Prepared files and infrastructure for i/o using MPI but not parallel-hdf5.

Former-commit-id: 62740d07c6cc875f716f2285dd2ef7674fe97fa9

examples/test.c

@@ -677,11 +677,16 @@ int main ( int argc , char *argv[] ) {
 
     /* Read particles and space information from (GADGET) IC */
     tic = getticks();
-#ifdef WITH_MPI
+#if defined( WITH_MPI ) 
+#if defined( HAVE_PARALLEL_HDF5 )
     read_ic_parallel( ICfileName , dim , &parts , &N , &periodic, myrank, nr_nodes, MPI_COMM_WORLD, MPI_INFO_NULL );
 #else
-    read_ic( ICfileName , dim , &parts , &N , &periodic );
+    read_ic_serial( ICfileName , dim , &parts , &N , &periodic, myrank, nr_nodes, MPI_COMM_WORLD, MPI_INFO_NULL );
+#endif
+#else
+    read_ic_single( ICfileName , dim , &parts , &N , &periodic );
 #endif
+
     if ( myrank == 0 )
         message( "reading particle properties took %.3f ms." , ((double)(getticks() - tic)) / CPU_TPS * 1000 ); fflush(stdout);
     
@@ -778,12 +783,17 @@ int main ( int argc , char *argv[] ) {
     engine_redistribute ( &e );
 #endif
 
+    message("Before write !");
     /* Write the state of the system as it is before starting time integration. */
     tic = getticks();
-#ifdef WITH_MPI
+#if defined( WITH_MPI ) 
+#if defined( HAVE_PARALLEL_HDF5 )
     write_output_parallel(&e, &us, myrank, nr_nodes, MPI_COMM_WORLD, MPI_INFO_NULL);
 #else
-    write_output(&e, &us);
+    write_output_serial(&e, &us, myrank, nr_nodes, MPI_COMM_WORLD, MPI_INFO_NULL);
+#endif
+#else
+    write_output_single(&e, &us);
 #endif
     message( "writing particle properties took %.3f ms." , ((double)(getticks() - tic)) / CPU_TPS * 1000 ); fflush(stdout);
     
@@ -837,11 +847,17 @@ int main ( int argc , char *argv[] ) {
         
         if ( j % 100 == 0 )
 	  {
-#ifdef WITH_MPI
-             write_output_parallel(&e, &us, myrank, nr_nodes, MPI_COMM_WORLD, MPI_INFO_NULL);
+
+#if defined( WITH_MPI ) 
+#if defined( HAVE_PARALLEL_HDF5 )
+	    write_output_parallel(&e, &us, myrank, nr_nodes, MPI_COMM_WORLD, MPI_INFO_NULL);
+#else
+	    write_output_serial(&e, &us, myrank, nr_nodes, MPI_COMM_WORLD, MPI_INFO_NULL);
+#endif
 #else
-             write_output(&e, &us);
+	    write_output_single(&e, &us);
 #endif
+
           }
                 
         /* Dump a line of agregate output. */
@@ -858,20 +874,18 @@ int main ( int argc , char *argv[] ) {
         /* for ( k = 0 ; k < 5 ; k++ )
             printgParticle( s.gparts , pid[k] , N ); */
         
-        }
+    }
         
     /* Print the values of the runner histogram. */
-    #ifdef HIST
-        printf( "main: runner histogram data:\n" );
-        for ( k = 0 ; k < runner_hist_N ; k++ )
-            printf( " %e %e %e\n" ,
-                runner_hist_a + k * (runner_hist_b - runner_hist_a) / runner_hist_N ,
-                runner_hist_a + (k + 1) * (runner_hist_b - runner_hist_a) / runner_hist_N ,
-                (double)runner_hist_bins[k] );
-    #endif
+#ifdef HIST
+    printf( "main: runner histogram data:\n" );
+    for ( k = 0 ; k < runner_hist_N ; k++ )
+      printf( " %e %e %e\n" ,
+	      runner_hist_a + k * (runner_hist_b - runner_hist_a) / runner_hist_N ,
+	      runner_hist_a + (k + 1) * (runner_hist_b - runner_hist_a) / runner_hist_N ,
+	      (double)runner_hist_bins[k] );
+#endif
 
-    // write_output( &e );
-        
     /* Loop over the parts directly. */
     // for ( k = 0 ; k < N ; k++ )
     //     printf( " %i %e %e\n" , s.parts[k].id , s.parts[k].count , s.parts[k].count_dh );
@@ -904,16 +918,20 @@ int main ( int argc , char *argv[] ) {
     #endif */
     
     /* Write final output. */
-#ifdef WITH_MPI
-	write_output_parallel( &e, &us, myrank, nr_nodes, MPI_COMM_WORLD, MPI_INFO_NULL );
+#if defined( WITH_MPI ) 
+#if defined( HAVE_PARALLEL_HDF5 )
+    write_output_parallel(&e, &us, myrank, nr_nodes, MPI_COMM_WORLD, MPI_INFO_NULL);
+#else
+    write_output_serial(&e, &us, myrank, nr_nodes, MPI_COMM_WORLD, MPI_INFO_NULL);
+#endif
 #else
-	write_output( &e , &us );
+    write_output_single(&e, &us);
 #endif
         
 #ifdef WITH_MPI
-        if ( MPI_Finalize() != MPI_SUCCESS )
-            error( "call to MPI_Finalize failed with error %i." , res );
-    #endif
+    if ( MPI_Finalize() != MPI_SUCCESS )
+      error( "call to MPI_Finalize failed with error %i." , res );
+#endif
     
     /* Say goodbye. */
     message( "done." );
@@ -921,4 +939,4 @@ int main ( int argc , char *argv[] ) {
     /* All is calm, all is bright. */
     return 0;
     
-    }
+}

src/Makefile.am

@@ -35,12 +35,12 @@ endif
 # List required headers
 include_HEADERS = space.h runner.h queue.h task.h lock.h cell.h part.h const.h \
     engine.h swift.h serial_io.h timers.h debug.h scheduler.h proxy.h parallel_io.h \
-    common_io.h multipole.h
+    common_io.h single_io.h multipole.h
 
 # Common source files
 AM_SOURCES = space.c runner.c queue.c task.c cell.c engine.c \
     serial_io.c timers.c debug.c scheduler.c proxy.c parallel_io.c \
-    units.c common_io.c multipole.c version.c
+    units.c common_io.c single_io.c multipole.c version.c
 
 # Include files for distribution, not installation.
 noinst_HEADERS = atomic.h cycle.h error.h inline.h kernel.h vector.h \

src/parallel_io.c

@@ -21,7 +21,7 @@
 /* Config parameters. */
 #include "../config.h"
 
-#if defined(HAVE_HDF5) && defined(WITH_MPI)
+#if defined(HAVE_HDF5) && defined(WITH_MPI) && defined(HAVE_PARALLEL_HDF5)
 
 /* Tell hdf5 that we intend to use shared-memory parallel stuff. */
 #define H5_HAVE_PARALLEL

src/parallel_io.h

@@ -18,7 +18,7 @@
  ******************************************************************************/
 
 
-#if defined(HAVE_HDF5) && defined(WITH_MPI)
+#if defined(HAVE_HDF5) && defined(WITH_MPI) && defined(HAVE_PARALLEL_HDF5)
 
 void read_ic_parallel ( char* fileName, double dim[3], struct part **parts,  int* N, int* periodic, int mpi_rank, int mpi_size, MPI_Comm comm, MPI_Info info);
 

src/serial_io.c

@@ -21,7 +21,7 @@
 /* Config parameters. */
 #include "../config.h"
 
-#if defined(HAVE_HDF5) && !defined(WITH_MPI)
+#if defined(HAVE_HDF5) && defined(WITH_MPI) && !defined(HAVE_PARALLEL_HDF5)
 
 
 /* Some standard headers. */
@@ -175,7 +175,7 @@ void readArrayBackEnd(hid_t grp, char* name, enum DATA_TYPE type, int N, int dim
  * Calls #error() if an error occurs.
  *
  */
-void read_ic ( char* fileName, double dim[3], struct part **parts,  int* N, int* periodic)
+void read_ic_serial ( char* fileName, double dim[3], struct part **parts,  int* N, int* periodic, int mpi_rank, int mpi_size, MPI_Comm comm, MPI_Info info)
 {
   hid_t h_file=0, h_grp=0;
   double boxSize[3]={0.0,-1.0,-1.0};         /* GADGET has only cubic boxes (in cosmological mode) */
@@ -390,7 +390,7 @@ void writeArrayBackEnd(hid_t grp, char* fileName, FILE* xmfFile, char* name, enu
  * Calls #error() if an error occurs.
  *
  */
-void write_output (struct engine *e, struct UnitSystem* us)
+void write_output_serial ( struct engine* e, struct UnitSystem* us, int mpi_rank, int mpi_size, MPI_Comm comm, MPI_Info info )
 {
   
   hid_t h_file=0, h_grp=0;

src/serial_io.h

@@ -18,11 +18,11 @@
  ******************************************************************************/
 
 
-#if defined(HAVE_HDF5) && !defined(WITH_MPI)
+#if defined(HAVE_HDF5) && defined(WITH_MPI) && !defined(HAVE_PARALLEL_HDF5)
 
-void read_ic ( char* fileName, double dim[3], struct part **parts,  int* N, int* periodic);
+void read_ic_serial ( char* fileName, double dim[3], struct part **parts,  int* N, int* periodic, int mpi_rank, int mpi_size, MPI_Comm comm, MPI_Info info);
 
-void write_output ( struct engine* e, struct UnitSystem* us );
+void write_output_serial ( struct engine* e, struct UnitSystem* us, int mpi_rank, int mpi_size, MPI_Comm comm, MPI_Info info );
 
 #endif
 

src/swift.h

@@ -38,6 +38,7 @@
 #include "runner.h"
 #include "engine.h"
 #include "units.h"
+#include "single_io.h"
 #include "serial_io.h"
 #include "parallel_io.h"
 #include "debug.h"