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netcdf-c/nczarr_test/test_zchunks2.c
Dennis Heimbigner df3636b959 Mitigate S3 test interference + Unlimited Dimensions in NCZarr 
This PR started as an attempt to add unlimited dimensions to NCZarr.
It did that, but this exposed significant problems with test interference.
So this PR is mostly about fixing -- well mitigating anyway -- test
interference.

The problem of test interference is now documented in the document docs/internal.md.
The solutions implemented here are also describe in that document.
The solution is somewhat fragile but multiple cleanup mechanisms
are provided. Note that this feature requires that the
AWS command line utility must be installed.

## Unlimited Dimensions.
The existing NCZarr extensions to Zarr are modified to support unlimited dimensions.
NCzarr extends the Zarr meta-data for the ".zgroup" object to include netcdf-4 model extensions. This information is stored in ".zgroup" as dictionary named "_nczarr_group".
Inside "_nczarr_group", there is a key named "dims" that stores information about netcdf-4 named dimensions. The value of "dims" is a dictionary whose keys are the named dimensions. The value associated with each dimension name has one of two forms
Form 1 is a special case of form 2, and is kept for backward compatibility. Whenever a new file is written, it uses format 1 if possible, otherwise format 2.
* Form 1: An integer representing the size of the dimension, which is used for simple named dimensions.
* Form 2: A dictionary with the following keys and values"
   - "size" with an integer value representing the (current) size of the dimension.
   - "unlimited" with a value of either "1" or "0" to indicate if this dimension is an unlimited dimension.

For Unlimited dimensions, the size is initially zero, and as variables extend the length of that dimension, the size value for the dimension increases.
That dimension size is shared by all arrays referencing that dimension, so if one array extends an unlimited dimension, it is implicitly extended for all other arrays that reference that dimension.
This is the standard semantics for unlimited dimensions.

Adding unlimited dimensions required a number of other changes to the NCZarr code-base. These included the following.
* Did a partial refactor of the slice handling code in zwalk.c to clean it up.
* Added a number of tests for unlimited dimensions derived from the same test in nc_test4.
* Added several NCZarr specific unlimited tests; more are needed.
* Add test of endianness.

## Misc. Other Changes
* Modify libdispatch/ncs3sdk_aws.cpp to optionally support use of the
   AWS Transfer Utility mechanism. This is controlled by the
   ```#define TRANSFER```` command in that file. It defaults to being disabled.
* Parameterize both the standard Unidata S3 bucket (S3TESTBUCKET) and the netcdf-c test data prefix (S3TESTSUBTREE).
* Fixed an obscure memory leak in ncdump.
* Removed some obsolete unit testing code and test cases.
* Uncovered a bug in the netcdf-c handling of big-endian floats and doubles. Have not fixed yet. See tst_h5_endians.c.
* Renamed some nczarr_tests testcases to avoid name conflicts with nc_test4.
* Modify the semantics of zmap\#ncsmap_write to only allow total rewrite of objects.
* Modify the semantics of zodom to properly handle stride > 1.
* Add a truncate operation to the libnczarr zmap code.
2023-09-26 16:56:48 -06:00

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/* This is part of the netCDF package.
Copyright 2018 University Corporation for Atmospheric Research/Unidata
See COPYRIGHT file for conditions of use.
Test netcdf-4 chunking.
Ed Hartnett, Dennis Heimbigner
modified version of nc_test4/tst_chunks2.c
*/
#include "ut_includes.h"
#include "test_nczarr_utils.h"
#define FILE_NAME "tst_chunks2"
#define MAX_WASTE 25.0
#define NUM_RANDOM_TESTS 3
#define NDIMS3 3
/* Calculate the waste of the chunking. A waste of 10% means the
* chunked data is 10% larger then the unchunked data. */
static int
calculate_waste(int ndims, size_t *dimlen, size_t *chunksize, float *waste)
{
int d;
float chunked = 1, unchunked = 1;
size_t *num_chunks;
size_t chunk_size = 1;
assert(waste && dimlen && chunksize && ndims);
if (!(num_chunks = calloc(ndims, sizeof(size_t)))) ERR;
#ifdef PRINT_CHUNK_WASTE_REPORT
printf("\n");
#endif
/* Caclulate the total space taken up by the chunked data. */
for (d = 0; d < ndims; d++)
{
/* How many chunks along this dimension are required to hold all the data? */
for (num_chunks[d] = 0; (num_chunks[d] * chunksize[d]) < (dimlen[d] ? dimlen[d] : 1);
num_chunks[d]++)
;
chunked *= (num_chunks[d] * chunksize[d]);
}
/* Calculate the minimum space required for this data
* (i.e. unchunked) or one record of it. */
for (d = 0; d < ndims; d++)
unchunked *= (dimlen[d] ? dimlen[d] : 1);
#ifdef PRINT_CHUNK_WASTE_REPORT
printf("size for unchunked %g elements; size for chunked %g elements\n",
unchunked, chunked);
#endif
/* Percent of the chunked file that is wasted space. */
*waste = ((float)(chunked - unchunked) / (float)chunked) * 100.0;
#ifdef PRINT_CHUNK_WASTE_REPORT
printf("\ndimlen\tchunksize\tnum_chunks\n");
#endif
for (d = 0; d < ndims; d++)
{
#ifdef PRINT_CHUNK_WASTE_REPORT
printf("%ld\t%ld\t\t%ld\n", (long int)dimlen[d], (long int)chunksize[d],
(long int)num_chunks[d]);
#endif
chunk_size *= chunksize[d];
}
#ifdef PRINT_CHUNK_WASTE_REPORT
printf("size of chunk: %ld elements; wasted space: %2.2f percent\n",
(long int)chunk_size, *waste);
#endif
free(num_chunks);
return 0;
}
int
main(int argc, char **argv)
{
processoptions(argc,argv,FILE_NAME);
printf("\n*** Testing netcdf-4 variable chunking.\n");
printf("**** testing default chunksizes...");
{
#define NDIMS3 3
#define NUM_VARS 1
#define Y_NAME "y"
#define X_NAME "x"
#define Z_NAME "z"
#define VAR_NAME_JOE "joe"
#define XDIM_LEN 2
#define YDIM_LEN 5
#define ZDIM_LEN 3000
int varid, ncid, dims[NDIMS3], dims_in[NDIMS3];
int ndims, nvars, ngatts, unlimdimid, natts;
char name_in[NC_MAX_NAME + 1];
nc_type type_in;
size_t len_in[NDIMS3];
int storage = 0;
size_t chunksizes[NDIMS3];
float waste = 0;
/* Create a file with 3D var, turn on chunking, but don't provide chunksizes. */
if (nc_create(itoptions.path, NC_NETCDF4 | NC_CLOBBER, &ncid)) ERR;
if (nc_def_dim(ncid, X_NAME, XDIM_LEN, &dims[0])) ERR;
if (nc_def_dim(ncid, Y_NAME, YDIM_LEN, &dims[1])) ERR;
if (nc_def_dim(ncid, Z_NAME, ZDIM_LEN, &dims[2])) ERR;
if (nc_def_var(ncid, VAR_NAME_JOE, NC_FLOAT, NDIMS3, dims, &varid)) ERR;
if (nc_def_var_chunking(ncid, 0, NC_CHUNKED, NULL)) ERR;
/* Check it out. */
if (nc_inq(ncid, &ndims, &nvars, &ngatts, &unlimdimid)) ERR;
if (nvars != NUM_VARS || ndims != NDIMS3 || ngatts != 0 || unlimdimid != -1) ERR;
if (nc_inq_var(ncid, 0, name_in, &type_in, &ndims, dims_in, &natts)) ERR;
if (strcmp(name_in, VAR_NAME_JOE) || type_in != NC_FLOAT || ndims != NDIMS3 ||
dims_in[0] != dims[0] || dims_in[1] != dims[1] || dims_in[2] != dims[2] || natts != 0) ERR;
if (nc_inq_dim(ncid, 0, name_in, &len_in[0])) ERR;
if (strcmp(name_in, X_NAME) || len_in[0] != XDIM_LEN) ERR;
if (nc_inq_dim(ncid, 1, name_in, &len_in[1])) ERR;
if (strcmp(name_in, Y_NAME) || len_in[1] != YDIM_LEN) ERR;
if (nc_inq_dim(ncid, 2, name_in, &len_in[2])) ERR;
if (strcmp(name_in, Z_NAME) || len_in[2] != ZDIM_LEN) ERR;
if (nc_inq_var_chunking(ncid, 0, &storage, chunksizes)) ERR;
if (storage != NC_CHUNKED) ERR;
if (nc_close(ncid)) ERR;
/* Open the file and check again. */
if (nc_open(itoptions.path, NC_WRITE, &ncid)) ERR;
if (nc_inq(ncid, &ndims, &nvars, &ngatts, &unlimdimid)) ERR;
if (nvars != NUM_VARS || ndims != NDIMS3 || ngatts != 0 || unlimdimid != -1) ERR;
if (nc_inq_var(ncid, 0, name_in, &type_in, &ndims, dims_in, &natts)) ERR;
if (strcmp(name_in, VAR_NAME_JOE) || type_in != NC_FLOAT || ndims != NDIMS3 ||
dims_in[0] != dims[0] || dims_in[1] != dims[1] || dims_in[2] != dims[2] || natts != 0) ERR;
if (nc_inq_dim(ncid, 0, name_in, &len_in[0])) ERR;
if (strcmp(name_in, X_NAME) || len_in[0] != XDIM_LEN) ERR;
if (nc_inq_dim(ncid, 1, name_in, &len_in[1])) ERR;
if (strcmp(name_in, Y_NAME) || len_in[1] != YDIM_LEN) ERR;
if (nc_inq_dim(ncid, 2, name_in, &len_in[2])) ERR;
if (strcmp(name_in, Z_NAME) || len_in[2] != ZDIM_LEN) ERR;
if (nc_inq_var_chunking(ncid, 0, &storage, chunksizes)) ERR;
if (storage != NC_CHUNKED) ERR;
if (calculate_waste(NDIMS3, len_in, chunksizes, &waste)) ERR;
/*if (waste > MAX_WASTE) ERR;*/
if (nc_close(ncid)) ERR;
}
SUMMARIZE_ERR;
printf("**** testing default chunksizes some more for a 3D var...");
{
#define NDIMS3 3
#define VAR_NAME "op-amp"
int varid, ncid;
int dimids[NDIMS3];
size_t dim_len[NDIMS3] = {1, 11, 152750};
int storage = 0;
size_t chunksizes[NDIMS3];
int d;
char dim_name[NC_MAX_NAME + 1];
float waste;
if (nc_create(itoptions.path, NC_NETCDF4 | NC_CLOBBER, &ncid)) ERR;
/* Create a few dimensions. */
for (d = 0; d < NDIMS3; d++)
{
sprintf(dim_name, "dim_%d", d);
if (nc_def_dim(ncid, dim_name, dim_len[d], &dimids[d])) ERR;
}
/* Define a var with these dimensions, and turn on chunking. */
if (nc_def_var(ncid, VAR_NAME, NC_FLOAT, NDIMS3, dimids, &varid)) ERR;
if (nc_def_var_chunking(ncid, varid, NC_CHUNKED, NULL)) ERR;
/* Check how default chunking worked. */
if (nc_inq_var_chunking(ncid, varid, &storage, chunksizes)) ERR;
if (storage != NC_CHUNKED) ERR;
if (calculate_waste(NDIMS3, dim_len, chunksizes, &waste)) ERR;
/* if (waste > MAX_WASTE) ERR;*/
if (nc_close(ncid)) ERR;
/* Open the file and check. */
if (nc_open(itoptions.path, NC_WRITE, &ncid)) ERR;
if (nc_close(ncid)) ERR;
}
SUMMARIZE_ERR;
printf("**** testing default chunksizes even more for a 3D var...");
{
int varid, ncid;
int dimids[NDIMS3];
size_t dim_len[NDIMS3] = {1804289383, 846930886, 1681692777};
int storage = 0;
size_t chunksizes[NDIMS3];
int d;
char dim_name[NC_MAX_NAME + 1];
float waste;
if (nc_create(itoptions.path, NC_NETCDF4 | NC_CLOBBER, &ncid)) ERR;
/* Create a few dimensions. */
for (d = 0; d < NDIMS3; d++)
{
sprintf(dim_name, "dim_%d", d);
if (nc_def_dim(ncid, dim_name, dim_len[d], &dimids[d])) ERR;
}
/* Define a var with these dimensions, and turn on chunking. */
if (nc_def_var(ncid, VAR_NAME, NC_FLOAT, NDIMS3, dimids, &varid)) ERR;
if (nc_def_var_chunking(ncid, varid, NC_CHUNKED, NULL)) ERR;
/* Check how default chunking worked. */
if (nc_inq_var_chunking(ncid, varid, &storage, chunksizes)) ERR;
if (storage != NC_CHUNKED) ERR;
if (calculate_waste(NDIMS3, dim_len, chunksizes, &waste)) ERR;
/* if (waste > MAX_WASTE) ERR;*/
if (nc_close(ncid)) ERR;
/* Open the file and check. */
if (nc_open(itoptions.path, NC_WRITE, &ncid)) ERR;
if (nc_close(ncid)) ERR;
}
SUMMARIZE_ERR;
printf("**** testing default chunksizes even even more for a 3D var...");
{
int varid, ncid;
int dimids[NDIMS3];
size_t dim_len[NDIMS3] = {1714636915, 1957747793, 424238335};
int storage = 0;
size_t chunksizes[NDIMS3];
int d;
char dim_name[NC_MAX_NAME + 1];
float waste;
if (nc_create(itoptions.path, NC_NETCDF4 | NC_CLOBBER, &ncid)) ERR;
/* Create a few dimensions. */
for (d = 0; d < NDIMS3; d++)
{
sprintf(dim_name, "dim_%d", d);
if (nc_def_dim(ncid, dim_name, dim_len[d], &dimids[d])) ERR;
}
/* Define a var with these dimensions, and turn on chunking. */
if (nc_def_var(ncid, VAR_NAME, NC_FLOAT, NDIMS3, dimids, &varid)) ERR;
if (nc_def_var_chunking(ncid, varid, NC_CHUNKED, NULL)) ERR;
/* Check how default chunking worked. */
if (nc_inq_var_chunking(ncid, varid, &storage, chunksizes)) ERR;
if (storage != NC_CHUNKED) ERR;
if (calculate_waste(NDIMS3, dim_len, chunksizes, &waste)) ERR;
/* if (waste > MAX_WASTE) ERR;*/
if (nc_close(ncid)) ERR;
/* Open the file and check. */
if (nc_open(itoptions.path, NC_WRITE, &ncid)) ERR;
if (nc_close(ncid)) ERR;
}
SUMMARIZE_ERR;
printf("**** testing default chunksizes some more for a 3D var...");
{
#define NDIMS3 3
#define VAR_NAME "op-amp"
int varid, ncid;
int dimids[NDIMS3];
size_t dim_len[NDIMS3] = {1967513926, 1365180540, 426};
int storage = 0;
size_t chunksizes[NDIMS3];
int d;
char dim_name[NC_MAX_NAME + 1];
float waste;
if (nc_create(itoptions.path, NC_NETCDF4 | NC_CLOBBER, &ncid)) ERR;
/* Create a few dimensions. */
for (d = 0; d < NDIMS3; d++)
{
sprintf(dim_name, "dim_%d", d);
if (nc_def_dim(ncid, dim_name, dim_len[d], &dimids[d])) ERR;
}
/* Define a var with these dimensions, and turn on chunking. */
if (nc_def_var(ncid, VAR_NAME, NC_FLOAT, NDIMS3, dimids, &varid)) ERR;
if (nc_def_var_chunking(ncid, varid, NC_CHUNKED, NULL)) ERR;
/* Check how default chunking worked. */
if (nc_inq_var_chunking(ncid, varid, &storage, chunksizes)) ERR;
if (storage != NC_CHUNKED) ERR;
if (calculate_waste(NDIMS3, dim_len, chunksizes, &waste)) ERR;
/* if (waste > MAX_WASTE) ERR;*/
if (nc_close(ncid)) ERR;
/* Open the file and check. */
if (nc_open(itoptions.path, NC_WRITE, &ncid)) ERR;
if (nc_close(ncid)) ERR;
}
SUMMARIZE_ERR;
printf("**** testing default chunksizes for very large 3D var...");
{
#define NDIMS3 3
int varid, ncid;
int dimids[NDIMS3];
size_t dim_len[NDIMS3] = {1804289383, 846930886, 1681692777};
int storage = 0;
size_t chunksizes[NDIMS3];
int d;
char dim_name[NC_MAX_NAME + 1];
float waste;
if (nc_create(itoptions.path, NC_NETCDF4 | NC_CLOBBER, &ncid)) ERR;
/* Create a few dimensions. */
for (d = 0; d < NDIMS3; d++)
{
sprintf(dim_name, "dim_%d", d);
if (nc_def_dim(ncid, dim_name, dim_len[d], &dimids[d])) ERR;
}
/* Define a var with these dimensions, and turn on chunking. */
if (nc_def_var(ncid, VAR_NAME, NC_FLOAT, NDIMS3, dimids, &varid)) ERR;
if (nc_def_var_chunking(ncid, varid, NC_CHUNKED, NULL)) ERR;
/* Check how default chunking worked. */
if (nc_inq_var_chunking(ncid, varid, &storage, chunksizes)) ERR;
if (storage != NC_CHUNKED) ERR;
if (calculate_waste(NDIMS3, dim_len, chunksizes, &waste)) ERR;
/* if (waste > MAX_WASTE) ERR;*/
if (nc_close(ncid)) ERR;
/* Open the file and check. */
if (nc_open(itoptions.path, NC_WRITE, &ncid)) ERR;
if (nc_close(ncid)) ERR;
}
SUMMARIZE_ERR;
printf("**** testing default chunksizes some randomly sized 3D vars...");
{
#define NDIMS3 3
int varid, ncid;
int dimids[NDIMS3];
size_t dim_len[NDIMS3];
int storage = 0;
size_t chunksizes[NDIMS3];
int d, t;
char dim_name[NC_MAX_NAME + 1];
float waste;
for (t = 0; t < NUM_RANDOM_TESTS; t++)
{
if (nc_create(itoptions.path, NC_NETCDF4 | NC_CLOBBER, &ncid)) ERR;
/* Create a few dimensions. */
for (d = 0; d < NDIMS3; d++)
{
dim_len[d] = rand();
sprintf(dim_name, "dim_%d", d);
if (nc_def_dim(ncid, dim_name, dim_len[d], &dimids[d])) ERR;
}
/* Define a var with these dimensions, and turn on chunking. */
if (nc_def_var(ncid, VAR_NAME, NC_FLOAT, NDIMS3, dimids, &varid)) ERR;
if (nc_def_var_chunking(ncid, varid, NC_CHUNKED, NULL)) ERR;
/* Check how well default chunking worked. */
if (nc_inq_var_chunking(ncid, varid, &storage, chunksizes)) ERR;
if (storage != NC_CHUNKED) ERR;
if (calculate_waste(NDIMS3, dim_len, chunksizes, &waste)) ERR;
if (waste > MAX_WASTE) ERR;
if (nc_close(ncid)) ERR;
}
}
SUMMARIZE_ERR;
printf("**** testing default chunksizes some randomly sized 3D vars, with one small dimension...");
{
int varid, ncid;
int dimids[NDIMS3];
size_t dim_len[NDIMS3];
int storage = 0;
size_t chunksizes[NDIMS3];
int d, t;
char dim_name[NC_MAX_NAME + 1];
float waste;
for (t = 0; t < NUM_RANDOM_TESTS; t++)
{
if (nc_create(itoptions.path, NC_NETCDF4 | NC_CLOBBER, &ncid)) ERR;
dim_len[0] = rand();
dim_len[1] = rand();
dim_len[2] = rand() % 1000;
/* Create a few dimensions. */
for (d = 0; d < NDIMS3; d++)
{
sprintf(dim_name, "dim_%d", d);
if (nc_def_dim(ncid, dim_name, dim_len[d], &dimids[d])) ERR;
}
/* Define a var with these dimensions, and turn on chunking. */
if (nc_def_var(ncid, VAR_NAME, NC_FLOAT, NDIMS3, dimids, &varid)) ERR;
if (nc_def_var_chunking(ncid, varid, NC_CHUNKED, NULL)) ERR;
/* Check how well default chunking worked. */
if (nc_inq_var_chunking(ncid, varid, &storage, chunksizes)) ERR;
if (storage != NC_CHUNKED) ERR;
if (calculate_waste(NDIMS3, dim_len, chunksizes, &waste)) ERR;
if (waste > MAX_WASTE) ERR;
if (nc_close(ncid)) ERR;
}
}
SUMMARIZE_ERR;
printf("**** testing default chunksizes some randomly sized 3D vars, with two small dimensions...");
{
int varid, ncid;
int dimids[NDIMS3];
size_t dim_len[NDIMS3];
int storage = 0;
size_t chunksizes[NDIMS3];
int d, t;
char dim_name[NC_MAX_NAME + 1];
float waste;
for (t = 0; t < NUM_RANDOM_TESTS; t++)
{
if (nc_create(itoptions.path, NC_NETCDF4 | NC_CLOBBER, &ncid)) ERR;
dim_len[0] = rand();
dim_len[1] = rand() % 1000;
dim_len[2] = rand() % 1000;
/* Create a few dimensions. */
for (d = 0; d < NDIMS3; d++)
{
sprintf(dim_name, "dim_%d", d);
if (nc_def_dim(ncid, dim_name, dim_len[d], &dimids[d])) ERR;
}
/* Define a var with these dimensions, and turn on chunking. */
if (nc_def_var(ncid, VAR_NAME, NC_FLOAT, NDIMS3, dimids, &varid)) ERR;
if (nc_def_var_chunking(ncid, varid, NC_CHUNKED, NULL)) ERR;
/* Check how well default chunking worked. */
if (nc_inq_var_chunking(ncid, varid, &storage, chunksizes)) ERR;
if (storage != NC_CHUNKED) ERR;
if (calculate_waste(NDIMS3, dim_len, chunksizes, &waste)) ERR;
if (waste > MAX_WASTE) ERR;
if (nc_close(ncid)) ERR;
}
}
clearoptions();
SUMMARIZE_ERR;
FINAL_RESULTS;
}
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