Merge branch 'master' of github.com:JamesEMcClure/LBPM-WIA
This commit is contained in:
James E McClure
commit
c5c35ff6d9
60
sample_scripts/config_build_rhea
Executable file
60
sample_scripts/config_build_rhea
Executable file
@ -0,0 +1,60 @@
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# Clear all modules (except modules)
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#for var in ${LOADEDMODULES//:/ }; do if [ " ${var///*/}" != " modules" ]; then module unload " ${var///*/}" > /dev/null 2>&1; fi; done
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source $MODULESHOME/init/bash
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module unload PE-intel
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module load PE-gnu/6.2.0-2.0.1
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#module load gcc/6.2.0
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module load cmake3/3.5.2
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module load openmpi netcdf hdf5
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export MPICH_RDMA_ENABLED_CUDA=0
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echo $GNU_VERSION
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module list
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# Remove CMake files from previous configures
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rm -rf CMake*
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# Configure
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cmake \
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-D CMAKE_BUILD_TYPE:STRING=Release \
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-D CMAKE_C_COMPILER:PATH=mpicc \
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-D CMAKE_CXX_COMPILER:PATH=mpicxx \
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-D CMAKE_CXX_COMPILER:PATH=mpicxx \
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-D CMAKE_CXX_STD=11 \
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-D USE_TIMER=false \
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-D TIMER_DIRECTORY=${HOME}/timerutility/build/opt \
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-D MPI_COMPILER:BOOL=TRUE \
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-D MPIEXEC=aprun \
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-D USE_EXT_MPI_FOR_SERIAL_TESTS:BOOL=TRUE \
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-D USE_CUDA=0 \
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-D CUDA_FLAGS="-arch sm_35" \
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-D USE_HDF5=1 \
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-D USE_SILO=1 \
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-D HDF5_DIRECTORY=/sw/rhea/hdf5/1.8.11/rhel6.6_gnu4.8.2/ \
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-D HDF5_LIB=/sw/rhea/hdf5/1.8.11/rhel6.6_gnu4.8.2/lib/libhdf5.so \
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-D SILO_DIRECTORY=/lustre/atlas1/geo106/proj-shared/rhea/silo\
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~/LBPM-WIA
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# -D PREFIX=$MEMBERWORK/geo106/eos-LBPM-WIA \
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#-D CUDA_HOST_COMPILER="/usr/bin/gcc" \
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# Build the code
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make install -j 8
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# Fix permissions
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#chmod -R g+w $PROJWORK/geo106/eos-LBPM-WIA
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# Run the fast tests
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# ctest -E WEEKLY
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# Run the slow tests
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# ctest -R WEEKLY -VV
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@ -41,6 +41,7 @@ ADD_LBPM_TEST( pmmc_cylinder )
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ADD_LBPM_TEST( TestTorus )
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ADD_LBPM_TEST( TestFluxBC )
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ADD_LBPM_TEST( TestMap )
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ADD_LBPM_TEST( TestMinkowski )
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#ADD_LBPM_TEST( TestMRT )
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#ADD_LBPM_TEST( TestColorGrad )
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#ADD_LBPM_TEST( TestColorGradDFH )
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222
tests/TestMinkowski.cpp
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222
tests/TestMinkowski.cpp
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// Sequential blob analysis
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// Reads parallel simulation data and performs connectivity analysis
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// and averaging on a blob-by-blob basis
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// James E. McClure 2014
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#include <stdio.h>
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#include <stdlib.h>
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#include <math.h>
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#include <iostream>
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#include <fstream>
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#include <sstream>
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#include <functional>
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#include "common/Array.h"
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#include "common/Domain.h"
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#include "common/Communication.h"
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#include "common/MPI_Helpers.h"
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#include "IO/MeshDatabase.h"
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#include "IO/Mesh.h"
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#include "IO/Writer.h"
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#include "IO/netcdf.h"
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#include "analysis/analysis.h"
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#include "analysis/filters.h"
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#include "analysis/distance.h"
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#include "analysis/Minkowski.h"
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#include "ProfilerApp.h"
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int main(int argc, char **argv)
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{
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// Initialize MPI
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int rank, nprocs;
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MPI_Init(&argc,&argv);
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MPI_Comm comm = MPI_COMM_WORLD;
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MPI_Comm_rank(comm,&rank);
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MPI_Comm_size(comm,&nprocs);
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{
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Utilities::setErrorHandlers();
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PROFILE_START("Main");
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//std::vector<std::string> filenames;
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if ( argc<2 ) {
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if ( rank == 0 ){
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printf("At least one filename must be specified\n");
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}
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return 1;
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}
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std::string filename = std::string(argv[1]);
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if ( rank == 0 ){
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printf("Input data file: %s\n",filename.c_str());
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}
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auto db = std::make_shared<Database>( filename );
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auto domain_db = db->getDatabase( "Domain" );
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// Read domain parameters
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auto Filename = domain_db->getScalar<std::string>( "Filename" );
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auto L = domain_db->getVector<double>( "L" );
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auto size = domain_db->getVector<int>( "n" );
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auto SIZE = domain_db->getVector<int>( "N" );
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auto nproc = domain_db->getVector<int>( "nproc" );
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auto ReadValues = domain_db->getVector<char>( "ReadValues" );
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auto WriteValues = domain_db->getVector<char>( "WriteValues" );
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auto nx = size[0];
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auto ny = size[1];
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auto nz = size[2];
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auto nprocx = nproc[0];
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auto nprocy = nproc[1];
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auto nprocz = nproc[2];
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auto Nx = SIZE[0];
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auto Ny = SIZE[1];
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auto Nz = SIZE[2];
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int i,j,k,n;
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char *SegData = NULL;
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// Rank=0 reads the entire segmented data and distributes to worker processes
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if (rank==0){
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printf("Dimensions of segmented image: %i x %i x %i \n",Nx,Ny,Nz);
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SegData = new char[Nx*Ny*Nz];
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FILE *SEGDAT = fopen(Filename.c_str(),"rb");
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if (SEGDAT==NULL) ERROR("Error reading segmented data");
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size_t ReadSeg;
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ReadSeg=fread(SegData,1,Nx*Ny*Nz,SEGDAT);
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if (ReadSeg != size_t(Nx*Ny*Nz)) printf("lbpm_segmented_decomp: Error reading segmented data (rank=%i)\n",rank);
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fclose(SEGDAT);
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printf("Read segmented data from %s \n",Filename.c_str());
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}
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MPI_Barrier(comm);
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// Get the rank info
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int N = (nx+2)*(ny+2)*(nz+2);
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std::shared_ptr<Domain> Dm (new Domain(domain_db,comm));
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for (k=0;k<nz+2;k++){
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for (j=0;j<ny+2;j++){
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for (i=0;i<nx+2;i++){
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n = k*(nx+2)*(ny+2)+j*(nx+2)+i;
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Dm->id[n] = 1;
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}
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}
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}
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Dm->CommInit();
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int z_transition_size = 0;
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int xStart = 0;
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int yStart = 0;
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int zStart = 0;
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// Set up the sub-domains
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if (rank==0){
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printf("Distributing subdomain across %i processors \n",nprocs);
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printf("Process grid: %i x %i x %i \n",Dm->nprocx(),Dm->nprocy(),Dm->nprocz());
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printf("Subdomain size: %i \n",N);
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//printf("Size of transition region: %i \n", z_transition_size);
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char *tmp;
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tmp = new char[N];
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for (int kp=0; kp<nprocz; kp++){
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for (int jp=0; jp<nprocy; jp++){
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for (int ip=0; ip<nprocx; ip++){
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// rank of the process that gets this subdomain
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int rnk = kp*Dm->nprocx()*Dm->nprocy() + jp*Dm->nprocx() + ip;
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// Pack and send the subdomain for rnk
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for (k=0;k<nz+2;k++){
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for (j=0;j<ny+2;j++){
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for (i=0;i<nx+2;i++){
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int x = xStart + ip*nx + i-1;
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int y = yStart + jp*ny + j-1;
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// int z = zStart + kp*nz + k-1;
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int z = zStart + kp*nz + k-1 - z_transition_size;
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if (x<xStart) x=xStart;
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if (!(x<Nx)) x=Nx-1;
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if (y<yStart) y=yStart;
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if (!(y<Ny)) y=Ny-1;
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if (z<zStart) z=zStart;
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if (!(z<Nz)) z=Nz-1;
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int nlocal = k*(nx+2)*(ny+2) + j*(nx+2) + i;
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int nglobal = z*Nx*Ny+y*Nx+x;
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tmp[nlocal] = SegData[nglobal];
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}
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}
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}
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if (rnk==0){
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for (k=0;k<nz+2;k++){
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for (j=0;j<ny+2;j++){
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for (i=0;i<nx+2;i++){
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int nlocal = k*(nx+2)*(ny+2) + j*(nx+2) + i;
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Dm->id[nlocal] = tmp[nlocal];
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}
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}
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}
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}
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else{
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printf("Sending data to process %i \n", rnk);
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MPI_Send(tmp,N,MPI_CHAR,rnk,15,comm);
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}
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}
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}
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}
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}
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else{
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// Recieve the subdomain from rank = 0
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printf("Ready to recieve data %i at process %i \n", N,rank);
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MPI_Recv(Dm->id,N,MPI_CHAR,0,15,comm,MPI_STATUS_IGNORE);
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}
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MPI_Barrier(comm);
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// Compute the Minkowski functionals
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MPI_Barrier(comm);
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std::shared_ptr<Minkowski> Averages(new Minkowski(Dm));
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// Calculate the distance
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// Initialize the domain and communication
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nx+=2; ny+=2; nz+=2;
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Array<char> id(nx,ny,nz);
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//if (rank==0){
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//printf("ID: %i, %i, %i \n",Dm->Nx, Dm->Ny, Dm->Nz);
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// printf("ID: %i, %i, %i \n",id.size(0),id.size(1),id.size(2));
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// printf("SDn: %i, %i, %i \n",Averages->SDn.size(0),Averages->SDn.size(1),Averages->SDn.size(2));
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//}
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// Solve for the position of the solid phase
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for (k=0;k<nz;k++){
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for (j=0;j<ny;j++){
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for (i=0;i<nx;i++){
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n = k*nx*ny+j*nx+i;
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// Initialize the object
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if (Dm->id[n] == ReadValues[0]) id(i,j,k) = 1;
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else id(i,j,k) = 0;
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}
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}
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}
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for (k=0;k<nz;k++){
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for (j=0;j<ny;j++){
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for (i=0;i<nx;i++){
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n=k*nx*ny+j*nx+i;
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// Initialize distance to +/- 1
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Averages->SDn(i,j,k) = 2.0*double(id(i,j,k))-1.0;
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}
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}
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}
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//MeanFilter(Averages->SDn);
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//std::array<bool> bc(3)={1,1,1};
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if (rank==0) printf("Initialized solid phase -- Converting to Signed Distance function \n");
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CalcDist(Averages->SDn,id,*Dm);
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if (rank==0) printf("Computing Minkowski functionals \n");
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Averages->Initialize();
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Averages->UpdateMeshValues();
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Averages->ComputeLocal();
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Averages->Reduce();
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Averages->PrintAll();
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}
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PROFILE_STOP("Main");
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PROFILE_SAVE("Minkowski",true);
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MPI_Barrier(comm);
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MPI_Finalize();
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return 0;
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}
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