ESMPy_memory_layout

ESMPy_memory_layout.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "collapsed": true
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   "source": [
    "import numpy as np\n",
    "import ESMF"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "Nlon, Nlat = 6001, 4001 # make a large grid"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "lon = np.linspace(-120, 120, Nlon)\n",
    "lat = np.linspace(-60, 60, Nlat)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "lons, lats = np.meshgrid(lon, lat) # don't use indexing='ij'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(4001, 6001)"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "lons.shape # (Nlat, Nlon), typical C-ordering"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "  C_CONTIGUOUS : True\n",
       "  F_CONTIGUOUS : False\n",
       "  OWNDATA : True\n",
       "  WRITEABLE : True\n",
       "  ALIGNED : True\n",
       "  UPDATEIFCOPY : False"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "lons.flags # C-ordering"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Inefficient memory layout"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [],
   "source": [
    "grid = ESMF.Grid(np.array(lons.shape), \n",
    "                 staggerloc = ESMF.StaggerLoc.CENTER,\n",
    "                 coord_sys = ESMF.CoordSys.SPH_DEG)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [],
   "source": [
    "lon_pointer = grid.get_coords(coord_dim=0, \n",
    "                              staggerloc=ESMF.StaggerLoc.CENTER)\n",
    "lat_pointer = grid.get_coords(coord_dim=1, \n",
    "                              staggerloc=ESMF.StaggerLoc.CENTER)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(4001, 6001)"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "lon_pointer.shape"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "  C_CONTIGUOUS : False\n",
       "  F_CONTIGUOUS : True\n",
       "  OWNDATA : False\n",
       "  WRITEABLE : True\n",
       "  ALIGNED : True\n",
       "  UPDATEIFCOPY : False"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "lon_pointer.flags # Fortran-ordering"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CPU times: user 480 ms, sys: 0 ns, total: 480 ms\n",
      "Wall time: 475 ms\n"
     ]
    }
   ],
   "source": [
    "# passing C-ordered array to F-ordered array is slow\n",
    "%time lon_pointer[:] = lons "
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Efficient memory layout"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "grid_T = ESMF.Grid(np.array(lons.T.shape), \n",
    "                  staggerloc = ESMF.StaggerLoc.CENTER,\n",
    "                  coord_sys = ESMF.CoordSys.SPH_DEG)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "lon_T_pointer = grid_T.get_coords(coord_dim=0, \n",
    "                              staggerloc=ESMF.StaggerLoc.CENTER)\n",
    "lat_T_pointer = grid_T.get_coords(coord_dim=1, \n",
    "                              staggerloc=ESMF.StaggerLoc.CENTER)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(6001, 4001)"
      ]
     },
     "execution_count": 14,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "lon_T_pointer.shape"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "  C_CONTIGUOUS : False\n",
       "  F_CONTIGUOUS : True\n",
       "  OWNDATA : False\n",
       "  WRITEABLE : True\n",
       "  ALIGNED : True\n",
       "  UPDATEIFCOPY : False"
      ]
     },
     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "lons.T.flags # Fortran-ordering"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CPU times: user 40 ms, sys: 0 ns, total: 40 ms\n",
      "Wall time: 40.9 ms\n"
     ]
    }
   ],
   "source": [
    "# passing F-ordered array to F-ordered array is fast\n",
    "%time lon_T_pointer[...] = lons.T "
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Mathematically, this is equivalent to using `indexing='ij'` at the beginning. For memory efficiency we should first create a normal, C-ordered numpy array and pass its transpose (which is F-ordered) to ESMPy."
   ]
  }
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