UltraScan III
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US_MPI_Analysis Class Reference

#include "us_mpi_analysis.h"

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Classes

class  Bucket
 
class  Fitness
 
class  MPI_GA_MSG
 
class  MPI_Job
 
class  Result
 
class  Sa_Job
 

Public Slots

void start (void)
 

Public Member Functions

 US_MPI_Analysis (int, QStringList &)
 

Private Types

enum  attr_type {
  ATTR_S, ATTR_K, ATTR_W, ATTR_V,
  ATTR_D, ATTR_F
}
 
enum  WorkerStatus { INIT, READY, WORKING }
 
enum  PMGTag {
  ADATESIZE =1000, ADATE, STARTITER, STARTLAST,
  UDPSIZE, UDPMSG, DONEITER, DONELAST
}
 
enum  {
  GENERATION, GENE, IMMIGRATE, EMMIGRATE,
  UPDATE, FINISHED
}
 
typedef QVector< US_Solute > Gene
 

Private Member Functions

void parse (const QString &)
 
void parse_job (QXmlStreamReader &)
 
void parse_dataset (QXmlStreamReader &, DATASET *)
 
void parse_files (QXmlStreamReader &, DATASET *)
 
void parse_solution (QXmlStreamReader &, DATASET *)
 
void send_udp (const QString &)
 
void abort (const QString &, int=-1)
 
long int max_rss (void)
 
QString par_key_value (const QString, const QString)
 
Gene create_solutes (double, double, double, double, double, double)
 
void init_solutes (void)
 
void fill_queue (void)
 
void limitBucket (Bucket &)
 
void _2dsa_master (void)
 
void submit (Sa_Job &, int)
 
void submit_pcsa (Sa_Job &, int)
 
void add_to_queue (Sa_Job &)
 
void process_results (int, const int *)
 
void shutdown_all (void)
 
void write_noise (US_Noise::NoiseType, const QVector< double > &)
 
void iterate (void)
 
void set_meniscus (void)
 
void set_monteCarlo (void)
 
void write_output (void)
 
void write_global (void)
 
void set_gaussians (void)
 
void global_fit (void)
 
void write_model (const SIMULATION &, US_Model::AnalysisType, bool=false)
 
void stats_output (int, int, int, QDateTime, QDateTime, QDateTime)
 
void pm_2dsa_master (void)
 
void pm_ga_master (void)
 
void pm_dmga_master (void)
 
int ready_worker (void)
 
int low_working_depth (void)
 
void cache_result (Result &)
 
void process_solutes (int &, int &, QVector< US_Solute > &)
 
void dset_matrices (int, int, QVector< double > &, QVector< double > &)
 
void update_outputs (bool=false)
 
US_Model::AnalysisType model_type (const QString)
 
void _2dsa_worker (void)
 
void calc_residuals (int, int, SIMULATION &)
 
void ga_master (void)
 
void ga_master_loop (void)
 
void ga_global_fit (void)
 
void set_gaMonteCarlo (void)
 
void ga_worker (void)
 
void ga_worker_loop (void)
 
Gene new_gene (void)
 
void mutate_s (US_Solute &, int)
 
void mutate_k (US_Solute &, int)
 
void mutate_gene (Gene &)
 
void cross_gene (Gene &, QList< Gene >)
 
int migrate_genes (void)
 
double random_01 (void)
 
int u_random (int=100)
 
int e_random (void)
 
double minimize (Gene &, double)
 
double get_fitness (const Gene &)
 
double get_fitness_v (const US_Vector &)
 
double update_fitness (int, US_Vector &)
 
void lamm_gsm_df (const US_Vector &, US_Vector &)
 
void align_gene (Gene &)
 
void vector_scaled_sum (US_Vector &, US_Vector &, double, US_Vector &, double=1.0)
 
void solutes_from_gene (Gene &, int)
 
void set_comp_attrib (US_Model::SimulationComponent &, double, int)
 
void build_component (US_Model::SimulationComponent &, US_Math2::SolutionData &, double, double)
 
void dmga_master (void)
 
void dmga_master_loop (void)
 
void dmga_global_fit (void)
 
void set_dmga_gaussians (void)
 
void set_dmga_MonteCarlo (void)
 
void marker_from_dgene (QVector< double > &, DGene &)
 
void dgene_from_marker (QVector< double > &, DGene &)
 
void dgenes_to_marker (QVector< double > &, QList< DGene > &, const int, const int)
 
void marker_to_dgenes (QVector< double > &, QList< DGene > &, const int, const int)
 
bool store_attr_value (double &, US_Model &, US_dmGA_Constraints::AttribType &, int &)
 
bool fetch_attr_value (double &, US_Model &, US_dmGA_Constraints::AttribType &, int &)
 
void model_from_dgene (US_Model &, DGene &dgene)
 
void dmga_worker (void)
 
void dmga_worker_loop (void)
 
DGene new_dmga_gene (void)
 
void mutate_dgene (DGene &)
 
void cross_dgene (DGene &, QList< DGene >)
 
int migrate_dgenes (void)
 
double get_fitness_dmga (DGene &)
 
double get_fitness_v_dmga (US_Vector &, US_Vector &)
 
void lamm_gsm_df_dmga (US_Vector &, US_Vector &, US_Vector &)
 
double minimize_dmga (DGene &, double)
 
QString dgene_key (DGene &)
 
void calc_residuals_dmga (int, int, SIMULATION &, DGene &)
 
void pcsa_master (void)
 
void init_pcsa_solutes (void)
 
void fill_pcsa_queue (void)
 
void process_pcsa_results (const int, const int *)
 
void process_pcsa_solutes (Result &)
 
void write_mrecs (void)
 
void iterate_pcsa (void)
 
void tikreg_pcsa (void)
 
void montecarlo_pcsa (void)
 
void pcsa_best_model (void)
 
void write_pcsa_aux_model (const int)
 
void filter_mrecs (const int, QVector< US_ModelRecord > &, QVector< US_ModelRecord > &)
 
void clean_mrecs (QVector< US_ModelRecord > &)
 
double alpha_scan (void)
 
void apply_alpha (const double, QVector< double > *, QVector< double > *, const int, const int, const int, double &, double &)
 
void pcsa_worker (void)
 
void pmasters_start (void)
 
void task_parse (const QString &)
 
void pmasters_supervisor (void)
 
void pmasters_master (void)
 
void pmasters_worker (void)
 
void time_mc_iterations (void)
 
void pm_cjobs_start (void)
 
void pm_cjobs_supervisor (void)
 
void pm_cjobs_master (void)
 
void pm_cjobs_worker (void)
 
void time_datasets_left (void)
 
void pm_2dsa_cjmast (void)
 
void pm_ga_cjmast (void)
 
void pm_dmga_cjmast (void)
 
void pm_pcsa_cjmast (void)
 
void dump_buckets (void)
 
void dump_genes (int)
 
void dump_fitness (const QList< Fitness > &)
 

Private Attributes

int proc_count
 
int my_rank
 
int my_group
 
int mgroup_count
 
int group_rank
 
int my_workers
 
int gcores_count
 
int max_walltime
 
int iterations
 
int max_iterations
 
int mc_iterations
 
int mc_iteration
 
int max_experiment_size
 
int total_points
 
int dbg_level
 
bool dbg_timing
 
bool glob_runid
 
bool do_astfem
 
bool is_global_fit
 
bool is_composite_job
 
MPI_Comm my_communicator
 
int current_dataset
 
int datasets_to_process
 
int count_calc_residuals
 
int count_datasets
 
int population
 
int generations
 
int crossover
 
int mutation
 
int plague
 
int migrate_count
 
int elitism
 
int attr_x
 
int attr_y
 
int attr_z
 
double mutate_sigma
 
double p_mutate_s
 
double p_mutate_k
 
double p_mutate_sk
 
double alpha
 
long int maxrss
 
QVector< int > worker_status
 
QVector< int > worker_depth
 
QList< int > ds_startx
 
QList< int > ds_points
 
QVector< double > gl_nnls_a
 
QVector< double > gl_nnls_b
 
int max_depth
 
int worknext
 
int meniscus_points
 
int meniscus_run
 
double meniscus_range
 
double meniscus_value
 
QVector< double > meniscus_values
 
QVector< double > concentrations
 
QVector< double > maxods
 
QVector< double > mc_data
 
QVector< double > sigmas
 
QVector< long > work_rss
 
US_DataIO::RawData * res_data
 
US_DataIO::RawData * sim_data
 
US_DataIO::RawData sim_data1
 
US_DataIO::RawData scaled_data
 
US_ModelRecord mrec
 
QVector< US_ModelRecord > mrecs
 
QStringList cm_files
 
double pararry [36]
 
QHostAddress server
 
quint16 port
 
QUdpSocket * socket
 
QString requestID
 
QString directory
 
QString analysis_type
 
QString cluster
 
QString db_name
 
QString modelGUID
 
QString requestGUID
 
QString analysisDate
 
QMap< QString, QString > parameters
 
QMap< QString, QString > task_params
 
QDateTime submitTime
 
QDateTime startTime
 
int set_count
 
QList< DATASET * > data_sets
 
QList< QVector< US_Solute > > orig_solutes
 
QVector< US_Solute > ljob_solutes
 
QList< QVector< US_ZSolute > > orig_zsolutes
 
QList< Sa_Job > job_queue
 
QList< QVector< US_Solute > > calculated_solutes
 
QList< QVector< US_Solute > > ds_calc_solutes
 
QVector< US_Solute > dset_calc_solutes
 
QList< QVector< US_ZSolute > > calculated_zsolutes
 
SIMULATION simulation_values
 
SIMULATION wksim_vals
 
SIMULATION previous_values
 
QList< Result > cached_results
 
int generation
 
int s_grid
 
int k_grid
 
int p_grid
 
int fitness_count
 
double regularization
 
double concentration_threshold
 
QList< Bucket > buckets
 
QList< Gene > genes
 
QList< Gene > best_genes
 
QList< SIMULATION > sim_values
 
QMap< QString, double > fitness_map
 
int fitness_hits
 
QList< DGene > dgenes
 
QList< DGene > best_dgenes
 
US_dmGA_Constraints constraints
 
US_Model wmodel
 
DGene dgene
 
QVector< double > dgmarker
 
QVector
< US_dmGA_Constraints::Constraint > 		cns_flt
 
QVector< int > lfvari
 
double base_sig
 
int nfloatc
 
int ncompc
 
int nassocc
 
int nfvari
 
int minimize_opt
 
int g_redo_inc
 
bool in_gsm
 
QList< Fitness > fitness
 
QList< Fitness > best_fitness
 

Static Private Attributes

static const int min_experiment_size = 100
 
static const double min_variance_improvement = 1.0e-100
 
static const double LARGE = 1.e39
 
static const int solute_doubles = sizeof( US_Solute ) / sizeof( double )
 
static const int zsolut_doubles = sizeof( US_ZSolute ) / sizeof( double )
 

Detailed Description

Definition at line 25 of file us_mpi_analysis.h.

Member Typedef Documentation

typedef QVector< US_Solute > US_MPI_Analysis::Gene
private

Definition at line 230 of file us_mpi_analysis.h.

Member Enumeration Documentation

anonymous enum
private
Enumerator
GENERATION 
GENE 
IMMIGRATE 
EMMIGRATE 
UPDATE 
FINISHED 

Definition at line 293 of file us_mpi_analysis.h.

enum US_MPI_Analysis::attr_type
private
Enumerator
ATTR_S 
ATTR_K 
ATTR_W 
ATTR_V 
ATTR_D 
ATTR_F 

Definition at line 37 of file us_mpi_analysis.h.

enum US_MPI_Analysis::PMGTag
private
Enumerator
ADATESIZE 
ADATE 
STARTITER 
STARTLAST 
UDPSIZE 
UDPMSG 
DONEITER 
DONELAST 

Definition at line 97 of file us_mpi_analysis.h.

enum US_MPI_Analysis::WorkerStatus
private
Enumerator
INIT 
READY 
WORKING 

Definition at line 96 of file us_mpi_analysis.h.

Constructor & Destructor Documentation

US_MPI_Analysis::US_MPI_Analysis ( int  nargs,
QStringList &  cmdargs 
)

Definition at line 27 of file us_mpi_analysis.cpp.

Member Function Documentation

void US_MPI_Analysis::_2dsa_master ( void  )
private

Definition at line 9 of file 2dsa_master.cpp.

void US_MPI_Analysis::_2dsa_worker ( void  )
private

Definition at line 7 of file 2dsa_worker.cpp.

void US_MPI_Analysis::abort ( const QString &  message,
int  error = -1 
)
private

Definition at line 792 of file us_mpi_analysis.cpp.

void US_MPI_Analysis::add_to_queue ( Sa_Job &  job)
private

Definition at line 1051 of file 2dsa_master.cpp.

void US_MPI_Analysis::align_gene ( Gene &  gene)
private

Definition at line 364 of file ga_worker.cpp.

double US_MPI_Analysis::alpha_scan ( void  )
private

Definition at line 1390 of file pcsa_master.cpp.

void US_MPI_Analysis::apply_alpha ( const double  alpha,
QVector< double > *  psv_nnls_a,
QVector< double > *  psv_nnls_b,
const int  nscans,
const int  npoints,
const int  nisols,
double &  variance,
double &  xnormsq 
)
private

Definition at line 1543 of file pcsa_master.cpp.

void US_MPI_Analysis::build_component ( US_Model::SimulationComponent &  mcomp,
US_Math2::SolutionData &  sd,
double  xval,
double  yval 
)
private

Definition at line 1550 of file ga_worker.cpp.

void US_MPI_Analysis::cache_result ( Result &  result)
private

Definition at line 1645 of file 2dsa_master.cpp.

void US_MPI_Analysis::calc_residuals ( int  ,
int  ,
SIMULATION &   
)
private

Definition at line 279 of file 2dsa_worker.cpp.

void US_MPI_Analysis::calc_residuals_dmga ( int  ,
int  ,
SIMULATION &  ,
DGene &   
)
private

Definition at line 1124 of file dmga_worker.cpp.

void US_MPI_Analysis::clean_mrecs ( QVector< US_ModelRecord > &  mrecs)
private

Definition at line 1100 of file pcsa_master.cpp.

Gene US_MPI_Analysis::create_solutes ( double  ,
double  ,
double  ,
double  ,
double  ,
double   
)
private
void US_MPI_Analysis::cross_dgene ( DGene &  dgene,
QList< DGene >  dgenes 
)
private

Definition at line 585 of file dmga_worker.cpp.

void US_MPI_Analysis::cross_gene ( Gene &  gene,
QList< Gene >  old_genes 
)
private

Definition at line 622 of file ga_worker.cpp.

void US_MPI_Analysis::dgene_from_marker ( QVector< double > &  dgm,
DGene &  dg 
)
private

Definition at line 904 of file dmga_master.cpp.

QString US_MPI_Analysis::dgene_key ( DGene &  dgene)
private

Definition at line 1107 of file dmga_worker.cpp.

void US_MPI_Analysis::dgenes_to_marker ( QVector< double > &  dgm,
QList< DGene > &  dgenes,
const int  stgx,
const int  ngenes 
)
private

Definition at line 918 of file dmga_master.cpp.

void US_MPI_Analysis::dmga_global_fit ( void  )
private

Definition at line 734 of file dmga_master.cpp.

void US_MPI_Analysis::dmga_master ( void  )
private

Definition at line 6 of file dmga_master.cpp.

void US_MPI_Analysis::dmga_master_loop ( void  )
private

Definition at line 459 of file dmga_master.cpp.

void US_MPI_Analysis::dmga_worker ( void  )
private

Definition at line 19 of file dmga_worker.cpp.

void US_MPI_Analysis::dmga_worker_loop ( void  )
private

Definition at line 199 of file dmga_worker.cpp.

void US_MPI_Analysis::dset_matrices ( int  dsx,
int  nsolutes,
QVector< double > &  nnls_a,
QVector< double > &  nnls_b 
)
private

Definition at line 917 of file us_mpi_analysis.cpp.

void US_MPI_Analysis::dump_buckets ( void  )
private

Definition at line 1451 of file ga_worker.cpp.

void US_MPI_Analysis::dump_fitness ( const QList< Fitness > &  fitness)
private

Definition at line 1505 of file ga_worker.cpp.

void US_MPI_Analysis::dump_genes ( int  gene)
private

Definition at line 1467 of file ga_worker.cpp.

int US_MPI_Analysis::e_random ( void  )
private

Definition at line 539 of file ga_worker.cpp.

bool US_MPI_Analysis::fetch_attr_value ( double &  aval,
US_Model &  model,
US_dmGA_Constraints::AttribType &  atype,
int &  mcompx 
)
private

Definition at line 1023 of file dmga_master.cpp.

void US_MPI_Analysis::fill_pcsa_queue ( void  )
private

Definition at line 1602 of file pcsa_master.cpp.

void US_MPI_Analysis::fill_queue ( void  )
private

Definition at line 366 of file 2dsa_master.cpp.

void US_MPI_Analysis::filter_mrecs ( const int  ctype,
QVector< US_ModelRecord > &  mrecs_a,
QVector< US_ModelRecord > &  mrecs_t 
)
private

Definition at line 1086 of file pcsa_master.cpp.

void US_MPI_Analysis::ga_global_fit ( void  )
private

Definition at line 426 of file ga_master.cpp.

void US_MPI_Analysis::ga_master ( void  )
private

Definition at line 6 of file ga_master.cpp.

void US_MPI_Analysis::ga_master_loop ( void  )
private

Definition at line 173 of file ga_master.cpp.

void US_MPI_Analysis::ga_worker ( void  )
private

Definition at line 18 of file ga_worker.cpp.

void US_MPI_Analysis::ga_worker_loop ( void  )
private

Definition at line 147 of file ga_worker.cpp.

double US_MPI_Analysis::get_fitness ( const Gene &  gene)
private

Definition at line 410 of file ga_worker.cpp.

double US_MPI_Analysis::get_fitness_dmga ( DGene &  dgene)
private

Definition at line 1082 of file dmga_worker.cpp.

double US_MPI_Analysis::get_fitness_v ( const US_Vector &  vv)
private

Definition at line 504 of file ga_worker.cpp.

double US_MPI_Analysis::get_fitness_v_dmga ( US_Vector &  vv,
US_Vector &  zz 
)
private

Definition at line 683 of file dmga_worker.cpp.

void US_MPI_Analysis::global_fit ( void  )
private

Definition at line 391 of file 2dsa_master.cpp.

void US_MPI_Analysis::init_pcsa_solutes ( void  )
private

Definition at line 247 of file pcsa_master.cpp.

void US_MPI_Analysis::init_solutes ( void  )
private

Definition at line 272 of file 2dsa_master.cpp.

void US_MPI_Analysis::iterate ( void  )
private

Definition at line 911 of file 2dsa_master.cpp.

void US_MPI_Analysis::iterate_pcsa ( void  )
private

Definition at line 554 of file pcsa_master.cpp.

void US_MPI_Analysis::lamm_gsm_df ( const US_Vector &  vv,
US_Vector &  vd 
)
private

Definition at line 1398 of file ga_worker.cpp.

void US_MPI_Analysis::lamm_gsm_df_dmga ( US_Vector &  vv,
US_Vector &  vd,
US_Vector &  zz 
)
private

Definition at line 703 of file dmga_worker.cpp.

void US_MPI_Analysis::limitBucket ( Bucket &  buk)
private

Definition at line 877 of file us_mpi_analysis.cpp.

int US_MPI_Analysis::low_working_depth ( void  )
private

Definition at line 1626 of file 2dsa_master.cpp.

void US_MPI_Analysis::marker_from_dgene ( QVector< double > &  dgm,
DGene &  dg 
)
private

Definition at line 893 of file dmga_master.cpp.

void US_MPI_Analysis::marker_to_dgenes ( QVector< double > &  dgm,
QList< DGene > &  dgenes,
const int  stgx,
const int  ngenes 
)
private

Definition at line 938 of file dmga_master.cpp.

long int US_MPI_Analysis::max_rss ( void  )
private

Definition at line 787 of file us_mpi_analysis.cpp.

int US_MPI_Analysis::migrate_dgenes ( void  )
private

Definition at line 614 of file dmga_worker.cpp.

int US_MPI_Analysis::migrate_genes ( void  )
private

Definition at line 654 of file ga_worker.cpp.

double US_MPI_Analysis::minimize ( Gene &  gene,
double  fitness 
)
private

Definition at line 767 of file ga_worker.cpp.

double US_MPI_Analysis::minimize_dmga ( DGene &  dgene,
double  fitness 
)
private

Definition at line 729 of file dmga_worker.cpp.

void US_MPI_Analysis::model_from_dgene ( US_Model &  model,
DGene &  dgene 
)
private

Definition at line 1076 of file dmga_master.cpp.

US_Model::AnalysisType US_MPI_Analysis::model_type ( const QString  a_type)
private

Definition at line 1808 of file 2dsa_master.cpp.

void US_MPI_Analysis::montecarlo_pcsa ( void  )
private

Definition at line 748 of file pcsa_master.cpp.

void US_MPI_Analysis::mutate_dgene ( DGene &  dgene)
private

Definition at line 526 of file dmga_worker.cpp.

void US_MPI_Analysis::mutate_gene ( Gene &  gene)
private

Definition at line 554 of file ga_worker.cpp.

void US_MPI_Analysis::mutate_k ( US_Solute &  solute,
int  b 
)
private

Definition at line 606 of file ga_worker.cpp.

void US_MPI_Analysis::mutate_s ( US_Solute &  solute,
int  b 
)
private

Definition at line 584 of file ga_worker.cpp.

DGene US_MPI_Analysis::new_dmga_gene ( void  )
private

Definition at line 485 of file dmga_worker.cpp.

US_MPI_Analysis::Gene US_MPI_Analysis::new_gene ( void  )
private

Definition at line 738 of file ga_worker.cpp.

QString US_MPI_Analysis::par_key_value ( const QString  kvtext,
const QString  key 
)
private

Definition at line 1251 of file dmga_worker.cpp.

void US_MPI_Analysis::parse ( const QString &  xmlfile)
private

Definition at line 7 of file us_mpi_parse.cpp.

void US_MPI_Analysis::parse_dataset ( QXmlStreamReader &  ,
DATASET *   
)
private

Definition at line 273 of file us_mpi_parse.cpp.

void US_MPI_Analysis::parse_files ( QXmlStreamReader &  ,
DATASET *   
)
private

Definition at line 394 of file us_mpi_parse.cpp.

void US_MPI_Analysis::parse_job ( QXmlStreamReader &  xml)
private

Definition at line 108 of file us_mpi_parse.cpp.

void US_MPI_Analysis::parse_solution ( QXmlStreamReader &  ,
DATASET *   
)
private

Definition at line 426 of file us_mpi_parse.cpp.

void US_MPI_Analysis::pcsa_best_model ( void  )
private

Definition at line 1186 of file pcsa_master.cpp.

void US_MPI_Analysis::pcsa_master ( void  )
private

Definition at line 10 of file pcsa_master.cpp.

void US_MPI_Analysis::pcsa_worker ( void  )
private

Definition at line 8 of file pcsa_worker.cpp.

void US_MPI_Analysis::pm_2dsa_cjmast ( void  )
private

Definition at line 428 of file pmasters_compjob.cpp.

void US_MPI_Analysis::pm_2dsa_master ( void  )
private

Definition at line 506 of file parallel_masters.cpp.

void US_MPI_Analysis::pm_cjobs_master ( void  )
private

Definition at line 298 of file pmasters_compjob.cpp.

void US_MPI_Analysis::pm_cjobs_start ( void  )
private

Definition at line 9 of file pmasters_compjob.cpp.

void US_MPI_Analysis::pm_cjobs_supervisor ( void  )
private

Definition at line 60 of file pmasters_compjob.cpp.

void US_MPI_Analysis::pm_cjobs_worker ( void  )
private

Definition at line 355 of file pmasters_compjob.cpp.

void US_MPI_Analysis::pm_dmga_cjmast ( void  )
private

Definition at line 916 of file pmasters_compjob.cpp.

void US_MPI_Analysis::pm_dmga_master ( void  )
private

Definition at line 866 of file parallel_masters.cpp.

void US_MPI_Analysis::pm_ga_cjmast ( void  )
private

Definition at line 719 of file pmasters_compjob.cpp.

void US_MPI_Analysis::pm_ga_master ( void  )
private

Definition at line 674 of file parallel_masters.cpp.

void US_MPI_Analysis::pm_pcsa_cjmast ( void  )
private

Definition at line 1104 of file pmasters_compjob.cpp.

void US_MPI_Analysis::pmasters_master ( void  )
private

Definition at line 384 of file parallel_masters.cpp.

void US_MPI_Analysis::pmasters_start ( void  )
private

Definition at line 9 of file parallel_masters.cpp.

void US_MPI_Analysis::pmasters_supervisor ( void  )
private

Definition at line 151 of file parallel_masters.cpp.

void US_MPI_Analysis::pmasters_worker ( void  )
private

Definition at line 436 of file parallel_masters.cpp.

void US_MPI_Analysis::process_pcsa_results ( const int  worker,
const int *  sizes 
)
private

Definition at line 392 of file pcsa_master.cpp.

void US_MPI_Analysis::process_pcsa_solutes ( Result &  result)
private

Definition at line 454 of file pcsa_master.cpp.

void US_MPI_Analysis::process_results ( int  worker,
const int *  size 
)
private

Definition at line 1070 of file 2dsa_master.cpp.

void US_MPI_Analysis::process_solutes ( int &  depth,
int &  worker,
QVector< US_Solute > &  result_solutes 
)
private

Definition at line 1169 of file 2dsa_master.cpp.

double US_MPI_Analysis::random_01 ( void  )
private
int US_MPI_Analysis::ready_worker ( void  )
private

Definition at line 1604 of file 2dsa_master.cpp.

void US_MPI_Analysis::send_udp ( const QString &  message)
private

Definition at line 750 of file us_mpi_analysis.cpp.

void US_MPI_Analysis::set_comp_attrib ( US_Model::SimulationComponent &  mcomp,
double  covalue,
int  attribx 
)
private

Definition at line 1522 of file ga_worker.cpp.

void US_MPI_Analysis::set_dmga_gaussians ( void  )
private

Definition at line 803 of file dmga_master.cpp.

void US_MPI_Analysis::set_dmga_MonteCarlo ( void  )
private

Definition at line 826 of file dmga_master.cpp.

void US_MPI_Analysis::set_gaMonteCarlo ( void  )
private

Definition at line 494 of file ga_master.cpp.

void US_MPI_Analysis::set_gaussians ( void  )
private

Definition at line 636 of file 2dsa_master.cpp.

void US_MPI_Analysis::set_meniscus ( void  )
private

Definition at line 496 of file 2dsa_master.cpp.

void US_MPI_Analysis::set_monteCarlo ( void  )
private

Definition at line 516 of file 2dsa_master.cpp.

void US_MPI_Analysis::shutdown_all ( void  )
private

Definition at line 990 of file 2dsa_master.cpp.

void US_MPI_Analysis::solutes_from_gene ( Gene &  solutes,
int  nsols 
)
private

Definition at line 1576 of file ga_worker.cpp.

void US_MPI_Analysis::start ( void  )
slot

Definition at line 624 of file us_mpi_analysis.cpp.

void US_MPI_Analysis::stats_output ( int  walltime,
int  cputime,
int  maxrssmb,
QDateTime  submitTime,
QDateTime  startTime,
QDateTime  endTime 
)
private

Definition at line 815 of file us_mpi_analysis.cpp.

bool US_MPI_Analysis::store_attr_value ( double &  aval,
US_Model &  model,
US_dmGA_Constraints::AttribType &  atype,
int &  mcompx 
)
private

Definition at line 966 of file dmga_master.cpp.

void US_MPI_Analysis::submit ( Sa_Job &  job,
int  worker 
)
private

Definition at line 1012 of file 2dsa_master.cpp.

void US_MPI_Analysis::submit_pcsa ( Sa_Job &  job,
int  worker 
)
private

Definition at line 348 of file pcsa_master.cpp.

void US_MPI_Analysis::task_parse ( const QString &  xmlfile)
private

Definition at line 60 of file parallel_masters.cpp.

void US_MPI_Analysis::tikreg_pcsa ( void  )
private

Definition at line 694 of file pcsa_master.cpp.

void US_MPI_Analysis::time_datasets_left ( void  )
private

Definition at line 384 of file pmasters_compjob.cpp.

void US_MPI_Analysis::time_mc_iterations ( void  )
private

Definition at line 460 of file parallel_masters.cpp.

int US_MPI_Analysis::u_random ( int  modulo = 100)
private

Definition at line 532 of file ga_worker.cpp.

double US_MPI_Analysis::update_fitness ( int  index,
US_Vector &  v 
)
private

Definition at line 1221 of file ga_worker.cpp.

void US_MPI_Analysis::update_outputs ( bool  is_final = false)
private

Definition at line 1666 of file 2dsa_master.cpp.

void US_MPI_Analysis::vector_scaled_sum ( US_Vector &  cc,
US_Vector &  aa,
double  sa,
US_Vector &  bb,
double  sb = 1.0 
)
private

Definition at line 1202 of file ga_worker.cpp.

void US_MPI_Analysis::write_global ( void  )
private

Definition at line 800 of file 2dsa_master.cpp.

void US_MPI_Analysis::write_model ( const SIMULATION &  ,
US_Model::AnalysisType  ,
bool  = false 
)
private

Definition at line 1330 of file 2dsa_master.cpp.

void US_MPI_Analysis::write_mrecs ( void  )
private

Definition at line 481 of file pcsa_master.cpp.

void US_MPI_Analysis::write_noise ( US_Noise::NoiseType  type,
const QVector< double > &  noise_data 
)
private

Definition at line 1508 of file 2dsa_master.cpp.

void US_MPI_Analysis::write_output ( void  )
private

Definition at line 689 of file 2dsa_master.cpp.

void US_MPI_Analysis::write_pcsa_aux_model ( const int  iter)
private

Definition at line 1298 of file pcsa_master.cpp.

Member Data Documentation

double US_MPI_Analysis::alpha
private

Definition at line 82 of file us_mpi_analysis.h.

QString US_MPI_Analysis::analysis_type
private

Definition at line 128 of file us_mpi_analysis.h.

QString US_MPI_Analysis::analysisDate
private

Definition at line 133 of file us_mpi_analysis.h.

int US_MPI_Analysis::attr_x
private

Definition at line 74 of file us_mpi_analysis.h.

int US_MPI_Analysis::attr_y
private

Definition at line 75 of file us_mpi_analysis.h.

int US_MPI_Analysis::attr_z
private

Definition at line 76 of file us_mpi_analysis.h.

double US_MPI_Analysis::base_sig
private

Definition at line 248 of file us_mpi_analysis.h.

QList< DGene > US_MPI_Analysis::best_dgenes
private

Definition at line 241 of file us_mpi_analysis.h.

QList< Fitness > US_MPI_Analysis::best_fitness
private

Definition at line 282 of file us_mpi_analysis.h.

QList< Gene > US_MPI_Analysis::best_genes
private

Definition at line 236 of file us_mpi_analysis.h.

QList< Bucket > US_MPI_Analysis::buckets
private

Definition at line 234 of file us_mpi_analysis.h.

QList< Result > US_MPI_Analysis::cached_results
private

Definition at line 209 of file us_mpi_analysis.h.

QList< QVector< US_Solute > > US_MPI_Analysis::calculated_solutes
private

Definition at line 190 of file us_mpi_analysis.h.

QList< QVector< US_ZSolute > > US_MPI_Analysis::calculated_zsolutes
private

Definition at line 193 of file us_mpi_analysis.h.

QString US_MPI_Analysis::cluster
private

Definition at line 129 of file us_mpi_analysis.h.

QStringList US_MPI_Analysis::cm_files
private

Definition at line 119 of file us_mpi_analysis.h.

QVector< US_dmGA_Constraints::Constraint > US_MPI_Analysis::cns_flt
private

Definition at line 246 of file us_mpi_analysis.h.

double US_MPI_Analysis::concentration_threshold
private

Definition at line 233 of file us_mpi_analysis.h.

QVector< double > US_MPI_Analysis::concentrations
private

Definition at line 106 of file us_mpi_analysis.h.

US_dmGA_Constraints US_MPI_Analysis::constraints
private

Definition at line 242 of file us_mpi_analysis.h.

int US_MPI_Analysis::count_calc_residuals
private

Definition at line 64 of file us_mpi_analysis.h.

int US_MPI_Analysis::count_datasets
private

Definition at line 65 of file us_mpi_analysis.h.

int US_MPI_Analysis::crossover
private

Definition at line 69 of file us_mpi_analysis.h.

int US_MPI_Analysis::current_dataset
private

Definition at line 62 of file us_mpi_analysis.h.

QList< DATASET* > US_MPI_Analysis::data_sets
private

Definition at line 142 of file us_mpi_analysis.h.

int US_MPI_Analysis::datasets_to_process
private

Definition at line 63 of file us_mpi_analysis.h.

QString US_MPI_Analysis::db_name
private

Definition at line 130 of file us_mpi_analysis.h.

int US_MPI_Analysis::dbg_level
private

Definition at line 53 of file us_mpi_analysis.h.

bool US_MPI_Analysis::dbg_timing
private

Definition at line 54 of file us_mpi_analysis.h.

DGene US_MPI_Analysis::dgene
private

Definition at line 244 of file us_mpi_analysis.h.

QList< DGene > US_MPI_Analysis::dgenes
private

Definition at line 240 of file us_mpi_analysis.h.

QVector< double > US_MPI_Analysis::dgmarker
private

Definition at line 245 of file us_mpi_analysis.h.

QString US_MPI_Analysis::directory
private

Definition at line 127 of file us_mpi_analysis.h.

bool US_MPI_Analysis::do_astfem
private

Definition at line 56 of file us_mpi_analysis.h.

QList< QVector< US_Solute > > US_MPI_Analysis::ds_calc_solutes
private

Definition at line 191 of file us_mpi_analysis.h.

QList< int > US_MPI_Analysis::ds_points
private

Definition at line 91 of file us_mpi_analysis.h.

QList< int > US_MPI_Analysis::ds_startx
private

Definition at line 90 of file us_mpi_analysis.h.

QVector< US_Solute > US_MPI_Analysis::dset_calc_solutes
private

Definition at line 192 of file us_mpi_analysis.h.

int US_MPI_Analysis::elitism
private

Definition at line 73 of file us_mpi_analysis.h.

QList< Fitness > US_MPI_Analysis::fitness
private

Definition at line 281 of file us_mpi_analysis.h.

int US_MPI_Analysis::fitness_count
private

Definition at line 228 of file us_mpi_analysis.h.

int US_MPI_Analysis::fitness_hits
private

Definition at line 239 of file us_mpi_analysis.h.

QMap< QString, double > US_MPI_Analysis::fitness_map
private

Definition at line 238 of file us_mpi_analysis.h.

int US_MPI_Analysis::g_redo_inc
private

Definition at line 254 of file us_mpi_analysis.h.

int US_MPI_Analysis::gcores_count
private

Definition at line 45 of file us_mpi_analysis.h.

int US_MPI_Analysis::generation
private

Definition at line 224 of file us_mpi_analysis.h.

int US_MPI_Analysis::generations
private

Definition at line 68 of file us_mpi_analysis.h.

QList< Gene > US_MPI_Analysis::genes
private

Definition at line 235 of file us_mpi_analysis.h.

QVector< double > US_MPI_Analysis::gl_nnls_a
private

Definition at line 92 of file us_mpi_analysis.h.

QVector< double > US_MPI_Analysis::gl_nnls_b
private

Definition at line 93 of file us_mpi_analysis.h.

bool US_MPI_Analysis::glob_runid
private

Definition at line 55 of file us_mpi_analysis.h.

int US_MPI_Analysis::group_rank
private

Definition at line 43 of file us_mpi_analysis.h.

bool US_MPI_Analysis::in_gsm
private

Definition at line 255 of file us_mpi_analysis.h.

bool US_MPI_Analysis::is_composite_job
private

Definition at line 58 of file us_mpi_analysis.h.

bool US_MPI_Analysis::is_global_fit
private

Definition at line 57 of file us_mpi_analysis.h.

int US_MPI_Analysis::iterations
private

Definition at line 47 of file us_mpi_analysis.h.

QList< Sa_Job > US_MPI_Analysis::job_queue
private

Definition at line 185 of file us_mpi_analysis.h.

int US_MPI_Analysis::k_grid
private

Definition at line 226 of file us_mpi_analysis.h.

const double US_MPI_Analysis::LARGE = 1.e39
staticprivate

Definition at line 187 of file us_mpi_analysis.h.

QVector< int > US_MPI_Analysis::lfvari
private

Definition at line 247 of file us_mpi_analysis.h.

QVector< US_Solute > US_MPI_Analysis::ljob_solutes
private

Definition at line 174 of file us_mpi_analysis.h.

int US_MPI_Analysis::max_depth
private

Definition at line 94 of file us_mpi_analysis.h.

int US_MPI_Analysis::max_experiment_size
private

Definition at line 51 of file us_mpi_analysis.h.

int US_MPI_Analysis::max_iterations
private

Definition at line 48 of file us_mpi_analysis.h.

int US_MPI_Analysis::max_walltime
private

Definition at line 46 of file us_mpi_analysis.h.

QVector< double > US_MPI_Analysis::maxods
private

Definition at line 107 of file us_mpi_analysis.h.

long int US_MPI_Analysis::maxrss
private

Definition at line 84 of file us_mpi_analysis.h.

QVector< double > US_MPI_Analysis::mc_data
private

Definition at line 108 of file us_mpi_analysis.h.

int US_MPI_Analysis::mc_iteration
private

Definition at line 50 of file us_mpi_analysis.h.

int US_MPI_Analysis::mc_iterations
private

Definition at line 49 of file us_mpi_analysis.h.

int US_MPI_Analysis::meniscus_points
private

Definition at line 100 of file us_mpi_analysis.h.

double US_MPI_Analysis::meniscus_range
private

Definition at line 102 of file us_mpi_analysis.h.

int US_MPI_Analysis::meniscus_run
private

Definition at line 101 of file us_mpi_analysis.h.

double US_MPI_Analysis::meniscus_value
private

Definition at line 103 of file us_mpi_analysis.h.

QVector< double > US_MPI_Analysis::meniscus_values
private

Definition at line 104 of file us_mpi_analysis.h.

int US_MPI_Analysis::mgroup_count
private

Definition at line 42 of file us_mpi_analysis.h.

int US_MPI_Analysis::migrate_count
private

Definition at line 72 of file us_mpi_analysis.h.

const int US_MPI_Analysis::min_experiment_size = 100
staticprivate

Definition at line 85 of file us_mpi_analysis.h.

const double US_MPI_Analysis::min_variance_improvement = 1.0e-100
staticprivate

Definition at line 86 of file us_mpi_analysis.h.

int US_MPI_Analysis::minimize_opt
private

Definition at line 253 of file us_mpi_analysis.h.

QString US_MPI_Analysis::modelGUID
private

Definition at line 131 of file us_mpi_analysis.h.

US_ModelRecord US_MPI_Analysis::mrec
private

Definition at line 117 of file us_mpi_analysis.h.

QVector< US_ModelRecord > US_MPI_Analysis::mrecs
private

Definition at line 118 of file us_mpi_analysis.h.

double US_MPI_Analysis::mutate_sigma
private

Definition at line 78 of file us_mpi_analysis.h.

int US_MPI_Analysis::mutation
private

Definition at line 70 of file us_mpi_analysis.h.

MPI_Comm US_MPI_Analysis::my_communicator
private

Definition at line 60 of file us_mpi_analysis.h.

int US_MPI_Analysis::my_group
private

Definition at line 41 of file us_mpi_analysis.h.

int US_MPI_Analysis::my_rank
private

Definition at line 40 of file us_mpi_analysis.h.

int US_MPI_Analysis::my_workers
private

Definition at line 44 of file us_mpi_analysis.h.

int US_MPI_Analysis::nassocc
private

Definition at line 251 of file us_mpi_analysis.h.

int US_MPI_Analysis::ncompc
private

Definition at line 250 of file us_mpi_analysis.h.

int US_MPI_Analysis::nfloatc
private

Definition at line 249 of file us_mpi_analysis.h.

int US_MPI_Analysis::nfvari
private

Definition at line 252 of file us_mpi_analysis.h.

QList< QVector< US_Solute > > US_MPI_Analysis::orig_solutes
private

Definition at line 173 of file us_mpi_analysis.h.

QList< QVector< US_ZSolute > > US_MPI_Analysis::orig_zsolutes
private

Definition at line 175 of file us_mpi_analysis.h.

int US_MPI_Analysis::p_grid
private

Definition at line 227 of file us_mpi_analysis.h.

double US_MPI_Analysis::p_mutate_k
private

Definition at line 80 of file us_mpi_analysis.h.

double US_MPI_Analysis::p_mutate_s
private

Definition at line 79 of file us_mpi_analysis.h.

double US_MPI_Analysis::p_mutate_sk
private

Definition at line 81 of file us_mpi_analysis.h.

QMap< QString, QString > US_MPI_Analysis::parameters
private

Definition at line 135 of file us_mpi_analysis.h.

double US_MPI_Analysis::pararry[36]
private

Definition at line 120 of file us_mpi_analysis.h.

int US_MPI_Analysis::plague
private

Definition at line 71 of file us_mpi_analysis.h.

int US_MPI_Analysis::population
private

Definition at line 67 of file us_mpi_analysis.h.

quint16 US_MPI_Analysis::port
private

Definition at line 123 of file us_mpi_analysis.h.

SIMULATION US_MPI_Analysis::previous_values
private

Definition at line 197 of file us_mpi_analysis.h.

int US_MPI_Analysis::proc_count
private

Definition at line 39 of file us_mpi_analysis.h.

double US_MPI_Analysis::regularization
private

Definition at line 232 of file us_mpi_analysis.h.

QString US_MPI_Analysis::requestGUID
private

Definition at line 132 of file us_mpi_analysis.h.

QString US_MPI_Analysis::requestID
private

Definition at line 126 of file us_mpi_analysis.h.

US_DataIO::RawData* US_MPI_Analysis::res_data
private

Definition at line 112 of file us_mpi_analysis.h.

int US_MPI_Analysis::s_grid
private

Definition at line 225 of file us_mpi_analysis.h.

US_DataIO::RawData US_MPI_Analysis::scaled_data
private

Definition at line 115 of file us_mpi_analysis.h.

QHostAddress US_MPI_Analysis::server
private

Definition at line 122 of file us_mpi_analysis.h.

int US_MPI_Analysis::set_count
private

Definition at line 141 of file us_mpi_analysis.h.

QVector< double > US_MPI_Analysis::sigmas
private

Definition at line 109 of file us_mpi_analysis.h.

US_DataIO::RawData* US_MPI_Analysis::sim_data
private

Definition at line 113 of file us_mpi_analysis.h.

US_DataIO::RawData US_MPI_Analysis::sim_data1
private

Definition at line 114 of file us_mpi_analysis.h.

QList< SIMULATION > US_MPI_Analysis::sim_values
private

Definition at line 237 of file us_mpi_analysis.h.

SIMULATION US_MPI_Analysis::simulation_values
private

Definition at line 195 of file us_mpi_analysis.h.

QUdpSocket* US_MPI_Analysis::socket
private

Definition at line 124 of file us_mpi_analysis.h.

const int US_MPI_Analysis::solute_doubles = sizeof( US_Solute ) / sizeof( double )
staticprivate

Definition at line 188 of file us_mpi_analysis.h.

QDateTime US_MPI_Analysis::startTime
private

Definition at line 139 of file us_mpi_analysis.h.

QDateTime US_MPI_Analysis::submitTime
private

Definition at line 138 of file us_mpi_analysis.h.

QMap< QString, QString > US_MPI_Analysis::task_params
private

Definition at line 136 of file us_mpi_analysis.h.

int US_MPI_Analysis::total_points
private

Definition at line 52 of file us_mpi_analysis.h.

SIMULATION US_MPI_Analysis::wksim_vals
private

Definition at line 196 of file us_mpi_analysis.h.

US_Model US_MPI_Analysis::wmodel
private

Definition at line 243 of file us_mpi_analysis.h.

QVector< long > US_MPI_Analysis::work_rss
private

Definition at line 110 of file us_mpi_analysis.h.

QVector< int > US_MPI_Analysis::worker_depth
private

Definition at line 89 of file us_mpi_analysis.h.

QVector< int > US_MPI_Analysis::worker_status
private

Definition at line 88 of file us_mpi_analysis.h.

int US_MPI_Analysis::worknext
private

Definition at line 95 of file us_mpi_analysis.h.

const int US_MPI_Analysis::zsolut_doubles = sizeof( US_ZSolute ) / sizeof( double )
staticprivate

Definition at line 189 of file us_mpi_analysis.h.

The documentation for this class was generated from the following files:
Generated on Sun Jun 21 2015 11:40:44 for UltraScan III by   doxygen 1.8.3.1-20130324