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/*
* Copyright (C) 2003, Northwestern University and Argonne National Laboratory
* See COPYRIGHT notice in top-level directory.
*
* $Id$
*/
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
*
* This program tests if the file header size and variable offsets are properly
* set when using a different set of alignment hints to open an existing file
* and entering the redef mode to add more dimensions, attributes, and
* variables, causing the expansion of the header.
*
* The compile and run commands are given below.
*
* % mpicc -g -o alignment_test alignment_test.c -lpnetcdf
*
* % mpiexec -l -n 4 alignment_test testfile.nc
*
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <libgen.h> /* basename() */
#include <assert.h>
#include <mpi.h>
#include <pnetcdf.h>
#include <testutils.h>
#define NVARS 8
#define NX 5
int main(int argc, char** argv) {
char filename[256];
int i, j, rank, nprocs, err, verbose=0, nerrs=0;
int ncid, cmode, varid[NVARS], dimid[2], *buf;
char str[32];
MPI_Offset start[2], count[2];
MPI_Offset new_var_off[NVARS*2], old_var_off[NVARS*2];
MPI_Offset header_size[2], header_extent[2];
MPI_Info info=MPI_INFO_NULL;
MPI_Init(&argc, &argv);
MPI_Comm_rank(MPI_COMM_WORLD, &rank);
MPI_Comm_size(MPI_COMM_WORLD, &nprocs);
if (argc > 2) {
if (!rank) printf("Usage: %s [filename]\n",argv[0]);
MPI_Finalize();
return 1;
}
if (argc == 2) snprintf(filename, 256, "%s", argv[1]);
else strcpy(filename, "redef1.nc");
if (rank == 0) {
char *cmd_str = (char*)malloc(strlen(argv[0]) + 256);
sprintf(cmd_str, "*** TESTING C %s for alignment ", basename(argv[0]));
printf("%-66s ------ ", cmd_str); fflush(stdout);
free(cmd_str);
}
/* create a new file for writing ----------------------------------------*/
cmode = NC_CLOBBER | NC_64BIT_DATA;
err = ncmpi_create(MPI_COMM_WORLD, filename, cmode, info, &ncid);
CHECK_ERROUT
/* define dimension */
err = ncmpi_def_dim(ncid, "Y", NC_UNLIMITED, &dimid[0]); CHECK_ERR
err = ncmpi_def_dim(ncid, "X", NX*nprocs, &dimid[1]); CHECK_ERR
#define TEST_FIXED_VAR
#define TEST_RECORD_VAR
/* Odd numbers are fixed variables, even numbers are record variables */
for (i=0; i<NVARS; i++) {
#ifdef TEST_FIXED_VAR
if (i%2) {
sprintf(str,"fixed_var_%d",i);
err = ncmpi_def_var(ncid, str, NC_INT, 1, dimid+1, &varid[i]); CHECK_ERR
}
#endif
#ifdef TEST_RECORD_VAR
if (i%2 == 0) {
sprintf(str,"record_var_%d",i);
err = ncmpi_def_var(ncid, str, NC_INT, 2, dimid, &varid[i]); CHECK_ERR
}
#endif
}
err = ncmpi_enddef(ncid); CHECK_ERR
/* write all variables */
buf = (int*) malloc(sizeof(int) * NX);
for (i=0; i<NVARS; i++) {
for (j=0; j<NX; j++) buf[j] = rank*1000 + i*10 + j;
#ifdef TEST_FIXED_VAR
if (i%2) {
start[0] = NX*rank;
count[0] = NX;
err = ncmpi_put_vara_int_all(ncid, varid[i], start, count, buf); CHECK_ERR
/* check if user put buffer contents altered */
for (j=0; j<NX; j++) {
if (buf[j] != rank*1000 + i*10 + j) {
printf("Error at line %d in %s: user put buffer[%d] altered from %d to %d\n",
__LINE__,__FILE__,j, rank*1000 + i*10 + j, buf[j]);
nerrs++;
}
}
}
#endif
#ifdef TEST_RECORD_VAR
if (i%2 == 0) {
start[0] = 0; start[1] = NX*rank;
count[0] = 1; count[1] = NX;
err = ncmpi_put_vara_int_all(ncid, varid[i], start, count, buf); CHECK_ERR
for (j=0; j<NX; j++) buf[j] = rank*1000 + 100 + i*10 + j;
start[0] = 1; /* write 2nd record */
err = ncmpi_put_vara_int_all(ncid, varid[i], start, count, buf); CHECK_ERR
/* check if user put buffer contents altered */
for (j=0; j<NX; j++) {
if (buf[j] != rank*1000 + 100 + i*10 + j) {
printf("Error at line %d in %s: user put buffer[%d] altered from %d to %d\n",
__LINE__,__FILE__,j, rank*1000 + 100 + i*10 + j, buf[j]);
nerrs++;
}
}
}
#endif
}
err = ncmpi_close(ncid); CHECK_ERR
/* Now, reopen the file and grow the header and read data back */
/* mimic netCDF that does not do alignments */
MPI_Info_create(&info);
MPI_Info_set(info, "nc_var_align_size", "197"); /* size in bytes */
/* open the file for adding more metadata */
err = ncmpi_open(MPI_COMM_WORLD, filename, NC_WRITE, info, &ncid);
CHECK_ERROUT
/* get header size and extent, and offsets of all variables */
err = ncmpi_inq_header_size(ncid, &header_size[0]); CHECK_ERR
err = ncmpi_inq_header_extent(ncid, &header_extent[0]); CHECK_ERR
for (i=0; i<NVARS; i++) {
#ifdef TEST_FIXED_VAR
if (i%2)
err = ncmpi_inq_varoffset(ncid, varid[i], &old_var_off[i]);
#endif
#ifdef TEST_RECORD_VAR
if (i%2==0)
err = ncmpi_inq_varoffset(ncid, varid[i], &old_var_off[i]);
#endif
CHECK_ERR
}
/* enter redef mode */
err = ncmpi_redef(ncid); CHECK_ERR
/* add attributes to make header grow */
for (i=0; i<NVARS; i++) {
sprintf(str, "annotation_for_var_%d",i);
#ifdef TEST_FIXED_VAR
if (i%2)
err = ncmpi_put_att_text(ncid, varid[i], "text_attr", strlen(str), str);
#endif
#ifdef TEST_RECORD_VAR
if (i%2==0)
err = ncmpi_put_att_text(ncid, varid[i], "text_attr", strlen(str), str);
#endif
CHECK_ERR
}
/* add new dimensions */
int new_dimid[3];
err = ncmpi_def_dim(ncid, "new_dim_a", 5, &new_dimid[0]); CHECK_ERR
err = ncmpi_def_dim(ncid, "new_dim_b", 4, &new_dimid[1]); CHECK_ERR
err = ncmpi_def_dim(ncid, "new_dim_c", NX*nprocs, &new_dimid[2]); CHECK_ERR
/* add new variables */
int new_varid[NVARS];
for (i=0; i<NVARS; i++) {
#ifdef TEST_FIXED_VAR
if (i%2 == 0) {
sprintf(str,"fixed_var_%d",i+NVARS);
err = ncmpi_def_var(ncid, str, NC_INT, 1, new_dimid+2, &new_varid[i]); CHECK_ERR
}
#endif
#ifdef TEST_RECORD_VAR
if (i%2 == 1) {
sprintf(str,"record_var_%d",i+NVARS);
err = ncmpi_def_var(ncid, str, NC_INT, 2, dimid, &new_varid[i]); CHECK_ERR
}
#endif
}
err = ncmpi_enddef(ncid); CHECK_ERR
/* get the new header size and extent, also all variables' starting
file offsets */
err = ncmpi_inq_header_size(ncid, &header_size[1]); CHECK_ERR
err = ncmpi_inq_header_extent(ncid, &header_extent[1]); CHECK_ERR
if (rank == 0 && verbose) {
printf("NX = %d (integer type)\n",NX);
printf("old header_size =%lld new header_size =%lld\n",header_size[0],header_size[1]);
printf("old header_extent=%lld new header_extent=%lld\n",header_extent[0],header_extent[1]);
#ifdef TEST_FIXED_VAR
for (i=1; i<NVARS; i+=2) {
err = ncmpi_inq_varoffset(ncid, varid[i], &new_var_off[i]); CHECK_ERR
printf("old fixed var[%2d] old offset=%4lld new offset=%4lld\n",i,old_var_off[i],new_var_off[i]);
}
for (i=NVARS; i<2*NVARS; i++) {
if (i%2 == 0) {
err = ncmpi_inq_varoffset(ncid, new_varid[i-NVARS], &new_var_off[i]); CHECK_ERR
printf("new fixed var[%2d] new offset=%4lld\n",i,new_var_off[i]);
}
}
#endif
#ifdef TEST_RECORD_VAR
for (i=0; i<NVARS; i+=2) {
err = ncmpi_inq_varoffset(ncid, varid[i], &new_var_off[i]); CHECK_ERR
printf("old record var[%2d] old offset=%4lld new offset=%4lld\n",i,old_var_off[i],new_var_off[i]);
}
for (i=NVARS; i<2*NVARS; i++) {
if (i%2) {
err = ncmpi_inq_varoffset(ncid, new_varid[i-NVARS], &new_var_off[i]); CHECK_ERR
printf("new record var[%2d] new offset=%4lld\n",i,new_var_off[i]);
}
}
#endif
}
/* write to the new variables */
for (i=0; i<NVARS; i++) {
for (j=0; j<NX; j++) buf[j] = -1 * (i*10 + j);
#ifdef TEST_FIXED_VAR
if (i%2 == 0) {
start[0] = NX*rank;
count[0] = NX;
err = ncmpi_put_vara_int_all(ncid, new_varid[i], start, count, buf); CHECK_ERR
sprintf(str,"fixed_var_%d",i);
/* check if user put buffer contents altered */
for (j=0; j<NX; j++) {
if (buf[j] != -1 * (i*10 + j)) {
printf("Error at %d in %s: var %s put buffer[%d] altered from %d to %d\n",
__LINE__,__FILE__, str, j, -1 * (i*10 + j), buf[j]);
nerrs++;
}
}
}
#endif
#ifdef TEST_RECORD_VAR
if (i%2 == 1) {
start[0] = 0; start[1] = NX*rank;
count[0] = 1; count[1] = NX;
err = ncmpi_put_vara_int_all(ncid, new_varid[i], start, count, buf); CHECK_ERR
for (j=0; j<NX; j++) buf[j] = -1 * (100 + i*10 + j);
start[0] = 1; /* write 2nd record */
err = ncmpi_put_vara_int_all(ncid, new_varid[i], start, count, buf); CHECK_ERR
sprintf(str,"record_var_%d",i);
/* check if user put buffer contents altered */
for (j=0; j<NX; j++) {
if (buf[j] != -1 * (100 + i*10 + j)) {
printf("Error at %d in %s: var %s put buffer[%d] altered from %d to %d\n",
__LINE__,__FILE__, str, j, -1 * (100 + i*10 + j), buf[j]);
nerrs++;
}
}
}
#endif
}
/* read old variables and check their contents */
for (i=0; i<NVARS; i++) {
#ifdef TEST_FIXED_VAR
if (i%2) {
start[0] = NX*rank;
count[0] = NX;
for (j=0; j<NX; j++) buf[j] = -1;
err = ncmpi_get_vara_int_all(ncid, varid[i], start, count, buf); CHECK_ERR
sprintf(str,"fixed_var_%d",i);
for (j=0; j<NX; j++)
if (buf[j] != rank*1000 + i*10 + j) {
printf("Error at %d: var %s i=%d buf[j=%d]=%d != %d\n",
__LINE__,str,i,j,buf[j],rank*1000+i*10+j);
nerrs++;
break;
}
}
#endif
#ifdef TEST_RECORD_VAR
if (i%2 == 0) {
start[0] = 0; start[1] = NX*rank;
count[0] = 1; count[1] = NX;
err = ncmpi_get_vara_int_all(ncid, varid[i], start, count, buf); CHECK_ERR
for (j=0; j<NX; j++)
if (buf[j] != rank*1000+i*10+j) {
printf("read error at %d: i=%d buf[j=%d]=%d != %d\n",__LINE__,i,j,buf[j],rank*1000+i*10+j);
nerrs++;
break;
}
start[0] = 1;
err = ncmpi_get_vara_int_all(ncid, varid[i], start, count, buf); CHECK_ERR
sprintf(str,"record_var_%d",i);
for (j=0; j<NX; j++)
if (buf[j] != rank*1000 + 100 + i*10 + j) {
printf("Error at %d: var %s i=%d buf[j=%d]=%d != %d\n",
__LINE__, str,i,j,buf[j],rank*1000+100+i*10+j);
nerrs++;
break;
}
}
#endif
}
err = ncmpi_close(ncid); CHECK_ERR
MPI_Info_free(&info);
free(buf);
/* check if PnetCDF freed all internal malloc */
MPI_Offset malloc_size, sum_size;
err = ncmpi_inq_malloc_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 && sum_size > 0)
printf("heap memory allocated by PnetCDF internally has %lld bytes yet to be freed\n",
sum_size);
if (malloc_size > 0) ncmpi_inq_malloc_list();
}
MPI_Allreduce(MPI_IN_PLACE, &nerrs, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
if (rank == 0) {
if (nerrs) printf(FAIL_STR,nerrs);
else printf(PASS_STR);
}
err_out:
MPI_Finalize();
return (nerrs > 0);
}
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