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computeStats not working correctly, Unit Tests added

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rastogi 2025-09-01 12:39:01 +02:00 committed by Max Lübke
parent 3500a24b4b
commit 858da525d7
12 changed files with 789 additions and 510 deletions
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4
CMakeLists.txt
View File

@ -28,12 +28,12 @@ if (POET_PREPROCESS_BENCHS)
endif()
# as tug will also pull in doctest as a dependency
set(TUG_ENABLE_TESTING OFF CACHE BOOL "" FORCE)
set(TUG_ENABLE_TESTING ON CACHE BOOL "" FORCE)
add_subdirectory(ext/tug EXCLUDE_FROM_ALL)
add_subdirectory(ext/iphreeqc EXCLUDE_FROM_ALL)
option(POET_ENABLE_TESTING "Build test suite for POET" OFF)
option(POET_ENABLE_TESTING "Build test suite for POET" ON)
if (POET_ENABLE_TESTING)
add_subdirectory(test)

1
src/CMakeLists.txt
View File

@ -22,6 +22,7 @@ add_library(POETLib
Init/DiffusionInit.cpp
Init/ChemistryInit.cpp
IO/checkpoint.cpp
IO/StatsIO.cpp
DataStructures/Field.cpp
Transport/DiffusionModule.cpp
Chemistry/ChemistryModule.cpp

768
src/Chemistry/ChemistryModule.hpp
View File

@ -23,392 +23,432 @@
#include <string>
#include <vector>
namespace poet {
/**
* \brief Wrapper around PhreeqcRM to provide POET specific parallelization with
* easy access.
*/
class ChemistryModule {
public:
namespace poet
{
/**
* Creates a new instance of Chemistry module with given grid cell count, work
* package size and communicator.
*
* This constructor shall only be called by the master. To create workers, see
* ChemistryModule::createWorker .
*
* When the use of parallelization is intended, the nxyz value shall be set to
* 1 to save memory and only one node is needed for initialization.
*
* \param nxyz Count of grid cells to allocate and initialize for each
* process. For parellel use set to 1 at the master.
* \param wp_size Count of grid cells to fill each work package at maximum.
* \param communicator MPI communicator to distribute work in.
* \brief Wrapper around PhreeqcRM to provide POET specific parallelization with
* easy access.
*/
ChemistryModule(uint32_t wp_size,
const InitialList::ChemistryInit chem_params,
MPI_Comm communicator);
class ChemistryModule
{
public:
/**
* Creates a new instance of Chemistry module with given grid cell count, work
* package size and communicator.
*
* This constructor shall only be called by the master. To create workers, see
* ChemistryModule::createWorker .
*
* When the use of parallelization is intended, the nxyz value shall be set to
* 1 to save memory and only one node is needed for initialization.
*
* \param nxyz Count of grid cells to allocate and initialize for each
* process. For parellel use set to 1 at the master.
* \param wp_size Count of grid cells to fill each work package at maximum.
* \param communicator MPI communicator to distribute work in.
*/
ChemistryModule(uint32_t wp_size,
const InitialList::ChemistryInit chem_params,
MPI_Comm communicator);
/**
* Deconstructor, which frees DHT data structure if used.
*/
~ChemistryModule();
/**
* Deconstructor, which frees DHT data structure if used.
*/
~ChemistryModule();
void masterSetField(Field field);
/**
* Run the chemical simulation with parameters set.
*/
void simulate(double dt);
void masterSetField(Field field);
/**
* Run the chemical simulation with parameters set.
*/
void simulate(double dt);
/**
* Returns all known species names, including not only aqueous species, but
* also equilibrium, exchange, surface and kinetic reactants.
*/
// auto GetPropNames() const { return this->prop_names; }
/**
* Returns all known species names, including not only aqueous species, but
* also equilibrium, exchange, surface and kinetic reactants.
*/
// auto GetPropNames() const { return this->prop_names; }
/**
* Return the accumulated runtime in seconds for chemical simulation.
*/
auto GetChemistryTime() const { return this->chem_t; }
/**
* Return the accumulated runtime in seconds for chemical simulation.
*/
auto GetChemistryTime() const { return this->chem_t; }
void setFilePadding(std::uint32_t maxiter) {
this->file_pad =
static_cast<std::uint8_t>(std::ceil(std::log10(maxiter + 1)));
}
void setFilePadding(std::uint32_t maxiter)
{
this->file_pad =
static_cast<std::uint8_t>(std::ceil(std::log10(maxiter + 1)));
}
struct SurrogateSetup {
std::vector<std::string> prop_names;
std::array<double, 2> base_totals;
bool has_het_ids;
struct SurrogateSetup
{
std::vector<std::string> prop_names;
std::array<double, 2> base_totals;
bool has_het_ids;
bool dht_enabled;
std::uint32_t dht_size_mb;
int dht_snaps;
std::string dht_out_dir;
bool dht_enabled;
std::uint32_t dht_size_mb;
int dht_snaps;
std::string dht_out_dir;
bool interp_enabled;
std::uint32_t interp_bucket_size;
std::uint32_t interp_size_mb;
std::uint32_t interp_min_entries;
bool ai_surrogate_enabled;
};
bool interp_enabled;
std::uint32_t interp_bucket_size;
std::uint32_t interp_size_mb;
std::uint32_t interp_min_entries;
bool ai_surrogate_enabled;
};
void masterEnableSurrogates(const SurrogateSetup &setup) {
// FIXME: This is a hack to get the prop_names and prop_count from the setup
this->prop_names = setup.prop_names;
this->prop_count = setup.prop_names.size();
void masterEnableSurrogates(const SurrogateSetup &setup)
{
// FIXME: This is a hack to get the prop_names and prop_count from the setup
this->prop_names = setup.prop_names;
this->prop_count = setup.prop_names.size();
this->dht_enabled = setup.dht_enabled;
this->interp_enabled = setup.interp_enabled;
this->ai_surrogate_enabled = setup.ai_surrogate_enabled;
this->dht_enabled = setup.dht_enabled;
this->interp_enabled = setup.interp_enabled;
this->ai_surrogate_enabled = setup.ai_surrogate_enabled;
this->base_totals = setup.base_totals;
this->base_totals = setup.base_totals;
if (this->dht_enabled || this->interp_enabled) {
this->initializeDHT(setup.dht_size_mb, this->params.dht_species,
setup.has_het_ids);
if (this->dht_enabled || this->interp_enabled)
{
this->initializeDHT(setup.dht_size_mb, this->params.dht_species,
setup.has_het_ids);
if (setup.dht_snaps != DHT_SNAPS_DISABLED) {
this->setDHTSnapshots(setup.dht_snaps, setup.dht_out_dir);
if (setup.dht_snaps != DHT_SNAPS_DISABLED)
{
this->setDHTSnapshots(setup.dht_snaps, setup.dht_out_dir);
}
}
if (this->interp_enabled)
{
this->initializeInterp(setup.interp_bucket_size, setup.interp_size_mb,
setup.interp_min_entries,
this->params.interp_species);
}
}
if (this->interp_enabled) {
this->initializeInterp(setup.interp_bucket_size, setup.interp_size_mb,
setup.interp_min_entries,
this->params.interp_species);
/**
* Intended to alias input parameters for grid initialization with a single
* value per species.
*/
using SingleCMap = std::unordered_map<std::string, double>;
/**
* Intended to alias input parameters for grid initialization with mutlitple
* values per species.
*/
using VectorCMap = std::unordered_map<std::string, std::vector<double>>;
/**
* Enumerating DHT file options
*/
enum
{
DHT_SNAPS_DISABLED = 0, //!< disabled file output
DHT_SNAPS_SIMEND, //!< only output of snapshot after simulation
DHT_SNAPS_ITEREND //!< output snapshots after each iteration
};
/**
* **Only called by workers!** Start the worker listening loop.
*/
void WorkerLoop();
/**
* **Called by master** Advise the workers to break the loop.
*/
void MasterLoopBreak();
/**
* **Master only** Return count of grid cells.
*/
auto GetNCells() const { return this->n_cells; }
/**
* **Master only** Return work package size.
*/
auto GetWPSize() const { return this->wp_size; }
/**
* **Master only** Return the time in seconds the master spent waiting for any
* free worker.
*/
auto GetMasterIdleTime() const { return this->idle_t; }
/**
* **Master only** Return the time in seconds the master spent in sequential
* part of the simulation, including times for shuffling/unshuffling field
* etc.
*/
auto GetMasterSequentialTime() const { return this->seq_t; }
/**
* **Master only** Return the time in seconds the master spent in the
* send/receive loop.
*/
auto GetMasterLoopTime() const { return this->send_recv_t; }
/**
* **Master only** Collect and return all accumulated timings recorded by
* workers to run Phreeqc simulation.
*
* \return Vector of all accumulated Phreeqc timings.
*/
std::vector<double> GetWorkerPhreeqcTimings() const;
/**
* **Master only** Collect and return all accumulated timings recorded by
* workers to get values from the DHT.
*
* \return Vector of all accumulated DHT get times.
*/
std::vector<double> GetWorkerDHTGetTimings() const;
/**
* **Master only** Collect and return all accumulated timings recorded by
* workers to write values to the DHT.
*
* \return Vector of all accumulated DHT fill times.
*/
std::vector<double> GetWorkerDHTFillTimings() const;
/**
* **Master only** Collect and return all accumulated timings recorded by
* workers waiting for work packages from the master.
*
* \return Vector of all accumulated waiting times.
*/
std::vector<double> GetWorkerIdleTimings() const;
/**
* **Master only** Collect and return DHT hits of all workers.
*
* \return Vector of all count of DHT hits.
*/
std::vector<uint32_t> GetWorkerDHTHits() const;
/**
* **Master only** Collect and return DHT evictions of all workers.
*
* \return Vector of all count of DHT evictions.
*/
std::vector<uint32_t> GetWorkerDHTEvictions() const;
/**
* **Master only** Returns the current state of the chemical field.
*
* \return Reference to the chemical field.
*/
Field &getField() { return this->chem_field; }
/**
* **Master only** Enable/disable progress bar.
*
* \param enabled True if print progressbar, false if not.
*/
void setProgressBarPrintout(bool enabled)
{
this->print_progessbar = enabled;
};
/**
* **Master only** Set the ai surrogate validity vector from R
*/
void set_ai_surrogate_validity_vector(std::vector<int> r_vector);
std::vector<uint32_t> GetWorkerInterpolationCalls() const;
std::vector<double> GetWorkerInterpolationWriteTimings() const;
std::vector<double> GetWorkerInterpolationReadTimings() const;
std::vector<double> GetWorkerInterpolationGatherTimings() const;
std::vector<double> GetWorkerInterpolationFunctionCallTimings() const;
std::vector<uint32_t> GetWorkerPHTCacheHits() const;
std::vector<int> ai_surrogate_validity_vector;
RuntimeParameters *runtime_params = nullptr;
uint32_t control_iteration_counter = 0;
struct error_stats
{
std::vector<double> mape;
std::vector<double> rrsme;
uint32_t iteration;
error_stats(size_t species_count, size_t iter)
: mape(species_count, 0.0), rrsme(species_count, 0.0), iteration(iter) {}
};
std::vector<error_stats> error_stats_history;
static void computeStats(const std::vector<double> &pqc_vector,
const std::vector<double> &sur_vector,
uint32_t size_per_prop, uint32_t species_count,
error_stats &stats);
protected:
void initializeDHT(uint32_t size_mb,
const NamedVector<std::uint32_t> &key_species,
bool has_het_ids);
void setDHTSnapshots(int type, const std::string &out_dir);
void setDHTReadFile(const std::string &input_file);
void initializeInterp(std::uint32_t bucket_size, std::uint32_t size_mb,
std::uint32_t min_entries,
const NamedVector<std::uint32_t> &key_species);
enum
{
CHEM_FIELD_INIT,
CHEM_DHT_ENABLE,
CHEM_DHT_SIGNIF_VEC,
CHEM_DHT_SNAPS,
CHEM_DHT_READ_FILE,
CHEM_IP_ENABLE,
CHEM_IP_MIN_ENTRIES,
CHEM_IP_SIGNIF_VEC,
CHEM_WORK_LOOP,
CHEM_PERF,
CHEM_BREAK_MAIN_LOOP,
CHEM_AI_BCAST_VALIDITY
};
enum
{
LOOP_WORK,
LOOP_END,
LOOP_CTRL
};
enum
{
WORKER_PHREEQC,
WORKER_DHT_GET,
WORKER_DHT_FILL,
WORKER_IDLE,
WORKER_IP_WRITE,
WORKER_IP_READ,
WORKER_IP_GATHER,
WORKER_IP_FC,
WORKER_DHT_HITS,
WORKER_DHT_EVICTIONS,
WORKER_PHT_CACHE_HITS,
WORKER_IP_CALLS
};
std::vector<uint32_t> interp_calls;
std::vector<uint32_t> dht_hits;
std::vector<uint32_t> dht_evictions;
struct worker_s
{
double phreeqc_t = 0.;
double dht_get = 0.;
double dht_fill = 0.;
double idle_t = 0.;
};
struct worker_info_s
{
char has_work = 0;
double *send_addr;
};
using worker_list_t = std::vector<struct worker_info_s>;
using workpointer_t = std::vector<double>::iterator;
void MasterRunParallel(double dt);
void MasterRunSequential();
void MasterSendPkgs(worker_list_t &w_list, workpointer_t &work_pointer,
int &pkg_to_send, int &count_pkgs, int &free_workers,
double dt, uint32_t iteration, uint32_t control_iteration,
const std::vector<uint32_t> &wp_sizes_vector);
void MasterRecvPkgs(worker_list_t &w_list, int &pkg_to_recv, bool to_send,
int &free_workers);
std::vector<double> MasterGatherWorkerTimings(int type) const;
std::vector<uint32_t> MasterGatherWorkerMetrics(int type) const;
void WorkerProcessPkgs(struct worker_s &timings, uint32_t &iteration);
void WorkerDoWork(MPI_Status &probe_status, int double_count,
struct worker_s &timings);
void WorkerPostIter(MPI_Status &prope_status, uint32_t iteration);
void WorkerPostSim(uint32_t iteration);
void WorkerWriteDHTDump(uint32_t iteration);
void WorkerReadDHTDump(const std::string &dht_input_file);
void WorkerPerfToMaster(int type, const struct worker_s &timings);
void WorkerMetricsToMaster(int type);
void WorkerRunWorkPackage(WorkPackage &work_package, double dSimTime,
double dTimestep);
std::vector<uint32_t> CalculateWPSizesVector(uint32_t n_cells,
uint32_t wp_size) const;
std::vector<double> shuffleField(const std::vector<double> &in_field,
uint32_t size_per_prop, uint32_t prop_count,
uint32_t wp_count);
void unshuffleField(const std::vector<double> &in_buffer,
uint32_t size_per_prop, uint32_t prop_count,
uint32_t wp_count, std::vector<double> &out_field);
std::vector<std::int32_t>
parseDHTSpeciesVec(const NamedVector<std::uint32_t> &key_species,
const std::vector<std::string> &to_compare) const;
void BCastStringVec(std::vector<std::string> &io);
int comm_size, comm_rank;
MPI_Comm group_comm;
bool is_sequential;
bool is_master;
uint32_t wp_size;
bool dht_enabled{false};
int dht_snaps_type{DHT_SNAPS_DISABLED};
std::string dht_file_out_dir;
poet::DHT_Wrapper *dht = nullptr;
bool interp_enabled{false};
std::unique_ptr<poet::InterpolationModule> interp;
bool ai_surrogate_enabled{false};
static constexpr uint32_t BUFFER_OFFSET = 6;
inline void ChemBCast(void *buf, int count, MPI_Datatype datatype) const
{
MPI_Bcast(buf, count, datatype, 0, this->group_comm);
}
}
/**
* Intended to alias input parameters for grid initialization with a single
* value per species.
*/
using SingleCMap = std::unordered_map<std::string, double>;
/**
* Intended to alias input parameters for grid initialization with mutlitple
* values per species.
*/
using VectorCMap = std::unordered_map<std::string, std::vector<double>>;
/**
* Enumerating DHT file options
*/
enum {
DHT_SNAPS_DISABLED = 0, //!< disabled file output
DHT_SNAPS_SIMEND, //!< only output of snapshot after simulation
DHT_SNAPS_ITEREND //!< output snapshots after each iteration
};
/**
* **Only called by workers!** Start the worker listening loop.
*/
void WorkerLoop();
/**
* **Called by master** Advise the workers to break the loop.
*/
void MasterLoopBreak();
/**
* **Master only** Return count of grid cells.
*/
auto GetNCells() const { return this->n_cells; }
/**
* **Master only** Return work package size.
*/
auto GetWPSize() const { return this->wp_size; }
/**
* **Master only** Return the time in seconds the master spent waiting for any
* free worker.
*/
auto GetMasterIdleTime() const { return this->idle_t; }
/**
* **Master only** Return the time in seconds the master spent in sequential
* part of the simulation, including times for shuffling/unshuffling field
* etc.
*/
auto GetMasterSequentialTime() const { return this->seq_t; }
/**
* **Master only** Return the time in seconds the master spent in the
* send/receive loop.
*/
auto GetMasterLoopTime() const { return this->send_recv_t; }
/**
* **Master only** Collect and return all accumulated timings recorded by
* workers to run Phreeqc simulation.
*
* \return Vector of all accumulated Phreeqc timings.
*/
std::vector<double> GetWorkerPhreeqcTimings() const;
/**
* **Master only** Collect and return all accumulated timings recorded by
* workers to get values from the DHT.
*
* \return Vector of all accumulated DHT get times.
*/
std::vector<double> GetWorkerDHTGetTimings() const;
/**
* **Master only** Collect and return all accumulated timings recorded by
* workers to write values to the DHT.
*
* \return Vector of all accumulated DHT fill times.
*/
std::vector<double> GetWorkerDHTFillTimings() const;
/**
* **Master only** Collect and return all accumulated timings recorded by
* workers waiting for work packages from the master.
*
* \return Vector of all accumulated waiting times.
*/
std::vector<double> GetWorkerIdleTimings() const;
/**
* **Master only** Collect and return DHT hits of all workers.
*
* \return Vector of all count of DHT hits.
*/
std::vector<uint32_t> GetWorkerDHTHits() const;
/**
* **Master only** Collect and return DHT evictions of all workers.
*
* \return Vector of all count of DHT evictions.
*/
std::vector<uint32_t> GetWorkerDHTEvictions() const;
/**
* **Master only** Returns the current state of the chemical field.
*
* \return Reference to the chemical field.
*/
Field &getField() { return this->chem_field; }
/**
* **Master only** Enable/disable progress bar.
*
* \param enabled True if print progressbar, false if not.
*/
void setProgressBarPrintout(bool enabled) {
this->print_progessbar = enabled;
};
/**
* **Master only** Set the ai surrogate validity vector from R
*/
void set_ai_surrogate_validity_vector(std::vector<int> r_vector);
std::vector<uint32_t> GetWorkerInterpolationCalls() const;
std::vector<double> GetWorkerInterpolationWriteTimings() const;
std::vector<double> GetWorkerInterpolationReadTimings() const;
std::vector<double> GetWorkerInterpolationGatherTimings() const;
std::vector<double> GetWorkerInterpolationFunctionCallTimings() const;
std::vector<uint32_t> GetWorkerPHTCacheHits() const;
std::vector<int> ai_surrogate_validity_vector;
RuntimeParameters *runtime_params = nullptr;
protected:
void initializeDHT(uint32_t size_mb,
const NamedVector<std::uint32_t> &key_species,
bool has_het_ids);
void setDHTSnapshots(int type, const std::string &out_dir);
void setDHTReadFile(const std::string &input_file);
void initializeInterp(std::uint32_t bucket_size, std::uint32_t size_mb,
std::uint32_t min_entries,
const NamedVector<std::uint32_t> &key_species);
enum {
CHEM_FIELD_INIT,
CHEM_DHT_ENABLE,
CHEM_DHT_SIGNIF_VEC,
CHEM_DHT_SNAPS,
CHEM_DHT_READ_FILE,
CHEM_IP_ENABLE,
CHEM_IP_MIN_ENTRIES,
CHEM_IP_SIGNIF_VEC,
CHEM_WORK_LOOP,
CHEM_PERF,
CHEM_BREAK_MAIN_LOOP,
CHEM_AI_BCAST_VALIDITY
};
enum { LOOP_WORK, LOOP_END, WITH_REL_ERROR };
enum {
WORKER_PHREEQC,
WORKER_DHT_GET,
WORKER_DHT_FILL,
WORKER_IDLE,
WORKER_IP_WRITE,
WORKER_IP_READ,
WORKER_IP_GATHER,
WORKER_IP_FC,
WORKER_DHT_HITS,
WORKER_DHT_EVICTIONS,
WORKER_PHT_CACHE_HITS,
WORKER_IP_CALLS
};
std::vector<uint32_t> interp_calls;
std::vector<uint32_t> dht_hits;
std::vector<uint32_t> dht_evictions;
struct worker_s {
double phreeqc_t = 0.;
double dht_get = 0.;
double dht_fill = 0.;
inline void PropagateFunctionType(int &type) const
{
ChemBCast(&type, 1, MPI_INT);
}
double simtime = 0.;
double idle_t = 0.;
double seq_t = 0.;
double send_recv_t = 0.;
std::array<double, 2> base_totals{0};
bool print_progessbar{false};
std::uint8_t file_pad{1};
double chem_t{0.};
uint32_t n_cells = 0;
uint32_t prop_count = 0;
std::vector<std::string> prop_names;
Field chem_field;
const InitialList::ChemistryInit params;
std::unique_ptr<PhreeqcRunner> pqc_runner;
std::vector<double> sur_shuffled;
};
struct worker_info_s {
char has_work = 0;
double *send_addr;
};
using worker_list_t = std::vector<struct worker_info_s>;
using workpointer_t = std::vector<double>::iterator;
void MasterRunParallel(double dt);
void MasterRunSequential();
void MasterSendPkgs(worker_list_t &w_list, workpointer_t &work_pointer,
int &pkg_to_send, int &count_pkgs, int &free_workers,
double dt, uint32_t iteration, uint32_t control_iter,
const std::vector<uint32_t> &wp_sizes_vector);
void MasterRecvPkgs(worker_list_t &w_list, int &pkg_to_recv, bool to_send,
int &free_workers);
std::vector<double> MasterGatherWorkerTimings(int type) const;
std::vector<uint32_t> MasterGatherWorkerMetrics(int type) const;
void WorkerProcessPkgs(struct worker_s &timings, uint32_t &iteration);
void WorkerDoWork(MPI_Status &probe_status, int double_count,
struct worker_s &timings);
void WorkerPostIter(MPI_Status &prope_status, uint32_t iteration);
void WorkerPostSim(uint32_t iteration);
void WorkerWriteDHTDump(uint32_t iteration);
void WorkerReadDHTDump(const std::string &dht_input_file);
void WorkerPerfToMaster(int type, const struct worker_s &timings);
void WorkerMetricsToMaster(int type);
void WorkerRunWorkPackage(WorkPackage &work_package, double dSimTime,
double dTimestep);
std::vector<uint32_t> CalculateWPSizesVector(uint32_t n_cells,
uint32_t wp_size) const;
std::vector<double> shuffleField(const std::vector<double> &in_field,
uint32_t size_per_prop, uint32_t prop_count,
uint32_t wp_count);
void unshuffleField(const std::vector<double> &in_buffer,
uint32_t size_per_prop, uint32_t prop_count,
uint32_t wp_count, std::vector<double> &out_field);
std::vector<std::int32_t>
parseDHTSpeciesVec(const NamedVector<std::uint32_t> &key_species,
const std::vector<std::string> &to_compare) const;
void BCastStringVec(std::vector<std::string> &io);
int comm_size, comm_rank;
MPI_Comm group_comm;
bool is_sequential;
bool is_master;
uint32_t wp_size;
bool dht_enabled{false};
int dht_snaps_type{DHT_SNAPS_DISABLED};
std::string dht_file_out_dir;
poet::DHT_Wrapper *dht = nullptr;
bool interp_enabled{false};
std::unique_ptr<poet::InterpolationModule> interp;
bool ai_surrogate_enabled{false};
static constexpr uint32_t BUFFER_OFFSET = 6;
inline void ChemBCast(void *buf, int count, MPI_Datatype datatype) const {
MPI_Bcast(buf, count, datatype, 0, this->group_comm);
}
inline void PropagateFunctionType(int &type) const {
ChemBCast(&type, 1, MPI_INT);
}
double simtime = 0.;
double idle_t = 0.;
double seq_t = 0.;
double send_recv_t = 0.;
std::array<double, 2> base_totals{0};
bool print_progessbar{false};
std::uint8_t file_pad{1};
double chem_t{0.};
uint32_t n_cells = 0;
uint32_t prop_count = 0;
std::vector<std::string> prop_names;
Field chem_field;
const InitialList::ChemistryInit params;
std::unique_ptr<PhreeqcRunner> pqc_runner;
};
} // namespace poet
#endif // CHEMISTRYMODULE_H_

128
src/Chemistry/MasterFunctions.cpp
View File

@ -3,6 +3,7 @@
#include <algorithm>
#include <cstddef>
#include <cstdint>
#include <iomanip>
#include <mpi.h>
#include <vector>
@ -172,6 +173,61 @@ std::vector<uint32_t> poet::ChemistryModule::GetWorkerPHTCacheHits() const
return ret;
}
void poet::ChemistryModule::computeStats(const std::vector<double> &pqc_vector,
const std::vector<double> &sur_vector,
uint32_t size_per_prop, uint32_t species_count,
error_stats &stats)
{
for (uint32_t i = 0; i < species_count; i++)
{
double err_sum = 0.0;
double sqr_err_sum = 0.0;
int count = 0;
for (uint32_t j = 0; j < size_per_prop; j++)
{
double pqc_value = pqc_vector[i * size_per_prop + j];
double sur_value = sur_vector[i * size_per_prop + j];
if (i == 0 && (j % 10000 == 0)) {
std::cout << "i=" << i << ", j=" << j
<< ", idx=" << i * size_per_prop + j
<< ", pqc=" << pqc_value
<< ", sur=" << sur_value
<< std::endl;
}
if (pqc_value != 0)
{
double rel_err = (pqc_value - sur_value) / pqc_value;
err_sum += std::abs(rel_err);
sqr_err_sum += rel_err * rel_err;
count++;
}
if (pqc_value == 0 && sur_value != 0)
{
err_sum += 1.0;
sqr_err_sum += 1.0;
count++;
}
if (pqc_value == 0 && sur_value == 0)
{
}
// else: both cases are zero, skip (no error)
}
if (i == 0)
{
std::cout << "computeStats, i==0, err_sum: " << err_sum << std::endl;
std::cout << "computeStats, i==0, sqr_err_sum: " << sqr_err_sum << std::endl;
}
stats.mape[i] = (count > 0) ? (100.0 / count) * err_sum : 0.0;
stats.rrsme[i] = (count > 0) ? std::sqrt(sqr_err_sum / count) : 0.0;
}
}
inline std::vector<int> shuffleVector(const std::vector<int> &in_vector,
uint32_t size_per_prop,
@ -355,30 +411,21 @@ inline void poet::ChemistryModule::MasterRecvPkgs(worker_list_t &w_list,
pkg_to_recv -= 1;
free_workers++;
}
if (probe_status.MPI_TAG == WITH_REL_ERROR)
if (probe_status.MPI_TAG == LOOP_CTRL)
{
MPI_Get_count(&probe_status, MPI_DOUBLE, &size);
std::cout << "[Master] Probed rel error from worker " << p
<< ", size = " << size << std::endl;
// layout of buffer is [phreeqc][surrogate]
std::vector<double> recv_buffer(size);
int half = size/2;
std::vector<double> rel_err_buffer(size);
std::vector<double> rel_error(half);
MPI_Recv(rel_err_buffer.data(), size, MPI_DOUBLE, p, WITH_REL_ERROR,
MPI_Recv(recv_buffer.data(), size, MPI_DOUBLE, p, LOOP_CTRL,
this->group_comm, MPI_STATUS_IGNORE);
std::copy(recv_buffer.begin(), recv_buffer.begin() + (size / 2),
w_list[p - 1].send_addr);
std::copy(rel_err_buffer.begin(), rel_err_buffer.begin() + half,
w_list[p - 1].send_addr);
std::copy(rel_err_buffer.begin() + half, rel_err_buffer.end(), rel_error.begin());
std::cout << "[Master] Received rel error buffer from worker " << p
<< ", first value = " << (rel_err_buffer.empty() ? -1 : rel_err_buffer[0])
<< std::endl;
sur_shuffled.insert(sur_shuffled.end(), recv_buffer.begin() + (size / 2),
recv_buffer.begin() + size);
w_list[p - 1].has_work = 0;
pkg_to_recv -= 1;
@ -461,12 +508,18 @@ void poet::ChemistryModule::MasterRunParallel(double dt)
static uint32_t iteration = 0;
uint32_t control_iteration = static_cast<uint32_t>(this->runtime_params->control_iteration_active ? 1 : 0);
if (control_iteration)
{
sur_shuffled.clear();
sur_shuffled.reserve(this->n_cells * this->prop_count);
}
/* start time measurement of sequential part */
seq_a = MPI_Wtime();
/* shuffle grid */
// grid.shuffleAndExport(mpi_buffer);
std::vector<double> mpi_buffer =
shuffleField(chem_field.AsVector(), this->n_cells, this->prop_count,
wp_sizes_vector.size());
@ -507,30 +560,6 @@ void poet::ChemistryModule::MasterRunParallel(double dt)
// ... and try to receive them from workers who has finished their work
MasterRecvPkgs(worker_list, pkg_to_recv, pkg_to_send > 0, free_workers);
}
// to do: Statistik
/* if control_iteration_active is true receive rel. error data and compare with epsilon */
if (this->runtime_params->control_iteration_active)
{
// do Statistik
/**
int rel_err_offset = size / 2; // or calculate as needed
for (std::size_t ep_i = 0; ep_i < this->runtime_params->species_epsilon.size(); ep_i++)
{
if (rel_err_buffer[rel_err_offset + ep_i] > this->runtime_params->species_epsilon[ep_i])
{
std::cout << "[Master] At least one relative error exceeded epsilon threshold!"
<< std::endl;
std::cout << "value: " << rel_err_buffer[rel_err_offset + ep_i] << " epsilon: "
<< this->runtime_params->species_epsilon[ep_i] << std::endl;
break;
}
}
*/
}
// Just to complete the progressbar
std::cout << std::endl;
@ -551,6 +580,23 @@ void poet::ChemistryModule::MasterRunParallel(double dt)
/* do master stuff */
if (control_iteration)
{
control_iteration_counter++;
std::vector<double> sur_unshuffled{sur_shuffled};
unshuffleField(sur_shuffled, this->n_cells, this->prop_count,
wp_sizes_vector.size(), sur_unshuffled);
error_stats stats(this->prop_count, control_iteration_counter * runtime_params->control_iteration);
computeStats(out_vec, sur_unshuffled, this->n_cells, this->prop_count, stats);
error_stats_history.push_back(stats);
// to do: control values to epsilon
}
/* start time measurement of master chemistry */
sim_e_chemistry = MPI_Wtime();

75
src/Chemistry/WorkerFunctions.cpp
View File

@ -239,76 +239,47 @@ namespace poet
if (control_iteration_active)
{
// increase size for relative error
std::size_t rel_error_size = s_curr_wp.size * this->prop_count;
std::size_t sur_wp_offset = s_curr_wp.size * this->prop_count;
// extend mpi_buffer, for rel. error for every species
mpi_buffer.resize(count + rel_error_size);
std::size_t offset = count;
count += rel_error_size;
mpi_buffer.resize(count + sur_wp_offset);
// calc rel. error if phreeqc != surrogate
for (std::size_t wp_i = 0; wp_i < s_curr_wp_pqc.size; wp_i++)
{
const auto &surrogate_result = s_curr_wp.output[wp_i];
const auto &phreeqc_result = s_curr_wp_pqc.output[wp_i];
// std::cout << "surrogate_result.size() " << surrogate_result.size() << ", phreeqc_result " << phreeqc_result.size() << std::endl;
// fill NaNs
if (surrogate_result.size() == 0)
{
for (std::size_t i = 0; i < this->prop_count; i++)
{
mpi_buffer[offset++] = std::numeric_limits<double>::quiet_NaN();
}
}
// compute rel error
if (surrogate_result.size() == phreeqc_result.size())
{
for (std::size_t i = 0; i < this->prop_count; i++)
{
double ref = phreeqc_result[i];
double surrogate = surrogate_result[i];
if (std::abs(ref) > 1e-9)
{
mpi_buffer[offset++] = std::abs((surrogate - ref) / ref);
}
else
{
mpi_buffer[offset++] = 0.0;
}
}
}
std::copy(s_curr_wp_pqc.output[wp_i].begin(), s_curr_wp_pqc.output[wp_i].end(),
mpi_buffer.begin() + this->prop_count * wp_i);
}
// s_curr_wp only contains the interpolated data
// copy surrogate output after the the pqc output, mpi_buffer[pqc][interp]
for (std::size_t wp_i = 0; wp_i < s_curr_wp.size; wp_i++)
{
std::copy(s_curr_wp.output[wp_i].begin(), s_curr_wp.output[wp_i].end(),
mpi_buffer.begin() + sur_wp_offset + this->prop_count * wp_i);
}
count += sur_wp_offset;
}
poet::WorkPackage &s_curr_wp_copy = control_iteration_active ? s_curr_wp_pqc : s_curr_wp;
for (std::size_t wp_i = 0; wp_i < s_curr_wp_copy.size; wp_i++)
else
{
std::copy(s_curr_wp_copy.output[wp_i].begin(), s_curr_wp_copy.output[wp_i].end(),
mpi_buffer.begin() + this->prop_count * wp_i);
for (std::size_t wp_i = 0; wp_i < s_curr_wp.size; wp_i++)
{
std::copy(s_curr_wp.output[wp_i].begin(), s_curr_wp.output[wp_i].end(),
mpi_buffer.begin() + this->prop_count * wp_i);
}
}
/* send results to master */
MPI_Request send_req;
int mpi_tag = control_iteration_active ? WITH_REL_ERROR : LOOP_WORK;
int mpi_tag = control_iteration_active ? LOOP_CTRL : LOOP_WORK;
MPI_Isend(mpi_buffer.data(), count, MPI_DOUBLE, 0, mpi_tag, MPI_COMM_WORLD, &send_req);
if (control_iteration_active)
{
std::cout << "[Worker " << this->comm_rank << "] Sent results." << std::endl;
}
if (dht_enabled || interp_enabled)
{
/* write results to DHT */
dht_fill_start = MPI_Wtime();
dht->fillDHT(s_curr_wp_copy);
dht->fillDHT(control_iteration_active ? s_curr_wp_pqc : s_curr_wp);
dht_fill_end = MPI_Wtime();
if (interp_enabled)

1
src/IO/HDF5Functions.hpp
View File

@ -6,3 +6,4 @@
int write_checkpoint(const std::string &file_path, struct Checkpoint_s &&checkpoint);
int read_checkpoint(const std::string &file_path, struct Checkpoint_s &checkpoint);

37
src/IO/StatsIO.cpp Normal file
View File

@ -0,0 +1,37 @@
#include "IO/StatsIO.hpp"
#include <fstream>
#include <iostream>
#include <string>
namespace poet
{
void writeStatsToCSV(const std::vector<ChemistryModule::error_stats> &all_stats,
const std::vector<std::string> &species_names,
const std::string &filename)
{
std::ofstream out(filename);
if (!out.is_open())
{
std::cerr << "Could not open " << filename << " !" << std::endl;
return;
}
// header
out << "Iteration, Species, MAPE, RRSME \n";
for (size_t i = 0; i < all_stats.size(); ++i)
{
for (size_t j = 0; j < species_names.size(); ++j)
{
out << all_stats[i].iteration << ",\t"
<< species_names[j] << ",\t"
<< all_stats[i].mape[j] << ",\t"
<< all_stats[i].rrsme[j] << "\n";
}
out << std::endl;
}
out.close();
std::cout << "Stats written to " << filename << "\n";
}
} // namespace poet

9
src/IO/StatsIO.hpp Normal file
View File

@ -0,0 +1,9 @@
#include <string>
#include "Chemistry/ChemistryModule.hpp"
namespace poet
{
void writeStatsToCSV(const std::vector<ChemistryModule::error_stats> &all_stats,
const std::vector<std::string> &species_names,
const std::string &filename);
} // namespace poet

137
src/poet.cpp
View File

@ -28,6 +28,7 @@
#include "DataStructures/Field.hpp"
#include "IO/Datatypes.hpp"
#include "IO/HDF5Functions.hpp"
#include "IO/StatsIO.hpp"
#include "Init/InitialList.hpp"
#include "Transport/DiffusionModule.hpp"
@ -67,7 +68,8 @@ static poet::DEFunc ReadRObj_R;
static poet::DEFunc SaveRObj_R;
static poet::DEFunc source_R;
static void init_global_functions(RInside &R) {
static void init_global_functions(RInside &R)
{
R.parseEval(kin_r_library);
master_init_R = DEFunc("master_init");
master_iteration_end_R = DEFunc("master_iteration_end");
@ -90,9 +92,15 @@ static void init_global_functions(RInside &R) {
// R.parseEval("mysetup$state_C <- TMP");
// }
enum ParseRet { PARSER_OK, PARSER_ERROR, PARSER_HELP };
enum ParseRet
{
PARSER_OK,
PARSER_ERROR,
PARSER_HELP
};
int parseInitValues(int argc, char **argv, RuntimeParameters &params) {
int parseInitValues(int argc, char **argv, RuntimeParameters &params)
{
CLI::App app{"POET - Potsdam rEactive Transport simulator"};
@ -174,9 +182,12 @@ int parseInitValues(int argc, char **argv, RuntimeParameters &params) {
"Output directory of the simulation")
->required();
try {
try
{
app.parse(argc, argv);
} catch (const CLI::ParseError &e) {
}
catch (const CLI::ParseError &e)
{
app.exit(e);
return -1;
}
@ -188,14 +199,16 @@ int parseInitValues(int argc, char **argv, RuntimeParameters &params) {
if (params.as_qs)
params.out_ext = "qs";
if (MY_RANK == 0) {
if (MY_RANK == 0)
{
// MSG("Complete results storage is " + BOOL_PRINT(simparams.store_result));
MSG("Output format/extension is " + params.out_ext);
MSG("Work Package Size: " + std::to_string(params.work_package_size));
MSG("DHT is " + BOOL_PRINT(params.use_dht));
MSG("AI Surrogate is " + BOOL_PRINT(params.use_ai_surrogate));
if (params.use_dht) {
if (params.use_dht)
{
// MSG("DHT strategy is " + std::to_string(simparams.dht_strategy));
// MDL: these should be outdated (?)
// MSG("DHT key default digits (ignored if 'signif_vector' is "
@ -209,7 +222,8 @@ int parseInitValues(int argc, char **argv, RuntimeParameters &params) {
// MSG("DHT load file is " + chem_params.dht_file);
}
if (params.use_interp) {
if (params.use_interp)
{
MSG("PHT interpolation enabled: " + BOOL_PRINT(params.use_interp));
MSG("PHT interp-size = " + std::to_string(params.interp_size));
MSG("PHT interp-min = " + std::to_string(params.interp_min_entries));
@ -237,7 +251,8 @@ int parseInitValues(int argc, char **argv, RuntimeParameters &params) {
// // log before rounding?
// R["dht_log"] = simparams.dht_log;
try {
try
{
Rcpp::List init_params_(ReadRObj_R(init_file));
params.init_params = init_params_;
@ -252,11 +267,12 @@ int parseInitValues(int argc, char **argv, RuntimeParameters &params) {
params.timesteps =
Rcpp::as<std::vector<double>>(global_rt_setup->operator[]("timesteps"));
params.control_iteration =
Rcpp::as<int>(global_rt_setup->operator[]("control_iteration"));
Rcpp::as<uint32_t>(global_rt_setup->operator[]("control_iteration"));
params.species_epsilon =
Rcpp::as<std::vector<double>>(global_rt_setup->operator[]("species_epsilon"));
} catch (const std::exception &e) {
}
catch (const std::exception &e)
{
ERRMSG("Error while parsing R scripts: " + std::string(e.what()));
return ParseRet::PARSER_ERROR;
}
@ -266,7 +282,8 @@ int parseInitValues(int argc, char **argv, RuntimeParameters &params) {
// HACK: this is a step back as the order and also the count of fields is
// predefined, but it will change in the future
void call_master_iter_end(RInside &R, const Field &trans, const Field &chem) {
void call_master_iter_end(RInside &R, const Field &trans, const Field &chem)
{
R["TMP"] = Rcpp::wrap(trans.AsVector());
R["TMP_PROPS"] = Rcpp::wrap(trans.GetProps());
R.parseEval(std::string("state_T <- setNames(data.frame(matrix(TMP, nrow=" +
@ -285,13 +302,15 @@ void call_master_iter_end(RInside &R, const Field &trans, const Field &chem) {
static Rcpp::List RunMasterLoop(RInsidePOET &R, RuntimeParameters &params,
DiffusionModule &diffusion,
ChemistryModule &chem) {
ChemistryModule &chem)
{
/* Iteration Count is dynamic, retrieving value from R (is only needed by
* master for the following loop) */
uint32_t maxiter = params.timesteps.size();
if (params.print_progress) {
if (params.print_progress)
{
chem.setProgressBarPrintout(true);
}
R["TMP_PROPS"] = Rcpp::wrap(chem.getField().GetProps());
@ -299,9 +318,10 @@ static Rcpp::List RunMasterLoop(RInsidePOET &R, RuntimeParameters &params,
/* SIMULATION LOOP */
double dSimTime{0};
for (uint32_t iter = 1; iter < maxiter + 1; iter++) {
for (uint32_t iter = 1; iter < maxiter + 1; iter++)
{
params.control_iteration_active = (iter % params.control_iteration == 0);
params.control_iteration_active = (iter % params.control_iteration == 0 && iter != 0);
double start_t = MPI_Wtime();
@ -323,7 +343,8 @@ static Rcpp::List RunMasterLoop(RInsidePOET &R, RuntimeParameters &params,
chem.getField().update(diffusion.getField());
// MSG("Chemistry start");
if (params.use_ai_surrogate) {
if (params.use_ai_surrogate)
{
double ai_start_t = MPI_Wtime();
// Save current values from the tug field as predictor for the ai step
R["TMP"] = Rcpp::wrap(chem.getField().AsVector());
@ -374,7 +395,8 @@ static Rcpp::List RunMasterLoop(RInsidePOET &R, RuntimeParameters &params,
chem.simulate(dt);
/* AI surrogate iterative training*/
if (params.use_ai_surrogate) {
if (params.use_ai_surrogate)
{
double ai_start_t = MPI_Wtime();
R["TMP"] = Rcpp::wrap(chem.getField().AsVector());
@ -408,19 +430,32 @@ static Rcpp::List RunMasterLoop(RInsidePOET &R, RuntimeParameters &params,
// TODO: write checkpoint
// checkpoint struct --> field and iteration
if (iter == 1) {
write_checkpoint("checkpoint1.hdf5",
{.field = chem.getField(), .iteration = iter});
} else if (iter == 2) {
/*else if (iter == 2) {
Checkpoint_s checkpoint_read{.field = chem.getField()};
read_checkpoint("checkpoint1.hdf5", checkpoint_read);
iter = checkpoint_read.iteration;
}
}*/
diffusion.getField().update(chem.getField());
MSG("End of *coupling* iteration " + std::to_string(iter) + "/" +
std::to_string(maxiter));
/*
if (params.control_iteration_active)
{
std::string file_path = "checkpoint" + std::to_string(iter) + ".hdf5";
write_checkpoint(file_path,
{.field = chem.getField(), .iteration = iter});
}
if (iter % params.control_iteration == 0 && iter != 0)
{
write_checkpoint("checkpoint" + std::to_string(iter) + ".hdf5",
{.field = chem.getField(), .iteration = iter});
}
*/
// MSG();
} // END SIMULATION LOOP
@ -437,7 +472,8 @@ static Rcpp::List RunMasterLoop(RInsidePOET &R, RuntimeParameters &params,
Rcpp::List diffusion_profiling;
diffusion_profiling["simtime"] = diffusion.getTransportTime();
if (params.use_dht) {
if (params.use_dht)
{
chem_profiling["dht_hits"] = Rcpp::wrap(chem.GetWorkerDHTHits());
chem_profiling["dht_evictions"] = Rcpp::wrap(chem.GetWorkerDHTEvictions());
chem_profiling["dht_get_time"] = Rcpp::wrap(chem.GetWorkerDHTGetTimings());
@ -445,7 +481,8 @@ static Rcpp::List RunMasterLoop(RInsidePOET &R, RuntimeParameters &params,
Rcpp::wrap(chem.GetWorkerDHTFillTimings());
}
if (params.use_interp) {
if (params.use_interp)
{
chem_profiling["interp_w"] =
Rcpp::wrap(chem.GetWorkerInterpolationWriteTimings());
chem_profiling["interp_r"] =
@ -466,11 +503,14 @@ static Rcpp::List RunMasterLoop(RInsidePOET &R, RuntimeParameters &params,
chem.MasterLoopBreak();
writeStatsToCSV(chem.error_stats_history, chem.getField().GetProps(), "stats_overview");
return profiling;
}
std::vector<std::string> getSpeciesNames(const Field &&field, int root,
MPI_Comm comm) {
MPI_Comm comm)
{
std::uint32_t n_elements;
std::uint32_t n_string_size;
@ -480,11 +520,13 @@ std::vector<std::string> getSpeciesNames(const Field &&field, int root,
const bool is_master = root == rank;
// first, the master sends all the species names iterative
if (is_master) {
if (is_master)
{
n_elements = field.GetProps().size();
MPI_Bcast(&n_elements, 1, MPI_UINT32_T, root, MPI_COMM_WORLD);
for (std::uint32_t i = 0; i < n_elements; i++) {
for (std::uint32_t i = 0; i < n_elements; i++)
{
n_string_size = field.GetProps()[i].size();
MPI_Bcast(&n_string_size, 1, MPI_UINT32_T, root, MPI_COMM_WORLD);
MPI_Bcast(const_cast<char *>(field.GetProps()[i].c_str()), n_string_size,
@ -499,7 +541,8 @@ std::vector<std::string> getSpeciesNames(const Field &&field, int root,
std::vector<std::string> species_names_out(n_elements);
for (std::uint32_t i = 0; i < n_elements; i++) {
for (std::uint32_t i = 0; i < n_elements; i++)
{
MPI_Bcast(&n_string_size, 1, MPI_UINT32_T, root, MPI_COMM_WORLD);
char recv_buf[n_string_size];
@ -512,7 +555,8 @@ std::vector<std::string> getSpeciesNames(const Field &&field, int root,
return species_names_out;
}
std::array<double, 2> getBaseTotals(Field &&field, int root, MPI_Comm comm) {
std::array<double, 2> getBaseTotals(Field &&field, int root, MPI_Comm comm)
{
std::array<double, 2> base_totals;
int rank;
@ -520,7 +564,8 @@ std::array<double, 2> getBaseTotals(Field &&field, int root, MPI_Comm comm) {
const bool is_master = root == rank;
if (is_master) {
if (is_master)
{
const auto h_col = field["H"];
const auto o_col = field["O"];
@ -535,7 +580,8 @@ std::array<double, 2> getBaseTotals(Field &&field, int root, MPI_Comm comm) {
return base_totals;
}
bool getHasID(Field &&field, int root, MPI_Comm comm) {
bool getHasID(Field &&field, int root, MPI_Comm comm)
{
bool has_id;
int rank;
@ -543,7 +589,8 @@ bool getHasID(Field &&field, int root, MPI_Comm comm) {
const bool is_master = root == rank;
if (is_master) {
if (is_master)
{
const auto ID_field = field["ID"];
std::set<double> unique_IDs(ID_field.begin(), ID_field.end());
@ -560,7 +607,8 @@ bool getHasID(Field &&field, int root, MPI_Comm comm) {
return has_id;
}
int main(int argc, char *argv[]) {
int main(int argc, char *argv[])
{
int world_size;
MPI_Init(&argc, &argv);
@ -571,7 +619,8 @@ int main(int argc, char *argv[]) {
RInsidePOET &R = RInsidePOET::getInstance();
if (MY_RANK == 0) {
if (MY_RANK == 0)
{
MSG("Running POET version " + std::string(poet_version));
}
@ -579,7 +628,8 @@ int main(int argc, char *argv[]) {
RuntimeParameters run_params;
if (parseInitValues(argc, argv, run_params) != 0) {
if (parseInitValues(argc, argv, run_params) != 0)
{
MPI_Finalize();
return 0;
}
@ -621,9 +671,12 @@ int main(int argc, char *argv[]) {
chemistry.masterEnableSurrogates(surr_setup);
if (MY_RANK > 0) {
if (MY_RANK > 0)
{
chemistry.WorkerLoop();
} else {
}
else
{
// R.parseEvalQ("mysetup <- setup");
// // if (MY_RANK == 0) { // get timestep vector from
// // grid_init function ... //
@ -637,7 +690,8 @@ int main(int argc, char *argv[]) {
R["out_ext"] = run_params.out_ext;
R["out_dir"] = run_params.out_dir;
if (run_params.use_ai_surrogate) {
if (run_params.use_ai_surrogate)
{
/* Incorporate ai surrogate from R */
R.parseEvalQ(ai_surrogate_r_library);
/* Use dht species for model input and output */
@ -686,7 +740,8 @@ int main(int argc, char *argv[]) {
MPI_Finalize();
if (MY_RANK == 0) {
if (MY_RANK == 0)
{
MSG("done, bye!");
}

2
src/poet.hpp.in
View File

@ -53,7 +53,7 @@ struct RuntimeParameters {
bool print_progress = false;
bool control_iteration_active = false;
std::uint32_t control_iteration = 25;
std::uint32_t control_iteration = 1;
static constexpr std::uint32_t WORK_PACKAGE_SIZE_DEFAULT = 32;
std::uint32_t work_package_size = WORK_PACKAGE_SIZE_DEFAULT;

2
test/CMakeLists.txt
View File

@ -12,7 +12,7 @@ get_filename_component(TEST_RInsideSourceFile "RInsidePOET_funcs.R" REALPATH)
configure_file(testDataStructures.hpp.in testDataStructures.hpp)
target_include_directories(testPOET PRIVATE "${CMAKE_CURRENT_BINARY_DIR}")
add_custom_target(check
add_custom_target(check_poet
COMMAND $<TARGET_FILE:testPOET>
DEPENDS testPOET
)

119
test/testStats.cpp Normal file
View File

@ -0,0 +1,119 @@
#include <cmath>
#include <cstddef>
#include <doctest/doctest.h>
#include <vector>
#include <Chemistry/ChemistryModule.hpp>
TEST_CASE("Stats calculation")
{
std::vector<double> real =
{
2, 2, 2, 2, // species 1
2.0, 0.01, 0.7, 0.5, // species 2
0.0, 0.0, 0.0, 0.0, // species 3
0.0, 0.0, 0.0, 0.0, // species 4
-2.5, -0.02, -0.7, -0.5, // species 5
7.7, 6.01, 4.7, 0.5 // species 6
};
std::vector<double> pred =
{
2, 2, 2, 2,
2.0, 0.02, 0.6, 0.5,
0.1, 0.0, 0.0, 0.0,
0.0, 0.0, 0.0, 0.0,
2.5, 0.01, 0.6, 0.5,
2.8, 0.02, 0.7, 0.5
};
poet::ChemistryModule::error_stats stats(6, 5);
poet::ChemistryModule::computeStats(real, pred, /*size_per_prop*/ 4, /*species_count*/ 6, stats);
SUBCASE("Non-zero values")
{
// species 1 is ID, should stay 0
CHECK_EQ(stats.mape[0], 0);
CHECK_EQ(stats.rrsme[0], 0);
/*
mape species 2
cell0: |(2.0 - 2.0)/2.0| = 0
cell1: |(0.01 - 0.02)/0.01| = 1
cell2: |(0.7 - 0.6)/0.7| = 0.142857143
cell3: |(0.5 - 0.5)/0.5| = 0
mape = 1.142857143/ 4 = 0.285714286 *100
rrsme species 1
squared err sum = 1.02040816
rrsme = sqrt(1.02040816/4) = 0.50507627
*/
CHECK_EQ(stats.mape[1], doctest::Approx(28.5714286).epsilon(1e-6));
CHECK_EQ(stats.rrsme[1], doctest::Approx(0.50507627).epsilon(1e-6));
}
SUBCASE("Zero-denominator case")
{
/*
mape species 3
cell0: |(0.0 - 0.1)/0.0|
cell1: |(0.0 - 0.0)/0.0|
cell2: |(0.0 - 0.0)/0.0|
cell3: |(0.0 - 0.0)/0.0|
mape = 1 *100
rrsme = 1
*/
CHECK_EQ(stats.mape[2], 100.0);
CHECK_EQ(stats.rrsme[2], 1.0);
}
SUBCASE("True and predicted values are zero")
{
/*
mape species 4
cell0: |(0.0 - 0.0)/0.0|
cell1: |(0.0 - 0.0)/0.0|
cell2: |(0.0 - 0.0)/0.0|
cell3: |(0.0 - 0.0)/0.0|
mape = 0.0
rrsme = 0.0
*/
CHECK_EQ(stats.mape[3], 0.0);
CHECK_EQ(stats.rrsme[3], 0.0);
}
SUBCASE("Negative values")
{
/*
mape species 5
cell0: |(-2.5 - 2.5)/-2.5| = 2
cell1: |(-0.02 - 0.01)/-0.02| = 1.5
cell2: |(-0.7 - 0.6)/-0.7| = 1.85714286
cell3: |(-0.5 - 0.5)/-0.5| = 2
mape = (100.0 / 4) * 7.35714286 = 183.92857143
rrsme = sqrt(13.6989796 / 4) = 1.85060663
*/
CHECK_EQ(stats.mape[4], doctest::Approx(183.92857143).epsilon(1e-6));
CHECK_EQ(stats.rrsme[4], doctest::Approx(1.85060663).epsilon(1e-6));
}
SUBCASE("Large differences")
{
/*
mape species 6
cell0: |(7.7 - 2.8)/7.7| = 0.63636364
cell1: |(6.01 - 0.02)/6.01| = 0.99667221
cell2: |(4.7 - 0.7)/4.7| = 0.85106383
cell3: |(0.5 - 0.5)/0.5| = 0
mape = (100.0 / 4) * 2.48409968 = 62.102492
rrsme = sqrt(2,12262382 / 4) = 0.72846136
*/
CHECK_EQ(stats.mape[5], doctest::Approx(62.102492).epsilon(1e-6));
CHECK_EQ(stats.rrsme[5], doctest::Approx(0.72846136).epsilon(1e-6));
}
}