Merge branch 'devel_drohr' of gitta.rzg.mpg.de:BioEM into devel_drohr

bioem.cpp

@@ -7,6 +7,14 @@
 
    ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++*/
 
+#include <mpi.h>
+
+#define MPI_CHK(expr) \
+	if (expr != MPI_SUCCESS) \
+	{ \
+		fprintf(stderr, "Error in MPI function %s: %d\n", __FILE__, __LINE__); \
+	}
+
 #include <fstream>
 #include <boost/program_options.hpp>
 #include <iostream>
@@ -215,7 +223,14 @@ int bioem::configure(int ac, char* av[])
 	}
 
 #ifdef WITH_MPI
-
+	MPI_Bcast(&param, sizeof(param), MPI_BYTE, 0, MPI_COMM_WORLD);
+	//refCtf, CtfParam, angles automatically filled by precalculare function below
+	
+	MPI_Bcast(&Model, sizeof(Model), MPI_BYTE, 0, MPI_COMM_WORLD);
+	Model.points = (bioem_model::bioem_model_point*) mallocchk(sizeof(bioem_model::bioem_model_point) * Model.nPointsModel);
+	MPI_Bcast(Model.points, sizeof(bioem_model::bioem_model_point) * Model.nPointsModel, MPI_BYTE, 0, MPI_COMM_WORLD);
+	
+	
 #endif
 	if (mpi_rank != 0) return(1);
 

include/bioem.h

 #ifndef BIOEM_H
 #define BIOEM_H
-#include <fstream>
-#include <iostream>
-#include <complex>
 
 #include "defs.h"
 #include "bioem.h"

include/defs.h

@@ -99,15 +99,6 @@ static inline void* reallocchk(void* oldptr, size_t size)
 #define omp_get_thread_num() 0
 #endif
 
-#ifdef WITH_MPI
-#include <mpi.h>
-
-#define MPI_CHK(expr) \
-	if (expr != MPI_SUCCESS) \
-	{ \
-		fprintf(stderr, "Error in MPI function %s: %d\n", __FILE__, __LINE__); \
-	}
-#endif
 extern int mpi_rank;
 extern int mpi_size;
 

include/param.h

@@ -39,6 +39,8 @@ public:
 	int Alignment;
 	mycomplex_t* refCTF;
 	myfloat3_t* CtfParam;
+	size_t getRefCtfCount() {return nTotCTFs * FFTMapSize;}
+	size_t getCtfParamCount() {return nTotCTFs;}
 
 	myfloat_t pixelSize;
 // Grid Points in Euler angles, assuming uniform sampling d_alpha=d_gamma (in 2pi) & cos(beta)=-1,1

main.cpp

+#include <mpi.h>
+
+#define MPI_CHK(expr) \
+	if (expr != MPI_SUCCESS) \
+	{ \
+		fprintf(stderr, "Error in MPI function %s: %d\n", __FILE__, __LINE__); \
+	}
+
 #include <stdio.h>
 #include <stdlib.h>
 #include <string.h>

param.cpp

@@ -375,10 +375,10 @@ int bioem_param::CalculateRefCTF()
 
 	nTotCTFs = numberGridPointsCTF_amp * numberGridPointsCTF_phase * numberGridPointsEnvelop;
 	delete[] refCTF;
-	refCTF = new mycomplex_t[nTotCTFs * FFTMapSize];
+	refCTF = new mycomplex_t[getRefCtfCount()];
 	delete[] CtfParam;
-	CtfParam = new myfloat3_t[nTotCTFs];
-
+	CtfParam = new myfloat3_t[getCtfParamCount()];
+	
 	for (int iamp = 0; iamp <  numberGridPointsCTF_amp ; iamp++) //Loop over amplitud
 	{
 		amp = (myfloat_t) iamp * gridCTF_amp + startGridCTF_amp;