Merge pull request #159 from ludwig-cf/develop

Release 0.15.0

CHANGES.md

@@ -1,6 +1,22 @@
 
 ### Changes
 
+version 0.15.0
+
+- Active stress implementation is updated to conform to the documented
+  case; active emulsion stress is available.
+- Add ability to rotate BPI and BPII liquid crystal initial conditions
+  Thanks to Oliver H. for this. See Section 3 of web documentation.
+- A diagnostic computation and output of the force breakdown on each
+  colloid has been added. This is currently via a static switch in
+  stats_colloid_force_split.c
+- An option for a "lap timer" is now provided.
+- Some simple open boundary conditions for fluid and binary composition
+  are available. See the "Open boundaries" section at
+  https://ludwig.epcc.ed.ac.uk/
+- Some refactoring of the lattice Boltzmann basis information has been
+  performed in order to be able to move to a more flexible approach.
+  This should have no practical impact at present.
 
 version 0.14.0
 

config/codeql-g++.mk

@@ -9,7 +9,7 @@
 BUILD   = serial
 MODEL   = -D_D3Q19_
 
-CC      = g++
+CC      = g++ -fopenmp
 CFLAGS  = -O -g -Wall -Werror
 
 AR      = ar

config/epcc-archer2.mk

@@ -0,0 +1,26 @@
+##############################################################################
+#
+#  archer2
+#  https://www.archer2.ac.uk
+#
+#  PrgEnv-cray
+#    - Use cce >= 12 to avoid problem in openmp
+#    - "module load cce/12.0.3"
+#
+#  Same compiler options for all PrgEnv are available.
+#
+##############################################################################
+
+BUILD   = parallel
+MODEL   = -D_D3Q19_
+
+CC      = cc -fopenmp
+CFLAGS  = -g -O3 -Wall -DNSIMDVL=2 -DNDEBUG
+
+MPI_INC_PATH      =
+MPI_LIB_PATH      =
+MPI_LIB           =
+
+LAUNCH_SERIAL_CMD =
+LAUNCH_MPIRUN_CMD = srun
+MPIRUN_NTASK_FLAG = -n

mpi_s/mpi.h

@@ -37,6 +37,8 @@ typedef struct {
   int MPI_TAG;
 } MPI_Status;
 
+#define MPI_STATUS_IGNORE   ((MPI_Status *) 0)
+#define MPI_STATUSES_IGNORE ((MPI_Status *) 0)
 
 /* MPI_Aint is a signed integer. Prefer intmax_t over intptr_t as
    the latter is optional in the standard. */ 
@@ -88,11 +90,6 @@ enum collective_operations {MPI_MAX,
 			    MPI_LOR,
 			    MPI_LXOR};
 
-/* special datatypes for constructing derived datatypes */
-
-#define MPI_UB 0 
-#define MPI_LB 0
-
 /* reserved communicators */
 
 enum reserved_communicators{MPI_COMM_WORLD, MPI_COMM_SELF};
@@ -110,6 +107,13 @@ enum reserved_communicators{MPI_COMM_WORLD, MPI_COMM_SELF};
 
 #define MPI_IN_PLACE ((void *) 1)
 
+/* Thread support level */
+
+#define MPI_THREAD_SINGLE      1
+#define MPI_THREAD_FUNNELED    2
+#define MPI_THREAD_SERIALIZED  3
+#define MPI_THREAD_MULTIPLE    4
+
 /* Interface */
 
 int MPI_Barrier(MPI_Comm comm);
@@ -159,10 +163,6 @@ int MPI_Type_contiguous(int count, MPI_Datatype oldtype,
 			MPI_Datatype * newtype);
 int MPI_Type_vector(int count, int blocklength, int stride,
 		    MPI_Datatype oldtype, MPI_Datatype * newtype);
-int MPI_Type_struct(int count, int * array_of_blocklengths,
-		    MPI_Aint * array_of_displacements,
-		    MPI_Datatype * array_of_types, MPI_Datatype * newtype);
-int MPI_Address(void * location, MPI_Aint * address);
 int MPI_Type_commit(MPI_Datatype * datatype);
 int MPI_Type_free(MPI_Datatype * datatype);
 int MPI_Waitall(int count, MPI_Request * array_of_requests,
@@ -207,16 +207,13 @@ double MPI_Wtime(void);
 double MPI_Wtick(void);
 
 int MPI_Init(int * argc, char *** argv);
+int MPI_Init_thread(int * argc, char *** argv, int required, int * provided);
 int MPI_Finalize(void);
 int MPI_Initialized(int * flag);
 int MPI_Abort(MPI_Comm comm, int errorcode);
 
 /* MPI 2.0 */
 /* In particular, replacements for routines removed from MPI 3 */
-/* MPI_Address() -> MPI_Get_Address()
- * MPI_Type_struct() -> MPI_Type_create_struct()
- * MPI_Type_lb() and MPI_Type_ub() -> MPI_Type_get_extent()
- * See MPI 3 standard */
 
 int MPI_Comm_set_errhandler(MPI_Comm comm, MPI_Errhandler erhandler);
 int MPI_Get_address(const void * location, MPI_Aint * address);

mpi_s/mpi_serial.c

@@ -144,6 +144,29 @@ int MPI_Init(int * argc, char *** argv) {
   return MPI_SUCCESS;
 }
 
+/*****************************************************************************
+ *
+ *  MPI_Init_thread
+ *
+ *****************************************************************************/
+
+int MPI_Init_thread(int * argc, char *** argv, int required, int * provided) {
+
+  assert(argc);
+  assert(argv);
+  assert(MPI_THREAD_SINGLE <= required && required <= MPI_THREAD_MULTIPLE);
+  assert(provided);
+
+  MPI_Init(argc, argv);
+
+  /* We are going to say that MPI_THREAD_SERIALIZED is available */
+  /* Not MPI_THREAD_MULTIPLE */
+
+  *provided = MPI_THREAD_SERIALIZED;
+
+  return MPI_SUCCESS;
+}
+
 /*****************************************************************************
  *
  *  MPI_Initialized
@@ -290,7 +313,6 @@ int MPI_Recv(void * buf, int count, MPI_Datatype datatype, int source,
 	     int tag, MPI_Comm comm, MPI_Status * status) {
 
   assert(buf);
-  assert(status);
 
   printf("MPI_Recv should not be called in serial.\n");
   exit(0);
@@ -310,8 +332,8 @@ int MPI_Irecv(void * buf, int count, MPI_Datatype datatype, int source,
   assert(buf);
   assert(request);
 
-  printf("MPI_Irecv should not be called in serial.\n");
-  exit(0);
+  /* Could assert tag is ok */
+  *request = tag;
 
   return MPI_SUCCESS;
 }
@@ -346,8 +368,8 @@ int MPI_Isend(void * buf, int count, MPI_Datatype datatype, int dest,
   assert(buf);
   assert(request);
 
-  printf("MPI_Isend should not be called in serial\n");
-  exit(0);
+  /* Could assert tag is ok */
+  *request = tag;
 
   return MPI_SUCCESS;
 }
@@ -383,7 +405,6 @@ int MPI_Waitall(int count, MPI_Request * requests, MPI_Status * statuses) {
 
   assert(count >= 0);
   assert(requests);
-  assert(statuses);
 
   return MPI_SUCCESS;
 }
@@ -396,12 +417,25 @@ int MPI_Waitall(int count, MPI_Request * requests, MPI_Status * statuses) {
  *****************************************************************************/
 
 int MPI_Waitany(int count, MPI_Request requests[], int * index,
-		MPI_Status * statuses) {
+		MPI_Status * status) {
 
   assert(count >= 0);
   assert(requests);
   assert(index);
-  assert(statuses);
+
+  *index = MPI_UNDEFINED;
+
+  for (int ireq = 0; ireq < count; ireq++) {
+    if (requests[ireq] != MPI_REQUEST_NULL) {
+      *index = ireq;
+      requests[ireq] = MPI_REQUEST_NULL;
+      if (status) {
+	status->MPI_SOURCE = 0;
+	status->MPI_TAG = requests[ireq];
+      }
+      break;
+    }
+  }
 
   return MPI_SUCCESS;
 }
@@ -417,7 +451,6 @@ int MPI_Probe(int source, int tag, MPI_Comm comm, MPI_Status * status) {
 
   assert(source == 0);
   assert(mpi_is_valid_comm(comm));
-  assert(status);
 
   printf("MPI_Probe should not be called in serial\n");
   exit(0);
@@ -440,7 +473,6 @@ int MPI_Sendrecv(void * sendbuf, int sendcount, MPI_Datatype sendtype,
   assert(dest == source);
   assert(recvbuf);
   assert(recvcount == sendcount);
-  assert(status);
 
   printf("MPI_Sendrecv should not be called in serial\n");
   exit(0);
@@ -737,62 +769,6 @@ int MPI_Type_vector(int count, int blocklength, int stride,
   return MPI_SUCCESS;
 }
 
-/*****************************************************************************
- *
- *  MPI_Type_struct
- *
- *  Superceded by MPI_Type_create_struct.
- *
- *****************************************************************************/
-
-int MPI_Type_struct(int count, int * array_of_blocklengths,
-		    MPI_Aint * array_of_displacements,
-		    MPI_Datatype * array_of_types, MPI_Datatype * newtype) {
-
-  assert(count > 0);
-  assert(array_of_blocklengths);
-  assert(array_of_displacements);
-  assert(array_of_types);
-  assert(newtype);
-
-  printf("MPI_Type_struct: please use MPI_Type_create_struct instead\n");
-
-  return -1;
-}
-
-/*****************************************************************************
- *
- *  MPI_Address
- *
- *  Please use MPI_Get_Address().
- *
- *****************************************************************************/
-
-int MPI_Address(void * location, MPI_Aint * address) {
-
-  assert(location);
-  assert(address);
-
-  *address = 0;
-
-  return MPI_SUCCESS;
-}
-
-/*****************************************************************************
- *
- *  MPI_Errhandler_set
- *
- *****************************************************************************/
-
-int MPI_Errhandler_set(MPI_Comm comm, MPI_Errhandler errhandler) {
-
-  assert(mpi_info);
-  assert(comm != MPI_COMM_NULL);
-  assert(errhandler == MPI_ERRORS_ARE_FATAL);
-
-  return MPI_SUCCESS;
-}
-
 /*****************************************************************************
  *
  *  MPI_Cart_create

src/advection.c

@@ -471,7 +471,10 @@ int advection_x(advflux_t * obj, hydro_t * hydro, field_t * field) {
       advflux_memcpy(obj, tdpMemcpyHostToDevice);
       break;
     case 5:
+      /* Ditto */
+      advflux_memcpy(obj, tdpMemcpyDeviceToHost);
       advection_le_5th(obj, hydro, nf, field->data);
+      advflux_memcpy(obj, tdpMemcpyHostToDevice);
       break; 
     default:
       pe_fatal(obj->pe, "Unexpected advection scheme order\n");