1264 lines
49 KiB
C++
1264 lines
49 KiB
C++
/*
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Copyright 2013--2018 James E. McClure, Virginia Polytechnic & State University
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Copyright Equnior ASA
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This file is part of the Open Porous Media project (OPM).
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OPM is free software: you can redistribute it and/or modify
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it under the terms of the GNU General Public License as published by
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the Free Software Foundation, either version 3 of the License, or
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(at your option) any later version.
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OPM is distributed in the hope that it will be useful,
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but WITHOUT ANY WARRANTY; without even the implied warranty of
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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GNU General Public License for more details.
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You should have received a copy of the GNU General Public License
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along with OPM. If not, see <http://www.gnu.org/licenses/>.
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*/
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// Run the analysis, blob identification, and write restart files
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#include "analysis/runAnalysis.h"
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#include "analysis/analysis.h"
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#include "common/Array.h"
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#include "common/Communication.h"
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#include "common/MPI.h"
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#include "common/ScaLBL.h"
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#include "models/ColorModel.h"
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#include "IO/MeshDatabase.h"
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#include "threadpool/thread_pool.h"
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#include "ProfilerApp.h"
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AnalysisType &operator|=(AnalysisType &lhs, AnalysisType rhs) {
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lhs = static_cast<AnalysisType>(
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static_cast<std::underlying_type<AnalysisType>::type>(lhs) |
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static_cast<std::underlying_type<AnalysisType>::type>(rhs));
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return lhs;
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}
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bool matches(AnalysisType x, AnalysisType y) {
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return (static_cast<std::underlying_type<AnalysisType>::type>(x) &
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static_cast<std::underlying_type<AnalysisType>::type>(y)) != 0;
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}
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// Create a shared_ptr to an array of values
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template <class TYPE>
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static inline std::shared_ptr<TYPE> make_shared_array(size_t N) {
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return std::shared_ptr<TYPE>(new TYPE[N],
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[](const TYPE *p) { delete[] p; });
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}
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// Helper class to write the restart file from a seperate thread
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class WriteRestartWorkItem : public ThreadPool::WorkItemRet<void> {
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public:
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WriteRestartWorkItem(const std::string &filename_,
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std::shared_ptr<double> cDen_,
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std::shared_ptr<double> cfq_, int N_)
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: filename(filename_), cfq(cfq_), cDen(cDen_), N(N_) {}
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virtual void run() {
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PROFILE_START("Save Checkpoint", 1);
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double value;
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ofstream File(filename, ios::binary);
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for (int n = 0; n < N; n++) {
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// Write the two density values
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value = cDen.get()[n];
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File.write((char *)&value, sizeof(value));
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value = cDen.get()[N + n];
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File.write((char *)&value, sizeof(value));
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}
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for (int n = 0; n < N; n++) {
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// Write the distributions
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for (int q = 0; q < 19; q++) {
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value = cfq.get()[q * N + n];
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File.write((char *)&value, sizeof(value));
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}
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}
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File.close();
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PROFILE_STOP("Save Checkpoint", 1);
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};
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private:
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WriteRestartWorkItem();
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const std::string filename;
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std::shared_ptr<double> cfq, cDen;
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const int N;
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};
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// Helper class to compute the blob ids
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typedef std::shared_ptr<std::pair<int, IntArray>> BlobIDstruct;
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typedef std::shared_ptr<std::vector<BlobIDType>> BlobIDList;
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static const std::string id_map_filename = "lbpm_id_map.txt";
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class BlobIdentificationWorkItem1 : public ThreadPool::WorkItemRet<void> {
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public:
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BlobIdentificationWorkItem1(int timestep_, int Nx_, int Ny_, int Nz_,
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const RankInfoStruct &rank_info_,
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std::shared_ptr<const DoubleArray> phase_,
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const DoubleArray &dist_, BlobIDstruct last_id_,
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BlobIDstruct new_index_, BlobIDstruct new_id_,
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BlobIDList new_list_,
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runAnalysis::commWrapper &&comm_)
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: timestep(timestep_), Nx(Nx_), Ny(Ny_), Nz(Nz_), rank_info(rank_info_),
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phase(phase_), dist(dist_), last_id(last_id_), new_index(new_index_),
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new_id(new_id_), new_list(new_list_), comm(std::move(comm_)) {}
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~BlobIdentificationWorkItem1() {}
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virtual void run() {
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// Compute the global blob id and compare to the previous version
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PROFILE_START("Identify blobs", 1);
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double vF = 0.0;
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double vS = -1.0; // one voxel buffer region around solid
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IntArray &ids = new_index->second;
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new_index->first =
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ComputeGlobalBlobIDs(Nx - 2, Ny - 2, Nz - 2, rank_info, *phase,
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dist, vF, vS, ids, comm.comm);
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PROFILE_STOP("Identify blobs", 1);
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}
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private:
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BlobIdentificationWorkItem1();
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int timestep;
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int Nx, Ny, Nz;
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const RankInfoStruct rank_info;
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std::shared_ptr<const DoubleArray> phase;
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const DoubleArray &dist;
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BlobIDstruct last_id, new_index, new_id;
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BlobIDList new_list;
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runAnalysis::commWrapper comm;
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};
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class BlobIdentificationWorkItem2 : public ThreadPool::WorkItemRet<void> {
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public:
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BlobIdentificationWorkItem2(int timestep_, int Nx_, int Ny_, int Nz_,
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const RankInfoStruct &rank_info_,
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std::shared_ptr<const DoubleArray> phase_,
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const DoubleArray &dist_, BlobIDstruct last_id_,
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BlobIDstruct new_index_, BlobIDstruct new_id_,
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BlobIDList new_list_,
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runAnalysis::commWrapper &&comm_)
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: timestep(timestep_), Nx(Nx_), Ny(Ny_), Nz(Nz_), rank_info(rank_info_),
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phase(phase_), dist(dist_), last_id(last_id_), new_index(new_index_),
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new_id(new_id_), new_list(new_list_), comm(std::move(comm_)) {}
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~BlobIdentificationWorkItem2() {}
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virtual void run() {
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// Compute the global blob id and compare to the previous version
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PROFILE_START("Identify blobs maps", 1);
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const IntArray &ids = new_index->second;
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static int max_id = -1;
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new_id->first = new_index->first;
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new_id->second = new_index->second;
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if (last_id.get() != NULL) {
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// Compute the timestep-timestep map
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const IntArray &old_ids = last_id->second;
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ID_map_struct map =
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computeIDMap(Nx, Ny, Nz, old_ids, ids, comm.comm);
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// Renumber the current timestep's ids
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getNewIDs(map, max_id, *new_list);
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renumberIDs(*new_list, new_id->second);
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writeIDMap(map, timestep, id_map_filename);
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} else {
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max_id = -1;
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ID_map_struct map(new_id->first);
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getNewIDs(map, max_id, *new_list);
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writeIDMap(map, timestep, id_map_filename);
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}
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PROFILE_STOP("Identify blobs maps", 1);
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}
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private:
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BlobIdentificationWorkItem2();
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int timestep;
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int Nx, Ny, Nz;
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const RankInfoStruct rank_info;
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std::shared_ptr<const DoubleArray> phase;
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const DoubleArray &dist;
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BlobIDstruct last_id, new_index, new_id;
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BlobIDList new_list;
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runAnalysis::commWrapper comm;
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};
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// Helper class to write the vis file from a thread
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class WriteVisWorkItem : public ThreadPool::WorkItemRet<void> {
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public:
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WriteVisWorkItem(int timestep_, std::vector<IO::MeshDataStruct> &visData_,
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TwoPhase &Avgerages_, std::array<int, 3> n_,
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RankInfoStruct rank_info_,
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runAnalysis::commWrapper &&comm_)
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: timestep(timestep_), visData(visData_), Averages(Avgerages_),
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n(std::move(n_)), rank_info(std::move(rank_info_)),
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comm(std::move(comm_)) {}
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~WriteVisWorkItem() {}
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virtual void run() {
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PROFILE_START("Save Vis", 1);
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fillHalo<double> fillData(comm.comm, rank_info, n, {1, 1, 1}, 0, 1);
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ASSERT(visData[0].vars[0]->name == "phase");
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Array<double> &PhaseData = visData[0].vars[0]->data;
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fillData.copy(Averages.SDn, PhaseData);
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ASSERT(visData[0].vars[5]->name == "SignDist");
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Array<double> &SignData = visData[0].vars[5]->data;
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fillData.copy(Averages.SDs, SignData);
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ASSERT(visData[0].vars[1]->name == "Pressure");
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Array<double> &PressData = visData[0].vars[1]->data;
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fillData.copy(Averages.Press, PressData);
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ASSERT(visData[0].vars[2]->name == "Velocity_x");
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ASSERT(visData[0].vars[3]->name == "Velocity_y");
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ASSERT(visData[0].vars[4]->name == "Velocity_z");
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Array<double> &VelxData = visData[0].vars[2]->data;
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Array<double> &VelyData = visData[0].vars[3]->data;
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Array<double> &VelzData = visData[0].vars[4]->data;
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fillData.copy(Averages.Vel_x, VelxData);
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fillData.copy(Averages.Vel_y, VelyData);
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fillData.copy(Averages.Vel_z, VelzData);
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ASSERT(visData[0].vars[6]->name == "BlobID");
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Array<double> &BlobData = visData[0].vars[6]->data;
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fillData.copy(Averages.Label_NWP, BlobData);
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IO::writeData(timestep, visData, comm.comm);
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PROFILE_STOP("Save Vis", 1);
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};
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private:
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WriteVisWorkItem();
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int timestep;
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std::array<int, 3> n;
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RankInfoStruct rank_info;
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std::vector<IO::MeshDataStruct> &visData;
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TwoPhase &Averages;
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runAnalysis::commWrapper comm;
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};
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// Helper class to write the vis file from a thread
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class IOWorkItem : public ThreadPool::WorkItemRet<void> {
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public:
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IOWorkItem(int timestep_, std::shared_ptr<Database> input_db_,
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std::vector<IO::MeshDataStruct> &visData_, SubPhase &Averages_,
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std::array<int, 3> n_, RankInfoStruct rank_info_,
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runAnalysis::commWrapper &&comm_)
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: timestep(timestep_), input_db(input_db_), visData(visData_),
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Averages(Averages_), n(std::move(n_)),
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rank_info(std::move(rank_info_)), comm(std::move(comm_)) {}
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~IOWorkItem() {}
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virtual void run() {
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PROFILE_START("Save Vis", 1);
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auto color_db = input_db->getDatabase("Color");
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auto vis_db = input_db->getDatabase("Visualization");
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// int timestep = color_db->getWithDefault<int>( "timestep", 0 );
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fillHalo<double> fillData(comm.comm, rank_info, n, {1, 1, 1}, 0, 1);
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if (vis_db->getWithDefault<bool>("save_phase_field", true)) {
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ASSERT(visData[0].vars[0]->name == "phase");
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Array<double> &PhaseData = visData[0].vars[0]->data;
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fillData.copy(Averages.Phi, PhaseData);
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}
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if (vis_db->getWithDefault<bool>("save_pressure", false)) {
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ASSERT(visData[0].vars[1]->name == "Pressure");
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Array<double> &PressData = visData[0].vars[1]->data;
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fillData.copy(Averages.Pressure, PressData);
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}
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if (vis_db->getWithDefault<bool>("save_velocity", false)) {
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ASSERT(visData[0].vars[2]->name == "Velocity_x");
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ASSERT(visData[0].vars[3]->name == "Velocity_y");
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ASSERT(visData[0].vars[4]->name == "Velocity_z");
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Array<double> &VelxData = visData[0].vars[2]->data;
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Array<double> &VelyData = visData[0].vars[3]->data;
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Array<double> &VelzData = visData[0].vars[4]->data;
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fillData.copy(Averages.Vel_x, VelxData);
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fillData.copy(Averages.Vel_y, VelyData);
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fillData.copy(Averages.Vel_z, VelzData);
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}
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if (vis_db->getWithDefault<bool>("save_dissipation", false)) {
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ASSERT(visData[0].vars[5]->name == "ViscousDissipation");
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Array<double> &ViscousDissipation = visData[0].vars[5]->data;
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fillData.copy(Averages.Dissipation, ViscousDissipation);
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}
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if (vis_db->getWithDefault<bool>("save_distance", false)) {
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ASSERT(visData[0].vars[6]->name == "SignDist");
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Array<double> &SignData = visData[0].vars[6]->data;
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fillData.copy(Averages.SDs, SignData);
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}
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if (vis_db->getWithDefault<bool>("save_connected_components", false)) {
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ASSERT(visData[0].vars[7]->name == "BlobID");
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Array<double> &BlobData = visData[0].vars[7]->data;
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fillData.copy(Averages.morph_n->label, BlobData);
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}
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if (vis_db->getWithDefault<bool>("write_silo", true))
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IO::writeData(timestep, visData, comm.comm);
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if (vis_db->getWithDefault<bool>("save_8bit_raw", true)) {
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char CurrentIDFilename[40];
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sprintf(CurrentIDFilename, "id_t%d.raw", timestep);
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Averages.AggregateLabels(CurrentIDFilename);
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}
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PROFILE_STOP("Save Vis", 1);
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};
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private:
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IOWorkItem();
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int timestep;
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std::array<int, 3> n;
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RankInfoStruct rank_info;
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std::shared_ptr<Database> input_db;
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std::vector<IO::MeshDataStruct> &visData;
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SubPhase &Averages;
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runAnalysis::commWrapper comm;
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};
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// Helper class to run the analysis from within a thread
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// Note: Averages will be modified after the constructor is called
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class AnalysisWorkItem : public ThreadPool::WorkItemRet<void> {
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public:
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AnalysisWorkItem(AnalysisType type_, int timestep_, TwoPhase &Averages_,
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BlobIDstruct ids, BlobIDList id_list_, double beta_)
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: type(type_), timestep(timestep_), Averages(Averages_), blob_ids(ids),
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id_list(id_list_), beta(beta_) {}
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~AnalysisWorkItem() {}
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virtual void run() {
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Averages.NumberComponents_NWP = blob_ids->first;
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Averages.Label_NWP = blob_ids->second;
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Averages.Label_NWP_map = *id_list;
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Averages.NumberComponents_WP = 1;
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Averages.Label_WP.fill(0.0);
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if (matches(type, AnalysisType::CopyPhaseIndicator)) {
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// Averages.ColorToSignedDistance(beta,Averages.Phase,Averages.Phase_tplus);
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}
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if (matches(type, AnalysisType::ComputeAverages)) {
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PROFILE_START("Compute dist", 1);
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Averages.Initialize();
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Averages.ComputeDelPhi();
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Averages.ColorToSignedDistance(beta, Averages.Phase, Averages.SDn);
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Averages.ColorToSignedDistance(beta, Averages.Phase_tminus,
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Averages.Phase_tminus);
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Averages.ColorToSignedDistance(beta, Averages.Phase_tplus,
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Averages.Phase_tplus);
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Averages.UpdateMeshValues();
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Averages.ComputeLocal();
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Averages.Reduce();
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Averages.PrintAll(timestep);
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Averages.Initialize();
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Averages.ComponentAverages();
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Averages.SortBlobs();
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Averages.PrintComponents(timestep);
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PROFILE_STOP("Compute dist", 1);
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}
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}
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private:
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AnalysisWorkItem();
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AnalysisType type;
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int timestep;
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TwoPhase &Averages;
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BlobIDstruct blob_ids;
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BlobIDList id_list;
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double beta;
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};
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class TCATWorkItem : public ThreadPool::WorkItemRet<void> {
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public:
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TCATWorkItem(AnalysisType type_, int timestep_, TwoPhase &Averages_,
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BlobIDstruct ids, BlobIDList id_list_, double beta_)
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: type(type_), timestep(timestep_), Averages(Averages_), blob_ids(ids),
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id_list(id_list_), beta(beta_) {}
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~TCATWorkItem() {}
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virtual void run() {
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Averages.NumberComponents_NWP = blob_ids->first;
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Averages.Label_NWP = blob_ids->second;
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Averages.Label_NWP_map = *id_list;
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Averages.NumberComponents_WP = 1;
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Averages.Label_WP.fill(0.0);
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if (matches(type, AnalysisType::CopyPhaseIndicator)) {
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// Averages.ColorToSignedDistance(beta,Averages.Phase,Averages.Phase_tplus);
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}
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if (matches(type, AnalysisType::ComputeAverages)) {
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PROFILE_START("Compute TCAT", 1);
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Averages.Initialize();
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Averages.ComputeDelPhi();
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Averages.ColorToSignedDistance(beta, Averages.Phase, Averages.SDn);
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Averages.ColorToSignedDistance(beta, Averages.Phase_tminus,
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Averages.Phase_tminus);
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Averages.ColorToSignedDistance(beta, Averages.Phase_tplus,
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Averages.Phase_tplus);
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Averages.UpdateMeshValues();
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Averages.ComputeLocal();
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Averages.Reduce();
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Averages.PrintAll(timestep);
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PROFILE_STOP("Compute TCAT", 1);
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}
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}
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private:
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TCATWorkItem();
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AnalysisType type;
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int timestep;
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TwoPhase &Averages;
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BlobIDstruct blob_ids;
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BlobIDList id_list;
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double beta;
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};
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class GanglionTrackingWorkItem : public ThreadPool::WorkItemRet<void> {
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public:
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GanglionTrackingWorkItem(AnalysisType type_, int timestep_,
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TwoPhase &Averages_, BlobIDstruct ids,
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BlobIDList id_list_, double beta_)
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: type(type_), timestep(timestep_), Averages(Averages_), blob_ids(ids),
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id_list(id_list_), beta(beta_) {}
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~GanglionTrackingWorkItem() {}
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virtual void run() {
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Averages.NumberComponents_NWP = blob_ids->first;
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Averages.Label_NWP = blob_ids->second;
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Averages.Label_NWP_map = *id_list;
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Averages.NumberComponents_WP = 1;
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Averages.Label_WP.fill(0.0);
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if (matches(type, AnalysisType::CopyPhaseIndicator)) {
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// Averages.ColorToSignedDistance(beta,Averages.Phase,Averages.Phase_tplus);
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}
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if (matches(type, AnalysisType::ComputeAverages)) {
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PROFILE_START("Compute ganglion", 1);
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Averages.Initialize();
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Averages.ComputeDelPhi();
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Averages.ColorToSignedDistance(beta, Averages.Phase, Averages.SDn);
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Averages.ColorToSignedDistance(beta, Averages.Phase_tminus,
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Averages.Phase_tminus);
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Averages.ColorToSignedDistance(beta, Averages.Phase_tplus,
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Averages.Phase_tplus);
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Averages.UpdateMeshValues();
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Averages.ComponentAverages();
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Averages.SortBlobs();
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Averages.PrintComponents(timestep);
|
|
PROFILE_STOP("Compute ganglion", 1);
|
|
}
|
|
}
|
|
|
|
private:
|
|
GanglionTrackingWorkItem();
|
|
AnalysisType type;
|
|
int timestep;
|
|
TwoPhase &Averages;
|
|
BlobIDstruct blob_ids;
|
|
BlobIDList id_list;
|
|
double beta;
|
|
};
|
|
|
|
class BasicWorkItem : public ThreadPool::WorkItemRet<void> {
|
|
public:
|
|
BasicWorkItem(AnalysisType type_, int timestep_, SubPhase &Averages_)
|
|
: type(type_), timestep(timestep_), Averages(Averages_) {}
|
|
~BasicWorkItem() {}
|
|
virtual void run() {
|
|
|
|
if (matches(type, AnalysisType::CopyPhaseIndicator)) {
|
|
// Averages.ColorToSignedDistance(beta,Averages.Phase,Averages.Phase_tplus);
|
|
}
|
|
if (matches(type, AnalysisType::ComputeAverages)) {
|
|
PROFILE_START("Compute basic averages", 1);
|
|
Averages.Basic();
|
|
PROFILE_STOP("Compute basic averages", 1);
|
|
}
|
|
}
|
|
|
|
private:
|
|
BasicWorkItem();
|
|
AnalysisType type;
|
|
int timestep;
|
|
SubPhase &Averages;
|
|
double beta;
|
|
};
|
|
|
|
class SubphaseWorkItem : public ThreadPool::WorkItemRet<void> {
|
|
public:
|
|
SubphaseWorkItem(AnalysisType type_, int timestep_, SubPhase &Averages_)
|
|
: type(type_), timestep(timestep_), Averages(Averages_) {}
|
|
~SubphaseWorkItem() {}
|
|
virtual void run() {
|
|
|
|
PROFILE_START("Compute subphase", 1);
|
|
Averages.Full();
|
|
Averages.Write(timestep);
|
|
PROFILE_STOP("Compute subphase", 1);
|
|
}
|
|
|
|
private:
|
|
SubphaseWorkItem();
|
|
AnalysisType type;
|
|
int timestep;
|
|
SubPhase &Averages;
|
|
double beta;
|
|
};
|
|
|
|
/******************************************************************
|
|
* MPI comm wrapper for use with analysis *
|
|
******************************************************************/
|
|
runAnalysis::commWrapper::commWrapper(int tag_, const Utilities::MPI &comm_,
|
|
runAnalysis *analysis_)
|
|
: comm(comm_), tag(tag_), analysis(analysis_) {}
|
|
runAnalysis::commWrapper::commWrapper(commWrapper &&rhs)
|
|
: comm(rhs.comm), tag(rhs.tag), analysis(rhs.analysis) {
|
|
rhs.tag = -1;
|
|
}
|
|
runAnalysis::commWrapper::~commWrapper() {
|
|
if (tag == -1)
|
|
return;
|
|
comm.barrier();
|
|
analysis->d_comm_used[tag] = false;
|
|
}
|
|
runAnalysis::commWrapper runAnalysis::getComm() {
|
|
// Get a tag from root
|
|
int tag = -1;
|
|
if (d_rank == 0) {
|
|
for (int i = 0; i < 1024; i++) {
|
|
if (!d_comm_used[i]) {
|
|
tag = i;
|
|
break;
|
|
}
|
|
}
|
|
if (tag == -1)
|
|
ERROR("Unable to get comm");
|
|
}
|
|
tag = d_comm.bcast(tag, 0);
|
|
d_comm_used[tag] = true;
|
|
if (d_comms[tag].isNull())
|
|
d_comms[tag] = d_comm.dup();
|
|
return commWrapper(tag, d_comms[tag], this);
|
|
}
|
|
|
|
/******************************************************************
|
|
* Constructor/Destructors *
|
|
******************************************************************/
|
|
runAnalysis::runAnalysis(std::shared_ptr<Database> input_db,
|
|
const RankInfoStruct &rank_info,
|
|
std::shared_ptr<ScaLBL_Communicator> ScaLBL_Comm,
|
|
std::shared_ptr<Domain> Dm, int Np, bool Regular,
|
|
IntArray Map)
|
|
: d_Np(Np), d_regular(Regular), d_rank_info(rank_info), d_Map(Map),
|
|
d_comm(Dm->Comm.dup()), d_ScaLBL_Comm(ScaLBL_Comm) {
|
|
|
|
auto db = input_db->getDatabase("Analysis");
|
|
auto vis_db = input_db->getDatabase("Visualization");
|
|
|
|
/* set the I/O format */
|
|
format = vis_db->getWithDefault<string>("format", "silo");
|
|
|
|
// Ids of work items to use for dependencies
|
|
ThreadPool::thread_id_t d_wait_blobID;
|
|
ThreadPool::thread_id_t d_wait_analysis;
|
|
ThreadPool::thread_id_t d_wait_vis;
|
|
ThreadPool::thread_id_t d_wait_restart;
|
|
ThreadPool::thread_id_t d_wait_subphase;
|
|
|
|
char rankString[20];
|
|
sprintf(rankString, "%05d", Dm->rank());
|
|
d_n[0] = Dm->Nx - 2;
|
|
d_n[1] = Dm->Ny - 2;
|
|
d_n[2] = Dm->Nz - 2;
|
|
d_N[0] = Dm->Nx;
|
|
d_N[1] = Dm->Ny;
|
|
d_N[2] = Dm->Nz;
|
|
|
|
d_restart_interval = db->getWithDefault<int>("restart_interval", 100000);
|
|
d_analysis_interval = db->getWithDefault<int>("analysis_interval", 1000);
|
|
d_subphase_analysis_interval = INT_MAX;
|
|
d_visualization_interval = INT_MAX;
|
|
d_blobid_interval = INT_MAX;
|
|
if (db->keyExists("blobid_interval")) {
|
|
d_blobid_interval = db->getScalar<int>("blobid_interval");
|
|
}
|
|
if (db->keyExists("visualization_interval")) {
|
|
d_visualization_interval = db->getScalar<int>("visualization_interval");
|
|
}
|
|
if (db->keyExists("subphase_analysis_interval")) {
|
|
d_subphase_analysis_interval =
|
|
db->getScalar<int>("subphase_analysis_interval");
|
|
}
|
|
|
|
auto restart_file =
|
|
db->getWithDefault<std::string>("restart_file", "Restart");
|
|
d_restartFile = restart_file + "." + rankString;
|
|
|
|
d_rank = d_comm.getRank();
|
|
writeIDMap(ID_map_struct(), 0, id_map_filename);
|
|
|
|
// Initialize IO for silo
|
|
//std::string format = "silo";
|
|
format = vis_db->getWithDefault<string>("format", "silo");
|
|
|
|
IO::initialize("", format, "false");
|
|
// Create the MeshDataStruct
|
|
d_meshData.resize(1);
|
|
|
|
d_meshData[0].meshName = "domain";
|
|
d_meshData[0].mesh = std::make_shared<IO::DomainMesh>(
|
|
d_rank_info, d_n[0], d_n[1], d_n[2], Dm->Lx, Dm->Ly, Dm->Lz);
|
|
auto PhaseVar = std::make_shared<IO::Variable>();
|
|
auto PressVar = std::make_shared<IO::Variable>();
|
|
auto VxVar = std::make_shared<IO::Variable>();
|
|
auto VyVar = std::make_shared<IO::Variable>();
|
|
auto VzVar = std::make_shared<IO::Variable>();
|
|
auto ViscousDissipationVar = std::make_shared<IO::Variable>();
|
|
auto SignDistVar = std::make_shared<IO::Variable>();
|
|
auto BlobIDVar = std::make_shared<IO::Variable>();
|
|
|
|
if (vis_db->getWithDefault<bool>("save_phase_field", true)) {
|
|
PhaseVar->name = "phase";
|
|
PhaseVar->type = IO::VariableType::VolumeVariable;
|
|
PhaseVar->dim = 1;
|
|
PhaseVar->data.resize(d_n[0], d_n[1], d_n[2]);
|
|
d_meshData[0].vars.push_back(PhaseVar);
|
|
}
|
|
|
|
if (vis_db->getWithDefault<bool>("save_pressure", false)) {
|
|
PressVar->name = "Pressure";
|
|
PressVar->type = IO::VariableType::VolumeVariable;
|
|
PressVar->dim = 1;
|
|
PressVar->data.resize(d_n[0], d_n[1], d_n[2]);
|
|
d_meshData[0].vars.push_back(PressVar);
|
|
}
|
|
|
|
if (vis_db->getWithDefault<bool>("save_velocity", false)) {
|
|
VxVar->name = "Velocity_x";
|
|
VxVar->type = IO::VariableType::VolumeVariable;
|
|
VxVar->dim = 1;
|
|
VxVar->data.resize(d_n[0], d_n[1], d_n[2]);
|
|
d_meshData[0].vars.push_back(VxVar);
|
|
VyVar->name = "Velocity_y";
|
|
VyVar->type = IO::VariableType::VolumeVariable;
|
|
VyVar->dim = 1;
|
|
VyVar->data.resize(d_n[0], d_n[1], d_n[2]);
|
|
d_meshData[0].vars.push_back(VyVar);
|
|
VzVar->name = "Velocity_z";
|
|
VzVar->type = IO::VariableType::VolumeVariable;
|
|
VzVar->dim = 1;
|
|
VzVar->data.resize(d_n[0], d_n[1], d_n[2]);
|
|
d_meshData[0].vars.push_back(VzVar);
|
|
}
|
|
|
|
if (vis_db->getWithDefault<bool>("save_dissipation", false)) {
|
|
ViscousDissipationVar->name = "ViscousDissipation";
|
|
ViscousDissipationVar->type = IO::VariableType::VolumeVariable;
|
|
ViscousDissipationVar->dim = 1;
|
|
ViscousDissipationVar->data.resize(d_n[0], d_n[1], d_n[2]);
|
|
d_meshData[0].vars.push_back(ViscousDissipationVar);
|
|
}
|
|
|
|
if (vis_db->getWithDefault<bool>("save_distance", false)) {
|
|
SignDistVar->name = "SignDist";
|
|
SignDistVar->type = IO::VariableType::VolumeVariable;
|
|
SignDistVar->dim = 1;
|
|
SignDistVar->data.resize(d_n[0], d_n[1], d_n[2]);
|
|
d_meshData[0].vars.push_back(SignDistVar);
|
|
}
|
|
|
|
if (vis_db->getWithDefault<bool>("save_connected_components", false)) {
|
|
BlobIDVar->name = "BlobID";
|
|
BlobIDVar->type = IO::VariableType::VolumeVariable;
|
|
BlobIDVar->dim = 1;
|
|
BlobIDVar->data.resize(d_n[0], d_n[1], d_n[2]);
|
|
d_meshData[0].vars.push_back(BlobIDVar);
|
|
}
|
|
|
|
// Initialize the comms
|
|
for (int i = 0; i < 1024; i++)
|
|
d_comm_used[i] = false;
|
|
// Initialize the threads
|
|
int N_threads = db->getWithDefault<int>("N_threads", 4);
|
|
auto method = db->getWithDefault<std::string>("load_balance", "default");
|
|
createThreads(method, N_threads);
|
|
}
|
|
|
|
runAnalysis::runAnalysis(ScaLBL_ColorModel &ColorModel)
|
|
/* std::shared_ptr<Database> input_db, const RankInfoStruct &rank_info,
|
|
std::shared_ptr<ScaLBL_Communicator> ScaLBL_Comm, std::shared_ptr<Domain> Dm, int Np,
|
|
bool Regular, IntArray Map )
|
|
: d_Np( Np ),
|
|
d_regular( Regular ),
|
|
d_rank_info( rank_info ),
|
|
d_Map( Map ),
|
|
d_comm( Dm->Comm.dup() ),
|
|
d_ScaLBL_Comm( ScaLBL_Comm )*/
|
|
{
|
|
|
|
d_comm = ColorModel.Dm->Comm.dup();
|
|
d_Np = ColorModel.Np;
|
|
|
|
auto input_db = ColorModel.db;
|
|
auto db = input_db->getDatabase("Analysis");
|
|
auto vis_db = input_db->getDatabase("Visualization");
|
|
|
|
// Ids of work items to use for dependencies
|
|
ThreadPool::thread_id_t d_wait_blobID;
|
|
ThreadPool::thread_id_t d_wait_analysis;
|
|
ThreadPool::thread_id_t d_wait_vis;
|
|
ThreadPool::thread_id_t d_wait_restart;
|
|
ThreadPool::thread_id_t d_wait_subphase;
|
|
|
|
char rankString[20];
|
|
sprintf(rankString, "%05d", ColorModel.Dm->rank());
|
|
d_n[0] = ColorModel.Dm->Nx - 2;
|
|
d_n[1] = ColorModel.Dm->Ny - 2;
|
|
d_n[2] = ColorModel.Dm->Nz - 2;
|
|
d_N[0] = ColorModel.Dm->Nx;
|
|
d_N[1] = ColorModel.Dm->Ny;
|
|
d_N[2] = ColorModel.Dm->Nz;
|
|
|
|
d_restart_interval = db->getWithDefault<int>("restart_interval", 100000);
|
|
d_analysis_interval = db->getWithDefault<int>("analysis_interval", 1000);
|
|
d_subphase_analysis_interval = INT_MAX;
|
|
d_visualization_interval = INT_MAX;
|
|
d_blobid_interval = INT_MAX;
|
|
if (db->keyExists("blobid_interval")) {
|
|
d_blobid_interval = db->getScalar<int>("blobid_interval");
|
|
}
|
|
if (db->keyExists("visualization_interval")) {
|
|
d_visualization_interval = db->getScalar<int>("visualization_interval");
|
|
}
|
|
if (db->keyExists("subphase_analysis_interval")) {
|
|
d_subphase_analysis_interval =
|
|
db->getScalar<int>("subphase_analysis_interval");
|
|
}
|
|
|
|
auto restart_file =
|
|
db->getWithDefault<std::string>("restart_file", "Restart");
|
|
d_restartFile = restart_file + "." + rankString;
|
|
|
|
d_rank = d_comm.getRank();
|
|
writeIDMap(ID_map_struct(), 0, id_map_filename);
|
|
// Initialize IO for silo
|
|
//std::string format = "silo";
|
|
|
|
format = vis_db->getWithDefault<string>("format", "silo");
|
|
|
|
IO::initialize("", format, "false");
|
|
// Create the MeshDataStruct
|
|
d_meshData.resize(1);
|
|
|
|
d_meshData[0].meshName = "domain";
|
|
d_meshData[0].mesh = std::make_shared<IO::DomainMesh>(
|
|
d_rank_info, d_n[0], d_n[1], d_n[2], ColorModel.Dm->Lx,
|
|
ColorModel.Dm->Ly, ColorModel.Dm->Lz);
|
|
auto PhaseVar = std::make_shared<IO::Variable>();
|
|
auto PressVar = std::make_shared<IO::Variable>();
|
|
auto VxVar = std::make_shared<IO::Variable>();
|
|
auto VyVar = std::make_shared<IO::Variable>();
|
|
auto VzVar = std::make_shared<IO::Variable>();
|
|
auto SignDistVar = std::make_shared<IO::Variable>();
|
|
auto BlobIDVar = std::make_shared<IO::Variable>();
|
|
|
|
if (vis_db->getWithDefault<bool>("save_phase_field", true)) {
|
|
PhaseVar->name = "phase";
|
|
PhaseVar->type = IO::VariableType::VolumeVariable;
|
|
PhaseVar->dim = 1;
|
|
PhaseVar->data.resize(d_n[0], d_n[1], d_n[2]);
|
|
d_meshData[0].vars.push_back(PhaseVar);
|
|
}
|
|
|
|
if (vis_db->getWithDefault<bool>("save_pressure", false)) {
|
|
PressVar->name = "Pressure";
|
|
PressVar->type = IO::VariableType::VolumeVariable;
|
|
PressVar->dim = 1;
|
|
PressVar->data.resize(d_n[0], d_n[1], d_n[2]);
|
|
d_meshData[0].vars.push_back(PressVar);
|
|
}
|
|
|
|
if (vis_db->getWithDefault<bool>("save_velocity", false)) {
|
|
VxVar->name = "Velocity_x";
|
|
VxVar->type = IO::VariableType::VolumeVariable;
|
|
VxVar->dim = 1;
|
|
VxVar->data.resize(d_n[0], d_n[1], d_n[2]);
|
|
d_meshData[0].vars.push_back(VxVar);
|
|
VyVar->name = "Velocity_y";
|
|
VyVar->type = IO::VariableType::VolumeVariable;
|
|
VyVar->dim = 1;
|
|
VyVar->data.resize(d_n[0], d_n[1], d_n[2]);
|
|
d_meshData[0].vars.push_back(VyVar);
|
|
VzVar->name = "Velocity_z";
|
|
VzVar->type = IO::VariableType::VolumeVariable;
|
|
VzVar->dim = 1;
|
|
VzVar->data.resize(d_n[0], d_n[1], d_n[2]);
|
|
d_meshData[0].vars.push_back(VzVar);
|
|
}
|
|
|
|
if (vis_db->getWithDefault<bool>("save_distance", false)) {
|
|
SignDistVar->name = "SignDist";
|
|
SignDistVar->type = IO::VariableType::VolumeVariable;
|
|
SignDistVar->dim = 1;
|
|
SignDistVar->data.resize(d_n[0], d_n[1], d_n[2]);
|
|
d_meshData[0].vars.push_back(SignDistVar);
|
|
}
|
|
|
|
if (vis_db->getWithDefault<bool>("save_connected_components", false)) {
|
|
BlobIDVar->name = "BlobID";
|
|
BlobIDVar->type = IO::VariableType::VolumeVariable;
|
|
BlobIDVar->dim = 1;
|
|
BlobIDVar->data.resize(d_n[0], d_n[1], d_n[2]);
|
|
d_meshData[0].vars.push_back(BlobIDVar);
|
|
}
|
|
|
|
// Initialize the comms
|
|
for (int i = 0; i < 1024; i++)
|
|
d_comm_used[i] = false;
|
|
// Initialize the threads
|
|
int N_threads = db->getWithDefault<int>("N_threads", 4);
|
|
auto method = db->getWithDefault<std::string>("load_balance", "default");
|
|
createThreads(method, N_threads);
|
|
}
|
|
runAnalysis::~runAnalysis() {
|
|
// Finish processing analysis
|
|
finish();
|
|
}
|
|
void runAnalysis::finish() {
|
|
PROFILE_START("finish");
|
|
// Wait for the work items to finish
|
|
d_tpool.wait_pool_finished();
|
|
// Clear the wait ids
|
|
d_wait_blobID.reset();
|
|
d_wait_analysis.reset();
|
|
d_wait_vis.reset();
|
|
d_wait_subphase.reset();
|
|
d_wait_restart.reset();
|
|
// Syncronize
|
|
d_comm.barrier();
|
|
PROFILE_STOP("finish");
|
|
}
|
|
|
|
/******************************************************************
|
|
* Set the thread affinities *
|
|
******************************************************************/
|
|
void print(const std::vector<int> &ids) {
|
|
if (ids.empty())
|
|
return;
|
|
printf("%i", ids[0]);
|
|
for (size_t i = 1; i < ids.size(); i++)
|
|
printf(", %i", ids[i]);
|
|
printf("\n");
|
|
}
|
|
void runAnalysis::createThreads(const std::string &method, int N_threads) {
|
|
// Check if we are not using analysis threads
|
|
if (method == "none")
|
|
return;
|
|
// Check if we have thread support
|
|
auto thread_support = Utilities::MPI::queryThreadSupport();
|
|
if (thread_support != Utilities::MPI::ThreadSupport::MULTIPLE &&
|
|
N_threads > 0)
|
|
std::cerr << "Warning: Failed to start MPI with necessary thread "
|
|
"support, errors may occur\n";
|
|
// Create the threads
|
|
const auto cores = d_tpool.getProcessAffinity();
|
|
if (N_threads == 0) {
|
|
// Special case to serials the analysis for debugging
|
|
d_tpool.setNumThreads(0);
|
|
} else if (cores.empty()) {
|
|
// We were not able to get the cores for the process
|
|
d_tpool.setNumThreads(N_threads);
|
|
} else if (method == "default") {
|
|
// Create the given number of threads, but let the OS manage affinities
|
|
d_tpool.setNumThreads(N_threads);
|
|
} else if (method == "independent") {
|
|
int N = cores.size() - 1;
|
|
d_tpool.setNumThreads(N);
|
|
d_tpool.setThreadAffinity({cores[0]});
|
|
for (int i = 0; i < N; i++)
|
|
d_tpool.setThreadAffinity(i, {cores[i + 1]});
|
|
}
|
|
// Print the current affinities
|
|
if (d_rank == 0) {
|
|
printf("Affinities - rank 0:\n");
|
|
printf("Main: ");
|
|
print(d_tpool.getProcessAffinity());
|
|
for (int i = 0; i < d_tpool.getNumThreads(); i++) {
|
|
printf("Thread %i: ", i + 1);
|
|
print(d_tpool.getThreadAffinity(i));
|
|
}
|
|
}
|
|
}
|
|
|
|
/******************************************************************
|
|
* Check which analysis we want to perform *
|
|
******************************************************************/
|
|
AnalysisType runAnalysis::computeAnalysisType(int timestep) {
|
|
AnalysisType type = AnalysisType::AnalyzeNone;
|
|
if (timestep % d_analysis_interval + 8 == d_analysis_interval) {
|
|
// Copy the phase indicator field for the earlier timestep
|
|
// printf("Copy phase indicator,timestep=%i\n",timestep);
|
|
type |= AnalysisType::CopyPhaseIndicator;
|
|
}
|
|
if (timestep % d_blobid_interval == 0) {
|
|
// Identify blobs and update global ids in time
|
|
type |= AnalysisType::IdentifyBlobs;
|
|
}
|
|
/*#ifdef USE_CUDA
|
|
if ( tpool.getQueueSize()<=3 && tpool.getNumThreads()>0 && timestep%50==0 ) {
|
|
// Keep a few blob identifications queued up to keep the processors busy,
|
|
// allowing us to track the blobs as fast as possible
|
|
// Add more detailed estimates of the update frequency required to track blobs
|
|
type |= AnalysisType::IdentifyBlobs;
|
|
}
|
|
#endif */
|
|
if (timestep % d_analysis_interval + 4 == d_analysis_interval) {
|
|
// Copy the averages to the CPU (and identify blobs)
|
|
// printf("Copy sim state, timestep=%i \n",timestep);
|
|
type |= AnalysisType::CopySimState;
|
|
type |= AnalysisType::IdentifyBlobs;
|
|
}
|
|
if (timestep % d_analysis_interval == 0) {
|
|
// Run the analysis
|
|
// printf("Compute averages, timestep=%i \n",timestep);
|
|
type |= AnalysisType::ComputeAverages;
|
|
}
|
|
if (timestep % d_restart_interval == 0) {
|
|
// Write the restart file
|
|
type |= AnalysisType::CreateRestart;
|
|
}
|
|
if (timestep % d_visualization_interval == 0) {
|
|
// Write the visualization data
|
|
type |= AnalysisType::WriteVis;
|
|
type |= AnalysisType::CopySimState;
|
|
type |= AnalysisType::IdentifyBlobs;
|
|
}
|
|
return type;
|
|
}
|
|
|
|
/******************************************************************
|
|
* Run the analysis *
|
|
******************************************************************/
|
|
void runAnalysis::run(int timestep, std::shared_ptr<Database> input_db,
|
|
TwoPhase &Averages, const double *Phi, double *Pressure,
|
|
double *Velocity, double *fq, double *Den) {
|
|
int N = d_N[0] * d_N[1] * d_N[2];
|
|
NULL_USE(N);
|
|
NULL_USE(Phi);
|
|
|
|
auto db = input_db->getDatabase("Analysis");
|
|
// int timestep = db->getWithDefault<int>( "timestep", 0 );
|
|
|
|
// Check which analysis steps we need to perform
|
|
auto type = computeAnalysisType(timestep);
|
|
if (type == AnalysisType::AnalyzeNone)
|
|
return;
|
|
|
|
// Check how may queued items we have
|
|
if (d_tpool.N_queued() > 20) {
|
|
std::cerr << "Analysis queue is getting behind, waiting ...\n";
|
|
finish();
|
|
}
|
|
|
|
PROFILE_START("run");
|
|
|
|
// Copy the appropriate variables to the host (so we can spawn new threads)
|
|
ScaLBL_DeviceBarrier();
|
|
PROFILE_START("Copy data to host", 1);
|
|
std::shared_ptr<DoubleArray> phase;
|
|
/* if ( matches(type,AnalysisType::CopyPhaseIndicator) ||
|
|
matches(type,AnalysisType::ComputeAverages) ||
|
|
matches(type,AnalysisType::CopySimState) ||
|
|
matches(type,AnalysisType::IdentifyBlobs) )
|
|
{
|
|
phase = std::make_shared<DoubleArray>(d_N[0],d_N[1],d_N[2]);
|
|
//ScaLBL_CopyToHost(phase->data(),Phi,N*sizeof(double));
|
|
// try 2 d_ScaLBL_Comm.RegulLayout(d_Map,Phi,Averages.Phase);
|
|
// memcpy(Averages.Phase.data(),phase->data(),N*sizeof(double));
|
|
int Nx = d_N[0];
|
|
int Ny = d_N[1];
|
|
int Nz = d_N[2];
|
|
double *TmpDat;
|
|
TmpDat = new double [d_Np];
|
|
ScaLBL_CopyToHost(&TmpDat[0],&Phi[0], d_Np*sizeof(double));
|
|
for (int k=0; k<Nz; k++){
|
|
for (int j=0; j<Ny; j++){
|
|
for (int i=0; i<Nx; i++){
|
|
int n=k*Nx*Ny+j*Nx+i;
|
|
int idx=d_Map(i,j,k);
|
|
if (!(idx<0)){
|
|
double value=TmpDat[idx];
|
|
//regdata(i,j,k)=value;
|
|
phase->data()[n]=value;
|
|
}
|
|
}
|
|
}
|
|
}
|
|
delete [] TmpDat;
|
|
}
|
|
*/
|
|
// if ( matches(type,AnalysisType::CopyPhaseIndicator) ) {
|
|
if (timestep % d_analysis_interval + 8 == d_analysis_interval) {
|
|
if (d_regular)
|
|
d_ScaLBL_Comm->RegularLayout(d_Map, Phi, Averages.Phase_tplus);
|
|
else
|
|
ScaLBL_CopyToHost(Averages.Phase_tplus.data(), Phi,
|
|
N * sizeof(double));
|
|
// memcpy(Averages.Phase_tplus.data(),phase->data(),N*sizeof(double));
|
|
}
|
|
if (timestep % d_analysis_interval == 0) {
|
|
if (d_regular)
|
|
d_ScaLBL_Comm->RegularLayout(d_Map, Phi, Averages.Phase_tminus);
|
|
else
|
|
ScaLBL_CopyToHost(Averages.Phase_tminus.data(), Phi,
|
|
N * sizeof(double));
|
|
// memcpy(Averages.Phase_tminus.data(),phase->data(),N*sizeof(double));
|
|
}
|
|
// if ( matches(type,AnalysisType::CopySimState) ) {
|
|
if (timestep % d_analysis_interval + 4 == d_analysis_interval) {
|
|
// Copy the members of Averages to the cpu (phase was copied above)
|
|
PROFILE_START("Copy-Pressure", 1);
|
|
ScaLBL_D3Q19_Pressure(fq, Pressure, d_Np);
|
|
// ScaLBL_D3Q19_Momentum(fq,Velocity,d_Np);
|
|
ScaLBL_DeviceBarrier();
|
|
PROFILE_STOP("Copy-Pressure", 1);
|
|
PROFILE_START("Copy-Wait", 1);
|
|
PROFILE_STOP("Copy-Wait", 1);
|
|
PROFILE_START("Copy-State", 1);
|
|
// memcpy(Averages.Phase.data(),phase->data(),N*sizeof(double));
|
|
if (d_regular)
|
|
d_ScaLBL_Comm->RegularLayout(d_Map, Phi, Averages.Phase);
|
|
else
|
|
ScaLBL_CopyToHost(Averages.Phase.data(), Phi, N * sizeof(double));
|
|
// copy other variables
|
|
d_ScaLBL_Comm->RegularLayout(d_Map, Pressure, Averages.Press);
|
|
d_ScaLBL_Comm->RegularLayout(d_Map, &Velocity[0], Averages.Vel_x);
|
|
d_ScaLBL_Comm->RegularLayout(d_Map, &Velocity[d_Np], Averages.Vel_y);
|
|
d_ScaLBL_Comm->RegularLayout(d_Map, &Velocity[2 * d_Np],
|
|
Averages.Vel_z);
|
|
PROFILE_STOP("Copy-State", 1);
|
|
}
|
|
std::shared_ptr<double> cfq, cDen;
|
|
// if ( matches(type,AnalysisType::CreateRestart) ) {
|
|
if (timestep % d_restart_interval == 0) {
|
|
// Copy restart data to the CPU
|
|
cDen = make_shared_array<double>(2 * d_Np);
|
|
cfq = make_shared_array<double>(19 * d_Np);
|
|
ScaLBL_CopyToHost(cfq.get(), fq, 19 * d_Np * sizeof(double));
|
|
ScaLBL_CopyToHost(cDen.get(), Den, 2 * d_Np * sizeof(double));
|
|
}
|
|
PROFILE_STOP("Copy data to host", 1);
|
|
|
|
// Spawn threads to do blob identification work
|
|
if (matches(type, AnalysisType::IdentifyBlobs)) {
|
|
phase = std::make_shared<DoubleArray>(d_N[0], d_N[1], d_N[2]);
|
|
if (d_regular)
|
|
d_ScaLBL_Comm->RegularLayout(d_Map, Phi, *phase);
|
|
else
|
|
ScaLBL_CopyToHost(phase->data(), Phi, N * sizeof(double));
|
|
|
|
auto new_index =
|
|
std::make_shared<std::pair<int, IntArray>>(0, IntArray());
|
|
auto new_ids =
|
|
std::make_shared<std::pair<int, IntArray>>(0, IntArray());
|
|
auto new_list = std::make_shared<std::vector<BlobIDType>>();
|
|
auto work1 = new BlobIdentificationWorkItem1(
|
|
timestep, d_N[0], d_N[1], d_N[2], d_rank_info, phase, Averages.SDs,
|
|
d_last_ids, new_index, new_ids, new_list, getComm());
|
|
auto work2 = new BlobIdentificationWorkItem2(
|
|
timestep, d_N[0], d_N[1], d_N[2], d_rank_info, phase, Averages.SDs,
|
|
d_last_ids, new_index, new_ids, new_list, getComm());
|
|
work1->add_dependency(d_wait_blobID);
|
|
work2->add_dependency(d_tpool.add_work(work1));
|
|
d_wait_blobID = d_tpool.add_work(work2);
|
|
d_last_index = new_index;
|
|
d_last_ids = new_ids;
|
|
d_last_id_map = new_list;
|
|
}
|
|
|
|
// Spawn threads to do the analysis work
|
|
// if (timestep%d_restart_interval==0){
|
|
// if ( matches(type,AnalysisType::ComputeAverages) ) {
|
|
if (timestep % d_analysis_interval == 0) {
|
|
auto work = new AnalysisWorkItem(type, timestep, Averages, d_last_index,
|
|
d_last_id_map, d_beta);
|
|
work->add_dependency(d_wait_blobID);
|
|
work->add_dependency(d_wait_analysis);
|
|
work->add_dependency(
|
|
d_wait_vis); // Make sure we are done using analysis before modifying
|
|
d_wait_analysis = d_tpool.add_work(work);
|
|
}
|
|
|
|
// Spawn a thread to write the restart file
|
|
// if ( matches(type,AnalysisType::CreateRestart) ) {
|
|
if (timestep % d_restart_interval == 0) {
|
|
|
|
if (d_rank == 0) {
|
|
input_db->putScalar<bool>("Restart", true);
|
|
std::ofstream OutStream("Restart.db");
|
|
input_db->print(OutStream, "");
|
|
OutStream.close();
|
|
}
|
|
// Write the restart file (using a seperate thread)
|
|
auto work =
|
|
new WriteRestartWorkItem(d_restartFile.c_str(), cDen, cfq, d_Np);
|
|
work->add_dependency(d_wait_restart);
|
|
d_wait_restart = d_tpool.add_work(work);
|
|
}
|
|
|
|
// Save the results for visualization
|
|
// if ( matches(type,AnalysisType::CreateRestart) ) {
|
|
if (timestep % d_restart_interval == 0) {
|
|
// Write the vis files
|
|
auto work = new WriteVisWorkItem(timestep, d_meshData, Averages, d_n,
|
|
d_rank_info, getComm());
|
|
work->add_dependency(d_wait_blobID);
|
|
work->add_dependency(d_wait_analysis);
|
|
work->add_dependency(d_wait_vis);
|
|
d_wait_vis = d_tpool.add_work(work);
|
|
}
|
|
PROFILE_STOP("run");
|
|
}
|
|
|
|
/******************************************************************
|
|
* Run the analysis *
|
|
******************************************************************/
|
|
void runAnalysis::basic(int timestep, std::shared_ptr<Database> input_db,
|
|
SubPhase &Averages, const double *Phi, double *Pressure,
|
|
double *Velocity, double *fq, double *Den) {
|
|
int Nx = d_N[0];
|
|
int Ny = d_N[1];
|
|
int Nz = d_N[2];
|
|
int N = Nx * Ny * Nz;
|
|
NULL_USE(N);
|
|
// Check which analysis steps we need to perform
|
|
auto color_db = input_db->getDatabase("Color");
|
|
auto vis_db = input_db->getDatabase("Visualization");
|
|
|
|
// int timestep = color_db->getWithDefault<int>( "timestep", 0 );
|
|
auto type = computeAnalysisType(timestep);
|
|
if (type == AnalysisType::AnalyzeNone)
|
|
return;
|
|
|
|
// Check how may queued items we have
|
|
if (d_tpool.N_queued() > 20) {
|
|
std::cerr << "Analysis queue is getting behind, waiting ...\n";
|
|
finish();
|
|
}
|
|
|
|
PROFILE_START("basic");
|
|
|
|
// Copy the appropriate variables to the host (so we can spawn new threads)
|
|
ScaLBL_DeviceBarrier();
|
|
PROFILE_START("Copy data to host", 1);
|
|
|
|
// if ( matches(type,AnalysisType::CopySimState) ) {
|
|
if (timestep % d_analysis_interval == 0) {
|
|
finish(); // can't copy if threads are still working on data
|
|
// Copy the members of Averages to the cpu (phase was copied above)
|
|
PROFILE_START("Copy-Pressure", 1);
|
|
ScaLBL_D3Q19_Pressure(fq, Pressure, d_Np);
|
|
// ScaLBL_D3Q19_Momentum(fq,Velocity,d_Np);
|
|
ScaLBL_DeviceBarrier();
|
|
PROFILE_STOP("Copy-Pressure", 1);
|
|
PROFILE_START("Copy-Wait", 1);
|
|
PROFILE_STOP("Copy-Wait", 1);
|
|
PROFILE_START("Copy-State", 1);
|
|
/*if (d_regular)
|
|
d_ScaLBL_Comm->RegularLayout(d_Map,Phi,Averages.Phi);
|
|
else */
|
|
ScaLBL_CopyToHost(Averages.Phi.data(), Phi, N * sizeof(double));
|
|
// copy other variables
|
|
d_ScaLBL_Comm->RegularLayout(d_Map, Pressure, Averages.Pressure);
|
|
d_ScaLBL_Comm->RegularLayout(d_Map, &Den[0], Averages.Rho_n);
|
|
d_ScaLBL_Comm->RegularLayout(d_Map, &Den[d_Np], Averages.Rho_w);
|
|
d_ScaLBL_Comm->RegularLayout(d_Map, &Velocity[0], Averages.Vel_x);
|
|
d_ScaLBL_Comm->RegularLayout(d_Map, &Velocity[d_Np], Averages.Vel_y);
|
|
d_ScaLBL_Comm->RegularLayout(d_Map, &Velocity[2 * d_Np],
|
|
Averages.Vel_z);
|
|
PROFILE_STOP("Copy-State", 1);
|
|
}
|
|
PROFILE_STOP("Copy data to host");
|
|
|
|
// Spawn threads to do the analysis work
|
|
// if (timestep%d_restart_interval==0){
|
|
// if ( matches(type,AnalysisType::ComputeAverages) ) {
|
|
if (timestep % d_analysis_interval == 0) {
|
|
auto work = new BasicWorkItem(type, timestep, Averages);
|
|
work->add_dependency(
|
|
d_wait_subphase); // Make sure we are done using analysis before modifying
|
|
work->add_dependency(d_wait_analysis);
|
|
work->add_dependency(d_wait_vis);
|
|
d_wait_analysis = d_tpool.add_work(work);
|
|
}
|
|
|
|
if (timestep % d_subphase_analysis_interval == 0) {
|
|
auto work = new SubphaseWorkItem(type, timestep, Averages);
|
|
work->add_dependency(
|
|
d_wait_subphase); // Make sure we are done using analysis before modifying
|
|
work->add_dependency(d_wait_analysis);
|
|
work->add_dependency(d_wait_vis);
|
|
d_wait_subphase = d_tpool.add_work(work);
|
|
}
|
|
|
|
if (timestep % d_restart_interval == 0) {
|
|
std::shared_ptr<double> cfq, cDen;
|
|
// Copy restart data to the CPU
|
|
cDen = make_shared_array<double>(2 * d_Np);
|
|
cfq = make_shared_array<double>(19 * d_Np);
|
|
ScaLBL_CopyToHost(cfq.get(), fq, 19 * d_Np * sizeof(double));
|
|
ScaLBL_CopyToHost(cDen.get(), Den, 2 * d_Np * sizeof(double));
|
|
|
|
if (d_rank == 0) {
|
|
color_db->putScalar<int>("timestep", timestep);
|
|
color_db->putScalar<bool>("Restart", true);
|
|
input_db->putDatabase("Color", color_db);
|
|
std::ofstream OutStream("Restart.db");
|
|
input_db->print(OutStream, "");
|
|
OutStream.close();
|
|
}
|
|
// Write the restart file (using a seperate thread)
|
|
auto work1 =
|
|
new WriteRestartWorkItem(d_restartFile.c_str(), cDen, cfq, d_Np);
|
|
work1->add_dependency(d_wait_restart);
|
|
d_wait_restart = d_tpool.add_work(work1);
|
|
}
|
|
|
|
if (timestep % d_visualization_interval == 0) {
|
|
// Write the vis files
|
|
auto work = new IOWorkItem(timestep, input_db, d_meshData, Averages,
|
|
d_n, d_rank_info, getComm());
|
|
work->add_dependency(d_wait_analysis);
|
|
work->add_dependency(d_wait_subphase);
|
|
work->add_dependency(d_wait_vis);
|
|
d_wait_vis = d_tpool.add_work(work);
|
|
}
|
|
|
|
PROFILE_STOP("basic");
|
|
}
|
|
|
|
void runAnalysis::WriteVisData(int timestep, std::shared_ptr<Database> input_db,
|
|
SubPhase &Averages, const double *Phi,
|
|
double *Pressure, double *Velocity, double *fq,
|
|
double *Den) {
|
|
auto color_db = input_db->getDatabase("Color");
|
|
auto vis_db = input_db->getDatabase("Visualization");
|
|
// int timestep = color_db->getWithDefault<int>( "timestep", 0 );
|
|
|
|
// Check which analysis steps we need to perform
|
|
auto type = computeAnalysisType(timestep);
|
|
if (type == AnalysisType::AnalyzeNone)
|
|
return;
|
|
|
|
// Check how may queued items we have
|
|
if (d_tpool.N_queued() > 20) {
|
|
std::cerr << "Analysis queue is getting behind, waiting ...\n";
|
|
finish();
|
|
}
|
|
|
|
// Copy the appropriate variables to the host (so we can spawn new threads)
|
|
ScaLBL_DeviceBarrier();
|
|
|
|
PROFILE_START("write vis", 1);
|
|
|
|
// if (Averages.WriteVis == true){
|
|
auto work2 = new IOWorkItem(timestep, input_db, d_meshData, Averages, d_n,
|
|
d_rank_info, getComm());
|
|
work2->add_dependency(d_wait_vis);
|
|
d_wait_vis = d_tpool.add_work(work2);
|
|
|
|
// Averages.WriteVis = false;
|
|
|
|
PROFILE_STOP("write vis");
|
|
}
|