Download - DSD-INT 2016 The new parallel Krylov Solver package - Verkaik

The new Parallel Krylov Solver package

Jarno Verkaik (Deltares)

Joseph Hughes (USGS)

Edwin Sutanudjaja (UU)

Oliver Schmitz (UU)

Paul van Walsum (Alterra WUR)

Raju Ram (TUD)

1 November, 2016

Contents

• Problem statement and solution

• Short overview of (related) developments

• Concept of domain decomposition

• (Preliminary) results

• Practical usage with iMOD

Cartesius: the Dutch supercomputer

Problem statement and solution

Problem statement:

• In order to support decision makers in solving hydrological problems,

detailed high resolution models are often needed.

• These models typically consist of a large number of computational cells

and have large memory requirements and long run times.

Solution:

• An efficient technique for obtaining realistic run times and memory

requirements is parallel computing, where the problem is divided over

multiple processor cores.

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Short overview of developments

2010 ----- Deltares develops parallel MT3DMS using Message Passing Interface.

2012 ----- USGS develops parallel U(nstructured)PCG-solver using OpenMP.

2013 ----- Deltares & USGS start working on new Parallel Krylov Solver package

for MODFLOW-2005 based on UPCG (hybrid, combined MPI/OpenMP).

2013 ----- USGS releases MODFLOW-USG (UnStructured Grid) that includes the

PCGU-solver, a derivative solver of UPCG.

2015 ----- Deltares incorporates PKS in MODFLOW-USG. Cases: Indonesia and global.

2016 ----- Deltares incorporates PKS in iMODFLOW, together with Alterra for

MetaSWAP. Main case: Netherlands Hydrological Model.

2017 ----- Deltares releases iMODFLOW with PKS.

2017 ----- Deltares incorporates PKS in iMOD-SEAWAT. Cases: fresh-salt global Deltas.

(2017+---- Deltares & USGS incorporate PKS in new MODFLOW-6.)

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• Distribute the memory over multiple

(connected) processor cores.

• For this, partitionize the MODFLOW grid:

• iMODFLOW: uniform blocks,

Recursive Coordinate Bisection

• MODFLOW-USG: METIS library

Concept of domain decomposition (1/3)

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Example

MODFLOW-USG

METIS

Example

iMODFLOW

“uniform”

Example

iMODFLOW

RCB

• Distribute the linear system Ah = b over

the partitions, where h is the groundwater

head to be solved.

• Connect the partitions tightly through MPI,

using an overlap for exchanging data.

• Solve this system in parallel with exactly

the same accuracy as for the serial case.

• Krylov-Schwarz domain decomposition:

• Restricted Additive Schwarz

parallel preconditioner:

• Applied to CG/GCR Krylov methods

• Inaccurate subdomain solve: ILU only

• Dirichlet transmission condition


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www.ddm.org

Example structure additive

Schwarz preconditioner M

http://www.ddm.org/


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Results iMODFLOW: NHM (1)

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• Netherlands Hydrological Model for drought simulation

• iMODFLOW-MetaSWAP-TRANSOL-MOZART-DM

parallel PKS serial

• Simulation period: 2006, daily time-step

• MODFLOW: confined, 7 layers, 7x1300x1200 (~6.5M cells)

• MetaSWAP: ~0.5M cells

Results iMODFLOW: NHM (2)

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• Maximum measured speedup ~5.

• Maximum theoretical speedup is

limited by surface water (< 1/0.06 16.7).

• Exactly the same heads are computed

with PKS as for the serial case.

Amdahl’s law

Results MODFLOW-USG: global model

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• PCRGLOB-WB

• Period 1996-jan, transient with daily time-step,

confined, 2 layers, ~4.5M cells, 5 arc-min.

• Run 1: watershed-based input/output

(SIO, 53 watersheds)

• Run 2: Input/output clipped on METIS

partitions (NO_SIO)

Results MODFLOW-USG: Indonesia & synthetic

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• Indonesia model:

steady-state, confined, 1 layer, ~4M cells,

30 arc-sec.

• Synthetic:

steady-state, confined,

heterogeneous conductivity, 2 layers,

10 km x 10 km, ~112M cells (2x7500x7500)

Synthetic Indonesia

Practical usage with iMOD (Windows)

Easy-to-use in three steps:

1. Install Microsoft MPI:

https://msdn.microsoft.com/en-us/library/bb524831(v=vs.85).aspx

2. Modify your run-file, Dataset 5 (Solver Configuration)

3. Start your parallel job. E.g. starting from the DOS prompt using 4 cores:

mpiexec -n 4 iMODFLOW.exe imodflow.run

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Enable PKS

Same options as PCG

Partition method, flag for merging IDF output






!!! THANK YOU FOR YOUR ATTENTION !!!

1 November, 2016

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