Changeset 698

Timestamp:

10/30/09 05:36:47 (3 weeks ago)

Author:

kgao

Message:

add the binding of iput_vara_all, iget_vara_all, waitall, wait in order to support multi-variable I/O operations on Fortran

Location:

trunk

Files:

• src/lib/header.c (modified) (4 diffs)
• src/lib/mpinetcdf.c (modified) (3 diffs)
• src/lib/pnetcdf.h (modified) (3 diffs)
• src/libf/Makefile.in (modified) (1 diff)
• src/libf/createffiles (modified) (1 diff)
• src/libf/defs (modified) (3 diffs)
• src/libf/mpifnetcdf.h (modified) (2 diffs)
• src/libf/mpinetcdf_impl.h (modified) (1 diff)
• src/libf/put_mvara_allf.c (modified) (1 diff)
• src/libf/waitallf.c (modified) (2 diffs)
• src/libf/waitf.c (modified) (2 diffs)
• test/Makefile.in (modified) (1 diff)

trunk/src/lib/header.c

@@ -1120 +1120 @@
   NCtype type = NC_UNSPECIFIED;
   NC_var **vpp, **end;
+  int i;
 
   assert(gbp != NULL && gbp->pos != NULL);
@@ -1278 +1279 @@
         } else {        
            for (i=0; i<nc_dim1->nelems; i++){
-              if (nc_dim1->value[i]->size != nc_dim2->value[i]->size){
+              if (nc_dim1->value[i]->size != nc_dim2->value[i]->size)
                 return NC_EDIMS_SIZE_MULTIDEFINE;
-              } else {
+#define METADATA_CONSISTENCY_CHECK
+#ifdef METADATA_CONSISTENCY_CHECK
+              else {
                    if ((nc_dim1->value[i]->name->nchars != nc_dim1->value[i]->name->nchars)||(strcmp(nc_dim1->value[i]->name->cp, nc_dim2->value[i]->name->cp)!=0)){
-                      printf("Warning: The dimination name of NC definations on multiprocesses conflict. \nNOTE: Definitions across all processes must agree with one another\n");
+                      printf("Warning: The dimination name %s of NC definations on multiprocesses inconsistent.\n",nc_dim1->value[i]->name->cp);
                    } 
              }
+#endif
            } 
 
@@ -1293 +1297 @@
 int ncmpii_comp_attrs(NC_attrarray *nc_attr1, NC_attrarray *nc_attr2){
         int i;
+#ifdef METADATA_CONSISTENCY_CHECK
         if (nc_attr1->nelems != nc_attr2->nelems){
-           printf("Warning: The number of attributes of NC definations on multiprocesses conflict. \nNOTE: Definitions across all processes must agree with one another\n");
+           printf("Warning: The number of attributes (root=%d != %d) of NC definations on multiprocesses inconsistent.\n",nc_attr1->nelems,nc_attr2->nelems);
         } else {
                 for (i=0; i<nc_attr1->nelems; i++){
                    if (nc_attr1->value[i]->xsz != nc_attr2->value[i]->xsz){
-                       printf("Warning: The size of attribute of NC definations on multiprocesses conflict. \nNOTE: Definitions across all processes must agree with one another\n");
+                       printf("Warning: The size of attribute (root=%d != %d) of NC definations on multiprocesses inconsistent.\n",nc_attr1->value[i]->xsz,nc_attr2->value[i]->xsz);
                    }
                    if ((nc_attr1->value[i]->name->nchars != nc_attr2->value[i]->name->nchars)||(strcmp(nc_attr1->value[i]->name->cp, nc_attr2->value[i]->name->cp))){
-                       printf("Warning: The name of attribute of NC definations on multiprocesses conflict. \nNOTE: Definitions across all processes must agree with one another\n");
+                       printf("Warning: The name of attribute (root=%s != %s) of NC definations on multiprocesses inconsistent.\n",nc_attr1->value[i]->name->cp,nc_attr2->value[i]->name->cp);
                    }
                    if (strcmp(nc_attr1->value[i]->xvalue, nc_attr2->value[i]->xvalue)){
-                    printf("Warning: The value of attribute of NC definations on multiprocesses conflict. \nNOTE: Definitions across all processes must agree with one another\n");
+                    printf("Warning: The value of attribute (root=%s !=%s) of NC definations on multiprocesses inconsistent.\n",nc_attr1->value[i]->xvalue, nc_attr2->value[i]->xvalue);
                    }    
                    if (nc_attr1->value[i]->type != nc_attr2->value[i]->type){
-                    printf("Warning: The type of attribute of NC definations on multiprocesses conflict. \nNOTE: Definitions across all processes must agree with one another\n");
+                    printf("Warning: The type of attribute (root=%d != %d) of NC definations on multiprocesses inconsistent.\n",nc_attr1->value[i]->type,nc_attr2->value[i]->type);
                    }
                    if (nc_attr1->value[i]->nelems != nc_attr2->value[i]->nelems){
-                    printf("Warning: The length of attribute of NC definations on multiprocesses conflict. \nNOTE: Definitions across all processes must agree with one another\n");
+                    printf("Warning: The length of attribute (root=%d != %d) of NC definations on multiprocesses inconsistent.\n",nc_attr1->value[i]->nelems,nc_attr2->value[i]->nelems);
                    }
                 }
         }       
+#endif
     return NC_NOERR;
 }
@@ -1323 +1329 @@
         } else {
                 for (i=0; i<nc_var1->nelems; i++){
+#ifdef METADATA_CONSISTENCY_CHECK
                    if ((nc_var1->value[i]->name->nchars !=  nc_var2->value[i]->name->nchars)||strcmp(nc_var1->value[i]->name->cp,nc_var2->value[i]->name->cp))
                    {
-                    printf("Warning: The name of variable of NC definations on multiprocesses conflict. \nNOTE: Definitions across all processes must agree with one another\n");
+                    printf("Warning: The name of variable (root=%s) of NC definations on multiprocesses inconsistent.\n",nc_var1->value[i]->name->cp);
                    }
+#endif
                    if ((nc_var1->value[i]->ndims != nc_var2->value[i]->ndims)){
                         return NC_EVARS_NDIMS_MULTIDEFINE;

trunk/src/lib/mpinetcdf.c

@@ -13220 +13220 @@
       (*request)->count[dim]=count[dim];
   }
-  
+  (*request)->rw_flag = 1; 
+  return NC_NOERR;
+}
+
+int
+ncmpi_iget_vara_all(int ncid, int varid,
+                   const MPI_Offset start[], const MPI_Offset count[],
+                   const void *buf, MPI_Offset bufcount,
+                   MPI_Datatype datatype, NCMPI_Request *request) {
+
+  NC_var *varp;
+  NC *ncp;
+  int status = NC_NOERR;
+  int dim;
+
+  status = ncmpii_NC_check_id(ncid, &ncp);
+  if(status != NC_NOERR)
+    return status;
+
+  varp = ncmpii_NC_lookupvar(ncp, varid);
+  if(varp == NULL)
+    return NC_ENOTVAR;
+
+
+  *request = (NCMPI_Request)malloc(sizeof(struct NCMPI_Req));
+  if (*request == NULL) printf("no memory buffer\n");
+  (*request)->indep = 0;
+  (*request)->ncid = ncid;
+  (*request)->varid = varid;
+  (*request)->ndim = varp->ndims;
+  (*request)->start = (MPI_Offset *)malloc(varp->ndims*sizeof(MPI_Offset));
+  (*request)->count = (MPI_Offset *)malloc(varp->ndims*sizeof(MPI_Offset));
+  (*request)->buf = (void *)buf;
+  (*request)->bufcount = bufcount;
+  (*request)->vartype = datatype;
+  (*request)->next_req = NULL;
+  for (dim = 0; dim < varp->ndims; dim++){
+      (*request)->start[dim]=start[dim];
+      (*request)->count[dim]=count[dim];
+  }
+  (*request)->rw_flag = 0;
   return NC_NOERR;
 }
@@ -13227 +13267 @@
 static int
 ncmpi_coll_wait(NCMPI_Request request) {
+  if (request->rw_flag == 1)
   return (ncmpi_put_vara_all(request->ncid, request->varid,
+                   request->start, request->count,
+                   request->buf, request->bufcount,
+                   request->vartype));
+  if (request->rw_flag == 0)
+  return (ncmpi_get_vara_all(request->ncid, request->varid,
                    request->start, request->count,
                    request->buf, request->bufcount,
@@ -13270 +13316 @@
         datatype[i] = array_of_requests[i]->vartype;
   }
-
+  if (array_of_requests[0]->rw_flag == 1)
   ncmpi_put_mvara_all(ncid, count, varids,
                    starts, counts,
                    buf, bufcount,
                    datatype);
+
+  if (array_of_requests[0]->rw_flag == 0)
+  ncmpi_get_mvara_all(ncid, count, varids,
+                   starts, counts,
+                   buf, bufcount,
+                   datatype);
+
+  free(starts);
+  free(varids);
+  free(counts);
+  free(buf);
+  free(bufcount);
+  free(datatype);
   return NC_NOERR;
 }

trunk/src/lib/pnetcdf.h

@@ -86 +86 @@
   MPI_Offset* start;
   MPI_Offset* count;
+  int rw_flag;
 };
 typedef struct NCMPI_Req * NCMPI_Request;
+
 #define NCMPI_REQUEST_NULL ((NCMPI_Request)NULL)
 #define NCMPI_REQTYPE_READ      1
@@ -698 +700 @@
                    void **buffers, MPI_Offset *bufcounts,
                    MPI_Datatype *datatypes);
-int
-ncmpi_iput_vara_all(int ncid, int varid,
+
+int ncmpi_iput_vara_all(int ncid, int varid,
                    const MPI_Offset start[], const MPI_Offset count[],
                    const void *buf, MPI_Offset bufcount,
@@ -713 +715 @@
                    void **buffers, MPI_Offset *bufcounts,
                    MPI_Datatype *datatypes);
+
+int ncmpi_iget_vara_all(int ncid, int varid,
+                   const MPI_Offset start[], const MPI_Offset count[],
+                   const void *buf, MPI_Offset bufcount,
+                   MPI_Datatype datatype, NCMPI_Request *request);
 
 int ncmpi_put_vara(int ncid, int varid,

trunk/src/libf/Makefile.in

@@ -100 +100 @@
         issyserrf.c \
         get_file_infof.c \
-        deletef.c
+        deletef.c \
+        iput_vara_allf.c \
+        iget_vara_allf.c \
+        waitallf.c \
+        waitf.c \
+        mvar.c
 
 LIB_FSRCS = strerrorf.f inq_libversf.f

trunk/src/libf/createffiles

@@ -5 +5 @@
 # It makes use of an interface builder developed for MPICH2 and a set of 
 # NetCDF-specific descriptions in the file "defs".
-mpich2SourceDir=${MPICH2SRC:-/home/gropp/projects/software/mpich2}
+mpich2SourceDir=${MPICH2SRC:-/home/kgao/ChomboIO/mpich2-1.1.1p1}
 
 if [ ! -d "$mpich2SourceDir" ] ; then

trunk/src/libf/defs

@@ -21 +21 @@
 $free   = "free";
 $header_file = "mpinetcdf_impl.h";
+
+$tof77{"NCMPI_Request*"} = "int *";
+$tof77{"NCMPI_Request*"} = "int *";
+$tof77{"NCMPI_Request\[\]"} = "int *";
+$tof77{"MPI_Offset**"} = "MPI_Offset *";
 
 # Error return handling
@@ -216 +221 @@
                 'get_vara_all-3' => 'in:intToSizeTOffsetArr:ncmpixVardim(*v1,*v2-1)',
                 'get_vara_all-4' => 'in:intToSizeTArr:ncmpixVardim(*v1,*v2-1)',
+              'iget_vara_all' => '2:3:4', 
+                'iget_vara_all-2' => 'in:OffsetIndexIn',
+                'iget_vara_all-3' => 'in:intToSizeTOffsetArr:ncmpixVardim(*v1,*v2-1)',
+                'iget_vara_all-4' => 'in:intToSizeTArr:ncmpixVardim(*v1,*v2-1)',
               'get_vara' => '2:3:4', 
                 'get_vara-2' => 'in:OffsetIndexIn',
@@ -578 +587 @@
                 'put_vara_all-3' => 'in:intToSizeTOffsetArr:ncmpixVardim(*v1,*v2-1)',
                 'put_vara_all-4' => 'in:intToSizeTArr:ncmpixVardim(*v1,*v2-1)',
+              'put_mvara_all' => '3', 
+                'put_mvara_all-3' => 'in:OffsetIndexIn',
+              'iput_vara_all' => '2:3:4', 
+                'iput_vara_all-2' => 'in:OffsetIndexIn',
+                'iput_vara_all-3' => 'in:intToSizeTOffsetArr:ncmpixVardim(*v1,*v2-1)',
+                'iput_vara_all-4' => 'in:intToSizeTArr:ncmpixVardim(*v1,*v2-1)',
               'put_vara' => '2:3:4', 
                 'put_vara-2' => 'in:OffsetIndexIn',

trunk/src/libf/mpifnetcdf.h

@@ -21 +21 @@
 extern FORTRAN_API int FORT_CALL nfmpi_end_indep_data_ ( int *v1 );
 extern FORTRAN_API int FORT_CALL nfmpi_close_ ( int *v1 );
-extern FORTRAN_API int FORT_CALL nfmpi_wait_ ( NCMPI_Request*v1 );
-extern FORTRAN_API int FORT_CALL nfmpi_waitall_ ( int *v1, NCMPI_Request v2[] );
+extern FORTRAN_API int FORT_CALL nfmpi_wait_ ( MPI_Fint *v1 );
+extern FORTRAN_API int FORT_CALL nfmpi_waitall_ ( int *v1, MPI_Fint * v2 );
 extern FORTRAN_API int FORT_CALL nfmpi_set_fill_ ( int *v1, int *v2, MPI_Fint *v3 );
 extern FORTRAN_API int FORT_CALL nfmpi_def_dim_ ( int *v1, char *v2 FORT_MIXED_LEN(d2), MPI_Offset *v3, MPI_Fint *v4 FORT_END_LEN(d2) );
@@ -101 +101 @@
 extern FORTRAN_API int FORT_CALL nfmpi_get_var_double_all_ ( int *v1, int *v2, double*v3 );
 extern FORTRAN_API int FORT_CALL nfmpi_put_vara_all_ ( int *v1, int *v2, MPI_Offset v3[], MPI_Offset v4[], void*v5, MPI_Offset *v6, MPI_Fint *v7 );
-extern FORTRAN_API int FORT_CALL nfmpi_put_mvara_all_ ( int *v1, int *v2, MPI_Fint v3[], MPI_Offset**starts v4, MPI_Offset**counts v5, void**buffers v6, MPI_Offset*v7, MPI_Fint *v8 );
+extern FORTRAN_API int FORT_CALL nfmpi_put_mvara_all_ ( int *v1, int *v2, MPI_Fint v3[], MPI_Offset**v4, MPI_Offset**v5, void**v6, MPI_Offset*v7, MPI_Fint *v8 );
+extern FORTRAN_API int FORT_CALL nfmpi_iput_vara_all_ ( int *v1, int *v2, MPI_Offset v3[], MPI_Offset v4[], void*v5, MPI_Offset *v6, MPI_Fint *v7, MPI_Fint *v8 );
 extern FORTRAN_API int FORT_CALL nfmpi_get_vara_all_ ( int *v1, int *v2, MPI_Offset v3[], MPI_Offset v4[], void*v5, MPI_Offset *v6, MPI_Fint *v7 );
-extern FORTRAN_API int FORT_CALL nfmpi_get_mvara_all_ ( int *v1, int *v2, MPI_Fint v3[], MPI_Offset**starts v4, MPI_Offset**counts v5, void**buffers v6, MPI_Offset*v7, MPI_Fint *v8 );
+extern FORTRAN_API int FORT_CALL nfmpi_get_mvara_all_ ( int *v1, int *v2, MPI_Fint v3[], MPI_Offset**v4, MPI_Offset**v5, void**v6, MPI_Offset*v7, MPI_Fint *v8 );
+extern FORTRAN_API int FORT_CALL nfmpi_iget_vara_all_ ( int *v1, int *v2, MPI_Offset v3[], MPI_Offset v4[], void*v5, MPI_Offset *v6, MPI_Fint *v7, MPI_Fint *v8 );
 extern FORTRAN_API int FORT_CALL nfmpi_put_vara_ ( int *v1, int *v2, MPI_Offset v3[], MPI_Offset v4[], void*v5, MPI_Offset *v6, MPI_Fint *v7 );
 extern FORTRAN_API int FORT_CALL nfmpi_get_vara_ ( int *v1, int *v2, MPI_Offset v3[], MPI_Offset v4[], void*v5, MPI_Offset *v6, MPI_Fint *v7 );

trunk/src/libf/mpinetcdf_impl.h

@@ -66 +66 @@
 /* Fortran logical values */
 
+
 #endif
 

trunk/src/libf/put_mvara_allf.c

@@ -22 +22 @@
 /* Prototypes for the Fortran interfaces */
 #include "mpifnetcdf.h"
-FORTRAN_API int FORT_CALL nfmpi_put_mvara_all_ ( int *v1, int *v2, MPI_Fint v3[], MPI_Offset**starts v4, MPI_Offset**counts v5, void**buffers v6, MPI_Offset*v7, MPI_Fint *v8 ){
+FORTRAN_API int FORT_CALL nfmpi_put_mvara_all_ ( int *v1, int *v2, MPI_Fint v3[], MPI_Offset** v4, MPI_Offset** v5, void** v6, MPI_Offset*v7, MPI_Fint *v8 ){
     int ierr;
-    ierr = ncmpi_put_mvara_all( *v1, *v2, v3, v4, v5, v6, v7, (fixme][ *)(v8) );
+    int l3 = *v3 - 1;
+    ierr = ncmpi_put_mvara_all( *v1, *v2, l3, v4, v5, v6, v7, (fixme][ *)(v8) );
     return ierr;
 }

trunk/src/libf/waitallf.c

@@ -8 +8 @@
  */
 #include "mpinetcdf_impl.h"
+#include "mvar.h"
 
 
@@ -22 +23 @@
 /* Prototypes for the Fortran interfaces */
 #include "mpifnetcdf.h"
-FORTRAN_API int FORT_CALL nfmpi_waitall_ ( int *v1, NCMPI_Request v2[] ){
+FORTRAN_API int FORT_CALL nfmpi_waitall_ ( int *v1, MPI_Fint * v2 ){
+    extern lnc_req *req_head ;
+    extern lnc_req *req_tail ;
     int ierr;
-    ierr = ncmpi_waitall( *v1, *v2 );
+    NCMPI_Request *l2_req;
+    int i,j;
+    lnc_req *tmp_req = NULL;
+    l2_req = malloc((*v1)*sizeof(NCMPI_Request));
+    tmp_req = req_head;
+ 
+    i = 0;
+    while(tmp_req != NULL){
+           l2_req[i]=  tmp_req->req; 
+           tmp_req = tmp_req->next;
+           i++; 
+    }
+  
+    ierr = ncmpi_waitall( *v1, l2_req );
+   
+    while(req_head != NULL){
+           tmp_req = req_head;
+           req_head = req_head->next;
+           free(tmp_req);
+    }    
+        req_tail = NULL;
+
+    free(l2_req);
+        
     return ierr;
 }

trunk/src/libf/waitf.c

@@ -8 +8 @@
  */
 #include "mpinetcdf_impl.h"
-
+#include "mvar.h"
 
 #ifdef F77_NAME_UPPER
@@ -22 +22 @@
 /* Prototypes for the Fortran interfaces */
 #include "mpifnetcdf.h"
-FORTRAN_API int FORT_CALL nfmpi_wait_ ( NCMPI_Request*v1 ){
+FORTRAN_API int FORT_CALL nfmpi_wait_ ( MPI_Fint *v1 ){
     int ierr;
-    ierr = ncmpi_wait( v1 );
+    lnc_req *tmp_req1 = NULL;
+    lnc_req *tmp_req2 = NULL;
+    NCMPI_Request l1_req;
+    extern lnc_req *req_head ;
+    extern lnc_req *req_tail ;
+//    l1_req = nc_requset_list[*v1] ;
+    tmp_req1 = req_head;
+    while(tmp_req1 != NULL){
+        if (tmp_req1->reqid == *v1){
+                break;
+        } else { 
+           tmp_req2 = tmp_req1; 
+           tmp_req1 = tmp_req1->next; 
+        }
+    }  
+    l1_req = tmp_req1->req;
+    ierr = ncmpi_wait( &tmp_req1->req );
+    if (req_head->reqid == *v1){
+        if (req_head->next == NULL){
+                req_head = NULL;
+                req_tail = NULL;
+        } else {
+                req_head = req_head->next;
+        }
+        free(tmp_req1);
+    } else {
+        if (req_tail->reqid == tmp_req1->reqid)
+                req_tail = tmp_req2;
+        else 
+        tmp_req2 = tmp_req1->next;
+        free(tmp_req1);
+    } 
+
     return ierr;
+
 }

trunk/test/Makefile.in

@@ -1 +1 @@
 srcdir = @srcdir@
 VPATH = @srcdir@
-SUBDIRS = common test_double test_double_int test_float test_int test_dtype nc_test fandc nf_test largefile C mcoll_perf test_check_header testcases
+SUBDIRS = common test_double test_double_int test_float test_int test_dtype nc_test fandc nf_test largefile C mcoll_perf mcoll_fortran test_check_header testcases
 
 all: