report of the cemracs project hpc- ilbios: understanding...

OLGA ASSAINOVA / XAVIER PORTELL

Report of the CEMRACS project HPC-IlBios: understanding the best HPC strategy for the IlBioS approach.Olga Assainova*, Xavier Portell**

CEMRACS 2016. Numerical challenges in parallel scientific computing

August 19, 2016, Marseille

**UMR ECOSYS, AgroParisTech, INRA, Université Paris-SaclayF-78850 Thiverval-Grignon, France.E-mail: [email protected]

*Université de BourgogneFaculté des Sciences Mirande9 avenue Alain SavaryBP 47870 21078 Dijon CedexE-mail: [email protected]

mailto:[email protected]

mailto:[email protected]

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SUMMARY

Introduction and background

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An overview of StarPU

Model versions produced in CEMRACS

4 Pending work

Introduction and background_01

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The CO2 and N2O as main GHG


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Riebbek (2011)

An important part of the CO2 emissions are due to the activity of the soil microorganisms


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0,03 % of the total GHG emissions but with a 300-fold greater potential for global warming (Thomson et al 2012)

Hu et al (2015)

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The soil matrix

The soil matrix

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The complex geometry of the pore space can now be characterized to a high level of detail and quantify its connectivity and topology

characterized.

X-ray Computed Tomography

The soil matrix

The morphology of the soil matrix affects microbial activity and the gas emissions dynamics to the atmosphere

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1 Compute-aided Detection - Fluorescence In Situ Hybridization

CAD-FISH1

Imaging of thin soil sections

Microorganisms in soil tend to be found in microcolonies, this means that “identical organisms” will face different microhabitat

conditions

The individuality of the microorganisms plays a role

The soil matrix

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Mass transport processes modelling in soil

Mass transport processes modelling in soil

.0‹N°›Mass transport processes modelling in soil

Lattice-Boltzmann modelling Fluid Node (D3Q19)

Solid Sites

Solid Sites

From: www.egr.msu.edu/ ~kutay/Lbsite/

.0‹N°›Mass transport processes modelling in soil

Lattice-Boltzmann modelling

Solid Sites

Solid Sites


AdvantageComplex pore space geometry easy

to handleIssues

Computationally demanding, but easy to parallelize (GPU or

accelerators)

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IlBioS conceptualization and description


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The model ILBioS is built coupling an Individual-based Model of the soil bacteria to a lattice-Boltzmann

model simulating the fluid dynamics and mass transport processes of soluble substrates


.0‹N°›Model conceptualization and description

Lattice-Boltzmann Nodes

Three dimensional lattice-Boltzmann (D3Q7)



Connected Lattice-Boltzmann Nodes



Fluid nodes

Solid nodes

Dissolved Organic Carbon (DOC)



Fluid nodes

Boundary Solid nodes

Solid nodes

Boundary Fluid nodes



Particulate Organic Matter:

Soil bacteria:

Uptake DOC from the boundary fluid nodes.

Release DOC to the boundary fluid nodes.



mj mass of the POM agent.

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mi mass of the bacterium

Model conceptualization and description


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Computing time requirements: antecedents

Computing time requirements: antecedents

.0‹N°›Computing time requirements: antecedents

Computing time requirements of lBioS❑3D CT image of 2003 nodes.❑10% of porosity.❑10 bacterial nodes.❑5 to 15 POM nodes.❑DOC as a single soluble lattice-Boltzmann substrate.❑Single desktop computer.

25 hours of processing time.

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Model complexity of upcoming IlBioS models

Model complexity of upcoming IlBioS models

.0‹N°›Model complexity of upcoming IlBioS models

Microbial regulation of the terrestrial Nitrous oxide formation (Hu et al., 2015)

106 – 109 bacteria / gram of soil


Initial (minimal) conceptualization of a multispecies IbM to reproduce CO2 and N2O flow in natural samples

NH3/NH4 NO2 /NO3

N2O

Denitrifying heterotroph(CO2 producing, aerobic (O2) and anaerobic (NO2)

respiration)

Nitrifying autotroph (Aerobic, CO2 consuming)


Initial (minimal) conceptualization of a multispecies IbM to reproduce CO2 and N2O flow in natural samples

CO2, O2, DOC, NH4, NO2/ NO3, N2O

Required lattice-Boltzmann substrates in the minimal system:

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Future computing time requirements

Future computing time requirements

.0‹N°›Future computing time requirements

Computing time requirements of llBioS❑3D CT image of 2003 nodes.❑10 % of porosity.❑1 000 000 bacterial nodes❑5 to 25 POM nodes.❑O2, DOC, NH4, NO2/ NO3

125-150 hours of processing time.

In any case, a non practical amount of time to perform

simulation experiments

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Parallelisation strategy of HPC-IlBioS


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Tiling of the data in subdomains

StarPU

CPU functions


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StarPU

100 xSpeed up for lattice-Boltzmann models using GPU

(Banari et al., 2014)

CUDA functions

CPU functions


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MPIStarPU

CUDA functions

CPU functions

CUDA functions

CPU functions

CUDA functions

CPU functions

Future need of increasing the resolution of the 3D CT images


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SUMMARY


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4 Pending work

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StarPU Introduction

StarPU Introduction

.0‹N°›StarPU Introduction

The basics of StarPU syntax and tools

❑Codelet❑Task❑Buffer❑Handle❑CPU/CUDA functions


StarPU preparation task routine

Registration of the data starpu_init(NULL);

starpu_data_handle_t f_handle; starpu_data_handle_t fn_handle;

starpu_vector_data_register(&ToV_handle, STARPU_MAIN_RAM, (uintptr_t)ToV, nsite, sizeof(ToV[0]));

starpu_matrix_data_register(&f_handle, STARPU_MAIN_RAM, (uintptr_t)f, Q, Q, nsite, sizeof(f[0][0]));

..=>

starpu_data_unregister(f_handle); starpu_data_unregister(f_handle); starpu_shutdown();


StarPU preparation task routine

Codelet

struct starpu_codelet bounceback_codelet = { .cpu_funcs = { bounceback_spu }, .cpu_funcs_name = {"bounceback_spu"}, .nbuffers = 2,

.modes = { R, RW } };

Task insert starpu_task_insert(&bounceback_codelet, STARPU_R, ToV_handle, STARPU_RW, f_handle, STARPU_VALUE, &SbD, sizeof(unsigned int), STARPU_VALUE, &nfluidsite, sizeof(unsigned long), STARPU_VALUE, &nsite, sizeof(unsigned long),

STARPU_VALUE, &Q, sizeof(int), 0);

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void bounceback_spu(void *buffers[], void *cl_arg){

unsigned int SubD=0; unsigned long nfluidsite=0; unsigned long nsite=0; int Q=0;

/* Unpacking arguments to their local copy */ starpu_codelet_unpack_args(cl_arg, &SubD,&nfluidsite, &nsite,&Q);

/* Unpacking buffers to to their local copy */ struct starpu_vector_interface *ToV_v =(struct starpu_vector_interface *) buffers[0]; unsigned long* ToV = (unsigned long *)STARPU_VECTOR_GET_PTR(ToV_v);

struct starpu_matrix_interface **f_m =(struct starpu_matrix_interface **) buffers[1]; double **f= (double **) STARPU_MATRIX_GET_PTR(f_m);

/* Beginning of the computations */ register unsigned long ns; for(ns=nfluidsite;ns<nsite;ns++){ if (SubD!=ToV[ns]) continue; /*Skipping computation of LB Nodes not in the current sub domain*/ register int q; for(q=0;q<Q;q++){ f[q][ns]=0.; } } } // end of bounceback_step_spu() function

StarPUexecutivefunction

StarPU Introduction

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void bounceback_spu(void *buffers[], void *cl_arg){

unsigned int SubD=0; unsigned long nfluidsite=0; unsigned long nsite=0; int Q=0;

/* Unpacking arguments to their local copy */ starpu_codelet_unpack_args(cl_arg, &SubD,&nfluidsite, &nsite,&Q);

/* Unpacking buffers to to their local copy */ struct starpu_vector_interface *ToV_v =(struct starpu_vector_interface *) buffers[0]; unsigned long* ToV = (unsigned long *)STARPU_VECTOR_GET_PTR(ToV_v);

struct starpu_matrix_interface **f_m =(struct starpu_matrix_interface **) buffers[1]; double **f= (double **) STARPU_MATRIX_GET_PTR(f_m);

/* Beginning of the computations */ register unsigned long ns; for(ns=nfluidsite;ns<nsite;ns++){ if (SubD!=ToV[ns]) continue; /*Skipping computation of LB Nodes not in the current sub domain*/ register int q; for(q=0;q<Q;q++){ f[q][ns]=0.; } } } // end of bounceback_step_spu() function

StarPU Introduction

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SUMMARY


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4 Pending work

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ILBios

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Spatial cells (LB Nodes)

NBULK

• Water (DOC) • Air • Solid • (agents)

NBOUND NBOUNDS

0 (NX*NY*NZ)-1LBNode

nfluidsites

Bacteria (many individuals/node)

POM

ILBios

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ILBios

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Typedef struct BiologicalAgent { unsigned long Who; /* ID of the individual */ unsigned long LBNode; /* lattice-Boltzmann Node */ double Mass; double Active_Fraction; double Respired_CO2; /* technical variable */

} type_bacteria;

Vector holding the individual bacteria properties

General workflow of the model IlBioS

ILBios

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Typedef struct POMAgent { unsigned long pWho; /* ID */ unsigned long pLBNode; /* lattice-Boltzmann Node */ double pMass; int pFluidNeigh; /* Number of fluid neighbors */ unsigned long *pFluidNeighID; /* technical variable */

} type_POM;

Vector holding the POM properties

ILBios

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Initialization of the DOC = population Boltzmann

Solid Sites

Solid Sites


ILBios

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Initialization of the DOC = population Boltzmann Fluid Node (D3Q19)

Solid Sites

Solid Sites


ILBios

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double *rho = (double *) calloc(nsite, sizeof(double));

Fluid Node (D3Q19)

Solid Sites

Solid Sites


double **f = (double **) calloc(Q, sizeof(double*)); for (q = 0; q < Q; q++) { f[q] = (double *) calloc(nsite, sizeof (double)); }

Initialization of the DOC = population Boltzmann

ILBios

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Time step (TS) or main loop

ILBios

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The State of the bacterial and POM agents and the global out-fluxes are stored in

appropriate data arrays every sampling time.

ILBios

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ILBios

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Mass of DOC particles moving in the unitary directions

D2Q5

ILBios

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ILBios

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The mass of DOC particles is propagated to the neighbors

ILBios

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Solid nodes

ILBios

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The DOC particles bounce back on the solid nodes directions

Solid nodes

ILBios

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ILBios

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Increase the DOC content of all fluid neighbors

ILBios

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Decreases the DOC content of the LBNode

ILBios

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Writing the sampled output in files.

ILBios

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ILBios

ILBios SbD

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ILBios

ILBios SbD

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3 4

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ILBios

ILBios SbD

ILBios SPU

One task for every function in the time step loop

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for(t=0;t<TMAX+1;t++) { ..=> starpu_task_insert(&POM_agents_loop_codelet, STARPU_R, tw_handle, STARPU_W, rho_handle, STARPU_RW, f_handle, STARPU_RW, POMPopul_handle, STARPU_VALUE, &POM_ts, sizeof(unsigned long), STARPU_VALUE, &Q, sizeof(int), STARPU_VALUE, &Q2, sizeof(int), STARPU_VALUE, &KPOM, sizeof(double), STARPU_VALUE, &MIN_POS_DBL, sizeof(double), 0);

Examplesofthecodelet

starpu_task_insert(&propagation_codelet, STARPU_R, neighbour_handle, STARPU_RW, f_handle, STARPU_VALUE, &Q, sizeof(int), STARPU_VALUE, &nfluidsite, sizeof(unsigned long), STARPU_VALUE, &nsite, sizeof(unsigned long), 0);

}

ILBios

ILBios SbD

ILBios SPU

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ILBios

ILBios SbD

ILBios SPU One task for every function and many tasks for collision function

HPC-ILBios (collision)

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for(int step=0; step<PARTS; step++) { struct starpu_task *task = starpu_task_create(); task->cl = &collision_vSubD_codelet;

task->handles[0] = ToV_handle; task->handles[1] = rho_handle; task->handles[2] = uw_handle; task->handles[3] = c_handle; task->handles[4] = twstar_handle; task->handles[5] = jo2_handle; task->handles[6] = jo_q_handle; task->handles[7] = f_handle; task->handles[8] = j_q_handle; task->handles[9] = evenf_handle; task->handles[10] = oddf_handle; task->handles[11] = fn_handle; // The only one changing parameter param.min = min; param.lenth =lenth; task->cl_arg = &param; task->cl_arg_size = sizeof(param); task->synchronous = 1; ret =starpu_task_submit(task)

}

ILBios

ILBios SbD

ILBios SPU

HPC-ILBios (collision)

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SUMMARY


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4 Pending work

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Domaindecompositionapproach

❑ Partial domain decompositionof the liquid parts of the cub❑Implementing MPI

R1

R2

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Thank you very much for your attention.

But, before we finish …

A big thanks to all people that has helped us !!

Alexandre Ancel

Herbert Oberlin

David Coulette

Philippe Helluy and all SCHNAPS members

Matthieu Boileau

Laura Grigori

Camile Coti

report of the cemracs project hpc- ilbios: understanding...

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