Inheritance diagram for ProgMpiAngularProjectLibrary:

Collaboration diagram for ProgMpiAngularProjectLibrary:

Public Member Functions
	ProgMpiAngularProjectLibrary ()

void	readParams ()

void	defineParams ()

void	show ()

void	preRun ()

void	process ()

void	createGroupSamplingFiles (void)

void	error_exit (const char *msg)

void	run ()

Public Member Functions inherited from ProgAngularProjectLibrary
	ProgAngularProjectLibrary ()

	ProgAngularProjectLibrary (const ProgAngularProjectLibrary &)=delete

	ProgAngularProjectLibrary (const ProgAngularProjectLibrary &&)=delete

	~ProgAngularProjectLibrary ()

ProgAngularProjectLibrary &	operator= (const ProgAngularProjectLibrary &)=delete

ProgAngularProjectLibrary &	operator= (const ProgAngularProjectLibrary &&)=delete

void	readParams ()

void	defineParams ()

void	show ()

void	run ()

void	createGroupSamplingFiles (void)

void	get_sym_vectors (std::vector< Matrix1D< double > > &sym_points)

void	project_angle_vector (int my_init, int my_end, bool verbose=true)

Public Member Functions inherited from XmippProgram
const char *	getParam (const char *param, int arg=0)

const char *	getParam (const char param, const char subparam, int arg=0)

int	getIntParam (const char *param, int arg=0)

int	getIntParam (const char param, const char subparam, int arg=0)

double	getDoubleParam (const char *param, int arg=0)

double	getDoubleParam (const char param, const char subparam, int arg=0)

float	getFloatParam (const char *param, int arg=0)

float	getFloatParam (const char param, const char subparam, int arg=0)

void	getListParam (const char *param, StringVector &list)

int	getCountParam (const char *param)

bool	checkParam (const char *param)

bool	existsParam (const char *param)

void	addParamsLine (const String &line)

void	addParamsLine (const char *line)

ParamDef *	getParamDef (const char *param) const

virtual void	quit (int exit_code=0) const

virtual int	tryRun ()

void	initProgress (size_t total, size_t stepBin=60)

void	setProgress (size_t value=0)

void	endProgress ()

void	processDefaultComment (const char param, const char left)

void	setDefaultComment (const char param, const char comment)

virtual void	initComments ()

void	setProgramName (const char *name)

void	addUsageLine (const char *line, bool verbatim=false)

void	clearUsage ()

void	addExampleLine (const char *example, bool verbatim=true)

void	addSeeAlsoLine (const char *seeAlso)

void	addKeywords (const char *keywords)

const char *	name () const

virtual void	usage (int verb=0) const

virtual void	usage (const String &param, int verb=2)

int	version () const

virtual void	show () const

virtual void	read (int argc, const char **argv, bool reportErrors=true)

virtual void	read (int argc, char **argv, bool reportErrors=true)

void	read (const String &argumentsLine)

	XmippProgram ()

	XmippProgram (int argc, const char **argv)

virtual	~XmippProgram ()

Public Attributes
int	nProcs

int	mpi_job_size

int	numberOfJobs

int	rank

MPI_Status	status

Public Attributes inherited from ProgAngularProjectLibrary
Sampling	mysampling

double	sampling

double	perturb_projection_vector

double	psi_sampling

double	max_tilt_angle

double	min_tilt_angle

FileName	output_file

FileName	output_file_root

FileName	fn_groups

projectionType	projType
	Type of projection algorithm: More...

double	paddFactor
	The padding factor for Fourier projection. More...

double	maxFrequency
	The maximum frequency for Fourier projection. More...

int	BSplineDeg
	The type of interpolation (NEAR. More...

FileName	FnexperimentalImages

bool	angular_distance_bool

bool	remove_points_far_away_from_experimental_data_bool

double	angular_distance

bool	compute_closer_sampling_point_bool

bool	compute_neighbors_bool

int	symmetry

FileName	fn_sym
	symmetry file for sampling More...

FileName	fn_sym_neigh
	symmetry file for heighbors computation More...

int	sym_order

FileName	input_volume

Image< double >	inputVol

int	Xdim

int	Ydim

bool	only_winner

RealShearsInfo *	Vshears

FourierProjector *	Vfourier

Public Attributes inherited from XmippProgram
bool	doRun

bool	runWithoutArgs

int	verbose
	Verbosity level. More...

int	debug

Additional Inherited Members
Protected Member Functions inherited from XmippProgram
void	defineCommons ()

Protected Attributes inherited from XmippProgram
int	errorCode

ProgramDef *	progDef
	Program definition and arguments parser. More...

std::map< String, CommentList >	defaultComments

int	argc
	Original command line arguments. More...

const char **	argv

Detailed Description

Definition at line 46 of file mpi_angular_project_library.cpp.

Constructor & Destructor Documentation

◆ ProgMpiAngularProjectLibrary()

ProgMpiAngularProjectLibrary::ProgMpiAngularProjectLibrary ( )

inline

Definition at line 68 of file mpi_angular_project_library.cpp.

     {
         //parent class constructor will be called by deault without parameters
         MPI_Comm_size(MPI_COMM_WORLD, &nProcs);
         MPI_Comm_rank(MPI_COMM_WORLD, &rank);
         //Blocks until all process have reached this routine.
         //very likelly this is
         MPI_Barrier(MPI_COMM_WORLD);
     }

Member Function Documentation

◆ createGroupSamplingFiles()

void ProgMpiAngularProjectLibrary::createGroupSamplingFiles ( void )

inline

Definition at line 481 of file mpi_angular_project_library.cpp.

     {
         if (rank==0 && fn_groups!="")
             ProgAngularProjectLibrary::createGroupSamplingFiles();
     }

◆ defineParams()

void ProgMpiAngularProjectLibrary::defineParams ( )

inlinevirtual

Function in which the param of each Program are defined.

Reimplemented from XmippProgram.

Definition at line 89 of file mpi_angular_project_library.cpp.

     {
         ProgAngularProjectLibrary::defineParams();
         addParamsLine("  [--mpi_job_size <size=10>]: Number of images sent to a cpu in a single job");
         addParamsLine("                            : 10 may be a good value");
         addParamsLine("                            : if  -1 the computer will put the maximum");
         addParamsLine("                            : posible value that may not be the best option");
     }

◆ error_exit()

void ProgMpiAngularProjectLibrary::error_exit ( const char * msg )

inline

Definition at line 488 of file mpi_angular_project_library.cpp.

     {
         fprintf(stderr, "%s", msg);
         MPI_Abort(MPI_COMM_WORLD, EXIT_FAILURE);
     }

◆ preRun()

void ProgMpiAngularProjectLibrary::preRun ( )

inline

Definition at line 107 of file mpi_angular_project_library.cpp.

     {
         //do not use rank 0 here, since rank 1 will manipulate this file later
         if (rank == 1)
         {
             unlink(output_file.c_str());
         }
 
 
         //#define DEBUGTIME
 #ifdef  DEBUGTIME
 #include <ctime>
 
         time_t start,end;
         double time_dif;
         time (&start);
         time (&end);
         time_dif = difftime (end,start);
         start=end;
         std::cerr<<" starting prerun rank= "<<rank<<std::endl;
 #endif
 
         int my_seed;
         if (rank == 0)
         {
             show();
             //random numbers must be the same in all nodes
             if(perturb_projection_vector!=0)
             {
                 srand(getpid());
                 my_seed = rand();
             }
         }
 #ifdef  DEBUGTIME
         time (&end);
         time_dif = difftime (end,start);
         start=end;
         std::cerr<<" set rand seed rank= "<<rank<<std::endl;
 #endif
         //Bcast must be seem by all processors
         if(perturb_projection_vector!=0)
         {
             MPI_Bcast (&my_seed, 1, MPI_INT, 0, MPI_COMM_WORLD);
             mysampling.setNoise(perturb_projection_vector,my_seed);
 #ifdef  DEBUGTIME
 
             time (&end);
             time_dif = difftime (end,start);
             start=end;
             std::cerr<<" after perturb rank= "<<rank<<std::endl;
 #endif
 
         }
         //all ranks
         mysampling.setSampling(sampling);
         //symmetry for sampling may be different from neighbourhs
         if (!mysampling.SL.isSymmetryGroup(fn_sym, symmetry, sym_order))
             REPORT_ERROR(ERR_NUMERICAL, (std::string)"angular_project_library::run Invalid symmetry" +  fn_sym);//set sampling must go before set noise
         if(angular_distance_bool!=0)
             mysampling.setNeighborhoodRadius(angular_distance);//irelevant
 
 #ifdef  DEBUGTIME
 
         time (&end);
         time_dif = difftime (end,start);
         start=end;
         std::cerr<<" setsampling rank= "<<rank<<std::endl;
 #endif
         //true -> half_sphere
         mysampling.computeSamplingPoints(false,max_tilt_angle,min_tilt_angle);
         mysampling.SL.readSymmetryFile(fn_sym);
         //store symmetry matrices, this is faster than computing them each time
         mysampling.fillLRRepository();
 
 #ifdef  DEBUGTIME
 
         time (&end);
         time_dif = difftime (end,start);
         start=end;
         std::cerr<<" compute sampling points rank= "<<rank<<std::endl;
 #endif
 
         // We first sample The  whole sphere
         // Then we remove point redundant due to sampling symmetry
         // use old symmetry, this is geometric does not use L_R
         mysampling.removeRedundantPoints(symmetry, sym_order);
 
         //=========================
         //======================
         //recompute symmetry with neigh symmetry
         if (!mysampling.SL.isSymmetryGroup(fn_sym_neigh, symmetry, sym_order))
             REPORT_ERROR(ERR_NUMERICAL, (std::string)"angular_project_library::run Invalid neig symmetry" +  fn_sym_neigh);
         mysampling.SL.readSymmetryFile(fn_sym_neigh);
         mysampling.fillLRRepository();
         //precompute product between symmetry matrices and experimental data
         if (FnexperimentalImages.size() > 0)
             mysampling.fillExpDataProjectionDirectionByLR(FnexperimentalImages);
 #ifdef  DEBUGTIME
 
         time (&end);
         time_dif = difftime (end,start);
         start=end;
         std::cerr<<" remove redundant rank= "<<rank<<std::endl;
 #endif
 
         if (FnexperimentalImages.size() > 0 &&
             remove_points_far_away_from_experimental_data_bool)
         {
             mysampling.removePointsFarAwayFromExperimentalData();
 #ifdef  DEBUGTIME
 
             time (&end);
             time_dif = difftime (end,start);
             start=end;
             std::cerr<<" remove points far away rank= "<<rank<<std::endl;
 #endif
 
         }
 
         /* save files */
         if (rank == 0)
         {
             if(compute_closer_sampling_point_bool)
             {
                 //find sampling point closer to experimental point (only 0) and bool
                 //and save docfile with this information
                 mysampling.findClosestSamplingPoint(FnexperimentalImages,output_file_root);
             }
             //mysampling.createSymFile(symmetry, sym_order);
             mysampling.createAsymUnitFile(output_file_root);
         }
 
         if (rank != 0)
         {
             inputVol.read(input_volume);
             inputVol().setXmippOrigin();
             Xdim = XSIZE(inputVol());
             Ydim = YSIZE(inputVol());
         }
         if (rank == 0)
         {
             if (compute_neighbors_bool)
             {
                 mysampling.computeNeighbors(only_winner);
                 mysampling.saveSamplingFile(output_file_root,false);
             }
         }
         //release some memory
         mysampling.exp_data_projection_direction_by_L_R.clear();
 
         if (mpi_job_size != -1)
         {
             numberOfJobs = (int)ceil((double)(mysampling.no_redundant_sampling_points_angles.size())/mpi_job_size);
         }
         else
         {
             numberOfJobs=nProcs-1;//one node is the master
             mpi_job_size=(int)ceil((double)mysampling.no_redundant_sampling_points_angles.size()/numberOfJobs);
         }
 
         verbose=false;
         #define DEBUG
 #ifdef DEBUG
 
         if (rank == 1)
         {
             std::cerr << "numberOfJobs: " << numberOfJobs << std::endl
             << "number of projections to be created: " <<  mysampling.no_redundant_sampling_points_angles.size()
             <<std::endl;
         }
 #endif
         #undef DEBUG
 
         //create blanck outfile so main header does not need to be re-writen
         //rank 1 has already xdim and ydim.
         if (rank == 1)
         {
             int  numberProjections = std::ceil(360.0 / psi_sampling);
             numberProjections *= mysampling.no_redundant_sampling_points_angles.size();
             std::cerr   << "creating Blank file: "
             << output_file << " for "
             << numberProjections << "  projections of size: " << Xdim << " " << Ydim
             << std::endl;
             createEmptyFile(output_file,Xdim,Ydim,1,numberProjections,true,WRITE_REPLACE);
         }
 
         MPI_Barrier(MPI_COMM_WORLD);
     }

◆ process()

void ProgMpiAngularProjectLibrary::process ( )

inline

Definition at line 296 of file mpi_angular_project_library.cpp.

     {
         if (rank == 0)
         {
             int stopTagsSent =0;
             int c = XMIPP_MAX(1, numberOfJobs / 60);
             init_progress_bar(numberOfJobs);
             for (int i=0;i<numberOfJobs;)
             {
                 //collect data if available
                 //be aware that mpi_Probe will block the program until a message is received
                 MPI_Probe(MPI_ANY_SOURCE, MPI_ANY_TAG, MPI_COMM_WORLD, &status);
                 // worker is free
                 if (status.MPI_TAG == TAG_FREEWORKER)
                 {
                     MPI_Recv(nullptr, 0, MPI_INT, MPI_ANY_SOURCE, TAG_FREEWORKER,
                              MPI_COMM_WORLD, &status);
                     //#define DEBUG
 #ifdef DEBUG
 
                     std::cerr << "Mr_f received TAG_FREEWORKER from worker " <<  status.MPI_SOURCE << std::endl;
 #endif
                     //send work
                     MPI_Send(&i,
                              1,
                              MPI_INT,
                              status.MPI_SOURCE,
                              TAG_WORKFORWORKER,
                              MPI_COMM_WORLD);
                     i++; //increase job number
                     //#define DEBUG
 #ifdef DEBUG
 
                     std::cerr << "Ms_f sent TAG_WORKFORWORKER to worker " <<  status.MPI_SOURCE << std::endl;
                     std::cerr << "Sent jobNo " <<  i << std::endl;
 #endif
                     //#undef DEBUG
                 }
                 else
                 {
                     std::cerr << "M_f Received unknown TAG" << std::endl;
                     exit(0);
                 }
 
                 if (i % c == 0)
                     progress_bar(i);
             }
             progress_bar(numberOfJobs);
 
             //send TAG_STOP
             while (stopTagsSent < (nProcs-1))
             {
                 MPI_Recv(nullptr, 0, MPI_INT, MPI_ANY_SOURCE, TAG_FREEWORKER,
                          MPI_COMM_WORLD, &status);
 #ifdef DEBUG
 
                 std::cerr << "Mr received TAG_FREEWORKER from worker " <<  status.MPI_SOURCE << std::endl;
                 std::cerr << "Ms sent TAG_STOP to worker" << status.MPI_SOURCE << std::endl;
 #endif
     #undef DEBUG
 
                 MPI_Send(nullptr, 0, MPI_INT, status.MPI_SOURCE, TAG_STOP, MPI_COMM_WORLD);
                 stopTagsSent++;
             }
             //only rank 0 create sel file
             if(rank==0)
             {
 
                 MetaDataVec  mySFin;
                 mySFin.read(output_file_root + "_angles.doc");
 #define ANGLESDOC
 #ifdef ANGLESDOC
 //       std::cerr << "DEBUG_ROB, output_file_root + angle.doc:"
 //               << output_file_root + "_angles.doc" << std::endl;
 #endif
                 MetaDataVec  mySF;
                 FileName fn_temp;
 
                 size_t myCounter = 0;
                 size_t id;
                 int ref;
 
                 for (size_t objId : mySFin.ids())
                 {
                     // FIXME: read whole row at once
                     double x,y,z, rot, tilt, psi;
                     mySFin.getValue(MDL_ANGLE_ROT,rot,objId);
                     mySFin.getValue(MDL_ANGLE_TILT,tilt,objId);
                     mySFin.getValue(MDL_ANGLE_PSI,psi,objId);
                     mySFin.getValue(MDL_X,x,objId);
                     mySFin.getValue(MDL_Y,y,objId);
                     mySFin.getValue(MDL_Z,z,objId);
                     mySFin.getValue(MDL_REF,ref,objId);
 
                     for (int i = 0; i < std::ceil(360.0 / psi_sampling); ++i) {
                         //FIXME, do I have order?
                         fn_temp.compose(++myCounter,output_file);
                         id = mySF.addObject();
                         mySF.setValue(MDL_IMAGE,fn_temp, id);
                         mySF.setValue(MDL_ENABLED,1, id);
 
                         mySF.setValue(MDL_ANGLE_ROT,rot, id);
                         mySF.setValue(MDL_ANGLE_TILT,tilt, id);
                         mySF.setValue(MDL_ANGLE_PSI,psi + i * psi_sampling, id);
                         mySF.setValue(MDL_X,x, id);
                         mySF.setValue(MDL_Y,y, id);
                         mySF.setValue(MDL_Z,z, id);
                         mySF.setValue(MDL_SCALE,1.0,id);
                         mySF.setValue(MDL_REF,ref,id);
                     }
                 }
                 fn_temp=output_file_root+".doc";
                 mySF.setComment("x,y,z refer to the coordinates of the unitary vector at direction given by the euler angles");
                 mySF.write(fn_temp);
 #ifndef ANGLESDOC
                 unlink((output_file_root+"_angles.doc").c_str());
 #endif
 #undef ANGLESDOC
             }
         }
         else
         {
             // Select only relevant part of selfile for this rank
             // job number
             // job size
             // aux variable
             while (1)
             {
                 int jobNumber;
                 //I am free
                 MPI_Send(nullptr, 0, MPI_INT, 0, TAG_FREEWORKER, MPI_COMM_WORLD);
                 //#define DEBUG
 #ifdef DEBUG
 
                 std::cerr << "W" << rank << " " << "sent TAG_FREEWORKER to master " << std::endl;
 #endif
 #undef DEBUG
                 //get yor next task
                 MPI_Probe(0, MPI_ANY_TAG, MPI_COMM_WORLD, &status);
 #ifdef DEBUG
 
                 std::cerr << "W" << rank << " " << "probe MPI_ANY_TAG " << std::endl;
 #endif
 
                 if (status.MPI_TAG == TAG_STOP)//no more jobs exit
                 {
                     //If I  do not read this tag
                     //master will no further process
                     //a posibility is a non-blocking send
                     MPI_Recv(nullptr, 0, MPI_INT, 0, TAG_STOP,
                              MPI_COMM_WORLD, &status);
 #ifdef DEBUG
 
                     std::cerr << "Wr" << rank << " " << "TAG_STOP" << std::endl;
 #endif
 
                     break;
                 }
                 if (status.MPI_TAG == TAG_WORKFORWORKER)
                     //there is still some work to be done
                 {
                     //get the jobs number
                     MPI_Recv(&jobNumber, 1, MPI_INT, 0, TAG_WORKFORWORKER, MPI_COMM_WORLD, &status);
 #ifdef DEBUG
 
                     std::cerr << "Wr" << rank << " " << "TAG_WORKFORWORKER" << std::endl;
                     std::cerr <<    "jobNumber "  << jobNumber << std::endl;
 #endif
 #undef DEBUG
                     // Process all images
                     project_angle_vector(jobNumber*mpi_job_size,
                                          std::min((size_t)((jobNumber+1)* mpi_job_size -1),
                                                    mysampling.no_redundant_sampling_points_angles.size()-1),
                                          verbose);
                     //get yor next task
                 }
                 else
                 {
                     std::cerr << "3) Received unknown TAG I quit" << std::endl;
                     exit(0);
                 }
             }
         }
     }

◆ readParams()

void ProgMpiAngularProjectLibrary::readParams ( )

inlinevirtual

Function in which each program will read parameters that it need. If some error occurs the usage will be printed out.

Reimplemented from XmippProgram.

Definition at line 80 of file mpi_angular_project_library.cpp.

     {
         if (nProcs < 2)
             error_exit("This program cannot be executed in a single working node");
         ProgAngularProjectLibrary::readParams();
         mpi_job_size = getIntParam("--mpi_job_size");
     }

◆ run()

void ProgMpiAngularProjectLibrary::run ( )

inlinevirtual

This function will be start running the program. it also should be implemented by derived classes.

Reimplemented from XmippProgram.

Definition at line 494 of file mpi_angular_project_library.cpp.

     {
       try
       {
           preRun();
           process();
           createGroupSamplingFiles();
       }
       catch (XmippError &XE)
       {
           std::cerr << "Error!" <<std::endl;
           std::cerr << XE.what();
           MPI_Finalize();
           exit(1);
       }
 
       if (rank == 0)
           std::cout << "Done!" <<std::endl;
     }

◆ show()

void ProgMpiAngularProjectLibrary::show ( )

inline

Definition at line 100 of file mpi_angular_project_library.cpp.

     {
         ProgAngularProjectLibrary::show();
         std::cerr << " Size of mpi jobs " << mpi_job_size <<std::endl;
     }

Member Data Documentation

◆ mpi_job_size

int ProgMpiAngularProjectLibrary::mpi_job_size

Dvide the job in this number block with this number of images

Definition at line 56 of file mpi_angular_project_library.cpp.

◆ nProcs

int ProgMpiAngularProjectLibrary::nProcs

Number of Procesors

Definition at line 53 of file mpi_angular_project_library.cpp.

◆ numberOfJobs

int ProgMpiAngularProjectLibrary::numberOfJobs

Number of jobs

Definition at line 59 of file mpi_angular_project_library.cpp.

◆ rank

int ProgMpiAngularProjectLibrary::rank

computing node number. Master=0

Definition at line 62 of file mpi_angular_project_library.cpp.

◆ status

MPI_Status ProgMpiAngularProjectLibrary::status

status after am MPI call

Definition at line 65 of file mpi_angular_project_library.cpp.

The documentation for this class was generated from the following file:

xmipp/libraries/parallel/mpi_angular_project_library.cpp

Public Member Functions

Public Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ ProgMpiAngularProjectLibrary()

Member Function Documentation

◆ createGroupSamplingFiles()

◆ defineParams()

◆ error_exit()

◆ preRun()

◆ process()

◆ readParams()

◆ run()

◆ show()

Member Data Documentation

◆ mpi_job_size

◆ nProcs

◆ numberOfJobs

◆ rank

◆ status