Performance Comparison

benchmark.f90

! Needs to go into ic.mod.f90 and then be called from default_ic


subroutine ball_of_cells
real*8::r,r_max,phi,theta

	nd = 10000
	nda = nd
	ncels = nd
	ncals = nd

    if (allocated(node)) deallocate(node)
    if (allocated(cels)) deallocate(cels)
    allocate(node(nda),cels(ncals)) 
    call iniarrays

   !******* #2 DEFINING MODEL PARAMETERS *******

    !implementation and initializations
    getot=0
    itacc=0
    nparti=1000
    idum=-11111
    idumoriginal=idum
    realtime=0

    nvarglobal_out=5

    !physical
    temp=1d0 !low value is low temperature	
    desmax=0.01
    resmax=1d-3
    prop_noise=0.0d0
    deltamax=1d-2 ! miguel 14-10-13   
    dmax=1
    screen_radius=0.85d0
    deltamin=1d-2
    khold=1d0
    angletor=0.05

    k_bu=5d0
    ramax=0.35d0
    k_press=0.0d0!5d-1
    m_xwall=0.0d0!0.75 !tooth
    mi_xwall=0d0 !tooth

    ndmax=9d4
    
    !biological
    !functions used
    
    
    ffu=0
     !spring of the ellipse
    ffu(1)=1
    ffu(2)=0 !to quit if there are too many cells
    ffu(3)=0 !screening
    ffu(4)=0 !torsion
    ffu(5)=0 !external signal source
    ffu(6)=0 !buoyancy

    ffu(11)=0 !epithelial node plastic deformation
    ffu(12)=1 !0 dynamic delta, 1 fixed delta
    ffu(13)=0 !neighboring by triangulation
    ffu(14)=1 !physical boundaries (walls)
    ffu(17)=0 !volume conservation (epithelial)
    ffu(22)=1 !0 = noise biased by energies , 1 = unbiased noise
    ffu(24)=0

       do i=1,nd
        node(i)%you=0d0 ; node(i)%adh=5d-1
        node(i)%rep=0d0 ; node(i)%repcel=5d-1
        node(i)%req=0.4d0
        node(i)%reqcr=0.4d0
        node(i)%reqs=0d0
        node(i)%da=0.5d0;
        node(i)%ke=5d0
        node(i)%tor=0d0
        node(i)%stor=0d0
        node(i)%mo=temp
        node(i)%dmo=0
        node(i)%diffe=0d0
        node(i)%khold=0d0
        node(i)%kplast=0d0
        node(i)%kvol=0d0
      end do
    
    !General parameters that depend on node parameters
    rv=2*maxval(node(:)%da)

    node(:)%hold=0


	r_max = (nd/ 0.64)**(1d0/3d0) * 0.4d0;
	do i=1,nd
		cels(i)%nunodes=1
		cels(i)%nodela=1
		allocate(cels(i)%node(1))

		call random_number(a)
		r = r_max * a**(1d0/3d0);
		call random_number(a)
		phi = a * 2d0 * pi;
		call random_number(a)
		theta = acos(2d0 * a - 1);

		node(i)%x=r * sin(theta) * cos(phi)
		node(i)%y=r * sin(theta) * sin(phi)
		node(i)%z=r * cos(theta)

        node(i)%marge=0
		node(i)%tipus=3
		cels(i)%node(1)=i
		node(i)%icel=i
		node(i)%altre=0

		cels(i)%ctipus=3
		cels(i)%cex=node(i)%x;cels(i)%cey=node(i)%y;cels(i)%cez=node(i)%z

	end do
   !******* #3 DEFINING CELL PARAMETERS *******
      do i=1,ncels
        cels(i)%fase=0d0
        mmae=node(cels(i)%node(1))%req
        cels(i)%minsize_for_div=cels(i)%nunodes*2
        cels(i)%maxsize_for_div=10000 !>>> Is 5-2-14
      end do

    do i=1,ncels !cells start with at random points of the cell cycle, so the divisions are not synchronous
      !if(i<=7.or.(i>ncelsepi.and.i<=ncelsepi+7))then
        call random_number(a)
        cels(i)%fase=a
      !end if
    end do
    
   !******* #4 DEFINING GENETIC PARAMETERS *******
    !Number of genes
    ng=1
    call initiate_gene
    !Gene parameters
      !gen(:)%kindof= ; gen(:)%diffu= ; gen(:)%mu=

      gen(1)%kindof=1 ; gen(1)%diffu=0d0 ; gen(1)%mu=0d0 ;gen(1)%name="does nothing"

    call update_npag


    node(:)%talone=0.0d0

end subroutine

performance.ipynb

springs.cu

// Integrate N-body problem with limited range springs between all bodies
#include "../include/dtypes.cuh"
#include "../include/inits.cuh"
#include "../include/solvers.cuh"
#include "../include/vtk.cuh"


const auto L_0 = 0.75f;  // Relaxed spring length
const auto n_cells = 1000;
const auto n_time_steps = 600u;  // Half of Chaste, because 2nd order
const auto dt = 0.001f;


__device__ float3 spring(float3 Xi, float3 r, float dist, int i, int j)
{
    float3 dF{0};
    if (i == j) return dF;

    if (dist > 1) return dF;

    dF = r * (L_0 - dist) / dist;
    return dF;
}


int main(int argc, const char* argv[])
{
    // Prepare initial state
    Solution<float3, Grid_solver> bolls{n_cells};
    random_sphere(L_0, bolls);

    // Integrate positions
    Vtk_output output("performance");
    for (auto time_step = 0; time_step <= n_time_steps; time_step++) {
        bolls.copy_to_host();
        bolls.take_step<spring, friction_on_background>(dt);
        output.write_positions(bolls);
    }

    return 0;
}

TestPerformance.hpp

/*

Copyright (c) 2017, European Molecular Biology Laboratory.
Copyright (c) 2005-2017, University of Oxford.
All rights reserved.

University of Oxford means the Chancellor, Masters and Scholars of the
University of Oxford, having an administrative office at Wellington
Square, Oxford OX1 2JD, UK.

This file is part of Chaste.

Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
 * Redistributions of source code must retain the above copyright notice,
   this list of conditions and the following disclaimer.
 * Redistributions in binary form must reproduce the above copyright notice,
   this list of conditions and the following disclaimer in the documentation
   and/or other materials provided with the distribution.
 * Neither the name of the University of Oxford nor the names of its
   contributors may be used to endorse or promote products derived from this
   software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

*/
#pragma once

#include <cxxtest/TestSuite.h>
#include "CheckpointArchiveTypes.hpp"

#include "AbstractCellBasedTestSuite.hpp"
#include "CellsGenerator.hpp"
#include "GeneralisedLinearSpringForce.hpp"
#include "HoneycombMeshGenerator.hpp"
#include "NodeBasedCellPopulation.hpp"
#include "NodesOnlyMesh.hpp"
#include "OffLatticeSimulation.hpp"
#include "SmartPointers.hpp"
#include "SphereGeometryBoundaryCondition.hpp"
#include "TransitCellProliferativeType.hpp"
#include "UniformCellCycleModel.hpp"
#include "PetscSetupAndFinalize.hpp"

#include "AbstractSimpleGenerationalCellCycleModel.hpp"

class TestPerformance : public AbstractCellBasedTestSuite
{
public:
    void TestSpheroid()
    {
        EXIT_IF_PARALLEL;

        // Prepare initial state
        auto t_0 = time(NULL);

        auto n_cells = 100;
        auto dist_to_nb = 0.75;
        auto r_max = pow(n_cells / 0.64, 1. / 3) * dist_to_nb / 2;
        std::vector<Node<3>*> nodes;
        for (auto i = 0; i < n_cells; i++)
        {
            auto r = r_max * pow(rand() / (RAND_MAX + 1.), 1. / 3);
            auto phi = rand() / (RAND_MAX + 1.) * 2 * M_PI;
            auto theta = acos(2. * rand() / (RAND_MAX + 1.) - 1);
            nodes.push_back(new Node<3>(i, false, r * sin(theta) * cos(phi),
                                        r * sin(theta) * sin(phi), r * cos(theta)));
        }

        NodesOnlyMesh<3> mesh;
        mesh.ConstructNodesWithoutMesh(nodes, 1.0); // Distance cut-off
        std::vector<CellPtr> cells;
        MAKE_PTR(TransitCellProliferativeType, p_transit_type);
        CellsGenerator<UniformCellCycleModel, 3> cells_generator;
        cells_generator.GenerateBasicRandom(cells, mesh.GetNumNodes(), p_transit_type);
        NodeBasedCellPopulation<3> cell_population(mesh, cells);

        // Setup simulation
        OffLatticeSimulation<3> simulator(cell_population);
        simulator.SetOutputDirectory("TestPerformance");
        simulator.SetSamplingTimestepMultiple(100); // Writes twelve timesteps
        simulator.SetEndTime(10.0);
        simulator.SetNoBirth(true);

        MAKE_PTR(GeneralisedLinearSpringForce<3>, p_force);
        p_force->SetMeinekeDivisionRestingSpringLength(0.75);
        simulator.AddForce(p_force);

        // Run simulation
        simulator.Solve();

        auto t_f = time(NULL);
        auto duration = t_f - t_0;
        if (duration < 60)
            std::cout << duration << " seconds";
        else if (duration < 60 * 60)
            std::cout << duration / 60 << "m " << duration % 60 << "s";
        else
            std::cout << duration / 60 / 60 << "h " << duration % 60 * 60 << "m";
        std::cout << " taken." << std::endl;

        std::cout << "Timestep: " << simulator.GetDt() << std::endl; // Is 0.00833333
    }
};