New i/o infrastructure now also for parallel writes

examples/main.c

@@ -336,9 +336,9 @@ int main(int argc, char *argv[]) {
   if (myrank == 0) clocks_gettime(&tic);
 #if defined(WITH_MPI)
 #if defined(HAVE_PARALLEL_HDF5)
-  read_ic_parallel(ICfileName, dim, &parts, &gparts, &Ngas, &Ngpart, &periodic,
-                   &flag_entropy_ICs, myrank, nr_nodes, MPI_COMM_WORLD,
-                   MPI_INFO_NULL, dry_run);
+  read_ic_parallel(ICfileName, &us, dim, &parts, &gparts, &Ngas, &Ngpart,
+                   &periodic, &flag_entropy_ICs, myrank, nr_nodes,
+                   MPI_COMM_WORLD, MPI_INFO_NULL, dry_run);
 #else
   read_ic_serial(ICfileName, dim, &parts, &gparts, &Ngas, &Ngpart, &periodic,
                  &flag_entropy_ICs, myrank, nr_nodes, MPI_COMM_WORLD,

src/engine.c

@@ -2672,8 +2672,9 @@ void engine_dump_snapshot(struct engine *e) {
 /* Dump... */
 #if defined(WITH_MPI)
 #if defined(HAVE_PARALLEL_HDF5)
-  write_output_parallel(e, e->snapshotBaseName, e->snapshotUnits, e->nodeID,
-                        e->nr_nodes, MPI_COMM_WORLD, MPI_INFO_NULL);
+  write_output_parallel(e, e->snapshotBaseName, e->internalUnits,
+                        e->snapshotUnits, e->nodeID, e->nr_nodes,
+                        MPI_COMM_WORLD, MPI_INFO_NULL);
 #else
   write_output_serial(e, e->snapshotBaseName, e->snapshotUnits, e->nodeID,
                       e->nr_nodes, MPI_COMM_WORLD, MPI_INFO_NULL);

src/parallel_io.h

@@ -34,15 +34,17 @@
 
 #if defined(HAVE_HDF5) && defined(WITH_MPI) && defined(HAVE_PARALLEL_HDF5)
 
-void read_ic_parallel(char* fileName, double dim[3], struct part** parts,
-                      struct gpart** gparts, size_t* Ngas, size_t* Ngparts,
-                      int* periodic, int* flag_entropy, int mpi_rank,
-                      int mpi_size, MPI_Comm comm, MPI_Info info, int dry_run);
+void read_ic_parallel(char* fileName, const struct UnitSystem* internal_units,
+                      double dim[3], struct part** parts, struct gpart** gparts,
+                      size_t* Ngas, size_t* Ngparts, int* periodic,
+                      int* flag_entropy, int mpi_rank, int mpi_size,
+                      MPI_Comm comm, MPI_Info info, int dry_run);
 
 void write_output_parallel(struct engine* e, const char* baseName,
-                           struct UnitSystem* us, int mpi_rank, int mpi_size,
-                           MPI_Comm comm, MPI_Info info);
-
+                           const struct UnitSystem* internal_units,
+                           const struct UnitSystem* snapshot_units,
+                           int mpi_rank, int mpi_size, MPI_Comm comm,
+                           MPI_Info info);
 #endif
 
 #endif /* SWIFT_PARALLEL_IO_H */

src/single_io.c

@@ -81,7 +81,7 @@ void readArray(hid_t h_grp, const struct io_props prop, size_t N,
       /* message("Optional data set '%s' not present. Zeroing this particle
        * prop...", name);	   */
 
-      for (int i = 0; i < N; ++i)
+      for (size_t i = 0; i < N; ++i)
         memset(prop.field + i * prop.partSize, 0, copySize);
 
       return;
@@ -126,16 +126,16 @@ void readArray(hid_t h_grp, const struct io_props prop, size_t N,
 
     if (isDoublePrecision(prop.type)) {
       double* temp_d = temp;
-      for (int i = 0; i < num_elements; ++i) temp_d[i] *= factor;
+      for (size_t i = 0; i < num_elements; ++i) temp_d[i] *= factor;
     } else {
       float* temp_f = temp;
-      for (int i = 0; i < num_elements; ++i) temp_f[i] *= factor;
+      for (size_t i = 0; i < num_elements; ++i) temp_f[i] *= factor;
     }
   }
 
   /* Copy temporary buffer to particle data */
   char* temp_c = temp;
-  for (int i = 0; i < N; ++i)
+  for (size_t i = 0; i < N; ++i)
     memcpy(prop.field + i * prop.partSize, &temp_c[i * copySize], copySize);
 
   /* Free and close everything */
@@ -162,8 +162,7 @@ void readArray(hid_t h_grp, const struct io_props prop, size_t N,
  * @param snapshot_units The #UnitSystem used in the snapshots
  *
  * @todo A better version using HDF5 hyper-slabs to write the file directly from
- * the part array
- * will be written once the structures have been stabilized.
+ * the part array will be written once the structures have been stabilized.
  */
 void writeArray(hid_t grp, char* fileName, FILE* xmfFile,
                 char* partTypeGroupName, const struct io_props props, size_t N,
@@ -182,7 +181,7 @@ void writeArray(hid_t grp, char* fileName, FILE* xmfFile,
 
   /* Copy particle data to temporary buffer */
   char* temp_c = temp;
-  for (int i = 0; i < N; ++i)
+  for (size_t i = 0; i < N; ++i)
     memcpy(&temp_c[i * copySize], props.field + i * props.partSize, copySize);
 
   /* Unit conversion if necessary */
@@ -194,10 +193,10 @@ void writeArray(hid_t grp, char* fileName, FILE* xmfFile,
 
     if (isDoublePrecision(props.type)) {
       double* temp_d = temp;
-      for (int i = 0; i < num_elements; ++i) temp_d[i] *= factor;
+      for (size_t i = 0; i < num_elements; ++i) temp_d[i] *= factor;
     } else {
       float* temp_f = temp;
-      for (int i = 0; i < num_elements; ++i) temp_f[i] *= factor;
+      for (size_t i = 0; i < num_elements; ++i) temp_f[i] *= factor;
     }
   }
 
@@ -297,7 +296,8 @@ void writeArray(hid_t grp, char* fileName, FILE* xmfFile,
  * @param Ngas (output) number of Gas particles read.
  * @param Ngparts (output) The number of #gpart read.
  * @param periodic (output) 1 if the volume is periodic, 0 if not.
- * @param flag_entropy 1 if the ICs contained Entropy in the InternalEnergy
+ * @param flag_entropy (output) 1 if the ICs contained Entropy in the
+ * InternalEnergy
  * field
  * @param dry_run If 1, don't read the particle. Only allocates the arrays.
  *
@@ -366,7 +366,7 @@ void read_ic_single(char* fileName, const struct UnitSystem* internal_units,
   /* Close header */
   H5Gclose(h_grp);
 
-  /* Read the unit system used in the snapshots */
+  /* Read the unit system used in the ICs */
   struct UnitSystem* ic_units = malloc(sizeof(struct UnitSystem));
   if (ic_units == NULL) error("Unable to allocate memory for IC unit system");
   readUnitSystem(h_file, ic_units);