fixed merge conflicts in lbpm_random_pp

README.visit

@@ -4,9 +4,10 @@ Checkout code and create a cmake script to compile plug-in.
 Example commands for Rhea:
 
 Load the proper modules
-   module load visit
+   module unload intel gcc
-   module load cmake
    module load gcc/4.8.2
+   module load cmake
+
 
 Configure cmake to build the plug-in
     cmake                                       \
@@ -16,20 +17,21 @@ Configure cmake to build the plug-in
         -D USE_MPI=false                        \
         -D USE_CUDA=false                       \
         -D USE_VISIT=true                       \
-            -D VISIT_ROOT_DIR=/sw/rhea/visit    \
+            -D VISIT_ROOT_DIR=/sw/redhat6/visit \
         -D USE_TIMER=false                      \
         ../../LBPM-WIA
 
 
-
 Build the visit plug-in
+    make install -j 8
     make visit
 
-Check that the visit plug-in installed in ~/.visit/2.7.1/linux-x86_64/plugins/databases
+Check that the visit plug-in installed in ~/.visit/2.9.0/linux-x86_64/plugins/databases
+where 2.9.0 is the current version of visit on rhea
 It should have created several shared libraries:
     libELBMDatabase_par.so  libELBMDatabase_ser.so  libILBMDatabase.so  libMLBMDatabase.so
 
-Install visit on local machine (2.7.3)
+Install visit on local machine (2.9.0)
 
 Start visit on local machine
 

cmake/FindVisIt.cmake

@@ -45,7 +45,7 @@ MACRO( VISIT_PLUGIN SRC_DIR TARGET )
     ENDFOREACH()
     ADD_CUSTOM_TARGET( 
         ${SRC_DIR}
-        COMMAND ${VISIT_XML_CMAKE} ${TARGET}.xml
+        COMMAND ${VISIT_XML_CMAKE} -clobber ${TARGET}.xml
         COMMAND ${CMAKE_COMMAND} -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
             -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER} -DCMAKE_C_FLAGS=${CMAKE_C_FLAGS}
             -DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER} -DCMAKE_CXX_FLAGS=${CMAKE_CXX_FLAGS}  .

common/MPI_Helpers.cpp

@@ -162,11 +162,27 @@ int MPI_Waitall( int, MPI_Request[], MPI_Status[] )
 {
     return 0;
 }
+int MPI_Wait( MPI_Request*, MPI_Status* )
+{
+    return 0;
+}
 int MPI_Bcast( void *buffer, int count, MPI_Datatype datatype, int root, MPI_Comm comm )
 {
     ERROR("Not implimented yet");
     return 0;
 }
+int MPI_Send(const void *buf, int count, MPI_Datatype datatype, int dest, int tag,
+         MPI_Comm comm)
+{
+    ERROR("Not implimented yet");
+    return 0;
+}
+int MPI_Recv(void *buf, int count, MPI_Datatype datatype, int source, int tag,
+         MPI_Comm comm, MPI_Status *status)
+{
+    ERROR("Not implimented yet");
+    return 0;
+}
 int MPI_Isend(const void *buf, int count, MPI_Datatype datatype, int dest, int tag,
               MPI_Comm comm, MPI_Request *request)
 {
@@ -185,6 +201,13 @@ int MPI_Allreduce(const void *sendbuf, void *recvbuf, int count,
     ERROR("Not implimented yet");
     return 0;
 }
+int MPI_Allgather(const void *sendbuf, int sendcount, MPI_Datatype sendtype,
+                  void *recvbuf, int recvcount, MPI_Datatype recvtype,
+                  MPI_Comm comm)
+{
+    ERROR("Not implimented yet");
+    return 0;
+}
 int MPI_Sendrecv(const void *sendbuf, int sendcount, MPI_Datatype sendtype,
                 int dest, int sendtag,
                 void *recvbuf, int recvcount, MPI_Datatype recvtype,
@@ -194,6 +217,16 @@ int MPI_Sendrecv(const void *sendbuf, int sendcount, MPI_Datatype sendtype,
     ERROR("Not implimented yet");
     return 0;
 }
+int MPI_Comm_group(MPI_Comm comm, MPI_Group *group)
+{
+    ERROR("Not implimented yet");
+    return 0;
+}
+int MPI_Comm_create(MPI_Comm comm, MPI_Group group, MPI_Comm *newcomm)
+{
+    ERROR("Not implimented yet");
+    return 0;
+}
 double MPI_Wtime( void )
 {
     return 0.0;

common/MPI_Helpers.h

@@ -18,28 +18,40 @@
     #define MPI_COMM_WORLD 0
     #define MPI_COMM_SELF 0
     #define MPI_STATUS_IGNORE NULL
-    enum MPI_Datatype { MPI_LOGICAL, MPI_CHAR, MPI_INT, MPI_DOUBLE };
+    enum MPI_Datatype { MPI_LOGICAL, MPI_CHAR, MPI_UNSIGNED_CHAR, MPI_INT, 
-    enum MPI_Op { MPI_SUM };
+        MPI_UNSIGNED, MPI_LONG, MPI_UNSIGNED_LONG, MPI_LONG_LONG, MPI_FLOAT, MPI_DOUBLE };
+    enum MPI_Op { MPI_MIN, MPI_MAX, MPI_SUM };
+    enum MPI_Group {  };
     // Fake MPI functions
 	int MPI_Init(int*,char***);
 	int MPI_Finalize();
     int MPI_Comm_size( MPI_Comm, int *size );
     int MPI_Comm_rank( MPI_Comm, int *rank );
     int MPI_Barrier(MPI_Comm);
+    int MPI_Wait(MPI_Request*,MPI_Status*);
     int MPI_Waitall(int,MPI_Request[],MPI_Status[]);
     int MPI_Bcast(void*,int,MPI_Datatype,int,MPI_Comm);
+    int MPI_Send(const void *buf, int count, MPI_Datatype datatype, int dest, int tag,
+             MPI_Comm comm);
+    int MPI_Recv(void *buf, int count, MPI_Datatype datatype, int source, int tag,
+             MPI_Comm comm, MPI_Status *status);
     int MPI_Isend(const void *buf, int count, MPI_Datatype datatype, int dest, int tag,
               MPI_Comm comm, MPI_Request *request);
     int MPI_Irecv(void *buf, int count, MPI_Datatype datatype, int source,
               int tag, MPI_Comm comm, MPI_Request *request);
     int MPI_Allreduce(const void *sendbuf, void *recvbuf, int count,
                   MPI_Datatype datatype, MPI_Op op, MPI_Comm comm);
+    int MPI_Allgather(const void *sendbuf, int sendcount, MPI_Datatype sendtype,
+                  void *recvbuf, int recvcount, MPI_Datatype recvtype,
+                  MPI_Comm comm);
     int MPI_Sendrecv(const void *sendbuf, int sendcount, MPI_Datatype sendtype,
                 int dest, int sendtag,
                 void *recvbuf, int recvcount, MPI_Datatype recvtype,
                 int source, int recvtag,
                 MPI_Comm comm, MPI_Status *status);
     double MPI_Wtime( void );
+    int MPI_Comm_group(MPI_Comm comm, MPI_Group *group);
+    int MPI_Comm_create(MPI_Comm comm, MPI_Group group, MPI_Comm *newcomm);
 #endif
 
 

tests/lbpm_disc_pp.cpp

@@ -5,11 +5,12 @@
 #include <exception>
 #include <stdexcept>
 #include <fstream>
-#include <mpi.h>
 
 #include "pmmc.h"
 #include "Domain.h"
 #include "Communication.h"
+#include "MPI_Helpers.h"    // This includes mpi.h
+
 
 /*
  * Pre-Processor to generate signed distance function from disc packing
@@ -151,6 +152,8 @@ int main(int argc, char **argv)
 	MPI_Request req1[18],req2[18];
 	MPI_Status stat1[18],stat2[18];
 
+	int depth;
+
 	if (rank == 0){
 		printf("********************************************************\n");
 		printf("Running Disc Packing Pre-Processor for LBPM-WIA	\n");
@@ -200,8 +203,10 @@ int main(int argc, char **argv)
 	MPI_Bcast(&Lz,1,MPI_DOUBLE,0,MPI_COMM_WORLD);
 	//.................................................
 	MPI_Barrier(MPI_COMM_WORLD);
-	
+
 	// **************************************************************
+	if (argc > 1)	depth=atoi(argv[1]);
+	else			depth=Nz;
 	
 	if (nprocs != nprocx*nprocy*nprocz){
 		printf("nprocx =  %i \n",nprocx);
@@ -227,6 +232,7 @@ int main(int argc, char **argv)
 		printf("Process grid = %ix%ix%i \n", nprocx,nprocy,nprocz);
 		printf("Sub-domain size = %ix%ix%i \n", Nx,Ny,Nz);
 		printf("Physical domain size = %fx%fx%f \n",Lx,Ly,Lz);
+		printf("Micromodel depth = %i voxels",depth);
 	}
 
 
@@ -284,6 +290,7 @@ int main(int argc, char **argv)
 		printf("************ \n");
 	}
 
+	if (nprocz > 1 && rank==0) printf("Disc packs are 2D -- are you sure you want nprocz > 1? \n");
 	//.......................................................................
 	SignedDistanceDiscPack(SignDist.get(),ndiscs,cx,cy,rad,Lx,Ly,Lz,Nx,Ny,Nz,
 					   iproc,jproc,kproc,nprocx,nprocy,nprocz);
@@ -293,8 +300,13 @@ int main(int argc, char **argv)
 	for (k=0;k<Nz;k++){
 		for (j=0;j<Ny;j++){
 			for (i=0;i<Nx;i++){
-				dst = (iproc*(Nx-2)+i-1)*1.0;
+				// Assign the micromodel depth
-				if ((Nx-2)*nprocx-2-iproc*(Nx-2)-i+1 < dst) 		dst = 1.0*((Nx-2)*nprocx-2-iproc*(Nx-2)-i+1);
+				dst = 1.0*(i-2);
+				if (1.0*(depth+2-i) < dst) dst = 1.0*(depth+2-i);
+				if (dst < SignDist(i,j,k)) 		SignDist(i,j,k) = dst;
+//				dst = (iproc*(Nx-2)+i-1)*1.0;
+//				if ((Nx-2)*nprocx-2-iproc*(Nx-2)-i+1 < dst) 		dst = 1.0*((Nx-2)*nprocx-2-iproc*(Nx-2)-i+1);
+				// Add walls at the boundary
 				if ( (jproc*(Ny-2)+ j-1)*1.0 < dst) 				dst = (jproc*(Ny-2)+j-2)*1.0;
 				if ((Ny-2)*nprocx-(jproc*(Ny-2)+j-2)*1.0 < dst) 	dst = ((Ny-2)*nprocy-(jproc*(Ny-2)+j-2))*1.0;
 				// Assign the Signed Distance where valid

tests/lbpm_random_pp.cpp

@@ -240,7 +240,6 @@ int main(int argc, char **argv)
 			for (int j=1; j<Ny-1; j++){
 				for (int i=1; i<Nx-1; i++){
 				  n=k*Nx*Ny+j*Nx+i;
-
 					if (id[n] == 1){
 						count++;
 					}