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GettingStarted.md

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Getting started

Quickstart

  1. check for the prerequisites
  2. compile using the Makefile (for help/instructions see Compilation.md
    • with the corresponding/wanted preprocessor directives in include/parameter.h
  3. provide/create/set
    • initial particle distribution
    • config file: especially output directory for the output files
    • material config file (for a simulation including SPH): especially sml in dependence of generated number of particles
  4. execute/run via mpirun -np <np> <binary> -n <#output files> -f <input hdf5 file> -C <config file> -m <material-config>
    • or by using an adequate batch script for the used queing system
  5. postprocess results

Generally

Preprocessor directives: parameter.h
  • see include/parameter.h
#define DEBUGGING 0

/**
 * * `SAFETY_LEVEL 0`: almost no safety measures
 * * `SAFETY_LEVEL 1`: most relevant/important safety measures
 * * `SAFETY_LEVEL 2`: more safety measures, including assertions
 * * `SAFETY_LEVEL 3`: many security measures, including all assertions
 */
#define SAFETY_LEVEL 2

/// Dimension of the problem
#define DIM 3

/// [0]: natural units, [1]: SI units
#define SI_UNITS 1

/// [0]: rectangular (and not necessarily cubic domains), [1]: cubic domains
#define CUBIC_DOMAINS 1

/// Simulation with gravitational forces
#define GRAVITY_SIM 1

/// SPH simulation
#define SPH_SIM 1

/// integrate energy equation
#define INTEGRATE_ENERGY 0

/// integrate density equation
#define INTEGRATE_DENSITY 1

/// integrate smoothing length
#define INTEGRATE_SML 0

/// decouple smoothing length for pc integrator(s)
#define DECOUPLE_SML 0

/// variable smoothing length
#define VARIABLE_SML 1

/// correct smoothing length
#define SML_CORRECTION 0

/**
 * Choose the SPH representation to solve the momentum and energy equation:
 * * **SPH_EQU_VERSION 1:** original version with
 *     * HYDRO $dv_a/dt ~ - (p_a/rho_a**2 + p_b/rho_b**2)  \nabla_a W_ab$
 *     * SOLID $dv_a/dt ~ (sigma_a/rho_a**2 + sigma_b/rho_b**2) \nabla_a W_ab$
 * * **SPH_EQU_VERSION 2:** slighty different version with
 *     * HYDRO $dv_a/dt ~ - (p_a+p_b)/(rho_a*rho_b)  \nabla_a W_ab$
 *     * SOLID $dv_a/dt ~ (sigma_a+sigma_b)/(rho_a*rho_b)  \nabla_a W_ab$
 */
#define SPH_EQU_VERSION 1
Input HDF5 file
  • for gravity only
    • provide mass "m", position "x" and velocity "v"
GROUP "/" {
   DATASET "m" {
      DATATYPE  H5T_IEEE_F64LE
      DATASPACE  SIMPLE { ( <num particles> ) / ( <num particles>  ) }
   }
   DATASET "v" {
      DATATYPE  H5T_IEEE_F64LE
      DATASPACE  SIMPLE { ( <num particles> , <dim> ) / ( <num particles> , <dim> ) }
   }
   DATASET "x" {
      DATATYPE  H5T_IEEE_F64LE
      DATASPACE  SIMPLE { ( <num particles> , <dim>  ) / (<num particles> , <dim>  ) }
   }
}
}
  • with SPH provide (at least)
    • provide mass "m", material identifier "materialId", internal energy "u", position "x" and velocity "v"
GROUP "/" {
   DATASET "m" {
      DATATYPE  H5T_IEEE_F64LE
      DATASPACE  SIMPLE { ( <num particles> ) / ( <num particles>  ) }
   }
   DATASET "materialId" {
      DATATYPE  H5T_STD_I8LE
      DATASPACE  SIMPLE { ( <num particles>  ) / ( <num particles>  ) }
   }
   DATASET "u" {
      DATATYPE  H5T_IEEE_F64LE
      DATASPACE  SIMPLE { ( <num particles>  ) / ( <num particles>  ) }
   }
   DATASET "v" {
      DATATYPE  H5T_IEEE_F64LE
      DATASPACE  SIMPLE { ( <num particles> , <dim> ) / ( <num particles> , <dim> ) }
   }
   DATASET "x" {
      DATATYPE  H5T_IEEE_F64LE
      DATASPACE  SIMPLE { ( <num particles> , <dim>  ) / (<num particles> , <dim>  ) }
   }
}
}
Config file 
; IO RELATED
; ------------------------------------------------------
; output directory (will be created if it does not exist)
directory bb/

; outputRank (-1 corresponds to all)
outputRank -1
; omit logType::TIME for standard output
omitTime true
; create log file (including warnings, errors, ...)
log true
; create performance log
performanceLog true
; write particles to be sent to h5 file
particlesSent2H5 true


; INTEGRATOR RELATED
; ------------------------------------------------------
; integrator selection
; explicit euler [0], predictor-corrector euler [1], leapfrog [2]
integrator 1
; initial time step
timeStep 1e-4
; max time step allowed
maxTimeStep 1e-4
; end time for simulation
;timeEnd 6e-2

; SIMULATION RELATED
; ------------------------------------------------------
; space-filling curve selection
; lebesgue [0], hilbert [1]
sfc 1

; theta-criterion for Barnes-Hut (approximative gravity)
theta 0.5
; smoothing parameter for gravitational forces
smoothing 2.56e+20

; SPH smoothing kernel selection
; spiky [0], cubic spline [1], wendlandc2 [3], wendlandc4 [4], wendlandc6 [5]
smoothingKernel 1

; remove particles (corresponding to some criterion)
removeParticles true
; spherically [0], cubic [1]
removeParticlesCriterion 0
; allowed distance to center (0, 0, 0)
removeParticlesDimension 3.6e14

; execute load balancing
loadBalancing false
; interval for executing load balancing (every Nth step)
loadBalancingInterval 1

; how much memory to allocate (1.0 -> all particles can in principle be on one process)
particleMemoryContingent 1.0

; calculate angular momentum (and save to output file)
calculateAngularMomentum true
; calculate (total) energy (and save to output file)
calculateEnergy true
; calculate center of mass (and save to output file)
calculateCenterOfMass false

; IMPLEMENTATION SELECTION
; ------------------------------------------------------
; force version for gravity (use [2])
; burtscher [0], burtscher without presorting [1], miluphcuda with presorting [2],
; miluphcuda without presorting [3], miluphcuda shared memory (experimental) [4]
gravityForceVersion 0
; fixed radius NN version for SPH (use [0])
; normal [0], brute-force [1], shared-memory [2], within-box [3]
sphFixedRadiusNNVersion 3
Material config file 
materials = (
{
    ID = 0
    name = "IsothermalGas"
    #sml = 1e12
    sml = 5.2e11
    interactions = 50
    artificial_viscosity = { alpha = 1.0; beta = 2.0; };
    eos = {
        type = 3
    };
}
);

...
Command line arguments
  • ./bin/runner -h gives help:
Multi-GPU CUDA Barnes-Hut NBody/SPH code
Usage:
  HPC NBody [OPTION...]

  -n, --number-output-files arg
                                number of output files (default: 100)
  -t, --max-time-step arg       time step (default: -1.)
  -l, --load-balancing          load balancing
  -L, --load-balancing-interval arg
                                load balancing interval (default: -1)
  -C, --config arg              config file (default: config/config.info)
  -m, --material-config arg     material config file (default: 
                                config/material.cfg)
  -c, --curve-type arg          curve type (Lebesgue: 0/Hilbert: 1) 
                                (default: -1)
  -f, --input-file arg          File name (default: -)
  -v, --verbosity arg           Verbosity level (default: 0)
  -h, --help                    Show this help

Test cases

Available test cases including instructions can be found within testcases/.

Currently available: