tadd several measures for reducing memory footprint - Granular.jl - Julia package for granular dynamics simulation
(HTM) git clone git://src.adamsgaard.dk/Granular.jl
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---
(DIR) commit aaacaf68ad468bebb4cb7024f63d193fa7d3b5f9
(DIR) parent f51076d53050ade8a00bc1216257be807a5df907
(HTM) Author: Anders Damsgaard <andersd@riseup.net>
Date: Fri, 23 Jun 2017 15:04:10 -0400
add several measures for reducing memory footprint
Diffstat:
M src/atmosphere.jl | 16 ++++++++++------
M src/grid.jl | 48 ++++++++++++++++++-------------
M src/icefloe.jl | 53 ++++++++++++++++++++++++++++++
M src/io.jl | 4 ++++
M src/ocean.jl | 14 ++++++++------
5 files changed, 103 insertions(+), 32 deletions(-)
---
(DIR) diff --git a/src/atmosphere.jl b/src/atmosphere.jl
t@@ -163,12 +163,16 @@ function addAtmosphereDrag!(simulation::Simulation)
""")
end
- u_local = bilinearInterpolation(u, x_tilde, y_tilde, i, j, k, 1)
- v_local = bilinearInterpolation(v, x_tilde, y_tilde, i, j, k, 1)
- vel_curl = curl(simulation.atmosphere, x_tilde, y_tilde, i, j, k, 1)
-
- applyAtmosphereDragToIceFloe!(ice_floe, u_local, v_local)
- applyAtmosphereVorticityToIceFloe!(ice_floe, vel_curl)
+ applyAtmosphereDragToIceFloe!(ice_floe,
+ bilinearInterpolation(u,
+ x_tilde, y_tilde,
+ i, j, k, 1),
+ bilinearInterpolation(v,
+ x_tilde, y_tilde,
+ i, j, k, 1))
+ applyAtmosphereVorticityToIceFloe!(ice_floe,
+ curl(simulation.atmosphere,
+ x_tilde, y_tilde, i, j, k, 1))
end
end
(DIR) diff --git a/src/grid.jl b/src/grid.jl
t@@ -21,9 +21,9 @@ function bilinearInterpolation(field::Array{Float64, 4},
k::Int,
it::Int)
- if x_tilde < 0. || x_tilde > 1. || y_tilde < 0. || y_tilde > 1.
- error("relative coordinates outside bounds ($(x_tilde), $(y_tilde))")
- end
+ #if x_tilde < 0. || x_tilde > 1. || y_tilde < 0. || y_tilde > 1.
+ #error("relative coordinates outside bounds ($(x_tilde), $(y_tilde))")
+ #end
return (field[i+1, j+1, k, it]*x_tilde +
field[i, j+1, k, it]*(1. - x_tilde))*y_tilde +
t@@ -86,12 +86,20 @@ Find ice-floe positions in grid, based on their center positions.
"""
function sortIceFloesInGrid!(simulation::Simulation, grid::Any; verbose=false)
- grid.ice_floe_list =
- Array{Array{Int, 1}}(size(grid.xh, 1), size(grid.xh, 2))
- #fill!(grid.ice_floe_list, Int[])
- for i=1:size(grid.xh, 1)
- for j=1:size(grid.xh, 2)
- grid.ice_floe_list[i, j] = Int[]
+ if simulation.time_iteration == 0
+ grid.ice_floe_list =
+ Array{Array{Int, 1}}(size(grid.xh, 1), size(grid.xh, 2))
+
+ for i=1:size(grid.xh, 1)
+ for j=1:size(grid.xh, 2)
+ grid.ice_floe_list[i, j] = Int[]
+ end
+ end
+ else
+ for i=1:size(grid.xh, 1)
+ for j=1:size(grid.xh, 2)
+ empty!(grid.ice_floe_list[i, j])
+ end
end
end
t@@ -146,7 +154,8 @@ function sortIceFloesInGrid!(simulation::Simulation, grid::Any; verbose=false)
if !found
i, j = findCellContainingPoint(grid,
- simulation.ice_floes[idx].lin_pos)
+ simulation.ice_floes[idx].
+ lin_pos)
end
# remove ice floe if it is outside of the grid
t@@ -211,8 +220,7 @@ function getNonDimensionalCellCoordinates(grid::Any, i::Int, j::Int,
point::Array{float, 1})
sw, se, ne, nw = getCellCornerCoordinates(grid.xq, grid.yq, i, j)
- x_tilde, y_tilde = conformalQuadrilateralCoordinates(sw, se, ne, nw, point)
- return [x_tilde, y_tilde]
+ return conformalQuadrilateralCoordinates(sw, se, ne, nw, point)
end
export isPointInCell
t@@ -264,13 +272,13 @@ south-east corner, north-east corner, north-west corner).
* `i::Int`: x-index of cell.
* `j::Int`: y-index of cell.
"""
-function getCellCornerCoordinates(xq::Array{Float64, 2}, yq::Array{Float64, 2},
- i::Int, j::Int)
- sw = [xq[ i, j], yq[ i, j]]
- se = [xq[i+1, j], yq[i+1, j]]
- ne = [xq[i+1, j+1], yq[i+1, j+1]]
- nw = [xq[ i, j+1], yq[ i, j+1]]
- return sw, se, ne, nw
+@inline function getCellCornerCoordinates(xq::Array{Float64, 2},
+ yq::Array{Float64, 2},
+ i::Int, j::Int)
+ return Float64[xq[ i, j], yq[ i, j]],
+ Float64[xq[i+1, j], yq[i+1, j]],
+ Float64[xq[i+1, j+1], yq[i+1, j+1]],
+ Float64[xq[ i, j+1], yq[ i, j+1]]
end
export getCellCenterCoordinates
t@@ -379,7 +387,7 @@ function conformalQuadrilateralCoordinates(A::Array{float, 1},
"alpha = $(alpha), beta = $(beta), gamma = $(gamma), ",
"delta = $(delta), epsilon = $(epsilon), kappa = $(kappa)")
end
- return [x_tilde, y_tilde]
+ return Float64[x_tilde, y_tilde]
end
export findEmptyPositionInGridCell
(DIR) diff --git a/src/icefloe.jl b/src/icefloe.jl
t@@ -317,6 +317,59 @@ function convertIceFloeDataToArrays(simulation::Simulation)
return ifarr
end
+function deleteIceFloeArrays!(ifarr::IceFloeArrays)
+ ifarr.density = 0
+
+ ifarr.thickness = 0
+ ifarr.contact_radius = 0
+ ifarr.areal_radius = 0
+ ifarr.circumreference = 0
+ ifarr.horizontal_surface_area = 0
+ ifarr.side_surface_area = 0
+ ifarr.volume = 0
+ ifarr.mass = 0
+ ifarr.moment_of_inertia = 0
+
+ ifarr.lin_pos = 0
+ ifarr.lin_vel = 0
+ ifarr.lin_acc = 0
+ ifarr.force = 0
+
+ ifarr.ang_pos = 0
+ ifarr.ang_vel = 0
+ ifarr.ang_acc = 0
+ ifarr.torque = 0
+
+ ifarr.fixed = 0
+ ifarr.rotating = 0
+ ifarr.enabled = 0
+
+ ifarr.contact_stiffness_normal = 0
+ ifarr.contact_stiffness_tangential = 0
+ ifarr.contact_viscosity_normal = 0
+ ifarr.contact_viscosity_tangential = 0
+ ifarr.contact_static_friction = 0
+ ifarr.contact_dynamic_friction = 0
+
+ ifarr.youngs_modulus = 0
+ ifarr.poissons_ratio = 0
+ ifarr.tensile_strength = 0
+ ifarr.compressive_strength_prefactor = 0
+
+ ifarr.ocean_drag_coeff_vert = 0
+ ifarr.ocean_drag_coeff_horiz = 0
+ ifarr.atmosphere_drag_coeff_vert = 0
+ ifarr.atmosphere_drag_coeff_horiz = 0
+
+ ifarr.pressure = 0
+ ifarr.n_contacts = 0
+
+ ifarr.granular_stress = 0
+ ifarr.ocean_stress = 0
+ ifarr.atmosphere_stress = 0
+ gc()
+end
+
export printIceFloeInfo
"""
printIceFloeInfo(icefloe::IceFloeCylindrical)
(DIR) diff --git a/src/io.jl b/src/io.jl
t@@ -336,6 +336,10 @@ function writeIceFloeVTK(simulation::Simulation,
WriteVTK.vtk_point_data(vtkfile, ifarr.atmosphere_stress,
"Atmosphere stress [Pa]")
+ deleteIceFloeArrays!(ifarr)
+ ifarr = 0
+ gc()
+
outfiles = WriteVTK.vtk_save(vtkfile)
if verbose
info("Output file: " * outfiles[1])
(DIR) diff --git a/src/ocean.jl b/src/ocean.jl
t@@ -274,12 +274,14 @@ function addOceanDrag!(simulation::Simulation)
""")
end
- u_local = bilinearInterpolation(u, x_tilde, y_tilde, i, j, k, 1)
- v_local = bilinearInterpolation(v, x_tilde, y_tilde, i, j, k, 1)
- vel_curl = curl(simulation.ocean, x_tilde, y_tilde, i, j, k, 1)
-
- applyOceanDragToIceFloe!(ice_floe, u_local, v_local)
- applyOceanVorticityToIceFloe!(ice_floe, vel_curl)
+ applyOceanDragToIceFloe!(ice_floe,
+ bilinearInterpolation(u, x_tilde, y_tilde,
+ i, j, k, 1),
+ bilinearInterpolation(v, x_tilde, y_tilde,
+ i, j, k, 1))
+ applyOceanVorticityToIceFloe!(ice_floe,
+ curl(simulation.ocean, x_tilde, y_tilde,
+ i, j, k, 1))
end
end