Local changes

.gitignore

@@ -11,3 +11,7 @@ slurm-*.out
 *~
 *.log
 .env
+# HON only
+config.yml
+config.aws.yml
+src/utilities/download_files.py

config.yml

@@ -2,23 +2,31 @@
 ## Documentation @ https://imi.readthedocs.io/en/latest/getting-started/imi-config-file.html
 
 ## General
-RunName: "Test_Permian_1week"
-Species: "CH4"
-isAWS: true
-SchedulerType: "slurm"
-SafeMode: true
+RunName: "Test_ICI_Global"
+Species: "CO2"
+isAWS: false
+SchedulerType: "PBS"
+SafeMode: false
 S3Upload: false
 
 ## Period of interest
-StartDate: 20180501
-EndDate: 20180508
+StartDate: 20221001
+EndDate: 20221003
 SpinupMonths: 1
 
-## Use blended TROPOMI+GOSAT data (true)? Or use operational TROPOMI data (false)?
-BlendedTROPOMI: false
+## What satellite data product should be used? Current options are: 
+##     "BlendedTROPOMI"  : The dataset generated by Balasus et al. in which
+##                         the TROPOMI data are fit to GOSAT data using ML
+##     "TROPOMI"         : The operational TROPOMI data
+##     "Other"           : Any other dataset
+## Currently, only "BlendedTROPOMI" and "TROPOMI" are supported on AWS. If 
+## "Other" is selected, the user must specify the path where observations are
+## located under "Advanced settings" in this file.
+SatelliteProduct: "Other"
+# BlendedTROPOMI: false
 
 ## Is this a regional inversion? Set to false for global inversion
-isRegional: true
+isRegional: false
 
 ## Select two character region ID (for using pre-cropped meteorological fields)
 ##   Current options are listed below with ([lat],[lon]) bounds:
@@ -32,15 +40,15 @@ isRegional: true
 ##     "SA" : South America ([-59,16], [-88,-31])
 ##     ""   : Use for global global simulation or custom regions
 ##   For example, if the region of interest is in Europe ([33,61],[-30,70]), select "EU".
-RegionID: "NA"
+RegionID: ""
 
 ## Region of interest
 ##   These lat/lon bounds are only used if CreateAutomaticRectilinearStateVectorFile: true
 ##   Otherwise lat/lon bounds are determined from StateVectorFile
-LonMin: -105
-LonMax: -103
-LatMin: 31
-LatMax: 33
+LonMin: -102.5
+LonMax: -87.5
+LatMin: 16
+LatMax: 24
 
 ## Kalman filter options
 KalmanMode: false
@@ -49,11 +57,11 @@ NudgeFactor: 0.1
 
 ## State vector
 CreateAutomaticRectilinearStateVectorFile: true
-nBufferClusters: 8
-BufferDeg: 5
+nBufferClusters: 
+BufferDeg: 0
+OptimizeBCs: false
 LandThreshold: 0.25
 OffshoreEmisThreshold: 0
-OptimizeBCs: false
 OptimizeOH: false
 
 ## Point source datasets
@@ -69,8 +77,8 @@ ForcedNativeResolutionElements:
   - [31.5, -104]
 
 ## Custom state vector
-StateVectorFile: "/home/ubuntu/integrated_methane_inversion/resources/statevectors/StateVector.nc"
-ShapeFile: "/home/ubuntu/integrated_methane_inversion/resources/shapefiles/PermianBasin_Extent_201712.shp"
+StateVectorFile: "/path/to/StateVector.nc"
+ShapeFile: "None"
 
 ## Inversion
 ## Note PriorError and PriorErrorOH are relative fractions (e.g. 0.5 = 50%)
@@ -84,25 +92,25 @@ PrecomputedJacobian: false
 
 ## Grid
 ##   Options are 0.25x0.3125 (GEOSFP only), 0.5x0.625, 2.0x2.5, or 4.0x5.0
-Res: "0.25x0.3125"
+Res: "2.0x2.5"
 
 ## Meteorology
 ##   Options are GEOSFP or MERRA2
-Met: "GEOSFP"
+Met: "MERRA2"
 
 ## Setup modules
 ##   Turn on/off different steps in setting up the inversion 
 SetupTemplateRundir: true
-SetupSpinupRun: false
-SetupJacobianRuns: false
+SetupSpinupRun: true
+SetupJacobianRuns: true
 SetupInversion: false
 SetupPosteriorRun: false
 
 ## Run modules
 ##   Turn on/off different steps in performing the inversion
-RunSetup: true
-DoSpinup: false
-DoJacobian: false
+RunSetup: false
+DoSpinup: true
+DoJacobian: true
 DoInversion: false
 DoPosterior: false
 
@@ -113,14 +121,14 @@ DOFSThreshold: 0
 
 ## Resource allocation settings for slurm jobs
 SimulationCPUs: 32
-SimulationMemory: 32000
+SimulationMemory: "32gb"
 JacobianCPUs: 1
 JacobianMemory: 2000
-RequestedTime: "0-24:00"
+RequestedTime: "01:00:00"
 SchedulerPartition: "debug"
 
 ## Max number of simultaneous Jacobian runs from the job array (-1: no limit)
-MaxSimultaneousRuns: -1
+MaxSimultaneousRuns: 50
 
 ##====================================================================
 ##
@@ -151,7 +159,7 @@ UseOHSF: false
 ## Save out hourly diagnostics from GEOS-Chem?
 ## For use in satellite operators via post-processing -- required for TROPOMI
 ## inversions
-HourlyCH4: true
+HourlySpecies: true
 
 ## Turn on planeflight diagnostic in GEOS-Chem?
 ## For use in comparing GEOS-Chem against planeflight data. The path
@@ -165,38 +173,48 @@ GOSAT: false
 TCCON: false
 AIRS: false
 
+## Use global boundary condition files for initial conditions
+UseBCsForRestart: False
+
 ##------------------------------------------------------------------
 ## Settings for running on local cluster
 ##------------------------------------------------------------------
 
 ## Path for IMI runs and output
-OutputPath: "/home/ubuntu/imi_output_dir"
+OutputPath: "/nobackupp27/$USER/IMI_demo"
 
 ## Path to GEOS-Chem input data
-DataPath: "/home/ubuntu/ExtData"
+DataPath: "/nobackupp27/$USER/ExtData"
+
+## Path to satellite data
+# DataPathObs: "/nobackup/$USER/CO2_inversion/observations/OCO-2"
+DataPathObs: "/nobackupp27/$USER/IMI_demo/data_TROPOMI"
+
+## GEOS-Chem environment file (with fortran compiler, netcdf libraries, etc.)
+##   NOTE: Copy your own file in the envs/ directory within the IMI
+GEOSChemEnv: "envs/NASA-Pleiades/gcclassic.pleiades.env"
 
-## Conda environment file
-PythonEnv: "/home/ubuntu/integrated_methane_inversion/envs/aws/python.env"
+## Python environment file (this is normally one or two lines)
+PythonEnv: "envs/NASA-Pleiades/python.env"
 
 ## Download initial restart file from AWS S3?
-##  NOTE: Must have AWS CLI enabled
-RestartDownload: true
+##   NOTE: Must have AWS CLI enabled
+RestartDownload: false
 
 ## Path to initial GEOS-Chem restart file + prefix
 ##   ("YYYYMMDD_0000z.nc4" will be appended)
-RestartFilePrefix: "/home/ubuntu/ExtData/BoundaryConditions/GEOSChem.BoundaryConditions."
-RestartFilePreviewPrefix: "/home/ubuntu/ExtData/BoundaryConditions/GEOSChem.BoundaryConditions."
+RestartFilePrefix: "/nobackup/$USER/CO2_inversion/restart_"
+RestartFilePreviewPrefix: "/nobackup/$USER/CO2_inversion/restart_"
 
 ## Path to GEOS-Chem boundary condition files (for regional simulations)
 ## BCversion will be appended to the end of this path. ${BCpath}/${BCversion}
-BCpath: "/home/ubuntu/ExtData/BoundaryConditions"
-BCversion: "v2023-06"
+BCpath: "/nobackup/$USER"
+BCversion: "v2023-10"
 
 ## Options to download missing GEOS-Chem input data from AWS S3
-##   NOTE: You will be charged if your ec2 instance is not in the
-##         us-east-1 region.
-PreviewDryRun: true
-SpinupDryrun: true
-ProductionDryRun: true
-PosteriorDryRun: true
-BCdryrun: true
+##   NOTE: Must have AWS CLI enabled
+PreviewDryRun: false
+SpinupDryrun: false
+ProductionDryRun: false
+PosteriorDryRun: false
+BCdryrun: false