/covariances/gridded_NH/
bio.cov.prefix : cov_ecoregion
!regtype : gridded_oif30
nparameters : 11
!random.seed : 4385
regionsfile : /store/empa/em05/parsenov/CTDAS/ctdas-py3/da/analysis/regions_ok.nc
!extendedregionsfile : /store/empa/em05/parsenov/CTDAS/ctdas-py3/da/analysis/regions_ok.nc
!regionsfile : ${datadir}/covariances/gridded_NH/griddedNHparameters.nc
regtype : gridded_oif30
nparameters : 9835
random.seed : 4385
regionsfile : ${datadir}/covariances/gridded_NH/griddedNHparameters.nc
!random.seed.init: ${datadir}/randomseedinit.pickle
! Include a naming scheme for the variables
......
......@@ -5,10 +5,8 @@
#$ 06:30:00
#$ /bin/sh
echo "All output piped to file template.log"
source /usr/local/Modules/3.2.8/init/sh
source /opt/intel/bin/ifortvars.sh intel64
export HOST='daint'
module load python
export icycle_in_job=999
echo "All output piped to file ct_base_test.log"
export HOST='capegrim'
export icycle_in_job=1
python --version
python template.py rc=template.rc -v $1 >& template.log &
......@@ -27,14 +27,13 @@ sys.path.append(os.getcwd())
from da.tools.initexit import start_logger, validate_opts_args, parse_options, CycleControl
from da.tools.pipeline import ensemble_smoother_pipeline, header, footer
from da.platform.capegrim import CapeGrimPlatform
from da.baseclasses.dasystem import DaSystem
from da.baseclasses.statevector import StateVector
from da.carbondioxide.obspack_globalviewplus2 import ObsPackObservations
from da.carbondioxide.optimizer import CO2Optimizer
from da.baseclasses.observationoperator import ObservationOperator
#from da.analysis.expand_fluxes import save_weekly_avg_1x1_data, save_weekly_avg_state_data, save_weekly_avg_tc_data, save_weekly_avg_ext_tc_data
#from da.analysis.expand_molefractions import write_mole_fractions
from da.platform.capegrim import CapeGrimPlatform
from da.baseclasses.dasystem import DaSystem
from da.co2gridded.statevector import CO2GriddedStateVector
from da.carbondioxide.obspack_globalviewplus2 import ObsPackObservations
from da.baseclasses.optimizer import Optimizer
from da.baseclasses.observationoperator import RandomizerObservationOperator
#################################################################################################
......@@ -51,13 +50,12 @@ opts, args = validate_opts_args(opts, args)
dacycle = CycleControl(opts, args)
platform = MaunaloaPlatform()
platform = CapeGrimPlatform()
dasystem = DaSystem(dacycle['da.system.rc'])
obsoperator = ObservationOperator(dacycle['da.obsoperator.rc'])
obsoperator = RandomizerObservationOperator(dacycle['da.obsoperator.rc'])
samples = ObsPackObservations()
statevector = StateVector()
optimizer = CO2Optimizer()
statevector = CO2GriddedStateVector()
optimizer = Optimizer()
##########################################################################################
################### ENTER THE PIPELINE WITH THE OBJECTS PASSED BY THE USER ###############
......
......@@ -28,8 +28,8 @@
!
! The time for which to start and end the data assimilation experiment in format YYYY-MM-DD HH:MM:SS
time.start : 2016-01-01 00:00:00
time.finish : 2016-02-01 00:00:00
time.start : 2012-01-01 00:00:00
time.finish : 2012-02-01 00:00:00
! Whether to restart the CTDAS system from a previous cycle, or to start the sequence fresh. Valid entries are T/F/True/False/TRUE/FALSE
......@@ -37,16 +37,16 @@ time.restart : False
! The length of a cycle is given in days, such that the integer 7 denotes the typically used weekly cycle. Valid entries are integers > 1
time.cycle : 7
time.cycle : 1
! The number of cycles of lag to use for a smoother version of CTDAS. CarbonTracker CO2 typically uses 5 weeks of lag. Valid entries are integers > 0
time.nlag : 3
time.nlag : 2
! The directory under which the code, input, and output will be stored. This is the base directory for a run. The word
! '/' will be replaced through the start_ctdas.sh script by a user-specified folder name. DO NOT REPLACE
dir.da_run : /scratch/snx3000/parsenov/projname
dir.da_run : template
! The resources used to complete the data assimilation experiment. This depends on your computing platform.
! The number of cycles per job denotes how many cycles should be completed before starting a new process or job, this
......
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