Merge pull request #148 from Parallel-NetCDF/mpi_address

Use MPI_Aint_diff and MPI_Aint_add

examples/C/Makefile.am

@@ -18,6 +18,7 @@ check_PROGRAMS = collective_write \
                  column_wise \
                  block_cyclic \
                  flexible_api \
+                 flexible_bottom \
                  get_info \
                  hints \
                  mput \
@@ -30,6 +31,7 @@ check_PROGRAMS = collective_write \
                  transpose \
                  transpose2D \
                  vard_int \
+                 vard_bottom \
                  i_varn_int64 \
                  bput_varn_uint \
                  bput_varn_int64 \

examples/C/flexible_bottom.c

@@ -0,0 +1,215 @@
+/*********************************************************************
+ *
+ *  Copyright (C) 2024, Northwestern University and Argonne National Laboratory
+ *  See COPYRIGHT notice in top-level directory.
+ *
+ *********************************************************************/
+
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ *
+ * This example shows how to use PnetCDF blocking and nonblocking flexible APIs
+ * by supplying an MPI derived datatype and MPI_BOTTOM in the buffer argument.
+ * The MPI derived datatype is constructed through MPI_Type_create_hindexed(),
+ * which defines a noncontiguous memory space consisting of two separate blocks.
+ *
+ * A 2D global variable of size NY * NX * nprocs of type float is defined in
+ * the file. Each process allocates two write buffers and constructs an MPI
+ * derived datatype for the two buffers.
+ *
+ * The compile and run commands are given below.
+ *
+ *    % mpicc -O2 -o flexible_bottom flexible_bottom.c -lpnetcdf
+ *
+ *    % mpiexec -l -n 4 ./flexible_bottom ./testfile.nc
+ *
+ *    % ncmpidump ./testfile.nc
+ *    netcdf testfile {
+ *    // file format: CDF-5 (big variables)
+ *    dimensions:
+ *            Y = 4 ;
+ *            X = 16 ;
+ *    variables:
+ *            float var(Y, X) ;
+ *    data:
+ *
+ *     var =
+ *      10, 10, 10, 10, 11, 11, 11, 11, 12, 12, 12, 12, 13, 13, 13, 13,
+ *      10, 10, 10, 10, 11, 11, 11, 11, 12, 12, 12, 12, 13, 13, 13, 13,
+ *      50, 50, 50, 50, 51, 51, 51, 51, 52, 52, 52, 52, 53, 53, 53, 53,
+ *      50, 50, 50, 50, 51, 51, 51, 51, 52, 52, 52, 52, 53, 53, 53, 53 ;
+ *    }
+ *
+ * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h> /* strcpy(), strncpy() */
+#include <unistd.h> /* getopt() */
+#include <mpi.h>
+#include <pnetcdf.h>
+
+#define NY 4
+#define NX 4
+
+static int verbose;
+
+#define ERR {if(err!=NC_NOERR){printf("Error at %s:%d : %s\n", __FILE__,__LINE__, ncmpi_strerror(err));nerrs++;}}
+
+#define CHECK_MPI_ERR \
+    if (err != MPI_SUCCESS) { \
+        int errorStringLen; \
+        char errorString[MPI_MAX_ERROR_STRING]; \
+        MPI_Error_string(err, errorString, &errorStringLen); \
+        printf("Error at line %d: %s\n",__LINE__, errorString); \
+    }
+
+static void
+usage(char *argv0)
+{
+    char *help =
+    "Usage: %s [-h] | [-q] [file_name]\n"
+    "       [-h] Print help\n"
+    "       [-q] Quiet mode (reports when fail)\n"
+    "       [filename] output netCDF file name\n";
+    fprintf(stderr, help, argv0);
+}
+
+/*----< pnetcdf_check_mem_usage() >------------------------------------------*/
+/* check PnetCDF library internal memory usage */
+static int
+pnetcdf_check_mem_usage(MPI_Comm comm)
+{
+    int err, nerrs=0, rank;
+    MPI_Offset malloc_size, sum_size;
+
+    MPI_Comm_rank(comm, &rank);
+
+    /* print info about PnetCDF internal malloc usage */
+    err = ncmpi_inq_malloc_max_size(&malloc_size);
+    if (err == NC_NOERR) {
+        MPI_Reduce(&malloc_size, &sum_size, 1, MPI_OFFSET, MPI_SUM, 0, MPI_COMM_WORLD);
+        if (rank == 0 && verbose)
+            printf("maximum heap memory allocated by PnetCDF internally is %lld bytes\n",
+                   sum_size);
+
+        /* check if there is any PnetCDF internal malloc residue */
+        err = ncmpi_inq_malloc_size(&malloc_size);
+        MPI_Reduce(&malloc_size, &sum_size, 1, MPI_OFFSET, MPI_SUM, 0, MPI_COMM_WORLD);
+        if (rank == 0 && sum_size > 0)
+            printf("heap memory allocated by PnetCDF internally has %lld bytes yet to be freed\n",
+                   sum_size);
+    }
+    else if (err != NC_ENOTENABLED) {
+        printf("Error at %s:%d: %s\n", __FILE__,__LINE__,ncmpi_strerror(err));
+        nerrs++;
+    }
+    return nerrs;
+}
+
+int main(int argc, char** argv)
+{
+    extern int optind;
+    char filename[256];
+    int i, rank, nprocs, err, nerrs=0, req, status;
+    int ncid, cmode, varid, dimid[2];
+    float *buf[2];
+    MPI_Offset start[2], count[2];
+    MPI_Datatype btype;
+    int array_of_blocklengths[2];
+    MPI_Aint array_of_displacements[2];
+
+    MPI_Init(&argc, &argv);
+    MPI_Comm_rank(MPI_COMM_WORLD, &rank);
+    MPI_Comm_size(MPI_COMM_WORLD, &nprocs);
+
+    verbose = 1;
+
+    /* get command-line arguments */
+    while ((i = getopt(argc, argv, "hq")) != EOF)
+        switch(i) {
+            case 'q': verbose = 0;
+                      break;
+            case 'h':
+            default:  if (rank==0) usage(argv[0]);
+                      MPI_Finalize();
+                      return 1;
+        }
+    if (argv[optind] == NULL) strcpy(filename, "testfile.nc");
+    else                      snprintf(filename, 256, "%s", argv[optind]);
+
+    if (verbose && rank == 0) printf("%s: example of using MPI_BOTTOM in flexible APIs\n",__FILE__);
+
+    /* create a new file for writing ----------------------------------------*/
+    cmode = NC_CLOBBER | NC_64BIT_DATA;
+    err = ncmpi_create(MPI_COMM_WORLD, filename, cmode, MPI_INFO_NULL, &ncid);
+    ERR
+
+    /* define dimensions */
+    err = ncmpi_def_dim(ncid, "Y", NY,        &dimid[0]); ERR
+    err = ncmpi_def_dim(ncid, "X", NX*nprocs, &dimid[1]); ERR
+
+    /* define a variable of size NY * (NX * nprocs) */
+    err = ncmpi_def_var(ncid, "var", NC_FLOAT, 2, dimid, &varid); ERR
+
+    /* exit define mode */
+    err = ncmpi_enddef(ncid); ERR
+
+    /* allocate two buffers */
+    buf[0] = (float*) malloc(sizeof(float) * NY * NX / 2);
+    buf[1] = (float*) malloc(sizeof(float) * NY * NX / 2);
+    for (i=0; i<NY*NX/2; i++) {
+        buf[0][i] = rank + 10;
+        buf[1][i] = rank + 50;
+    }
+
+    /* create a noncontiguous buffer datatype consisting 2 blocks */
+    MPI_Get_address(buf[0], &array_of_displacements[0]);
+    MPI_Get_address(buf[1], &array_of_displacements[1]);
+    array_of_blocklengths[0] = NY * NX / 2;
+    array_of_blocklengths[1] = NY * NX / 2;
+
+    err = MPI_Type_create_hindexed(2, array_of_blocklengths,
+                                   array_of_displacements,
+                                   MPI_FLOAT, &btype);
+    CHECK_MPI_ERR
+
+    err = MPI_Type_commit(&btype);
+    CHECK_MPI_ERR
+
+    start[0] = 0;
+    start[1] = NX * rank;
+    count[0] = NY;
+    count[1] = NX;
+
+    /* calling a blocking flexible API */
+    err = ncmpi_put_vara_all(ncid, varid, start, count, MPI_BOTTOM, 1, btype);
+    ERR
+
+    /* calling a blocking flexible API */
+    err = ncmpi_get_vara_all(ncid, varid, start, count, MPI_BOTTOM, 1, btype);
+    ERR
+
+    /* calling a nonblocking flexible API */
+    err = ncmpi_iput_vara(ncid, varid, start, count, MPI_BOTTOM, 1, btype, &req);
+    ERR
+
+    err = ncmpi_wait_all(ncid, 1, &req, &status); ERR
+
+    /* calling a nonblocking flexible API */
+    err = ncmpi_iget_vara(ncid, varid, start, count, MPI_BOTTOM, 1, btype, &req);
+    ERR
+
+    err = ncmpi_wait_all(ncid, 1, &req, &status); ERR
+
+    free(buf[0]);
+    free(buf[1]);
+    MPI_Type_free(&btype);
+
+    err = ncmpi_close(ncid); ERR
+
+    nerrs += pnetcdf_check_mem_usage(MPI_COMM_WORLD);
+
+    MPI_Finalize();
+    return (nerrs > 0);
+}
+