first sample script proposed.

DocumentationInterface

+initatmgrid(polygons_in,centre_in,area_in,contfrac_in,neighbours_in,[nbpt,nbseg])
+
+Wrapper for ``initatmgrid``.
+
+Parameters
+----------
+polygons_in : input rank-3 array('f') with bounds (nbpt,2 * nbseg + 1,2)
+centre_in : input rank-2 array('f') with bounds (nbpt,2)
+area_in : input rank-1 array('f') with bounds (nbpt)
+contfrac_in : input rank-1 array('f') with bounds (nbpt)
+neighbours_in : input rank-2 array('i') with bounds (nbpt,2 * nbseg)
+
+Other Parameters
+----------------
+nbpt : input int, optional
+    Default: shape(polygons_in,0)
+nbseg : input int, optional
+    Default: (shape(polygons_in,1)-1)/(2)
+====================================================================
+nbi,nbj,area_bx,trip_bx,basin_bx,topoind_bx,fac_bx,hierarchy_bx,lon_bx,lat_bx,lshead_bx,nwbas = gethydrogrid(nbxmax_in,sub_pts,sub_index,sub_area,max_basins,min_topoind,lon_rel,lat_rel,trip,basins,topoindex,fac,hierarchy,[nbpt,nbvmax_in])
+
+Wrapper for ``gethydrogrid``.
+
+Parameters
+----------
+nbxmax_in : input int
+sub_pts : input rank-1 array('i') with bounds (nbpt)
+sub_index : input rank-3 array('i') with bounds (nbpt,nbvmax_in,2)
+sub_area : input rank-2 array('f') with bounds (nbpt,nbvmax_in)
+max_basins : in/output rank-0 array(float,'f')
+min_topoind : input float
+lon_rel : input rank-2 array('f') with bounds (nbpt,nbvmax_in)
+lat_rel : input rank-2 array('f') with bounds (nbpt,nbvmax_in)
+trip : in/output rank-2 array('f') with bounds (nbpt,nbvmax_in)
+basins : in/output rank-2 array('f') with bounds (nbpt,nbvmax_in)
+topoindex : in/output rank-2 array('f') with bounds (nbpt,nbvmax_in)
+fac : in/output rank-2 array('f') with bounds (nbpt,nbvmax_in)
+hierarchy : in/output rank-2 array('f') with bounds (nbpt,nbvmax_in)
+
+Other Parameters
+----------------
+nbpt : input int, optional
+    Default: len(sub_pts)
+nbvmax_in : input int, optional
+    Default: shape(sub_index,1)
+
+Returns
+-------
+nbi : rank-1 array('i') with bounds (nbpt)
+nbj : rank-1 array('i') with bounds (nbpt)
+area_bx : rank-3 array('f') with bounds (nbpt,nbxmax_in,nbxmax_in)
+trip_bx : rank-3 array('i') with bounds (nbpt,nbxmax_in,nbxmax_in)
+basin_bx : rank-3 array('i') with bounds (nbpt,nbxmax_in,nbxmax_in)
+topoind_bx : rank-3 array('f') with bounds (nbpt,nbxmax_in,nbxmax_in)
+fac_bx : rank-3 array('f') with bounds (nbpt,nbxmax_in,nbxmax_in)
+hierarchy_bx : rank-3 array('f') with bounds (nbpt,nbxmax_in,nbxmax_in)
+lon_bx : rank-3 array('f') with bounds (nbpt,nbxmax_in,nbxmax_in)
+lat_bx : rank-3 array('f') with bounds (nbpt,nbxmax_in,nbxmax_in)
+lshead_bx : rank-3 array('f') with bounds (nbpt,nbxmax_in,nbxmax_in)
+nwbas : int
+====================================================================
+nb_basin,basin_inbxid,basin_outlet,basin_outtp,basin_sz,basin_bxout,basin_bbout,basin_pts,basin_lshead,coast_pts = findbasins(nbvmax_in,nbi,nbj,trip_bx,basin_bx,fac_bx,hierarchy_bx,topoind_bx,lshead_bx,lontmp,lattmp,[nbpt,nbxmax_in])
+
+Wrapper for ``findbasins``.
+
+Parameters
+----------
+nbvmax_in : input int
+nbi : input rank-1 array('i') with bounds (nbpt)
+nbj : input rank-1 array('i') with bounds (nbpt)
+trip_bx : in/output rank-3 array('i') with bounds (nbpt,nbxmax_in,nbxmax_in)
+basin_bx : in/output rank-3 array('i') with bounds (nbpt,nbxmax_in,nbxmax_in)
+fac_bx : input rank-3 array('f') with bounds (nbpt,nbxmax_in,nbxmax_in)
+hierarchy_bx : input rank-3 array('f') with bounds (nbpt,nbxmax_in,nbxmax_in)
+topoind_bx : in/output rank-3 array('f') with bounds (nbpt,nbxmax_in,nbxmax_in)
+lshead_bx : input rank-3 array('f') with bounds (nbpt,nbxmax_in,nbxmax_in)
+lontmp : input rank-3 array('f') with bounds (nbpt,nbxmax_in,nbxmax_in)
+lattmp : input rank-3 array('f') with bounds (nbpt,nbxmax_in,nbxmax_in)
+
+Other Parameters
+----------------
+nbpt : input int, optional
+    Default: len(nbi)
+nbxmax_in : input int, optional
+    Default: shape(trip_bx,1)
+
+Returns
+-------
+nb_basin : rank-1 array('i') with bounds (nbpt)
+basin_inbxid : rank-2 array('i') with bounds (nbpt,nbvmax_in)
+basin_outlet : rank-3 array('f') with bounds (nbpt,nbvmax_in,2)
+basin_outtp : rank-2 array('f') with bounds (nbpt,nbvmax_in)
+basin_sz : rank-2 array('i') with bounds (nbpt,nbvmax_in)
+basin_bxout : rank-2 array('i') with bounds (nbpt,nbvmax_in)
+basin_bbout : rank-2 array('i') with bounds (nbpt,nbvmax_in)
+basin_pts : rank-4 array('i') with bounds (nbpt,nbvmax_in,nbvmax_in,2)
+basin_lshead : rank-2 array('f') with bounds (nbpt,nbvmax_in)
+coast_pts : rank-2 array('i') with bounds (nbpt,nbvmax_in)
+====================================================================
+basin_count,basin_notrun,basin_area,basin_hierarchy,basin_fac,basin_topoind,basin_id,basin_coor,basin_type,basin_flowdir,basin_lshead,outflow_grid,outflow_basin,nbcoastal,coastal_basin = globalize(area_bx,trip_bx,hierarchy_bx,fac_bx,topoind_bx,min_topoind,nb_basin,basin_inbxid,basin_outlet,basin_outtp,basin_sz,basin_pts,basin_bxout,basin_bbout,lshead,coast_pts,nwbas,[nbpt,nbvmax_in,nbxmax_in])
+
+Wrapper for ``globalize``.
+
+Parameters
+----------
+area_bx : input rank-3 array('f') with bounds (nbpt,nbxmax_in,nbxmax_in)
+trip_bx : input rank-3 array('i') with bounds (nbpt,nbxmax_in,nbxmax_in)
+hierarchy_bx : input rank-3 array('f') with bounds (nbpt,nbxmax_in,nbxmax_in)
+fac_bx : input rank-3 array('f') with bounds (nbpt,nbxmax_in,nbxmax_in)
+topoind_bx : input rank-3 array('f') with bounds (nbpt,nbxmax_in,nbxmax_in)
+min_topoind : input float
+nb_basin : input rank-1 array('i') with bounds (nbpt)
+basin_inbxid : input rank-2 array('i') with bounds (nbpt,nbvmax_in)
+basin_outlet : input rank-3 array('f') with bounds (nbpt,nbvmax_in,2)
+basin_outtp : input rank-2 array('f') with bounds (nbpt,nbvmax_in)
+basin_sz : input rank-2 array('i') with bounds (nbpt,nbvmax_in)
+basin_pts : input rank-4 array('i') with bounds (nbpt,nbvmax_in,nbvmax_in,2)
+basin_bxout : input rank-2 array('i') with bounds (nbpt,nbvmax_in)
+basin_bbout : input rank-2 array('i') with bounds (nbpt,nbvmax_in)
+lshead : input rank-2 array('f') with bounds (nbpt,nbvmax_in)
+coast_pts : input rank-2 array('i') with bounds (nbpt,nbvmax_in)
+nwbas : input int
+
+Other Parameters
+----------------
+nbpt : input int, optional
+    Default: shape(area_bx,0)
+nbvmax_in : input int, optional
+    Default: shape(basin_inbxid,1)
+nbxmax_in : input int, optional
+    Default: shape(area_bx,1)
+
+Returns
+-------
+basin_count : rank-1 array('i') with bounds (nbpt)
+basin_notrun : rank-1 array('i') with bounds (nbpt)
+basin_area : rank-2 array('f') with bounds (nbpt,nwbas)
+basin_hierarchy : rank-2 array('f') with bounds (nbpt,nwbas)
+basin_fac : rank-2 array('f') with bounds (nbpt,nwbas)
+basin_topoind : rank-2 array('f') with bounds (nbpt,nwbas)
+basin_id : rank-2 array('i') with bounds (nbpt,nwbas)
+basin_coor : rank-3 array('f') with bounds (nbpt,nwbas,2)
+basin_type : rank-2 array('f') with bounds (nbpt,nwbas)
+basin_flowdir : rank-2 array('i') with bounds (nbpt,nwbas)
+basin_lshead : rank-2 array('f') with bounds (nbpt,nwbas)
+outflow_grid : rank-2 array('i') with bounds (nbpt,nwbas)
+outflow_basin : rank-2 array('i') with bounds (nbpt,nwbas)
+nbcoastal : rank-1 array('i') with bounds (nbpt)
+coastal_basin : rank-2 array('i') with bounds (nbpt,nwbas)
+====================================================================
+inflow_number,inflow_grid,inflow_basin = linkup(nbxmax_in,basin_count,basin_area,basin_id,basin_flowdir,basin_lshead,basin_hierarchy,basin_fac,outflow_grid,outflow_basin,nbcoastal,coastal_basin,invented_basins,[nbpt,nwbas])
+
+Wrapper for ``linkup``.
+
+Parameters
+----------
+nbxmax_in : input int
+basin_count : input rank-1 array('i') with bounds (nbpt)
+basin_area : input rank-2 array('f') with bounds (nbpt,nwbas)
+basin_id : input rank-2 array('i') with bounds (nbpt,nwbas)
+basin_flowdir : input rank-2 array('i') with bounds (nbpt,nwbas)
+basin_lshead : input rank-2 array('f') with bounds (nbpt,nwbas)
+basin_hierarchy : in/output rank-2 array('f') with bounds (nbpt,nwbas)
+basin_fac : input rank-2 array('f') with bounds (nbpt,nwbas)
+outflow_grid : in/output rank-2 array('i') with bounds (nbpt,nwbas)
+outflow_basin : in/output rank-2 array('i') with bounds (nbpt,nwbas)
+nbcoastal : in/output rank-1 array('i') with bounds (nbpt)
+coastal_basin : in/output rank-2 array('i') with bounds (nbpt,nwbas)
+invented_basins : input float
+
+Other Parameters
+----------------
+nbpt : input int, optional
+    Default: len(basin_count)
+nwbas : input int, optional
+    Default: shape(basin_area,1)
+
+Returns
+-------
+inflow_number : rank-2 array('i') with bounds (nbpt,8 * nbxmax_in)
+inflow_grid : rank-3 array('i') with bounds (nbpt,8 * nbxmax_in,8 * nbxmax_in)
+inflow_basin : rank-3 array('i') with bounds (nbpt,8 * nbxmax_in,8 * nbxmax_in)
+====================================================================
+fetch_basin = fetch(basin_count,basin_area,basin_id,basin_hierarchy,basin_fac,outflow_grid,outflow_basin,[nbpt,nwbas])
+
+Wrapper for ``fetch``.
+
+Parameters
+----------
+basin_count : input rank-1 array('i') with bounds (nbpt)
+basin_area : in/output rank-2 array('f') with bounds (nbpt,nwbas)
+basin_id : input rank-2 array('i') with bounds (nbpt,nwbas)
+basin_hierarchy : input rank-2 array('f') with bounds (nbpt,nwbas)
+basin_fac : input rank-2 array('f') with bounds (nbpt,nwbas)
+outflow_grid : in/output rank-2 array('i') with bounds (nbpt,nwbas)
+outflow_basin : input rank-2 array('i') with bounds (nbpt,nwbas)
+
+Other Parameters
+----------------
+nbpt : input int, optional
+    Default: len(basin_count)
+nwbas : input int, optional
+    Default: shape(basin_area,1)
+
+Returns
+-------
+fetch_basin : rank-2 array('f') with bounds (nbpt,nwbas)
+====================================================================
+routing_area,topo_resid,route_togrid,route_tobasin,route_nbintobas,global_basinid,route_outlet,route_type,origin_nbintobas = truncate(nbasmax,basin_count,basin_notrun,basin_area,basin_topoind,fetch_basin,basin_id,basin_coor,basin_type,basin_flowdir,outflow_grid,outflow_basin,inflow_number,inflow_grid,inflow_basin,[nbpt,nbxmax_in,nwbas])
+
+Wrapper for ``truncate``.
+
+Parameters
+----------
+nbasmax : input int
+basin_count : in/output rank-1 array('i') with bounds (nbpt)
+basin_notrun : in/output rank-1 array('i') with bounds (nbpt)
+basin_area : in/output rank-2 array('f') with bounds (nbpt,nwbas)
+basin_topoind : in/output rank-2 array('f') with bounds (nbpt,nwbas)
+fetch_basin : in/output rank-2 array('f') with bounds (nbpt,nwbas)
+basin_id : in/output rank-2 array('i') with bounds (nbpt,nwbas)
+basin_coor : in/output rank-3 array('f') with bounds (nbpt,nwbas,2)
+basin_type : in/output rank-2 array('f') with bounds (nbpt,nwbas)
+basin_flowdir : in/output rank-2 array('i') with bounds (nbpt,nwbas)
+outflow_grid : in/output rank-2 array('i') with bounds (nbpt,nwbas)
+outflow_basin : in/output rank-2 array('i') with bounds (nbpt,nwbas)
+inflow_number : in/output rank-2 array('i') with bounds (nbpt,8 * nbxmax_in)
+inflow_grid : in/output rank-3 array('i') with bounds (nbpt,8 * nbxmax_in,8 * nbxmax_in)
+inflow_basin : in/output rank-3 array('i') with bounds (nbpt,8 * nbxmax_in,8 * nbxmax_in)
+
+Other Parameters
+----------------
+nbpt : input int, optional
+    Default: len(basin_count)
+nbxmax_in : input int, optional
+    Default: (shape(inflow_number,1))/(8)
+nwbas : input int, optional
+    Default: shape(basin_area,1)
+
+Returns
+-------
+routing_area : rank-2 array('f') with bounds (nbpt,nbasmax)
+topo_resid : rank-2 array('f') with bounds (nbpt,nbasmax)
+route_togrid : rank-2 array('i') with bounds (nbpt,nbasmax)
+route_tobasin : rank-2 array('i') with bounds (nbpt,nbasmax)
+route_nbintobas : rank-1 array('i') with bounds (nbpt)
+global_basinid : rank-2 array('i') with bounds (nbpt,nbasmax)
+route_outlet : rank-3 array('f') with bounds (nbpt,nbasmax,2)
+route_type : rank-2 array('f') with bounds (nbpt,nbasmax)
+origin_nbintobas : rank-1 array('i') with bounds (nbpt)

RoutingPreProc.py

@@ -29,7 +29,6 @@ import RPPtools as RPP
 import HydroGrid as HG
 import diagplots as DP
 import Interface as IF
-import savefile
 #
 # Logging in MPI : https://groups.google.com/forum/#!topic/mpi4py/SaNzc8bdj6U
 #

SampleScripts/BuildHTUs.pbs

+#!/bin/bash
+#
+#PBS -N BuildHTUs
+#
+#PBS -j oe
+#PBS -l nodes=1:ppn=42
+#PBS -l walltime=48:00:00
+#PBS -l mem=120gb
+#PBS -l vmem=120gb
+#
+cd ${PBS_O_WORKDIR}/..
+
+cp ./TestConfigs/run.def.05_CS run.def
+#
+# Set the right Python 3 Anaconda environment
+#
+source ./Environment
+#
+# Run the Python code to generate the HTUs and write them into a netCDF file.
+#
+mpirun -n 42 python RoutingPreProc.py
+#
+ls -l

TestConfigs/run.def.05_CS

@@ -18,7 +18,7 @@ nbasmax = 35
 #
 # Output
 #
-GraphFile = test_graph.nc
+GraphFile = EM_WFDEI_test_graph.nc
 #
 # Diagnostics
 # You need to provide an interval in longitude and Latitude.

run.def

+[OverAll]
+#
+#
+EarthRadius = 6370000.
+#
+ModelGridFile = /bdd/MEDI/workspaces/polcher/NewRouting/EM_WFDEI_CRU_2000.nc
+##WEST_EAST = -9.75, 5.25
+##SOUTH_NORTH = 36.1, 44.2
+HydroFile = /bdd/MEDI/workspaces/polcher/NewRouting/routing_MED.nc
+#
+# FORTRAN interface parameters
+#
+Documentation = true
+#
+# Configuration for the graph to be generated
+#
+nbasmax = 35
+#
+# Output
+#
+GraphFile = EM_WFDEI_test_graph.nc
+#
+# Diagnostics
+# You need to provide an interval in longitude and Latitude.
+#
+DiagLon = 39.9, 39.9
+DiagLat = 40.0, 40.0