v.2.1-beta-1 (2.1.b1)

This fixes a critical bug affecting half-set (gold-standard) refinement.

Starting with version 2.0.4, each iteration of auto-refinement incorrectly
uses the same half-set reconstruction as for alignment of all data. The FSC
and resolution reported is however still based on comparing two half-set
reconstructions which contain completely separate image data. A
degree of reference-bias is however present.  The effect is to report
a resolution higher than what should be under gold-standard conditions,
since, reconstructions are subject to a degree of over-fitting.

In order to claim a so-called "gold-standard" resolution, use any version
before and including 2.0.3, or version 2.1b1 (this release).

src/macros.h

@@ -45,7 +45,7 @@
 #ifndef MACROS_H
 #define MACROS_H
 
-#define RELION_VERSION "2.1-beta-0"
+#define RELION_VERSION "2.1-beta-1"
 
 #include <math.h>
 #include "src/error.h"

src/ml_optimiser_mpi.cpp

@@ -664,21 +664,24 @@ void MlOptimiserMpi::initialiseWorkLoad()
 
     MPI_Barrier(MPI_COMM_WORLD);
 
-	if(!node->isMaster())
-	{
-		/* Set up a bool-array with reference responsibilities for each rank. That is;
-		 * if(PPrefRank[i]==true)  //on this rank
-		 * 		(set up reference vol and MPI_Bcast)
-		 * else()
-		 * 		(prepare to receive from MPI_Bcast)
-		 */
-		mymodel.PPrefRank.assign(mymodel.PPref.size(),true);
+    if(!do_split_random_halves) //only Bcast-prep on classification, in other cases halves have been separately made by all ranks after data exchange in maximization
+    {
+		if(!node->isMaster())
+		{
+			/* Set up a bool-array with reference responsibilities for each rank. That is;
+			 * if(PPrefRank[i]==true)  //on this rank
+			 * 		(set up reference vol and MPI_Bcast)
+			 * else()
+			 * 		(prepare to receive from MPI_Bcast)
+			 */
+			mymodel.PPrefRank.assign(mymodel.PPref.size(),true);
 
-		for(int i=0; i<mymodel.PPref.size(); i++)
-			mymodel.PPrefRank[i] = ((i)%(node->size-1) == node->rank-1);
-	}
+			for(int i=0; i<mymodel.PPref.size(); i++)
+				mymodel.PPrefRank[i] = ((i)%(node->size-1) == node->rank-1);
+		}
+		MPI_Barrier(MPI_COMM_WORLD);
+    }
 
-	 MPI_Barrier(MPI_COMM_WORLD);
 //#define DEBUG_WORKLOAD
 #ifdef DEBUG_WORKLOAD
 	std::cerr << " node->rank= " << node->rank << " my_first_ori_particle_id= " << my_first_ori_particle_id << " my_last_ori_particle_id= " << my_last_ori_particle_id << std::endl;
@@ -754,26 +757,29 @@ void MlOptimiserMpi::expectation()
 		timer.toc(TIMING_EXP_1a);
 #endif
 
-	if (!node->isMaster())
-		for(int i=0; i<mymodel.PPref.size(); i++)
+	if(!do_split_random_halves) //only Bcast on classification, in other cases halves have been separately made by all ranks after data exchange in maximization
+	{
+		if (!node->isMaster())
 		{
-			/* NOTE: the first slave has rank 0 on the slave communicator node->slaveC,
-			 *       that's why we don't have to add 1, like this;
-			 *       int sender = (i)%(node->size - 1)+1 ;
-			 */
-
-			int sender = (i)%(node->size - 1); // which rank did the heavy lifting? -> sender of information
+			for(int i=0; i<mymodel.PPref.size(); i++)
 			{
-				// Communicating over all slaves means we don't have to allocate on the master.
-				node->relion_MPI_Bcast(MULTIDIM_ARRAY(mymodel.PPref[i].data),
-						MULTIDIM_SIZE(mymodel.PPref[0].data), MY_MPI_COMPLEX, sender, node->slaveC);
-				node->relion_MPI_Bcast(MULTIDIM_ARRAY(mymodel.tau2_class[i]),
-						MULTIDIM_SIZE(mymodel.tau2_class[0]), MY_MPI_DOUBLE, sender, node->slaveC);
+				/* NOTE: the first slave has rank 0 on the slave communicator node->slaveC,
+				 *       that's why we don't have to add 1, like this;
+				 *       int sender = (i)%(node->size - 1)+1 ;
+				 */
+
+				int sender = (i)%(node->size - 1); // which rank did the heavy lifting? -> sender of information
+				{
+					// Communicating over all slaves means we don't have to allocate on the master.
+					node->relion_MPI_Bcast(MULTIDIM_ARRAY(mymodel.PPref[i].data),
+							MULTIDIM_SIZE(mymodel.PPref[0].data), MY_MPI_COMPLEX, sender, node->slaveC);
+					node->relion_MPI_Bcast(MULTIDIM_ARRAY(mymodel.tau2_class[i]),
+							MULTIDIM_SIZE(mymodel.tau2_class[0]), MY_MPI_DOUBLE, sender, node->slaveC);
+				}
 			}
 		}
-
-	MPI_Barrier(MPI_COMM_WORLD);
-
+		MPI_Barrier(MPI_COMM_WORLD);
+	}
 #ifdef DEBUG
 	if(node->rank==2)
 	{