//----------------------------------------------------------------
// Return a negative value when failed, otherwise return 0
int read_var_from_netcdf(int file_id, const char *var_name, struct Type type)
{
int TIMES=1;
int LATS=local_box_size[1];
int LONS=local_box_size[0];
assert(var_name != 0);
assert(var_data != 0);
int varidp,ndims,nvars,ngatts,unlimited;
nc_type xtypep;
//int dataset_id = H5Dopen2(file_id, var_name, H5P_DEFAULT);
int dataset_id = ncmpi_inq_varid(file_id, var_name, &varidp);
MPI_Offset start[]={local_box_offset[2],local_box_offset[1],local_box_offset[0]};
MPI_Offset count[]={TIMES,LATS,LONS};
dataset_id = ncmpi_inq_vartype(file_id,varidp, &xtypep);
// if (dataset_id !=0)
// terminate_with_error_msg("ERROR: Failed to open NetCDF dataset for variable %s\n", var_name);
int read_error = 0;
if (type.atomic_type == DOUBLE)
read_error = ncmpi_get_vara_double(file_id, varidp, start, count, var_data);
else if (type.atomic_type == FLOAT){
ncmpi_begin_indep_data(file_id);
read_error = ncmpi_get_vara_float(file_id, varidp, start, count, (float *)var_data);
ncmpi_end_indep_data(file_id);
if (read_error != NC_NOERR)
terminate_with_error_msg("ERROR: Can not read the data for the variable %s \n", var_name);
}
else if (type.atomic_type == INT)
read_error = ncmpi_get_vara_int(file_id, varidp, start, count, var_data);
// else if (type.atomic_type == UINT)
// read_error = ncmpi_get_vara_uint(file_id, varidp, start, count, var_data);
// else if (type.atomic_type == CHAR)
// read_error = ncmpi_get_vara_char(file_id, varidp, start, count, var_data);
else if (type.atomic_type == UCHAR)
read_error = ncmpi_get_vara_uchar(file_id, varidp, start, count, var_data);
else
terminate_with_error_msg("ERROR: Unsupported type. Type = %d\n", type.atomic_type);
if (read_error < 0)
return -1;
return 0;
}
//----------------------------------------------------------------
// Open the first NETCDF file and query all the types for all the variables
static void determine_var_types()
{
assert(netcdf_file_names != 0);
assert(netcdf_var_names != 0);
struct Type type;
int plist_id,i = 0,varidp,ndimsp;
int file_id = ncmpi_open(MPI_COMM_WORLD,netcdf_file_names[0], NC_NOWRITE, MPI_INFO_NULL, &plist_id);
if (file_id != NC_NOERR)
terminate_with_error_msg("ERROR: Cannot open file %s\n", netcdf_file_names[0]);
var_types = (struct Type *)calloc(var_count, sizeof(*var_types));
nc_type xtypep;
for (i = 0; i < var_count; ++i)
{
int dataset_id = ncmpi_inq_varid (plist_id, netcdf_var_names[i], &varidp);
dataset_id = ncmpi_inq_vartype(plist_id,varidp, &xtypep);
if (dataset_id != NC_NOERR)
terminate_with_error_msg("ERROR: Cannot read the datatype of the variable %s\n", netcdf_var_names[i]);
int num_dims = ncmpi_inq_varndims(plist_id,varidp,&ndimsp);
if (ndimsp > 3 )
{
//TODO:probably we can make it more clever to handle more dimensions as they are not related to the variable itself on netcdf
type.atomic_type = INVALID; // we don't support arrays of more than 3 dimension
return;
}
else if (xtypep == NC_FLOAT || xtypep == NC_INT)
{
type.num_values = 1;
}
else // we don't support HD5_COMPOUND datatype for example
{
type.atomic_type = INVALID;
}
type.atomic_type = from_netcdf_atomic_type(xtypep);
var_types[i] = type;
if (var_types[i].atomic_type == INVALID)
terminate_with_error_msg("ERROR: The datatype of the %s variable is not supported\n", netcdf_var_names[i]);
}
ncmpi_close(plist_id);
}
void BIL_Pio_read_nc_blocks(MPI_Comm all_readers_comm, MPI_Comm io_comm,
int num_blocks, BIL_Block* blocks) {
int i;
for (i = 0; i < num_blocks; i++) {
int fp;
BIL_Timing_fopen_start(all_readers_comm);
assert(ncmpi_open(io_comm, blocks[i].file_name, NC_NOWRITE,
BIL->io_hints, &fp) == NC_NOERR);
BIL_Timing_fopen_stop(all_readers_comm);
ncmpi_begin_indep_data(fp);
// Find the id, type, and size of the variable.
int var_id;
assert(ncmpi_inq_varid(fp, blocks[i].var_name, &var_id) == NC_NOERR);
nc_type var_type;
assert(ncmpi_inq_vartype(fp, var_id, &var_type) == NC_NOERR);
// Create extra variables specifically for the netCDF API.
MPI_Offset nc_dim_starts[BIL_MAX_NUM_DIMS];
MPI_Offset nc_dim_sizes[BIL_MAX_NUM_DIMS];
int j;
for (j = 0; j < blocks[i].num_dims; j++) {
nc_dim_starts[j] = blocks[i].starts[j];
nc_dim_sizes[j] = blocks[i].sizes[j];
}
MPI_Datatype nc_var_type;
BIL_Pio_nc_to_mpi_type(var_type, &nc_var_type, &(blocks[i].var_size));
// Allocate room for data and read it independently.
blocks[i].data = BIL_Misc_malloc(blocks[i].total_size * blocks[i].var_size);
BIL_Timing_io_start(all_readers_comm);
assert(ncmpi_get_vara(fp, var_id, nc_dim_starts, nc_dim_sizes,
blocks[i].data, blocks[i].total_size,
nc_var_type) == NC_NOERR);
BIL_Timing_io_stop(all_readers_comm,
blocks[i].total_size * blocks[i].var_size);
// Clean up.
ncmpi_end_indep_data(fp);
ncmpi_close(fp);
}
}
int main(int argc, char** argv)
{
char filename[256];
int i, j, rank, nprocs, err, nerrs=0, expected;
int ncid, cmode, varid[2], dimid[2], req[4], st[4], *buf;
int *buf0, *buf1, *buf2;
size_t len;
MPI_Offset start[2], count[2];
MPI_Info info;
MPI_Init(&argc, &argv);
MPI_Comm_rank(MPI_COMM_WORLD, &rank);
MPI_Comm_size(MPI_COMM_WORLD, &nprocs);
/* this program is intended to run on one process */
if (rank) goto fn_exit;
/* get command-line arguments */
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, "testfile.nc");
if (rank == 0) {
char *cmd_str = (char*)malloc(strlen(argv[0]) + 256);
sprintf(cmd_str, "*** TESTING C %s for writing interleaved fileviews ", basename(argv[0]));
printf("%-66s ------ ", cmd_str);
free(cmd_str);
}
MPI_Info_create(&info);
MPI_Info_set(info, "romio_cb_write", "disable");
MPI_Info_set(info, "ind_wr_buffer_size", "8");
/* these 2 hints are required to cause a core dump if r1758 fix is not
* presented */
/* create a new file for writing ----------------------------------------*/
cmode = NC_CLOBBER | NC_64BIT_DATA;
err = ncmpi_create(MPI_COMM_SELF, filename, cmode, info, &ncid); CHECK_ERR
MPI_Info_free(&info);
/* define dimensions Y and X */
err = ncmpi_def_dim(ncid, "Y", NY, &dimid[0]); CHECK_ERR
err = ncmpi_def_dim(ncid, "X", NX, &dimid[1]); CHECK_ERR
/* define 2D variables of integer type */
err = ncmpi_def_var(ncid, "var0", NC_INT, 2, dimid, &varid[0]); CHECK_ERR
err = ncmpi_def_var(ncid, "var1", NC_INT, 2, dimid, &varid[1]); CHECK_ERR
/* enable fill mode */
err = ncmpi_set_fill(ncid, NC_FILL, NULL); CHECK_ERR
/* do not forget to exit define mode */
err = ncmpi_enddef(ncid); CHECK_ERR
/* now we are in data mode */
buf = (int*) malloc(NY*NX * sizeof(int));
/* fill the entire variable var0 with -1s */
for (i=0; i<NY*NX; i++) buf[i] = -1;
err = ncmpi_put_var_int_all(ncid, varid[0], buf); CHECK_ERR
/* write 8 x 2 elements so this only interleaves the next two
* iput requests */
start[0] = 0; start[1] = 3;
count[0] = 8; count[1] = 2;
len = (size_t)(count[0] * count[1]);
buf0 = (int*) malloc(len * sizeof(int));
for (i=0; i<len; i++) buf0[i] = 50+i;
err = ncmpi_iput_vara_int(ncid, varid[0], start, count, buf0, &req[0]);
CHECK_ERR
/* write 1 x 3 elements */
start[0] = 1; start[1] = 8;
count[0] = 1; count[1] = 5;
len = (size_t)(count[0] * count[1]);
buf1 = (int*) malloc(len * sizeof(int));
for (i=0; i<len; i++) buf1[i] = 60+i;
err = ncmpi_iput_vara_int(ncid, varid[0], start, count, buf1, &req[1]);
CHECK_ERR
/* write 1 x 3 elements */
start[0] = 3; start[1] = 7;
count[0] = 1; count[1] = 5;
len = (size_t)(count[0] * count[1]);
buf2 = (int*) malloc(len * sizeof(int));
for (i=0; i<len; i++) buf2[i] = 70+i;
err = ncmpi_iput_vara_int(ncid, varid[0], start, count, buf2, &req[2]);
CHECK_ERR
err = ncmpi_wait_all(ncid, 3, req, st); CHECK_ERR
free(buf0); free(buf1); free(buf2);
/* fill the entire variable var1 with -1s */
for (i=0; i<NY*NX; i++) buf[i] = -1;
err = ncmpi_put_var_int_all(ncid, varid[1], buf); CHECK_ERR
/* write 8 x 2 elements so this only interleaves the next two iput
* requests */
start[0] = 0; start[1] = 3;
count[0] = 8; count[1] = 2;
len = (size_t)(count[0] * count[1]);
buf0 = (int*) malloc(len * sizeof(int));
for (i=0; i<count[0]*count[1]; i++) buf0[i] = 50+i;
err = ncmpi_iput_vara_int(ncid, varid[1], start, count, buf0, &req[0]);
CHECK_ERR
/* rearrange buffer contents, as buf is 2D */
for (i=0; i<5; i++) buf[i] = 10 + i;
for (i=5; i<10; i++) buf[i] = 10 + i + 5;
for (i=10; i<15; i++) buf[i] = 10 + i + 10;
start[0] = 6; start[1] = 7;
count[0] = 3; count[1] = 5;
err = ncmpi_iput_vara_int(ncid, varid[1], start, count, buf, &req[1]);
CHECK_ERR
for (i=15; i<20; i++) buf[i] = 10 + i - 10;
for (i=20; i<25; i++) buf[i] = 10 + i - 5;
start[0] = 6; start[1] = 12;
count[0] = 2; count[1] = 5;
err = ncmpi_iput_vara_int(ncid, varid[1], start, count, buf+15, &req[2]);
CHECK_ERR
for (i=25; i<30; i++) buf[i] = 10 + i;
start[0] = 8; start[1] = 12;
count[0] = 1; count[1] = 5;
err = ncmpi_iput_vara_int(ncid, varid[1], start, count, buf+25, &req[3]);
CHECK_ERR
err = ncmpi_wait_all(ncid, 4, req, st); CHECK_ERR
/* check if write buffer contents have been altered */
for (i=0; i<16; i++) CHECK_CONTENTS(buf0, 50 + i)
for (i=0; i<5; i++) CHECK_CONTENTS(buf, 10 + i)
for (i=5; i<10; i++) CHECK_CONTENTS(buf, 10 + i + 5)
for (i=10; i<15; i++) CHECK_CONTENTS(buf, 10 + i + 10)
for (i=15; i<20; i++) CHECK_CONTENTS(buf, 10 + i - 10)
for (i=20; i<25; i++) CHECK_CONTENTS(buf, 10 + i - 5)
for (i=25; i<30; i++) CHECK_CONTENTS(buf, 10 + i)
err = ncmpi_close(ncid); CHECK_ERR
free(buf0);
/* open the same file and read back for validate */
err = ncmpi_open(MPI_COMM_SELF, filename, NC_NOWRITE, MPI_INFO_NULL,
&ncid); CHECK_ERR
err = ncmpi_inq_varid(ncid, "var0", &varid[0]); CHECK_ERR
err = ncmpi_inq_varid(ncid, "var1", &varid[1]); CHECK_ERR
/* read the entire array */
for (i=0; i<NY*NX; i++) buf[i] = -1;
err = ncmpi_get_var_int_all(ncid, varid[0], buf); CHECK_ERR
/* check if the contents of buf are expected */
expected = 50;
for (j=0; j<8; j++) {
for (i=3; i<5; i++) {
if (buf[j*NX+i] != expected) {
printf("%d: Unexpected read buf[%d][%d]=%d, should be %d\n",
rank, j, i, buf[j*NX+i], expected);
nerrs++;
}
expected++;
}
}
expected = 60;
j = 1;
for (i=8; i<13; i++) {
if (buf[j*NX+i] != expected) {
printf("%d: Unexpected read buf[%d][%d]=%d, should be %d\n",
rank, j, i, buf[j*NX+i], expected);
nerrs++;
}
expected++;
}
expected = 70;
j = 3;
for (i=7; i<12; i++) {
if (buf[j*NX+i] != expected) {
printf("%d: Unexpected read buf[%d][%d]=%d, should be %d\n",
rank, j, i, buf[j*NX+i], expected);
nerrs++;
}
expected++;
}
/* initialize the contents of the array to a different value */
for (i=0; i<NY*NX; i++) buf[i] = -1;
/* read the entire array */
err = ncmpi_get_var_int_all(ncid, varid[1], buf); CHECK_ERR
/* check if the contents of buf are expected */
expected = 10;
for (j=6; j<9; j++) {
for (i=7; i<17; i++) {
if (buf[j*NX+i] != expected) {
printf("%d: Unexpected read buf[%d]=%d, should be %d\n",
rank, i, buf[j*NX+i], expected);
nerrs++;
}
expected++;
}
}
expected = 50;
for (j=0; j<8; j++) {
for (i=3; i<5; i++) {
if (buf[j*NX+i] != expected) {
printf("%d: Unexpected read buf[%d][%d]=%d, should be %d\n",
rank, j, i, buf[j*NX+i], expected);
nerrs++;
}
expected++;
}
}
err = ncmpi_close(ncid); CHECK_ERR
free(buf);
/* check if PnetCDF freed all internal malloc */
MPI_Offset malloc_size;
err = ncmpi_inq_malloc_size(&malloc_size);
if (err == NC_NOERR && malloc_size > 0) {
printf("heap memory allocated by PnetCDF internally has %lld bytes yet to be freed\n", malloc_size);
ncmpi_inq_malloc_list();
}
fn_exit:
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);
}
MPI_Finalize();
return (nerrs > 0);
}
IOR_offset_t
IOR_Xfer_NCMPI(int access,
void * fd,
IOR_size_t * buffer,
IOR_offset_t length,
IOR_param_t * param)
{
char * bufferPtr = (char *)buffer;
static int firstReadCheck = FALSE,
startDataSet;
int var_id,
dim_id[NUM_DIMS];
MPI_Offset bufSize[NUM_DIMS],
offset[NUM_DIMS];
IOR_offset_t segmentPosition;
int segmentNum,
transferNum;
/* Wei-keng Liao: In IOR.c line 1979 says "block size must be a multiple
of transfer size." Hence, length should always == param->transferSize
below. I leave it here to double check.
*/
if (length != param->transferSize) {
char errMsg[256];
sprintf(errMsg,"length(%lld) != param->transferSize(%lld)\n",
length, param->transferSize);
NCMPI_CHECK(-1, errMsg);
}
/* determine by offset if need to start data set */
if (param->filePerProc == TRUE) {
segmentPosition = (IOR_offset_t)0;
} else {
segmentPosition = (IOR_offset_t)((rank + rankOffset) % param->numTasks)
* param->blockSize;
}
if ((int)(param->offset - segmentPosition) == 0) {
startDataSet = TRUE;
/*
* this toggle is for the read check operation, which passes through
* this function twice; note that this function will open a data set
* only on the first read check and close only on the second
*/
if (access == READCHECK) {
if (firstReadCheck == TRUE) {
firstReadCheck = FALSE;
} else {
firstReadCheck = TRUE;
}
}
}
if (startDataSet == TRUE &&
(access != READCHECK || firstReadCheck == TRUE)) {
if (access == WRITE) {
int numTransfers = param->blockSize / param->transferSize;
/* Wei-keng Liao: change 1D array to 3D array of dimensions:
[segmentCount*numTasksWorld][numTransfers][transferSize]
Requirement: none of these dimensions should be > 4G,
*/
NCMPI_CHECK(ncmpi_def_dim(*(int *)fd, "segments_times_np",
NC_UNLIMITED, &dim_id[0]),
"cannot define data set dimensions");
NCMPI_CHECK(ncmpi_def_dim(*(int *)fd, "number_of_transfers",
numTransfers, &dim_id[1]),
"cannot define data set dimensions");
NCMPI_CHECK(ncmpi_def_dim(*(int *)fd, "transfer_size",
param->transferSize, &dim_id[2]),
"cannot define data set dimensions");
NCMPI_CHECK(ncmpi_def_var(*(int *)fd, "data_var", NC_BYTE,
NUM_DIMS, dim_id, &var_id),
"cannot define data set variables");
NCMPI_CHECK(ncmpi_enddef(*(int *)fd),
"cannot close data set define mode");
} else {
NCMPI_CHECK(ncmpi_inq_varid(*(int *)fd, "data_var", &var_id),
"cannot retrieve data set variable");
}
if (param->collective == FALSE) {
NCMPI_CHECK(ncmpi_begin_indep_data(*(int *)fd),
"cannot enable independent data mode");
}
param->var_id = var_id;
startDataSet = FALSE;
}
var_id = param->var_id;
/* Wei-keng Liao: calculate the segment number */
segmentNum = param->offset / (param->numTasks * param->blockSize);
/* Wei-keng Liao: calculate the transfer number in each block */
transferNum = param->offset % param->blockSize / param->transferSize;
/* Wei-keng Liao: read/write the 3rd dim of the dataset, each is of
amount param->transferSize */
bufSize[0] = 1;
bufSize[1] = 1;
bufSize[2] = param->transferSize;
offset[0] = segmentNum * numTasksWorld + rank;
offset[1] = transferNum;
offset[2] = 0;
/* access the file */
if (access == WRITE) { /* WRITE */
if (param->collective) {
NCMPI_CHECK(ncmpi_put_vara_all(*(int *)fd, var_id, offset, bufSize,
bufferPtr, length, MPI_BYTE),
"cannot write to data set");
} else {
NCMPI_CHECK(ncmpi_put_vara(*(int *)fd, var_id, offset, bufSize,
bufferPtr, length, MPI_BYTE),
"cannot write to data set");
}
} else { /* READ or CHECK */
if (param->collective == TRUE) {
NCMPI_CHECK(ncmpi_get_vara_all(*(int *)fd, var_id, offset, bufSize,
bufferPtr, length, MPI_BYTE),
"cannot read from data set");
} else {
NCMPI_CHECK(ncmpi_get_vara(*(int *)fd, var_id, offset, bufSize,
bufferPtr, length, MPI_BYTE),
"cannot read from data set");
}
}
return(length);
} /* IOR_Xfer_NCMPI() */
/**
* Read a single-precision parallel-nedcdf file.
*
* We assume here that localData is a scalar.
*
* Pnetcdf uses row-major format (same as FFTW).
*
* \param[in] filename : PnetCDF filename
* \param[in] starts : offset to where to start reading data
* \param[in] counts : number of elements read (3D sub-domain inside global)
* \param[in] gsizes : global sizes
* \param[out] localData : actual data buffer (size : nx*ny*nz*sizeof(float))
*
* localData must have been allocated prior to calling this routine.
*/
void read_pnetcdf(const std::string &filename,
MPI_Offset starts[3],
MPI_Offset counts[3],
int gsizes[3],
float *localData)
{
int myRank;
MPI_Comm_rank(MPI_COMM_WORLD, &myRank);
// netcdf file id
int ncFileId;
int err;
// file opening mode
int ncOpenMode = NC_NOWRITE;
int nbVar=1;
int varIds[nbVar];
MPI_Info mpi_info_used;
/*
* Open NetCDF file
*/
err = ncmpi_open(MPI_COMM_WORLD, filename.c_str(),
ncOpenMode,
MPI_INFO_NULL, &ncFileId);
if (err != NC_NOERR) {
printf("Error: ncmpi_open() file %s (%s)\n",filename.c_str(),ncmpi_strerror(err));
MPI_Abort(MPI_COMM_WORLD, -1);
exit(1);
}
/*
* Query NetCDF mode
*/
int NC_mode;
err = ncmpi_inq_version(ncFileId, &NC_mode);
if (myRank==0) {
if (NC_mode == NC_64BIT_DATA)
std::cout << "Pnetcdf Input mode : NC_64BIT_DATA (CDF-5)\n";
else if (NC_mode == NC_64BIT_OFFSET)
std::cout << "Pnetcdf Input mode : NC_64BIT_OFFSET (CDF-2)\n";
else
std::cout << "Pnetcdf Input mode : unknown\n";
}
/*
* Query information about variable named "data"
*/
{
int ndims, nvars, ngatts, unlimited;
err = ncmpi_inq(ncFileId, &ndims, &nvars, &ngatts, &unlimited);
PNETCDF_HANDLE_ERROR;
err = ncmpi_inq_varid(ncFileId, "data", &varIds[0]);
PNETCDF_HANDLE_ERROR;
}
/*
* Define expected data types (no conversion done here)
*/
MPI_Datatype mpiDataType = MPI_FLOAT;
/*
* Get all the MPI_IO hints used (just in case, we want to print it after
* reading data...
*/
err = ncmpi_get_file_info(ncFileId, &mpi_info_used);
PNETCDF_HANDLE_ERROR;
/*
* Read heavy data (take care of row-major / column major format !)
*/
int nItems = counts[IX]*counts[IY]*counts[IZ];
{
err = ncmpi_get_vara_all(ncFileId,
varIds[0],
starts,
counts,
localData,
nItems,
mpiDataType);
PNETCDF_HANDLE_ERROR;
} // end reading heavy data
/*
* close the file
*/
err = ncmpi_close(ncFileId);
PNETCDF_HANDLE_ERROR;
} // read_pnetcdf
int main(int argc, char ** argv)
{
int ncid, dimid, varid;
MPI_Init(&argc, &argv);
MPI_Datatype vtype, rtype, usertype;
MPI_Aint lb, extent;
int userbufsz, *userbuf, *cmpbuf, i, errs=0;
int count = 25;
double pi = 3.14159;
MPI_Offset start, acount;
ncmpi_create(MPI_COMM_WORLD, "vectors.nc", NC_CLOBBER, MPI_INFO_NULL,
&ncid);
ncmpi_def_dim(ncid, "50k", 1024*50, &dimid);
ncmpi_def_var(ncid, "vector", NC_DOUBLE, 1, &dimid, &varid);
ncmpi_enddef(ncid);
MPI_Type_vector(VECCOUNT, BLOCKLEN, STRIDE, MPI_INT, &vtype);
MPI_Type_create_resized(vtype, 0, STRIDE*VECCOUNT*sizeof(int), &rtype);
MPI_Type_contiguous(count, rtype, &usertype);
MPI_Type_commit(&usertype);
MPI_Type_free(&vtype);
MPI_Type_free(&rtype);
MPI_Type_get_extent(usertype, &lb, &extent);
userbufsz = extent;
userbuf = malloc(userbufsz);
cmpbuf = calloc(userbufsz, 1);
for (i=0; i< userbufsz/sizeof(int); i++) {
userbuf[i] = pi*i;
}
start = 10; acount = count*12;
ncmpi_begin_indep_data(ncid);
ncmpi_put_vara(ncid, varid, &start, &acount,
userbuf, 1, usertype);
ncmpi_close(ncid);
NC_CHECK(ncmpi_open(MPI_COMM_WORLD, "vectors.nc", NC_NOWRITE,
MPI_INFO_NULL, &ncid));
ncmpi_begin_indep_data(ncid);
NC_CHECK(ncmpi_inq_varid(ncid, "vector", &varid));
NC_CHECK(ncmpi_get_vara(ncid, varid, &start, &acount,
cmpbuf, 1, usertype));
ncmpi_close(ncid);
for (i=0; errs < 10 && i < acount; i++) {
/* vector of 4,3,5, so skip 4th and 5th items of every block */
if (i%STRIDE >= BLOCKLEN) continue;
if (userbuf[i] != cmpbuf[i]) {
errs++;
fprintf(stderr, "%d: expected 0x%x got 0x%x\n",
i, userbuf[i], cmpbuf[i]);
}
}
free(userbuf);
free(cmpbuf);
MPI_Type_free(&usertype);
MPI_Finalize();
return 0;
}
void read_pnetcdf(const std::string &filename,
int iVar,
ConfigMap &configMap,
HostArray<double> &localData)
{
int myRank;
MPI_Comm_rank(MPI_COMM_WORLD, &myRank);
int nbMpiProc;
MPI_Comm_size(MPI_COMM_WORLD, &nbMpiProc);
// netcdf file id
int ncFileId;
int err;
// ghostWidth
int ghostWidth = configMap.getInteger("mesh","ghostWidth",3);
// file creation mode
int ncOpenMode = NC_NOWRITE;
int varIds[8];
MPI_Offset starts[3], counts[3]; // read_size, sum_read_size;
MPI_Info mpi_info_used;
// domain local size
int nx,ny,nz;
// sizes to read
//int nx_r, ny_r, nz_r; // logical sizes / per sub-domain
//int nx_g, ny_g, nz_g; // sizes with ghost zones included / per sub-domain
/* read domain sizes */
nx=configMap.getInteger("mesh","nx",32);
ny=configMap.getInteger("mesh","ny",32);
nz=configMap.getInteger("mesh","nz",32);
// nx_g = nx+2*ghostWidth;
// ny_g = ny+2*ghostWidth;
// nz_g = nz+2*ghostWidth;
// get input filename from configMap
//std::string filename = configMap.getString("input", "filename", "");
/*
* Open NetCDF file
*/
err = ncmpi_open(MPI_COMM_WORLD, filename.c_str(),
ncOpenMode,
MPI_INFO_NULL, &ncFileId);
if (err != NC_NOERR) {
printf("Error: ncmpi_open() file %s (%s)\n",filename.c_str(),ncmpi_strerror(err));
MPI_Abort(MPI_COMM_WORLD, -1);
exit(1);
}
/*
* Query NetCDF mode
*/
int NC_mode;
err = ncmpi_inq_version(ncFileId, &NC_mode);
if (myRank==0) {
if (NC_mode == NC_64BIT_DATA)
std::cout << "Pnetcdf Input mode : NC_64BIT_DATA (CDF-5)\n";
else if (NC_mode == NC_64BIT_OFFSET)
std::cout << "Pnetcdf Input mode : NC_64BIT_OFFSET (CDF-2)\n";
else
std::cout << "Pnetcdf Input mode : unknown\n";
}
/*
* Query information about variables
*/
{
int ndims, nvars, ngatts, unlimited;
err = ncmpi_inq(ncFileId, &ndims, &nvars, &ngatts, &unlimited);
PNETCDF_HANDLE_ERROR;
err = ncmpi_inq_varid(ncFileId, "rho", &varIds[ID]);
PNETCDF_HANDLE_ERROR;
err = ncmpi_inq_varid(ncFileId, "E", &varIds[IP]);
PNETCDF_HANDLE_ERROR;
err = ncmpi_inq_varid(ncFileId, "rho_vx", &varIds[IU]);
PNETCDF_HANDLE_ERROR;
err = ncmpi_inq_varid(ncFileId, "rho_vy", &varIds[IV]);
PNETCDF_HANDLE_ERROR;
err = ncmpi_inq_varid(ncFileId, "rho_vz", &varIds[IW]);
PNETCDF_HANDLE_ERROR;
err = ncmpi_inq_varid(ncFileId, "Bx", &varIds[IA]);
PNETCDF_HANDLE_ERROR;
err = ncmpi_inq_varid(ncFileId, "By", &varIds[IB]);
PNETCDF_HANDLE_ERROR;
err = ncmpi_inq_varid(ncFileId, "Bz", &varIds[IC]);
PNETCDF_HANDLE_ERROR;
} // end query information
/*
* Define expected data types (no conversion done here)
*/
//nc_type ncDataType;
MPI_Datatype mpiDataType;
//ncDataType = NC_DOUBLE;
mpiDataType = MPI_DOUBLE;
/*
* Get all the MPI_IO hints used (just in case, we want to print it after
* reading data...
*/
err = ncmpi_get_file_info(ncFileId, &mpi_info_used);
PNETCDF_HANDLE_ERROR;
/*
* Read heavy data (take care of row-major / column major format !)
*/
// use overlapping domains
// counts[IZ] = nx_rg;
// counts[IY] = ny_rg;
// counts[IX] = nz_rg;
// starts[IZ] = 0;
// starts[IY] = 0;
// starts[IX] = myRank*nz_r;
counts[IZ] = nx;
counts[IY] = ny;
counts[IX] = nz;
starts[IZ] = ghostWidth;
starts[IY] = ghostWidth;
starts[IX] = ghostWidth+myRank*nz;
int nItems = counts[IX]*counts[IY]*counts[IZ];
/*
* Actual reading
*/
{
double* data;
//data = &(localData(0,0,0,0));
data = localData.data();
err = ncmpi_get_vara_all(ncFileId, varIds[iVar],
starts, counts, data, nItems, mpiDataType);
PNETCDF_HANDLE_ERROR;
} // end for loop reading heavy data
/*
* close the file
*/
err = ncmpi_close(ncFileId);
PNETCDF_HANDLE_ERROR;
} // read_pnetcdf
/*----< main() >------------------------------------------------------------*/
int main(int argc, char **argv) {
char filename[256];
int i, j, err, ncid, varid0, varid1, varid2, dimids[2], nerrs=0;
int rank, nprocs, debug=0, blocklengths[2], **buf, *bufptr;
int array_of_sizes[2], array_of_subsizes[2], array_of_starts[2];
MPI_Offset start[2], count[2];
MPI_Aint a0, a1, disps[2];
MPI_Datatype buftype, ghost_buftype, rec_filetype, fix_filetype;
MPI_Init(&argc, &argv);
MPI_Comm_size(MPI_COMM_WORLD, &nprocs);
MPI_Comm_rank(MPI_COMM_WORLD, &rank);
if (argc > 2) {
if (!rank) printf("Usage: %s [filename]\n",argv[0]);
MPI_Finalize();
return 0;
}
strcpy(filename, "testfile.nc");
if (argc == 2) strcpy(filename, argv[1]);
MPI_Bcast(filename, 256, MPI_CHAR, 0, MPI_COMM_WORLD);
if (rank == 0) {
char cmd_str[256];
sprintf(cmd_str, "*** TESTING C %s for flexible put and get ", argv[0]);
printf("%-66s ------ ", cmd_str); fflush(stdout);
}
buf = (int**)malloc(NY * sizeof(int*));
buf[0] = (int*)malloc(NY * NX * sizeof(int));
for (i=1; i<NY; i++) buf[i] = buf[i-1] + NX;
/* construct various MPI derived data types */
/* construct an MPI derived data type for swapping 1st row with 2nd row */
blocklengths[0] = blocklengths[1] = NX;
MPI_Get_address(buf[1], &a0);
MPI_Get_address(buf[0], &a1);
disps[0] = 0;
disps[1] = a1 - a0;
bufptr = buf[1];
err = MPI_Type_create_hindexed(2, blocklengths, disps, MPI_INT, &buftype);
if (err != MPI_SUCCESS) printf("MPI error MPI_Type_create_hindexed\n");
MPI_Type_commit(&buftype);
start[0] = 0; start[1] = NX*rank;
count[0] = 2; count[1] = NX;
if (debug) printf("put start=%lld %lld count=%lld %lld\n",start[0],start[1],count[0],count[1]);
/* create a file type for the fixed-size variable */
array_of_sizes[0] = 2;
array_of_sizes[1] = NX*nprocs;
array_of_subsizes[0] = count[0];
array_of_subsizes[1] = count[1];
array_of_starts[0] = start[0];
array_of_starts[1] = start[1];
MPI_Type_create_subarray(2, array_of_sizes, array_of_subsizes,
array_of_starts, MPI_ORDER_C,
MPI_INT, &fix_filetype);
MPI_Type_commit(&fix_filetype);
/* create a buftype with ghost cells on each side */
array_of_sizes[0] = count[0]+4;
array_of_sizes[1] = count[1]+4;
array_of_subsizes[0] = count[0];
array_of_subsizes[1] = count[1];
array_of_starts[0] = 2;
array_of_starts[1] = 2;
MPI_Type_create_subarray(2, array_of_sizes, array_of_subsizes,
array_of_starts, MPI_ORDER_C,
MPI_INT, &ghost_buftype);
MPI_Type_commit(&ghost_buftype);
/* create a new file for write */
err = ncmpi_create(MPI_COMM_WORLD, filename, NC_CLOBBER, MPI_INFO_NULL,
&ncid); ERR
/* define a 2D array */
err = ncmpi_def_dim(ncid, "REC_DIM", NC_UNLIMITED, &dimids[0]); ERR
err = ncmpi_def_dim(ncid, "X", NX*nprocs, &dimids[1]); ERR
err = ncmpi_def_var(ncid, "rec_var", NC_INT, 2, dimids, &varid0); ERR
err = ncmpi_def_var(ncid, "dummy_rec", NC_INT, 2, dimids, &varid2); ERR
err = ncmpi_def_dim(ncid, "FIX_DIM", 2, &dimids[0]); ERR
err = ncmpi_def_var(ncid, "fix_var", NC_INT, 2, dimids, &varid1); ERR
err = ncmpi_enddef(ncid); ERR
/* create a file type for the record variable */
int *array_of_blocklengths=(int*) malloc(count[0]*sizeof(int));
MPI_Aint *array_of_displacements=(MPI_Aint*) malloc(count[0]*sizeof(MPI_Aint));
MPI_Offset recsize;
err = ncmpi_inq_recsize(ncid, &recsize);
for (i=0; i<count[0]; i++) {
array_of_blocklengths[i] = count[1];
array_of_displacements[i] = start[1]*sizeof(int) + recsize * i;
}
MPI_Type_create_hindexed(2, array_of_blocklengths, array_of_displacements,
MPI_INT, &rec_filetype);
MPI_Type_commit(&rec_filetype);
free(array_of_blocklengths);
free(array_of_displacements);
/* initialize the contents of the array */
for (j=0; j<NY; j++) for (i=0; i<NX; i++) buf[j][i] = rank*100 + j*10 + i;
/* write the record variable */
err = ncmpi_put_vard_all(ncid, varid0, rec_filetype, bufptr, 1, buftype); ERR
/* check if the contents of buf are altered */
CHECK_VALUE
/* check if root process can write to file header in data mode */
err = ncmpi_rename_var(ncid, varid0, "rec_VAR"); ERR
/* write the fixed-size variable */
err = ncmpi_put_vard_all(ncid, varid1, fix_filetype, bufptr, 1, buftype); ERR
/* check if the contents of buf are altered */
CHECK_VALUE
/* check if root process can write to file header in data mode */
err = ncmpi_rename_var(ncid, varid0, "rec_var"); ERR
/* test the same routines in independent data mode */
err = ncmpi_begin_indep_data(ncid); ERR
err = ncmpi_put_vard(ncid, varid0, rec_filetype, bufptr, 1, buftype); ERR
CHECK_VALUE
err = ncmpi_rename_var(ncid, varid0, "rec_VAR"); ERR
err = ncmpi_put_vard(ncid, varid1, fix_filetype, bufptr, 1, buftype); ERR
CHECK_VALUE
err = ncmpi_rename_var(ncid, varid0, "rec_var"); ERR
err = ncmpi_end_indep_data(ncid); ERR
err = ncmpi_close(ncid); ERR
/* open the same file and read back for validate */
err = ncmpi_open(MPI_COMM_WORLD, filename, NC_NOWRITE, MPI_INFO_NULL,
&ncid); ERR
err = ncmpi_inq_varid(ncid, "rec_var", &varid0); ERR
err = ncmpi_inq_varid(ncid, "fix_var", &varid1); ERR
nerrs += get_var_and_verify(ncid, varid0, start, count, buf, buftype, ghost_buftype, rec_filetype);
nerrs += get_var_and_verify(ncid, varid1, start, count, buf, buftype, ghost_buftype, fix_filetype);
err = ncmpi_close(ncid); ERR
MPI_Type_free(&rec_filetype);
MPI_Type_free(&fix_filetype);
MPI_Type_free(&buftype);
MPI_Type_free(&ghost_buftype);
free(buf[0]); 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);
}
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);
}
MPI_Finalize();
return 0;
}
static
int tst_norm(char *filename, int cmode)
{
int ncid, dimid, varid;
int dimids[NDIMS];
/* unnormalized UTF-8 encoding for Unicode 8-character "Hello" in Greek: */
unsigned char uname_utf8[] = {
0x41, /* LATIN CAPITAL LETTER A */
0xCC, 0x80, /* COMBINING GRAVE ACCENT */
0x41, /* LATIN CAPITAL LETTER A */
0xCC, 0x81, /* COMBINING ACUTE ACCENT */
0x41, /* LATIN CAPITAL LETTER A */
0xCC, 0x82, /* COMBINING CIRCUMFLEX ACCENT */
0x41, /* LATIN CAPITAL LETTER A */
0xCC, 0x83, /* COMBINING TILDE */
0x41, /* LATIN CAPITAL LETTER A */
0xCC, 0x88, /* COMBINING DIAERESIS */
0x41, /* LATIN CAPITAL LETTER A */
0xCC, 0x8A, /* COMBINING RING ABOVE */
0x43, /* LATIN CAPITAL LETTER C */
0xCC, 0xA7, /* COMBINING CEDILLA */
0x45, /* LATIN CAPITAL LETTER E */
0xCC, 0x80, /* COMBINING GRAVE ACCENT */
0x45, /* LATIN CAPITAL LETTER E */
0xCC, 0x81, /* COMBINING ACUTE ACCENT */
0x45, /* LATIN CAPITAL LETTER E */
0xCC, 0x82, /* COMBINING CIRCUMFLEX ACCENT */
0x45, /* LATIN CAPITAL LETTER E */
0xCC, 0x88, /* COMBINING DIAERESIS */
0x49, /* LATIN CAPITAL LETTER I */
0xCC, 0x80, /* COMBINING GRAVE ACCENT */
0x49, /* LATIN CAPITAL LETTER I */
0xCC, 0x81, /* COMBINING ACUTE ACCENT */
0x49, /* LATIN CAPITAL LETTER I */
0xCC, 0x82, /* COMBINING CIRCUMFLEX ACCENT */
0x49, /* LATIN CAPITAL LETTER I */
0xCC, 0x88, /* COMBINING DIAERESIS */
0x4E, /* LATIN CAPITAL LETTER N */
0xCC, 0x83, /* COMBINING TILDE */
0x00
};
/* NFC normalized UTF-8 encoding for same Unicode string: */
unsigned char nname_utf8[] = {
0xC3, 0x80, /* LATIN CAPITAL LETTER A WITH GRAVE */
0xC3, 0x81, /* LATIN CAPITAL LETTER A WITH ACUTE */
0xC3, 0x82, /* LATIN CAPITAL LETTER A WITH CIRCUMFLEX */
0xC3, 0x83, /* LATIN CAPITAL LETTER A WITH TILDE */
0xC3, 0x84, /* LATIN CAPITAL LETTER A WITH DIAERESIS */
0xC3, 0x85, /* LATIN CAPITAL LETTER A WITH RING ABOVE */
0xC3, 0x87, /* LATIN CAPITAL LETTER C WITH CEDILLA */
0xC3, 0x88, /* LATIN CAPITAL LETTER E WITH GRAVE */
0xC3, 0x89, /* LATIN CAPITAL LETTER E WITH ACUTE */
0xC3, 0x8A, /* LATIN CAPITAL LETTER E WITH CIRCUMFLEX */
0xC3, 0x8B, /* LATIN CAPITAL LETTER E WITH DIAERESIS */
0xC3, 0x8C, /* LATIN CAPITAL LETTER I WITH GRAVE */
0xC3, 0x8D, /* LATIN CAPITAL LETTER I WITH ACUTE */
0xC3, 0x8E, /* LATIN CAPITAL LETTER I WITH CIRCUMFLEX */
0xC3, 0x8F, /* LATIN CAPITAL LETTER I WITH DIAERESIS */
0xC3, 0x91, /* LATIN CAPITAL LETTER N WITH TILDE */
0x00
};
/* Unnormalized name used for dimension, variable, and attribute value */
#define UNAME ((char *) uname_utf8)
#define UNAMELEN (sizeof uname_utf8)
/* Normalized name */
#define NNAME ((char *) nname_utf8)
#define NNAMELEN (sizeof nname_utf8)
char name_in[UNAMELEN + 1], strings_in[UNAMELEN + 1];
nc_type att_type;
MPI_Offset att_len;
int err, dimid_in, varid_in, attnum_in;
int attvals[] = {42};
#define ATTNUM ((sizeof attvals)/(sizeof attvals[0]))
err = ncmpi_create(MPI_COMM_WORLD, filename, cmode, MPI_INFO_NULL,&ncid); ERR
/* Define dimension with unnormalized Unicode UTF-8 encoded name */
err = ncmpi_def_dim(ncid, UNAME, NX, &dimid); ERR
dimids[0] = dimid;
/* Define variable with same name */
err = ncmpi_def_var(ncid, UNAME, NC_CHAR, NDIMS, dimids, &varid); ERR
/* Create string attribute with same value */
err = ncmpi_put_att_text(ncid, varid, UNITS, UNAMELEN, UNAME); ERR
/* Create int attribute with same name */
err = ncmpi_put_att_int(ncid, varid, UNAME, NC_INT, ATTNUM, attvals); ERR
/* Try to create dimension and variable with NFC-normalized
* version of same name. These should fail, as unnormalized name
* should have been normalized in library, so these are attempts to
* create duplicate netCDF objects. */
if ((err = ncmpi_def_dim(ncid, NNAME, NX, &dimid)) != NC_ENAMEINUSE) {
printf("Error at line %d: expecting error code %d but got %d\n",__LINE__,NC_ENAMEINUSE,err);
return 1;
}
if ((err=ncmpi_def_var(ncid, NNAME, NC_CHAR, NDIMS, dimids, &varid)) != NC_ENAMEINUSE) {
printf("Error at line %d: expecting error code %d but got %d\n",__LINE__,NC_ENAMEINUSE,err);
return 1;
}
err = ncmpi_enddef(ncid); ERR
/* Write string data, UTF-8 encoded, to the file */
err = ncmpi_put_var_text_all(ncid, varid, UNAME); ERR
err = ncmpi_close(ncid); ERR
/* Check it out. */
err = ncmpi_open(MPI_COMM_WORLD, filename, NC_NOWRITE, MPI_INFO_NULL, &ncid); ERR
err = ncmpi_inq_varid(ncid, UNAME, &varid); ERR
err = ncmpi_inq_varname(ncid, varid, name_in); ERR
err = strncmp(NNAME, name_in, NNAMELEN); ERR
err = ncmpi_inq_varid(ncid, NNAME, &varid_in); ERR
if ((err = ncmpi_inq_dimid(ncid, UNAME, &dimid_in)) || dimid != dimid_in)
{printf("Error at line %d\n",__LINE__);return 1;}
if ((err = ncmpi_inq_dimid(ncid, NNAME, &dimid_in)) || dimid != dimid_in)
{printf("Error at line %d\n",__LINE__);return 1;}
err = ncmpi_inq_att(ncid, varid, UNITS, &att_type, &att_len); ERR
if ( att_type != NC_CHAR || att_len != UNAMELEN)
{printf("Error at line %d\n",__LINE__);return 1;}
err = ncmpi_get_att_text(ncid, varid, UNITS, strings_in); ERR
strings_in[UNAMELEN] = '\0';
err = strncmp(UNAME, strings_in, UNAMELEN); ERR
if ((err = ncmpi_inq_attid(ncid, varid, UNAME, &attnum_in)) || ATTNUM != attnum_in)
{printf("Error at line %d\n",__LINE__);return 1;}
if ((err = ncmpi_inq_attid(ncid, varid, NNAME, &attnum_in)) || ATTNUM != attnum_in)
{printf("Error at line %d\n",__LINE__);return 1;}
err = ncmpi_close(ncid); ERR
return 0;
}
/*----< main() >------------------------------------------------------------*/
int main(int argc, char **argv)
{
int i, j, err, nerrs=0, rank, nprocs;
int ncid, dimid[2], varid, req, status;
MPI_Offset start[2], count[2], stride[2], imap[2];
int var[6][4];
float k, rh[4][6];
signed char varT[4][6];
char filename[256];
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, "testfile.nc");
if (rank == 0) {
char *cmd_str = (char*)malloc(strlen(argv[0]) + 256);
sprintf(cmd_str, "*** TESTING C %s for get/put varm ", basename(argv[0]));
printf("%-66s ------ ", cmd_str); fflush(stdout);
free(cmd_str);
}
#ifdef DEBUG
if (nprocs > 1 && rank == 0)
printf("Warning: %s is designed to run on 1 process\n", argv[0]);
#endif
err = ncmpi_create(MPI_COMM_WORLD, filename, NC_CLOBBER | NC_64BIT_DATA,
MPI_INFO_NULL, &ncid); CHECK_ERR
/* define a variable of a 6 x 4 integer array in the nc file */
err = ncmpi_def_dim(ncid, "Y", 6, &dimid[0]); CHECK_ERR
err = ncmpi_def_dim(ncid, "X", 4, &dimid[1]); CHECK_ERR
err = ncmpi_def_var(ncid, "var", NC_INT, 2, dimid, &varid); CHECK_ERR
err = ncmpi_enddef(ncid); CHECK_ERR
/* create a 6 x 4 integer variable in the file with contents:
0, 1, 2, 3,
4, 5, 6, 7,
8, 9, 10, 11,
12, 13, 14, 15,
16, 17, 18, 19,
20, 21, 22, 23
*/
for (j=0; j<6; j++) for (i=0; i<4; i++) var[j][i] = j*4+i;
start[0] = 0; start[1] = 0;
count[0] = 6; count[1] = 4;
if (rank > 0) count[0] = count[1] = 0;
err = ncmpi_put_vara_int_all(ncid, varid, start, count, &var[0][0]); CHECK_ERR
if (nprocs > 1) MPI_Barrier(MPI_COMM_WORLD);
err = ncmpi_close(ncid); CHECK_ERR
err = ncmpi_open(MPI_COMM_WORLD, filename, NC_NOWRITE, MPI_INFO_NULL, &ncid); CHECK_ERR
err = ncmpi_inq_varid(ncid, "var", &varid); CHECK_ERR
/* read the variable back in the matrix transposed way, rh is 4 x 6 */
count[0] = 6; count[1] = 4;
stride[0] = 1; stride[1] = 1;
imap[0] = 1; imap[1] = 6; /* would be {4, 1} if not transposing */
for (i=0; i<6; i++) for (j=0; j<4; j++) rh[j][i] = -1.0;
err = ncmpi_iget_varm_float(ncid, varid, start, count, stride, imap, &rh[0][0], &req); CHECK_ERR
err = ncmpi_wait_all(ncid, 1, &req, &status); CHECK_ERR
err = status; CHECK_ERR
/* check the contents of read */
k = 0.0;
for (i=0; i<6; i++) {
for (j=0; j<4; j++) {
if (rh[j][i] != k) {
#ifdef PRINT_ERR_ON_SCREEN
printf("Error at line %d in %s: expecting rh[%d][%d]=%f but got %f\n",
__LINE__,__FILE__,j,i,k,rh[j][i]);
#endif
nerrs++;
break;
}
k += 1.0;
}
}
#ifdef PRINT_ON_SCREEN
/* print the contents of read */
for (j=0; j<4; j++) {
printf("[%2d]: ",j);
for (i=0; i<6; i++) {
printf("%5.1f",rh[j][i]);
}
printf("\n");
}
#endif
/* the stdout should be:
[ 0]: 0.0 4.0 8.0 12.0 16.0 20.0
[ 1]: 1.0 5.0 9.0 13.0 17.0 21.0
[ 2]: 2.0 6.0 10.0 14.0 18.0 22.0
[ 3]: 3.0 7.0 11.0 15.0 19.0 23.0
*/
for (i=0; i<6; i++) for (j=0; j<4; j++) rh[j][i] = -1.0;
err = ncmpi_get_varm_float_all(ncid, varid, start, count, stride, imap, &rh[0][0]); CHECK_ERR
/* check the contents of read */
k = 0.0;
for (i=0; i<6; i++) {
for (j=0; j<4; j++) {
if (rh[j][i] != k) {
#ifdef PRINT_ERR_ON_SCREEN
printf("Error at line %d in %s: expecting rh[%d][%d]=%f but got %f\n",
__LINE__,__FILE__,j,i,k,rh[j][i]);
#endif
nerrs++;
break;
}
k += 1.0;
}
}
#ifdef PRINT_ON_SCREEN
/* print the contents of read */
for (j=0; j<4; j++) {
printf("[%2d]: ",j);
for (i=0; i<6; i++) {
printf("%5.1f",rh[j][i]);
}
printf("\n");
}
#endif
/* the stdout should be:
[ 0]: 0.0 4.0 8.0 12.0 16.0 20.0
[ 1]: 1.0 5.0 9.0 13.0 17.0 21.0
[ 2]: 2.0 6.0 10.0 14.0 18.0 22.0
[ 3]: 3.0 7.0 11.0 15.0 19.0 23.0
*/
err = ncmpi_close(ncid); CHECK_ERR
err = ncmpi_open(MPI_COMM_WORLD, filename, NC_WRITE, MPI_INFO_NULL, &ncid); CHECK_ERR
err = ncmpi_inq_varid(ncid, "var", &varid); CHECK_ERR
/* testing get_varm(), first zero-out the variable in the file */
memset(&var[0][0], 0, 6*4*sizeof(int));
start[0] = 0; start[1] = 0;
count[0] = 6; count[1] = 4;
if (rank > 0) count[0] = count[1] = 0;
err = ncmpi_put_vara_int_all(ncid, varid, start, count, &var[0][0]); CHECK_ERR
/* set the contents of the write buffer varT, a 4 x 6 char array
50, 51, 52, 53, 54, 55,
56, 57, 58, 59, 60, 61,
62, 63, 64, 65, 66, 67,
68, 69, 70, 71, 72, 73
*/
for (j=0; j<4; j++) for (i=0; i<6; i++) varT[j][i] = j*6+i + 50;
/* write varT to the NC variable in the matrix transposed way */
start[0] = 0; start[1] = 0;
count[0] = 6; count[1] = 4;
stride[0] = 1; stride[1] = 1;
imap[0] = 1; imap[1] = 6; /* would be {4, 1} if not transposing */
if (rank > 0) count[0] = count[1] = 0;
err = ncmpi_iput_varm_schar(ncid, varid, start, count, stride, imap, &varT[0][0], &req); CHECK_ERR
err = ncmpi_wait_all(ncid, 1, &req, &status); CHECK_ERR
err = status; CHECK_ERR
/* the output from command "ncmpidump -v var test.nc" should be:
var =
50, 56, 62, 68,
51, 57, 63, 69,
52, 58, 64, 70,
53, 59, 65, 71,
54, 60, 66, 72,
55, 61, 67, 73 ;
*/
/* check if the contents of write buffer have been altered */
for (j=0; j<4; j++) {
for (i=0; i<6; i++) {
if (varT[j][i] != j*6+i + 50) {
#ifdef PRINT_ERR_ON_SCREEN
/* this error is a pnetcdf internal error, if occurs */
printf("Error at line %d in %s: expecting varT[%d][%d]=%d but got %d\n",
__LINE__,__FILE__,j,i,j*6+i + 50,varT[j][i]);
#endif
nerrs++;
break;
}
}
}
err = ncmpi_put_varm_schar_all(ncid, varid, start, count, stride, imap, &varT[0][0]); CHECK_ERR
/* check if the contents of write buffer have been altered */
for (j=0; j<4; j++) {
for (i=0; i<6; i++) {
if (varT[j][i] != j*6+i + 50) {
#ifdef PRINT_ERR_ON_SCREEN
/* this error is a pnetcdf internal error, if occurs */
printf("Error at line %d in %s: expecting varT[%d][%d]=%d but got %d\n",
__LINE__,__FILE__,j,i,j*6+i + 50,varT[j][i]);
#endif
nerrs++;
break;
}
}
}
err = ncmpi_close(ncid); CHECK_ERR
/* 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);
}
MPI_Finalize();
return (nerrs > 0);
}
int
main(int argc, char **argv)
{
int rank, nprocs, ncid, pres_varid, temp_varid;
int lat_varid, lon_varid;
/* The start and count arrays will tell the netCDF library where to
read our data. */
MPI_Offset start[NDIMS], count[NDIMS];
/* Program variables to hold the data we will read. We will only
need enough space to hold one timestep of data; one record. */
float **pres_in=NULL; /* [NLVL/nprocs][NLAT][NLON] */
float **temp_in=NULL; /* [NLVL/nprocs][NLAT][NLON] */
/* These program variables hold the latitudes and longitudes. */
float lats[NLAT], lons[NLON];
/* Loop indexes. */
int lvl, lat, lon, rec, i = 0;
/* Error handling. */
int err, nerrs=0;
char *filename = FILE_NAME;
MPI_Init(&argc, &argv);
MPI_Comm_size(MPI_COMM_WORLD, &nprocs);
MPI_Comm_rank(MPI_COMM_WORLD, &rank);
if (argc > 2) {
if (!rank) printf("Usage: %s [filename]\n",argv[0]);
MPI_Finalize();
return 1;
}
if (argc == 2) filename = argv[1];
if (rank == 0) {
char *cmd_str = (char*)malloc(strlen(argv[0]) + 256);
sprintf(cmd_str, "*** TESTING C %s for reading file", basename(argv[0]));
printf("%-66s ------ ", cmd_str);
free(cmd_str);
}
/* Open the file. */
err = ncmpi_open(MPI_COMM_WORLD, filename, NC_NOWRITE, MPI_INFO_NULL, &ncid);
CHECK_ERR
/* Get the varids of the latitude and longitude coordinate
* variables. */
err = ncmpi_inq_varid(ncid, LAT_NAME, &lat_varid);
CHECK_ERR
err = ncmpi_inq_varid(ncid, LON_NAME, &lon_varid);
CHECK_ERR
/* Read the coordinate variable data. */
memset(lats, 0, sizeof(float)*NLAT);
memset(lons, 0, sizeof(float)*NLON);
err = ncmpi_get_var_float_all(ncid, lat_varid, &lats[0]);
CHECK_ERR
err = ncmpi_get_var_float_all(ncid, lon_varid, &lons[0]);
CHECK_ERR
/* Check the coordinate variable data. */
for (lat = 0; lat < NLAT; lat++)
if (lats[lat] != START_LAT + 5.*lat) {
printf("\nError at line %d in %s: expect %e but got %e\n", __LINE__,__FILE__, START_LAT+5.*lat,lats[lat]);
nerrs++;
goto fn_exit;
}
for (lon = 0; lon < NLON; lon++)
if (lons[lon] != START_LON + 5.*lon) {
printf("\nError at line %d in %s: expect %e but got %e\n", __LINE__,__FILE__, START_LON+5.*lon,lons[lon]);
nerrs++;
goto fn_exit;
}
/* Get the varids of the pressure and temperature netCDF
* variables. */
err = ncmpi_inq_varid(ncid, PRES_NAME, &pres_varid);
CHECK_ERR
err = ncmpi_inq_varid(ncid, TEMP_NAME, &temp_varid);
CHECK_ERR
/* Read the data. Since we know the contents of the file we know
* that the data arrays in this program are the correct size to
* hold one timestep. */
count[0] = 1;
count[2] = NLAT;
count[3] = NLON;
start[2] = 0;
start[3] = 0;
/* divide NLVL dimension among processes */
count[1] = NLVL / nprocs;
start[1] = count[1] * rank;
if (rank < NLVL % nprocs) {
start[1] += rank;
count[1]++;
}
else {
start[1] += NLVL % nprocs;
}
if (count[1] == 0) start[1] = 0;
/* allocate read buffers */
pres_in = (float**) malloc(count[1]*2 * sizeof(float*));
temp_in = pres_in + count[1];
if (count[1] > 0) {
pres_in[0] = (float*) malloc(count[1]*2 * NLAT*NLON * sizeof(float));
temp_in[0] = pres_in[0] + count[1] * NLAT*NLON;
for (i=1; i<count[1]; i++) {
pres_in[i] = pres_in[i-1] + NLAT*NLON;
temp_in[i] = temp_in[i-1] + NLAT*NLON;
}
}
/* Read and check one record at a time. */
for (rec = 0; rec < NREC; rec++)
{
start[0] = rec;
err = ncmpi_get_vara_float_all(ncid, pres_varid, start, count, &pres_in[0][0]);
CHECK_ERR
err = ncmpi_get_vara_float_all(ncid, temp_varid, start, count, &temp_in[0][0]);
CHECK_ERR
/* Check the data. */
i = (int)start[1] * NLAT * NLON;
for (lvl=0; lvl<count[1]; lvl++)
for (lat = 0; lat < NLAT; lat++)
for (lon = 0; lon < NLON; lon++) {
if (pres_in[lvl][lat*NLON+lon] != SAMPLE_PRESSURE + i) {
printf("\nError at line %d in %s: expect %e but got %e\n", __LINE__,__FILE__, SAMPLE_PRESSURE+i,pres_in[lvl][lat*NLON+lon]);
nerrs++;
goto fn_exit;
}
if (temp_in[lvl][lat*NLON+lon] != SAMPLE_TEMP + i) {
printf("\nError at line %d in %s: expect %e but got %e\n", __LINE__,__FILE__, SAMPLE_TEMP+i,temp_in[lvl][lat*NLON+lon]);
nerrs++;
goto fn_exit;
}
i++;
}
} /* next record */
fn_exit:
/* Close the file. */
err = ncmpi_close(ncid);
CHECK_ERR
if (pres_in != NULL) {
if (pres_in[0] != NULL) free(pres_in[0]);
free(pres_in);
}
/* check if there is any malloc residue */
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);
}
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);
}
MPI_Finalize();
return (nerrs > 0);
}
/*
reads input in pnetcdf format
nblocks: (output) local number of blocks
tot_blocks: (output) total number of blocks
vblocks: (output) pointer to array of vblocks
in_file: input file name
comm: MPI communicator
gids: (output) gids of local blocks (allocated by this function)
num_neighbors: (output) number of neighbors for each local block
(allocated by this function)
neighbors: (output) gids of neighbors of each local block
(allocated by this function)
side effects: allocates vblocks, gids, num_neighbors, neighbors
*/
void pnetcdf_read(int *nblocks, int *tot_blocks, struct vblock_t ***vblocks,
char *in_file, MPI_Comm comm, int *gids, int *num_neighbors,
int **neighbors) {
#ifdef USEPNETCDF
int err;
int ncid, varids[23], dimids[8];
MPI_Offset start[2], count[2];
nc_type type;
int ndims, natts;
int dims[2];
int rank, groupsize; /* MPI usual */
/* open file for reading */
err = ncmpi_open(comm, in_file, NC_NOWRITE, MPI_INFO_NULL, &ncid); ERR;
err = ncmpi_inq_varid(ncid, "block_off_num_verts", &varids[5]); ERR;
err = ncmpi_inq_varid(ncid, "block_off_num_complete_cells", &varids[6]); ERR;
err = ncmpi_inq_varid(ncid, "block_off_tot_num_cell_faces", &varids[7]); ERR;
err = ncmpi_inq_varid(ncid, "block_off_tot_num_face_verts", &varids[8]); ERR;
err = ncmpi_inq_varid(ncid, "block_off_num_orig_particles", &varids[9]); ERR;
/* get number of blocks */
MPI_Offset num_g_blocks; /* 64 bit version of tot_blcoks */
err = ncmpi_inq_dimlen(ncid, dimids[0], &num_g_blocks); ERR;
*tot_blocks = num_g_blocks;
MPI_Comm_rank(comm, &rank);
MPI_Comm_size(comm, &groupsize);
int start_block_ofst = rank * (*tot_blocks / groupsize);
*nblocks = (rank < groupsize - 1 ? (*tot_blocks / groupsize) :
*tot_blocks - (rank * *tot_blocks / groupsize));
/* block offsets */
int64_t *block_ofsts = (int64_t*)malloc(*tot_blocks * sizeof(int64_t));
*vblocks = (struct vblock_t**)malloc(*nblocks * sizeof(struct vblock_t*));
/* read all blocks */
gids = (int *)malloc(*nblocks * sizeof(int));
num_neighbors = (int *)malloc(*nblocks * sizeof(int));
neighbors = (int **)malloc(*nblocks * sizeof(int *));
int b;
for (b = 0; b < *nblocks; b++) {
struct vblock_t* v = (struct vblock_t*)malloc(sizeof(struct vblock_t));
/* quantities */
start[0] = start_block_ofst + b;
count[0] = 1;
err = ncmpi_inq_varid(ncid, "num_verts", &varids[0]); ERR;
err = ncmpi_get_vara_int_all(ncid, varids[0], start, count,
&(v->num_verts)); ERR;
err = ncmpi_inq_varid(ncid, "num_complete_cells", &varids[1]); ERR;
err = ncmpi_get_vara_int_all(ncid, varids[1], start, count,
&(v->num_complete_cells)); ERR;
err = ncmpi_inq_varid(ncid, "tot_num_cell_faces", &varids[2]); ERR;
err = ncmpi_get_vara_int_all(ncid, varids[2], start, count,
&(v->tot_num_cell_faces)); ERR;
err = ncmpi_inq_varid(ncid, "tot_num_face_verts", &varids[3]); ERR;
err = ncmpi_get_vara_int_all(ncid, varids[3], start, count,
&(v->tot_num_face_verts)); ERR;
err = ncmpi_inq_varid(ncid, "num_orig_particles", &varids[4]); ERR;
err = ncmpi_get_vara_int_all(ncid, varids[4], start, count,
&(v->num_orig_particles)); ERR;
err = ncmpi_inq_varid(ncid, "neighbors", &varids[21]); ERR;
err = ncmpi_inq_var(ncid, varids[21], 0, &type, &ndims,
dimids, &natts);
/* block bounds */
start[0] = start_block_ofst + b;
start[1] = 0;
count[0] = 1;
count[1] = 3;
err = ncmpi_inq_varid(ncid, "mins", &varids[11]); ERR;
err = ncmpi_get_vara_float_all(ncid, varids[11], start, count,
v->mins); ERR;
err = ncmpi_inq_varid(ncid, "maxs", &varids[12]); ERR;
err = ncmpi_get_vara_float_all(ncid, varids[12], start, count,
v->maxs); ERR;
/* save_verts */
start[0] = 0;
count[0] = *tot_blocks;
err = ncmpi_get_vara_longlong_all(ncid, varids[5], start, count,
block_ofsts); ERR;
v->save_verts = (float *)malloc(v->num_verts * 3 * sizeof(float));
start[0] = block_ofsts[start_block_ofst + b];
start[1] = 0;
count[0] = v->num_verts;
count[1] = 3;
err = ncmpi_inq_varid(ncid, "save_verts", &varids[13]); ERR;
err = ncmpi_get_vara_float_all(ncid, varids[13], start, count,
v->save_verts); ERR;
/* sites */
start[0] = 0;
count[0] = *tot_blocks;
err = ncmpi_get_vara_longlong_all(ncid, varids[9], start, count,
block_ofsts); ERR;
v->sites = (float *)malloc(v->num_orig_particles * 3 * sizeof(float));
start[0] = block_ofsts[start_block_ofst + b];
start[1] = 0;
count[0] = v->num_orig_particles;
count[1] = 3;
err = ncmpi_inq_varid(ncid, "sites", &varids[14]); ERR;
err = ncmpi_get_vara_float_all(ncid, varids[14], start, count,
v->sites); ERR;
/* complete cells */
start[0] = 0;
count[0] = *tot_blocks;
err = ncmpi_get_vara_longlong_all(ncid, varids[6], start, count,
block_ofsts); ERR;
v->complete_cells = (int *)malloc(v->num_complete_cells * sizeof(int));
start[0] = block_ofsts[start_block_ofst + b];
count[0] = v->num_complete_cells;
err = ncmpi_inq_varid(ncid, "complete_cells", &varids[15]); ERR;
err = ncmpi_get_vara_int_all(ncid, varids[15], start, count,
v->complete_cells); ERR;
/* areas, uses same block offsets as complete cells */
v->areas = (float *)malloc(v->num_complete_cells * sizeof(float));
start[0] = block_ofsts[start_block_ofst + b];
count[0] = v->num_complete_cells;
err = ncmpi_inq_varid(ncid, "areas", &varids[16]); ERR;
err = ncmpi_get_vara_float_all(ncid, varids[16], start, count,
v->areas); ERR;
/* volumes, uses same block offsets as complete cells */
v->vols = (float *)malloc(v->num_complete_cells * sizeof(float));
start[0] = block_ofsts[start_block_ofst + b];
count[0] = v->num_complete_cells;
err = ncmpi_inq_varid(ncid, "vols", &varids[17]); ERR;
err = ncmpi_get_vara_float_all(ncid, varids[17], start, count,
v->vols); ERR;
/* num_cell_faces, uses same block offsets as complete cells */
v->num_cell_faces = (int *)malloc(v->num_complete_cells * sizeof(int));
start[0] = block_ofsts[start_block_ofst + b];
count[0] = v->num_complete_cells;
err = ncmpi_inq_varid(ncid, "num_cell_faces", &varids[18]); ERR;
err = ncmpi_get_vara_int_all(ncid, varids[18], start, count,
v->num_cell_faces); ERR;
/* num_face_verts */
start[0] = 0;
count[0] = *tot_blocks;
err = ncmpi_get_vara_longlong_all(ncid, varids[7], start, count,
block_ofsts); ERR;
v->num_face_verts = (int *)malloc(v->tot_num_cell_faces * sizeof(int));
start[0] = block_ofsts[start_block_ofst + b];
count[0] = v->tot_num_cell_faces;
err = ncmpi_inq_varid(ncid, "num_face_verts", &varids[19]); ERR;
err = ncmpi_get_vara_int_all(ncid, varids[19], start, count,
v->num_face_verts); ERR;
/* face_verts */
start[0] = 0;
count[0] = *tot_blocks;
err = ncmpi_get_vara_longlong_all(ncid, varids[8], start, count,
block_ofsts); ERR;
v->face_verts = (int *)malloc(v->tot_num_face_verts * sizeof(int));
start[0] = block_ofsts[start_block_ofst + b];
count[0] = v->tot_num_face_verts;
err = ncmpi_inq_varid(ncid, "face_verts", &varids[20]); ERR;
err = ncmpi_get_vara_int_all(ncid, varids[20], start, count,
v->face_verts); ERR;
/* neighbors */
MPI_Offset n; /* temporary 64-bit version of number of neighbors */
err = ncmpi_inq_varid(ncid, "neighbors", &varids[21]); ERR;
err = ncmpi_inq_var(ncid, varids[2], 0, &type, &ndims,
dims, &natts); ERR;
err = ncmpi_inq_dimlen(ncid, dims[0], &n); ERR;
num_neighbors[b] = n;
neighbors[b] = (int *)malloc(num_neighbors[b] * sizeof(int));
start[0] = start_block_ofst + b;
count[0] = num_neighbors[b];
err = ncmpi_get_vara_int_all(ncid, varids[21], start, count,
neighbors[b]); ERR;
/* gids */
start[0] = start_block_ofst + b;
count[0] = 1;
err = ncmpi_inq_varid(ncid, "g_block_ids", &varids[22]); ERR;
err = ncmpi_get_vara_int_all(ncid, varids[22], start, count,
&gids[b]); ERR;
(*vblocks)[b] = v;
}
/* cleanup */
err = ncmpi_close(ncid); ERR;
free(block_ofsts);
#endif
}
int main(int argc, char** argv)
{
extern int optind;
char filename[256];
int i, j, verbose=1, rank, nprocs, err, nerrs=0;
int myNX, G_NX, myOff, num_reqs;
int ncid, cmode, varid, dimid[2], *reqs, *sts, **buf;
MPI_Offset start[2], count[2];
MPI_Info info;
MPI_Init(&argc, &argv);
MPI_Comm_rank(MPI_COMM_WORLD, &rank);
MPI_Comm_size(MPI_COMM_WORLD, &nprocs);
/* 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]);
/* set an MPI-IO hint to disable file offset alignment for fixed-size
* variables */
MPI_Info_create(&info);
MPI_Info_set(info, "nc_var_align_size", "1");
cmode = NC_CLOBBER | NC_64BIT_DATA;
err = ncmpi_create(MPI_COMM_WORLD, filename, cmode, info, &ncid);
ERR
MPI_Info_free(&info);
/* the global array is NY * (NX * nprocs) */
G_NX = NX * nprocs;
myOff = NX * rank;
myNX = NX;
if (verbose) printf("%2d: myOff=%3d myNX=%3d\n",rank,myOff,myNX);
err = ncmpi_def_dim(ncid, "Y", NY, &dimid[0]);
ERR
err = ncmpi_def_dim(ncid, "X", G_NX, &dimid[1]);
ERR
err = ncmpi_def_var(ncid, "var", NC_INT, 2, dimid, &varid);
ERR
err = ncmpi_enddef(ncid);
ERR
/* First, fill the entire array with zeros, using a blocking I/O.
Every process writes a subarray of size NY * myNX */
buf = (int**) malloc(myNX * sizeof(int*));
buf[0] = (int*) calloc(NY * myNX, sizeof(int));
start[0] = 0; start[1] = myOff;
count[0] = NY; count[1] = myNX;
err = ncmpi_put_vara_int_all(ncid, varid, start, count, buf[0]);
free(buf[0]);
/* initialize the buffer with rank ID. Also make the case interesting,
by allocating buffers separately */
for (i=0; i<myNX; i++) {
buf[i] = (int*) malloc(NY * sizeof(int));
for (j=0; j<NY; j++) buf[i][j] = rank;
}
reqs = (int*) malloc(myNX * sizeof(int));
sts = (int*) malloc(myNX * sizeof(int));
/* each proc writes myNX single columns of the 2D array */
start[0] = 0; start[1] = rank;
count[0] = NY; count[1] = 1;
if (verbose)
printf("%2d: start=%3lld %3lld count=%3lld %3lld\n",
rank, start[0],start[1], count[0],count[1]);
num_reqs = 0;
for (i=0; i<myNX; i++) {
err = ncmpi_iput_vara_int(ncid, varid, start, count, buf[i],
&reqs[num_reqs++]);
ERR
start[1] += nprocs;
}
err = ncmpi_wait_all(ncid, num_reqs, reqs, sts);
ERR
/* check status of all requests */
for (i=0; i<num_reqs; i++)
if (sts[i] != NC_NOERR)
printf("Error at line %d in %s: nonblocking write fails on request %d (%s)\n",
__LINE__,__FILE__,i, ncmpi_strerror(sts[i]));
err = ncmpi_close(ncid); ERR
/* read back using the same access pattern */
err = ncmpi_open(MPI_COMM_WORLD, filename, NC_NOWRITE, info, &ncid); ERR
err = ncmpi_inq_varid(ncid, "var", &varid); ERR
for (i=0; i<myNX; i++)
for (j=0; j<NY; j++) buf[i][j] = -1;
/* each proc reads myNX single columns of the 2D array */
start[0] = 0; start[1] = rank;
count[0] = NY; count[1] = 1;
num_reqs = 0;
for (i=0; i<myNX; i++) {
err = ncmpi_iget_vara_int(ncid, varid, start, count, buf[i],
&reqs[num_reqs++]);
ERR
start[1] += nprocs;
}
err = ncmpi_wait_all(ncid, num_reqs, reqs, sts);
ERR
/* check status of all requests */
for (i=0; i<num_reqs; i++)
if (sts[i] != NC_NOERR)
printf("Error at line %d in %s: nonblocking write fails on request %d (%s)\n",
__LINE__,__FILE__,i, ncmpi_strerror(sts[i]));
for (i=0; i<myNX; i++) {
for (j=0; j<NY; j++)
if (buf[i][j] != rank)
printf("Error at line %d in %s: expect buf[%d][%d]=%d but got %d\n",
__LINE__,__FILE__,i,j,rank,buf[i][j]);
}
err = ncmpi_close(ncid);
ERR
free(sts);
free(reqs);
for (i=0; i<myNX; i++) free(buf[i]);
free(buf);
/* check if there is any PnetCDF internal malloc residue */
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);
}
MPI_Finalize();
return (nerrs > 0);
}
/*----< main() >--------------------------------------------------------------*/
int main(int argc, char **argv)
{
int i, j, c, err, rank, nprocs, verbose, quiet;
int ncid1, ndims1, nvars1, natts1, unlimdimid1, *dimids1;
int ncid2, ndims2, nvars2, natts2, unlimdimid2, *dimids2;
char *name1, *name2;
MPI_Offset *shape=NULL, varsize, *start=NULL;
MPI_Offset attlen1, dimlen1, attlen2, dimlen2;
nc_type type1, type2;
MPI_Comm comm=MPI_COMM_WORLD;
int nvars, check_header, check_variable_list, check_entire_file;
long long numVarDIFF=0, numHeadDIFF=0, varDIFF, numDIFF;
struct vspec var_list;
extern char *optarg;
extern int optind;
MPI_Info info;
MPI_Init(&argc, &argv);
MPI_Comm_size(comm, &nprocs);
MPI_Comm_rank(comm, &rank);
progname = argv[0];
verbose = 0;
quiet = 0;
check_header = 0;
check_variable_list = 0;
check_entire_file = 0;
var_list.names = NULL;
var_list.nvars = 0;
while ((c = getopt(argc, argv, "bhqv:")) != -1)
switch(c) {
case 'h': /* compare header only */
check_header = 1;
break;
case 'v': /* variable names */
/* make list of names of variables specified */
get_var_names(optarg, &var_list);
check_variable_list = 1;
break;
case 'b':
verbose = 1;
break;
case 'q':
quiet = 1;
break;
case '?':
usage(rank, argv[0]);
break;
}
/* quiet overwrites verbose */
if (quiet) verbose = 0;
if (argc - optind != 2) usage(rank, argv[0]);
if (check_header == 0 && check_variable_list == 0) {
check_entire_file = 1;
check_header = 1;
}
name1 = (char*) malloc(NC_MAX_NAME);
if (!name1) OOM_ERROR
name2 = (char*) malloc(NC_MAX_NAME);
if (!name2) OOM_ERROR
/* Nov. 18, 2014 -- disable subfiling as it does not correctly handle the
* cases when nprocs < num_subfiles */
MPI_Info_create (&info);
MPI_Info_set (info, "pnetcdf_subfiling", "disable");
/* open files */
err = ncmpi_open(comm, argv[optind], NC_NOWRITE, info, &ncid1);
HANDLE_ERROR
err = ncmpi_open(comm, argv[optind+1], NC_NOWRITE, info, &ncid2);
HANDLE_ERROR
MPI_Info_free(&info);
/* check header */
if (check_header && rank == 0) { /* only root checks header */
int attnump;
err = ncmpi_inq(ncid1, &ndims1, &nvars1, &natts1, &unlimdimid1);
HANDLE_ERROR
err = ncmpi_inq(ncid2, &ndims2, &nvars2, &natts2, &unlimdimid2);
HANDLE_ERROR
if (ndims1 != ndims2) { /* check number of dimensions if equal */
if (!quiet) printf("DIFF: number of dimensions (%d) != (%d)\n",ndims1, ndims2);
numHeadDIFF++;
}
else if (verbose)
printf("SAME: number of dimensions (%d)\n",ndims1);
if (nvars1 != nvars2) { /* check number of variables if equal */
if (!quiet) printf("DIFF: number of variables (%d) != (%d)\n",nvars1, nvars2);
numHeadDIFF++;
}
else if (verbose)
printf("SAME: number of variables (%d)\n",nvars1);
if (natts1 != natts2) { /* check number of global attributes if equal */
if (!quiet) printf("DIFF: number of global attributes (%d) != (%d)\n",natts1, natts2);
numHeadDIFF++;
}
else if (verbose)
printf("SAME: number of global attributes (%d)\n",natts1);
/* Compare global attributes, assume CHAR attributes. */
for (i=0; i<natts1; i++) { /* check what's in file1 also in file2 */
err = ncmpi_inq_attname(ncid1, NC_GLOBAL, i, name1);
HANDLE_ERROR
/* find the attr with the same name from ncid2 */
err = ncmpi_inq_attid(ncid2, NC_GLOBAL, name1, &attnump);
if (err == NC_ENOTATT) {
if (!quiet) printf("DIFF: global attribute \"%s\" not found in file %s\n",
name1,argv[optind+1]);
numHeadDIFF++;
continue;
}
err = ncmpi_inq_att(ncid1, NC_GLOBAL, name1, &type1, &attlen1);
HANDLE_ERROR
err = ncmpi_inq_att(ncid2, NC_GLOBAL, name1, &type2, &attlen2);
HANDLE_ERROR
if (type1 != type2) {
if (!quiet) printf("DIFF: global attribute \"%s\" data type (%s) != (%s)\n",
name1,get_type(type1),get_type(type2));
numHeadDIFF++;
continue;
}
else if (verbose) {
printf("Global attribute \"%s\":\n",name1);
printf("\tSAME: data type (%s)\n",get_type(type1));
}
if (attlen1 != attlen2) {
if (!quiet) printf("DIFF: global attribute \"%s\" length (%lld) != (%lld)\n",
name1,attlen1,attlen2);
numHeadDIFF++;
continue;
}
else if (verbose)
printf("\tSAME: length (%lld)\n",attlen1);
switch (type1) {
case NC_CHAR: CHECK_GLOBAL_ATT_DIFF(char, ncmpi_get_att_text, NC_CHAR)
case NC_SHORT: CHECK_GLOBAL_ATT_DIFF(short, ncmpi_get_att_short, NC_SHORT)
case NC_INT: CHECK_GLOBAL_ATT_DIFF(int, ncmpi_get_att_int, NC_INT)
case NC_FLOAT: CHECK_GLOBAL_ATT_DIFF(float, ncmpi_get_att_float, NC_FLOAT)
case NC_DOUBLE: CHECK_GLOBAL_ATT_DIFF(double, ncmpi_get_att_double, NC_DOUBLE)
case NC_UBYTE: CHECK_GLOBAL_ATT_DIFF(ubyte, ncmpi_get_att_uchar, NC_UBYTE)
case NC_USHORT: CHECK_GLOBAL_ATT_DIFF(ushort, ncmpi_get_att_ushort, NC_USHORT)
case NC_UINT: CHECK_GLOBAL_ATT_DIFF(uint, ncmpi_get_att_uint, NC_UINT)
case NC_INT64: CHECK_GLOBAL_ATT_DIFF(int64, ncmpi_get_att_longlong, NC_INT64)
case NC_UINT64: CHECK_GLOBAL_ATT_DIFF(uint64, ncmpi_get_att_ulonglong, NC_UINT64)
default: ; /* TODO: handle unexpected types */
}
}
for (i=0; i<natts2; i++) { /* check attributes in file2 but not in file1 */
err = ncmpi_inq_attname(ncid2, NC_GLOBAL, i, name2);
HANDLE_ERROR
/* find the attr with the same name from ncid1 */
if (ncmpi_inq_attid(ncid1, NC_GLOBAL, name2, &attnump) == NC_ENOTATT) {
numHeadDIFF++;
if (!quiet) printf("DIFF: global attribute \"%s\" not found in file %s\n",
name1,argv[optind]);
}
}
/* Compare dimension */
if (ndims1 && verbose)
printf("Dimension:\n");
for (i=0; i<ndims1; i++) { /* check dimensions in file1 also in file2 */
int dimid;
err = ncmpi_inq_dim(ncid1, i, name1, &dimlen1);
HANDLE_ERROR
/* find the dim with the same name from ncid2 */
err = ncmpi_inq_dimid(ncid2, name1, &dimid);
if (err == NC_EBADDIM) {
if (!quiet) printf("DIFF: dimension \"%s\" not found in file %s\n",
name1,argv[optind+1]);
numHeadDIFF++;
continue;
}
err = ncmpi_inq_dimlen(ncid2, dimid, &dimlen2);
HANDLE_ERROR
if (dimlen1 != dimlen2) {
/* cast to quiet warning on 32 bit platforms */
if (!quiet) printf("DIFF: dimension \"%s\" length (%lld) != (%lld)\n",
name1,(long long int)dimlen1,(long long int)dimlen2);
numHeadDIFF++;
}
else if (verbose)
printf("\tSAME: dimension \"%s\" length (%lld)\n",
name1,(long long int)dimlen1);
}
for (i=0; i<ndims2; i++) { /* check dimensions in file2 but not in file1 */
int dimid;
err = ncmpi_inq_dim(ncid2, i, name2, &dimlen2);
HANDLE_ERROR
/* find the dim with the same name from ncid1 */
if (ncmpi_inq_dimid(ncid2, name1, &dimid) == NC_EBADDIM) {
if (!quiet) printf("DIFF: dimension \"%s\" not found in file %s\n",
name1,argv[optind]);
numHeadDIFF++;
}
}
/* Compare variables' metadata */
for (i=0; i<nvars1; i++) {
int varid;
err = ncmpi_inq_varndims(ncid1, i, &ndims1); HANDLE_ERROR
dimids1 = (int*) malloc((size_t)ndims1 * SIZEOF_INT);
if (!dimids1) OOM_ERROR
err = ncmpi_inq_var(ncid1, i, name1, &type1, &ndims1, dimids1, &natts1);
HANDLE_ERROR
/* find the variable with the same name from ncid2 */
err = ncmpi_inq_varid(ncid2, name1, &varid);
if (err == NC_ENOTVAR) {
if (!quiet) printf("DIFF: variable \"%s\" not found in file %s\n",
name1,argv[optind+1]);
numHeadDIFF++;
numVarDIFF++;
continue;
}
err = ncmpi_inq_varndims(ncid2, varid, &ndims2); HANDLE_ERROR
dimids2 = (int*) malloc((size_t)ndims2 * SIZEOF_INT);
if (!dimids2) OOM_ERROR
err = ncmpi_inq_var(ncid2, varid, name2, &type2, &ndims2, dimids2, &natts2);
HANDLE_ERROR
if (type1 != type2) {
if (!quiet) printf("DIFF: variable \"%s\" data type (%s) != (%s)\n",
name1,get_type(type1),get_type(type2));
numHeadDIFF++;
}
else if (verbose) {
printf("Variable \"%s\":\n",name1);
printf("\tSAME: data type (%s)\n",get_type(type1));
}
if (ndims1 != ndims2) {
if (!quiet) printf("DIFF: variable \"%s\" number of dimensions (%d) != (%d)\n",
name1,ndims1,ndims2);
numHeadDIFF++;
}
else {
if (verbose)
printf("\tSAME: number of dimensions (%d)\n",ndims1);
for (j=0; j<ndims1; j++) { /* check variable's dimensionality */
char dimname1[NC_MAX_NAME], dimname2[NC_MAX_NAME];
/* get dim name for each dim ID */
err = ncmpi_inq_dim(ncid1, dimids1[j], dimname1, &dimlen1);
HANDLE_ERROR
err = ncmpi_inq_dim(ncid1, dimids2[j], dimname2, &dimlen2);
HANDLE_ERROR
if (verbose)
printf("\tdimension %d:\n",j);
if (strcmp(dimname1, dimname2) != 0) {
if (!quiet) printf("DIFF: variable \"%s\" of type \"%s\" dimension %d's name (%s) != (%s)\n",
name1,get_type(type1),j,dimname1,dimname2);
numHeadDIFF++;
}
else if (verbose)
printf("\t\tSAME: name (%s)\n",dimname1);
if (dimlen1 != dimlen2) {
if (!quiet) printf("DIFF: variable \"%s\" of type \"%s\" dimension %d's length (%lld) != (%lld)\n",
name1,get_type(type1),j,(long long int)dimlen1,(long long int)dimlen2);
numHeadDIFF++;
}
else if (verbose)
printf("\t\tSAME: length (%lld)\n",(long long int)dimlen1);
}
}
if (natts1 != natts2) {
if (!quiet) printf("DIFF: variable \"%s\" number of attributes (%d) != (%d)\n",
name1,natts1,natts2);
numHeadDIFF++;
}
else if (verbose)
printf("\tSAME: number of attributes (%d)\n",natts1);
/* var attributes, assume CHAR attributes */
for (j=0; j<natts1; j++) {
char attrname[NC_MAX_NAME];
err = ncmpi_inq_attname(ncid1, i, j, attrname);
HANDLE_ERROR
err = ncmpi_inq_att(ncid1, i, attrname, &type1, &attlen1);
HANDLE_ERROR
/* find the variable attr with the same name from ncid2 */
err = ncmpi_inq_att(ncid2, varid, attrname, &type2, &attlen2);
if (err == NC_ENOTATT) {
if (!quiet) printf("DIFF: variable \"%s\" attribute \"%s\" not found in file %s\n",
name1,attrname,argv[optind+1]);
numHeadDIFF++;
continue;
}
if (verbose)
printf("\tattribute \"%s\":\n",attrname);
if (type1 != type2) {
if (!quiet) printf("DIFF: variable \"%s\" attribute \"%s\" data type (%s) != (%s)\n",
name1,attrname,get_type(type1),get_type(type2));
numHeadDIFF++;
continue; /* skip this attribute */
}
else if (verbose)
printf("\t\tSAME: data type (%s)\n",get_type(type1));
if (attlen1 != attlen2) {
if (!quiet) printf("DIFF: variable \"%s\" attribute \"%s\" length (%lld) != (%lld)\n",
name1,attrname,(long long int)attlen1,(long long int)attlen2);
numHeadDIFF++;
continue; /* skip this attribute */
}
else if (verbose)
printf("\t\tSAME: length (%lld)\n",(long long int)attlen1);
switch (type1) {
case NC_CHAR: CHECK_VAR_ATT_DIFF(char, ncmpi_get_att_text, NC_CHAR)
case NC_SHORT: CHECK_VAR_ATT_DIFF(short, ncmpi_get_att_short, NC_SHORT)
case NC_INT: CHECK_VAR_ATT_DIFF(int, ncmpi_get_att_int, NC_INT)
case NC_FLOAT: CHECK_VAR_ATT_DIFF(float, ncmpi_get_att_float, NC_FLOAT)
case NC_DOUBLE: CHECK_VAR_ATT_DIFF(double, ncmpi_get_att_double, NC_DOUBLE)
case NC_UBYTE: CHECK_VAR_ATT_DIFF(ubyte, ncmpi_get_att_uchar, NC_UBYTE)
case NC_USHORT: CHECK_VAR_ATT_DIFF(ushort, ncmpi_get_att_ushort, NC_USHORT)
case NC_UINT: CHECK_VAR_ATT_DIFF(uint, ncmpi_get_att_uint, NC_UINT)
case NC_INT64: CHECK_VAR_ATT_DIFF(int64, ncmpi_get_att_longlong, NC_INT64)
case NC_UINT64: CHECK_VAR_ATT_DIFF(uint64, ncmpi_get_att_ulonglong, NC_UINT64)
default: ; /* TODO: handle unexpected types */
}
}
for (j=0; j<natts2; j++) {
char attrname[NC_MAX_NAME];
err = ncmpi_inq_attname(ncid2, varid, j, attrname);
HANDLE_ERROR
/* find the variable attr with the same name from ncid1 */
err = ncmpi_inq_att(ncid1, i, attrname, &type1, &attlen1);
if (err == NC_ENOTATT) {
if (!quiet) printf("DIFF: variable \"%s\" attribute \"%s\" not found in file %s\n",
name1,attrname,argv[optind]);
numHeadDIFF++;
}
}
free(dimids1);
free(dimids2);
}
for (i=0; i<nvars2; i++) { /* check variables in file2 but not in file1 */
int varid;
err = ncmpi_inq_varname(ncid2, i, name2);
HANDLE_ERROR
/* find the variable with the same name from ncid1 */
err = ncmpi_inq_varid(ncid1, name2, &varid);
if (err == NC_ENOTVAR) {
if (!quiet) printf("DIFF: variable \"%s\" not found in file %s\n",
name2,argv[optind]);
numHeadDIFF++;
numVarDIFF++;
}
}
}