Chunks

configure.ac

@@ -28,8 +28,10 @@ AC_CHECK_HEADERS([stdint.h],
 )
 
 # Checks for library functions.
-AC_FUNC_MALLOC
-AC_CHECK_FUNCS([gettimeofday])
+# AC_FUNC_MALLOC disabled to ensure that cross-compilation works and autoconf does
+# not attempt to substitute 'rpl_malloc'
+##AC_FUNC_MALLOC
+AC_CHECK_FUNCS([malloc realloc calloc gettimeofday])
 
 AC_CONFIG_FILES([Makefile])
 AC_CONFIG_FILES([include/Makefile])

src/internal_LemonSetup.ih

@@ -36,6 +36,7 @@ typedef struct
   int ndims;
   int localVol;
   int totalVol;
+  int nranks;
 
   int *starts;
   int *localDims;

src/internal_setupIOTypes.static

@@ -42,6 +42,7 @@ static void lemonSetupIOTypes(LemonSetup *setup, MPI_Comm cartesian, MPI_Offset
 
   /* Gathering of the required MPI data from the cartesian communicator. */
   MPI_Cartdim_get(cartesian, &setup->ndims);
+  MPI_Comm_size(cartesian, &setup->nranks);
 
   setup->starts = (int*)malloc(setup->ndims * sizeof(int));
   setup->localDims = (int*)malloc(setup->ndims * sizeof(int));
@@ -72,4 +73,4 @@ static void lemonSetupIOTypes(LemonSetup *setup, MPI_Comm cartesian, MPI_Offset
   MPI_Type_create_subarray(setup->ndims, setup->mappedDims, setup->localDims, setup->starts,
 			   MPI_ORDER_C, setup->etype, &setup->ftype);
   MPI_Type_commit(&setup->ftype);
-}
+}

src/reader_latticeParallelMapped.c

@@ -27,6 +27,7 @@
 #include <config.h>
 #include <lemon.h>
 #include <stdio.h>
+#include <limits.h>
 
 #include "internal_LemonSetup.ih"
 #include "internal_clearReaderState.static"
@@ -45,18 +46,33 @@ int lemonReadLatticeParallelMapped(LemonReader *reader, void *data, MPI_Offset s
     return error;
 
   lemonSetupIOTypes(&setup, reader->cartesian, siteSize, latticeDims, mapping);
-
+  
   /* Install the data organization we worked out above on the file as a view.
-     We keep the individual file pointers synchronized explicitly, so assume they are here. */
-  MPI_File_set_view(*reader->fp, reader->off + reader->pos, setup.etype, setup.ftype, "native", MPI_INFO_NULL);
+       We keep the individual file pointers synchronized explicitly, so assume they are here. */
+  MPI_File_set_view(*reader->fp, reader->off + reader->pos,
+                    setup.etype, setup.ftype, "native", MPI_INFO_NULL);
 
-  /* Blast away! */
-  MPI_File_read_at_all(*reader->fp, reader->pos, data, setup.localVol, setup.etype, &status);
-  MPI_Barrier(reader->cartesian);
+  long int bytes = (long int)setup.localVol * (long int)siteSize;
+  long int buffer_offset = 0;
+  while( bytes > 0 ){
+    int chunk = bytes > (long int)INT_MAX ? (INT_MAX/siteSize)*siteSize : bytes;
+    bytes -= (long int)chunk;
 
-  /* Synchronize the file pointer */
-  MPI_Get_count(&status, MPI_BYTE, &read);
-  reader->pos += setup.totalVol * siteSize;
+    /* Blast away! */
+    MPI_File_read_at_all(*reader->fp, reader->pos, &data[buffer_offset], chunk/siteSize, setup.etype, &status);
+    MPI_Barrier(reader->cartesian);
+
+    /* Synchronize the file pointer */
+    MPI_Get_count(&status, MPI_BYTE, &read);
+    buffer_offset += (long int)read;
+    if (read != chunk)
+    {
+      fprintf(stderr, "[LEMON] Node %d reports in lemonReadLatticeParallel:\n"
+                      "        Could not read the required amount of data.\n", reader->my_rank);
+      return LEMON_ERR_READ;
+    }
+    reader->pos += (long int)chunk * (long int)setup.nranks;
+  }
 
   /* We want to leave the file in a well-defined state, so we reset the view to a default. */
   /* We don't want to reread any data, so we maximize the file pointer globally. */
@@ -66,7 +82,7 @@ int lemonReadLatticeParallelMapped(LemonReader *reader, void *data, MPI_Offset s
   lemonFreeIOTypes(&setup);
 
   /* Doing a data read should never get us to EOF, only header scanning -- any shortfall is an error */
-  if (read != siteSize * setup.localVol)
+  if (buffer_offset != (long int)siteSize * (long int)setup.localVol)
   {
     fprintf(stderr, "[LEMON] Node %d reports in lemonReadLatticeParallel:\n"
                     "        Could not read the required amount of data.\n", reader->my_rank);

src/writer_latticeParallelMapped.c

@@ -27,6 +27,7 @@
 #include <config.h>
 #include <lemon.h>
 #include <stdio.h>
+#include <limits.h>
 
 #include "internal_LemonSetup.ih"
 #include "internal_clearWriterState.static"
@@ -50,13 +51,31 @@ int lemonWriteLatticeParallelMapped(LemonWriter *writer, void *data, MPI_Offset
   MPI_Barrier(writer->cartesian);
   MPI_File_set_view(*writer->fp, writer->off + writer->pos, setup.etype, setup.ftype, "native", MPI_INFO_NULL);
 
-  /* Blast away! */
-  MPI_File_write_at_all(*writer->fp, writer->pos, data, setup.localVol, setup.etype, &status);
-  MPI_File_sync(*writer->fp);
+  long int bytes = (long int)setup.localVol * (long int)siteSize;
+  long int buffer_offset = 0;
 
-  MPI_Barrier(writer->cartesian);
+  while( bytes > 0 ){
+    int chunk = bytes > (long int)INT_MAX ? (INT_MAX/siteSize)*siteSize : bytes;
+    bytes -= (long int)chunk;
+
+    /* Blast away! */
+    MPI_File_write_at_all(*writer->fp, writer->pos, &data[buffer_offset], chunk/siteSize, setup.etype, &status);
+    MPI_File_sync(*writer->fp);
+
+    MPI_Barrier(writer->cartesian);
+
+    writer->pos += (long int)chunk * (long int)setup.nranks;
+
+    MPI_Get_count(&status, MPI_BYTE, &written);
 
-  writer->pos += setup.totalVol * siteSize;
+    buffer_offset += (long int)written;
+    if (written != chunk)
+    {
+      fprintf(stderr, "[LEMON] Node %d reports in lemonWriteLatticeParallel:\n"
+                      "        Could not write the required amount of data.\n", writer->my_rank);
+      return LEMON_ERR_WRITE;
+    }
+  }
 
   /* We should reset the shared file pointer, in an MPI_BYTE based view... */
   MPI_Barrier(writer->cartesian);
@@ -65,13 +84,5 @@ int lemonWriteLatticeParallelMapped(LemonWriter *writer, void *data, MPI_Offset
   /* Free up the resources we claimed for this operation. */
   lemonFreeIOTypes(&setup);
 
-  MPI_Get_count(&status, MPI_BYTE, &written);
-  if (written != siteSize * setup.localVol)
-  {
-    fprintf(stderr, "[LEMON] Node %d reports in lemonWriteLatticeParallel:\n"
-                    "        Could not write the required amount of data.\n", writer->my_rank);
-    return LEMON_ERR_WRITE;
-  }
-
   return LEMON_SUCCESS;
 }