mirror/netcdf-c
2
0
Fork 0
mirror of https://github.com/Unidata/netcdf-c.git synced 2024-12-09 08:11:38 +08:00
Code Issues Packages Projects Releases Wiki Activity
9cc8831fc8
netcdf-c/nc_test4/tst_parallel5.c
Dennis Heimbigner 3ffe7be446 Enhance/Fix filter support 
re: Discussion https://github.com/Unidata/netcdf-c/discussions/2214

The primary change is to support so-called "standard filters".
A standard filter is one that is defined by the following
netcdf-c API:
````
int nc_def_var_XXX(int ncid, int varid, size_t nparams, unsigned* params);
int nc_inq_var_XXXX(int ncid, int varid, int* usefilterp, unsigned* params);
````
So for example, zstandard would be a standard filter by defining
the functions *nc_def_var_zstandard* and *nc_inq_var_zstandard*.

In order to define these functions, we need a new dispatch function:
````
int nc_inq_filter_avail(int ncid, unsigned filterid);
````
This function, combined with the existing filter API can be used
to implement arbitrary standard filters using a simple code pattern.
Note that I would have preferred that this function return a list
of all available filters, but HDF5 does not support that functionality.

So this PR implements the dispatch function and implements
the following standard functions:
    + bzip2
    + zstandard
    + blosc
Specific test cases are also provided for HDF5 and NCZarr.
Over time, other specific standard filters will be defined.

## Primary Changes
* Add nc_inq_filter_avail() to netcdf-c API.
* Add standard filter implementations to test use of *nc_inq_filter_avail*.
* Bump the dispatch table version number and add to all the relevant
   dispatch tables (libsrc, libsrcp, etc).
* Create a program to invoke nc_inq_filter_avail so that it is accessible
  to shell scripts.
* Cleanup szip support to properly support szip
  when HDF5 is disabled. This involves detecting
  libsz separately from testing if HDF5 supports szip.
* Integrate shuffle and fletcher32 into the existing
  filter API. This means that, for example, nc_def_var_fletcher32
  is now a wrapper around nc_def_var_filter.
* Extend the Codec defaulting to allow multiple default shared libraries.

## Misc. Changes
* Modify configure.ac/CMakeLists.txt to look for the relevant
  libraries implementing standard filters.
* Modify libnetcdf.settings to list available standard filters
  (including deflate and szip).
* Add CMake test modules to locate libbz2 and libzstd.
* Cleanup the HDF5 memory manager function use in the plugins.
* remove unused file include//ncfilter.h
* remove tests for the HDF5 memory operations e.g. H5allocate_memory.
* Add flag to ncdump to force use of _Filter instead of _Deflate
  or _Shuffle or _Fletcher32. Used for testing.
2022-03-14 12:39:37 -06:00

482 lines
17 KiB
C
Raw Blame History

/* Copyright 2018, UCAR/Unidata See COPYRIGHT file for copying and
* redistribution conditions.
*
* This program tests netcdf-4 parallel I/O.
*
* Ed Hartnett
*/
#include <nc_tests.h>
#include "err_macros.h"
#include <mpi.h>
#define FILE "tst_parallel5.nc"
#define VAR_NAME "TheIrishRover"
#define DIM_NAME "number_of_masts"
#define MASTS 27
#define NDIMS1 1
#define DIMSIZE 4
#define NUM_PROC 4
#define NUM_SLABS 10
#define NUM_ACCESS_TESTS 2
#define HDF5_DEFAULT_CACHE_SIZE 1048576
#define HDF5_DEFAULT_NELEMS 521
#define HDF5_DEFAULT_PREEMPTION 0.75
int
nc4_hdf5_get_chunk_cache(int ncid, size_t *sizep, size_t *nelemsp,
float *preemptionp);
int
main(int argc, char **argv)
{
int mpi_size, mpi_rank;
MPI_Comm comm = MPI_COMM_WORLD;
MPI_Info info = MPI_INFO_NULL;
int ncid, v1id, dimid;
size_t start[NDIMS1] = {0}, count[NDIMS1] = {0};
int data = MASTS;
int data_in = TEST_VAL_42;
int acc;
/* Initialize MPI. */
MPI_Init(&argc, &argv);
MPI_Comm_size(MPI_COMM_WORLD, &mpi_size);
MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank);
/* Require exactly 4 tasks. */
if (mpi_size != NUM_PROC) ERR;
if (!mpi_rank)
printf("\n*** Testing parallel I/O.\n");
if (!mpi_rank)
printf("*** testing whether we can write 0 elements from some tasks...");
{
for (acc = 0; acc < NUM_ACCESS_TESTS; acc++)
{
/* Create a parallel netcdf-4 file. */
/* nc_set_log_level(3); */
if (nc_create_par(FILE, NC_NETCDF4, comm, info, &ncid)) ERR;
/* Create a dimension. */
if (nc_def_dim(ncid, DIM_NAME, DIMSIZE, &dimid)) ERR;
/* Create one var. */
if (nc_def_var(ncid, VAR_NAME, NC_INT, NDIMS1, &dimid, &v1id)) ERR;
/* Write metadata to file. */
if (nc_enddef(ncid)) ERR;
/* Set up slab for this process. */
if (!mpi_rank)
count[0] = 1;
if (nc_var_par_access(ncid, v1id, acc ? NC_COLLECTIVE : NC_INDEPENDENT)) ERR;
/* Write phoney data. */
if (nc_put_vara_int(ncid, v1id, start, count, &data)) ERR;
if (nc_sync(ncid)) ERR;
/* Read phoney data. */
if (nc_get_vara_int(ncid, v1id, start, count, &data_in)) ERR;
/* Task 0 has MASTS, the others have data_in remaining, as
* initialized, at TEST_VAL_42. */
if (data_in != (mpi_rank ? TEST_VAL_42 : MASTS)) ERR;
/* Close the netcdf file. */
if (nc_close(ncid)) ERR;
/* nc_set_log_level(-1); */
}
}
if (!mpi_rank)
SUMMARIZE_ERR;
if (!mpi_rank)
printf("*** testing enum type and parallel I/O...");
{
for (acc = 0; acc < NUM_ACCESS_TESTS; acc++)
{
#define ENUM_NAME "cargo"
#define ENUM_VAR_NAME "in_the_hold_of_the_Irish_Rover"
#define NUM_ENUM_FIELDS 8
int typeid;
int f;
char field_name[NUM_ENUM_FIELDS][NC_MAX_NAME + 1] = {"bags of the best Sligo rags", "barrels of bones",
"bails of old nanny goats' tails", "barrels of stones",
"dogs", "hogs", "barrels of porter",
"sides of old blind horses hides"};
unsigned long long field_value[NUM_ENUM_FIELDS] = {1000000, 2000000, 3000000, 4000000,
5000000, 6000000, 7000000, 8000000};
unsigned long long data = 1000000, data_in = TEST_VAL_42;
/* Create a parallel netcdf-4 file. */
if (nc_create_par(FILE, NC_NETCDF4, comm, info, &ncid)) ERR;
/* Create a dimension. */
if (nc_def_dim(ncid, DIM_NAME, DIMSIZE, &dimid)) ERR;
/* Create an enum type. */
if (nc_def_enum(ncid, NC_UINT64, ENUM_NAME, &typeid)) ERR;
for (f = 0; f < NUM_ENUM_FIELDS; f++)
if (nc_insert_enum(ncid, typeid, field_name[f], &field_value[f])) ERR;
/* Create one var. */
if (nc_def_var(ncid, ENUM_VAR_NAME, typeid, NDIMS1, &dimid, &v1id)) ERR;
/* Write metadata to file. */
if (nc_enddef(ncid)) ERR;
/* Set up slab for this process. */
if (!mpi_rank)
count[0] = 1;
if (nc_var_par_access(ncid, v1id, acc ? NC_COLLECTIVE : NC_INDEPENDENT)) ERR;
/* Write phoney data. */
if (nc_put_vara(ncid, v1id, start, count, &data)) ERR;
if (nc_sync(ncid)) ERR;
/* Read phoney data. */
if (nc_get_vara(ncid, v1id, start, count, &data_in)) ERR;
/* Task 0 has 1000000, the others have data_in remaining, as
* initialized, at TEST_VAL_42. */
if (data_in != (mpi_rank ? TEST_VAL_42 : 1000000)) ERR;
/* Close the netcdf file. */
if (nc_close(ncid)) ERR;
}
}
if (!mpi_rank)
SUMMARIZE_ERR;
if (!mpi_rank)
printf("*** testing compound type and parallel I/O...");
{
for (acc = 0; acc < NUM_ACCESS_TESTS; acc++)
{
#define COMPOUND_NAME "crew_info"
#define COMPOUND_VAR_NAME "whale_of_a_crew"
#define NUM_CREW 5
#define CREW_DIM_NAME "number_of_crew"
int typeid;
struct crew
{
char name[NC_MAX_NAME + 1];
char description[NC_MAX_NAME + 1];
char origin[NC_MAX_NAME + 1];
int age;
};
struct crew data = {"Mick McCann", "the skipper of the Irish Rover",
"from the banks of the Bann", 42};
struct crew data_in = {"", "", "", -42};
int dim_size = NC_MAX_NAME + 1;
/* Create a parallel netcdf-4 file. */
if (nc_create_par(FILE, NC_NETCDF4, comm, info, &ncid)) ERR;
/* Create a dimension. */
if (nc_def_dim(ncid, CREW_DIM_NAME, NUM_CREW, &dimid)) ERR;
/* Create a compound type. */
if (nc_def_compound(ncid, sizeof(struct crew), COMPOUND_NAME, &typeid)) ERR;
if (nc_insert_array_compound(ncid, typeid, "name", NC_COMPOUND_OFFSET(struct crew, name), NC_CHAR, 1, &dim_size)) ERR;
if (nc_insert_array_compound(ncid, typeid, "description", NC_COMPOUND_OFFSET(struct crew, description), NC_CHAR, 1, &dim_size)) ERR;
if (nc_insert_array_compound(ncid, typeid, "origin", NC_COMPOUND_OFFSET(struct crew, origin), NC_CHAR, 1, &dim_size)) ERR;
if (nc_insert_compound(ncid, typeid, "age", NC_COMPOUND_OFFSET(struct crew, age), NC_INT)) ERR;
/* Create one var. */
if (nc_def_var(ncid, COMPOUND_VAR_NAME, typeid, NDIMS1, &dimid, &v1id)) ERR;
/* Write metadata to file. */
if (nc_enddef(ncid)) ERR;
/* Set up slab for this process. */
if (!mpi_rank)
count[0] = 1;
if (nc_var_par_access(ncid, v1id, acc ? NC_COLLECTIVE : NC_INDEPENDENT)) ERR;
/* Write phoney data. */
if (nc_put_vara(ncid, v1id, start, count, &data)) ERR;
if (nc_sync(ncid)) ERR;
/* Read phoney data. */
if (nc_get_vara(ncid, v1id, start, count, &data_in)) ERR;
/* Task 0 has data, the others have nothing. */
if (!mpi_rank)
{
if (strcmp(data_in.name, data.name) || strcmp(data_in.description, data.description) ||
strcmp(data_in.origin, data.origin) || data_in.age != data.age) ERR;
}
else
{
if (strcmp(data_in.name, "") || strcmp(data_in.description, "") ||
strcmp(data_in.origin, "") || data_in.age != -42) ERR;
}
/* Close the netcdf file. */
if (nc_close(ncid)) ERR;
}
}
if (!mpi_rank)
SUMMARIZE_ERR;
if (!mpi_rank)
printf("*** testing string type and parallel I/O...");
{
for (acc = 0; acc < NUM_ACCESS_TESTS; acc++)
{
#define STORY_VAR_NAME "fate_of_the_Irish_Rover"
#define STORY_DIM_NAME "number_of_lines"
#define STORY_LEN 8
char *story[STORY_LEN] = {"We had sailed seven years when the measles broke out",
"And the ship lost it's way in the fog",
"And that whale of the crew was reduced down to two",
"Just myself and the captain's old dog",
"Then the ship struck a rock, oh Lord what a shock",
"The bulkhead was turned right over",
"Turned nine times around, and the poor dog was drowned",
"I'm the last of the Irish Rover"};
char *story_in[STORY_LEN];
int s;
/* Create a netcdf-4 file. Turns out that HDF5 does not
* support VLEN writes with parallel I/O. Strings are
* VLENS. So here I write a file with task 0 and then read it
* with all tasks. */
if (!mpi_rank)
{
if (nc_create(FILE, NC_NETCDF4, &ncid)) ERR;
/* Create a dimension. */
if (nc_def_dim(ncid, STORY_DIM_NAME, STORY_LEN, &dimid)) ERR;
/* Create one var. */
if (nc_def_var(ncid, STORY_VAR_NAME, NC_STRING, NDIMS1, &dimid, &v1id)) ERR;
/* Write metadata to file. */
if (nc_enddef(ncid)) ERR;
/* Set up slab for this process. */
count[0] = STORY_LEN;
/* Write phoney data. */
if (nc_put_vara(ncid, v1id, start, count, story)) ERR;
/* Close the netcdf file. */
if (nc_close(ncid)) ERR;
}
/* Now try parallel read. */
if (nc_open_par(FILE, 0, comm, info, &ncid)) ERR;
/* Task 0 reads all 8 lines, other tasks read 0. */
if (nc_get_vara(ncid, v1id, start, count, story_in)) ERR;
if (!mpi_rank)
{
for (s = 0; s < STORY_LEN; s++)
if (strcmp(story_in[s], story[s])) ERR;
if (nc_free_string(STORY_LEN, (char **)story_in)) ERR;
}
/* Close the netcdf file. */
if (nc_close(ncid)) ERR;
}
}
if (!mpi_rank)
SUMMARIZE_ERR;
if (!mpi_rank)
printf("*** testing NC_BYTE type and parallel I/O...");
{
/* This test is related to
* https://github.com/Unidata/netcdf-c/issues/1462. */
int ncid, varid;
signed char test_data_in, test_data = 42;
/* Crate a file with a scalar NC_BYTE value. */
if (nc_create_par(FILE, NC_NETCDF4, MPI_COMM_WORLD, MPI_INFO_NULL,
&ncid)) ERR;
if (nc_def_var(ncid, VAR_NAME, NC_BYTE, 0, NULL, &varid)) ERR;
if (nc_enddef(ncid)) ERR;
if (nc_put_var_schar(ncid, varid, &test_data)) ERR;
if (nc_close(ncid)) ERR;
/* Reopen the file and check. */
if (nc_open_par(FILE, 0, comm, info, &ncid)) ERR;
if (nc_get_var_schar(ncid, varid, &test_data_in)) ERR;
if (test_data_in != test_data) ERR;
if (nc_close(ncid)) ERR;
}
if (!mpi_rank)
SUMMARIZE_ERR;
if (!mpi_rank)
printf("*** testing cache settings for sequentially-opened files...");
{
/* This test is related to
* https://github.com/Unidata/netcdf-c/issues/1715. */
int ncid;
size_t size, nelems;
float preemption;
/* Create a file with parallel I/O and check cache settings. */
if (nc_create_par(FILE, NC_NETCDF4|NC_CLOBBER, MPI_COMM_WORLD, MPI_INFO_NULL,
&ncid)) ERR;
if (nc4_hdf5_get_chunk_cache(ncid, &size, &nelems, &preemption)) ERR;
if (size != HDF5_DEFAULT_CACHE_SIZE || nelems != HDF5_DEFAULT_NELEMS ||
preemption != HDF5_DEFAULT_PREEMPTION) ERR;
/* printf("%ld %ld %g\n", size, nelems, preemption); */
if (nc_close(ncid)) ERR;
/* Create a file with sequential I/O and check cache settings
* on processor 0. Now, instead of being set to the HDF5
* defaults, the chunk settings are set to the netCDF
* defaults. */
if (!mpi_rank)
{
if (nc_create(FILE, NC_NETCDF4|NC_CLOBBER, &ncid)) ERR;
if (nc4_hdf5_get_chunk_cache(ncid, &size, &nelems, &preemption)) ERR;
/* printf("%ld %ld %g\n", size, nelems, preemption); */
if (size != CHUNK_CACHE_SIZE || nelems != CHUNK_CACHE_NELEMS ||
preemption != CHUNK_CACHE_PREEMPTION) ERR;
if (nc_close(ncid)) ERR;
}
/* Reopen the file and check. */
if (nc_open_par(FILE, 0, comm, info, &ncid)) ERR;
if (nc4_hdf5_get_chunk_cache(ncid, &size, &nelems, &preemption)) ERR;
if (size != HDF5_DEFAULT_CACHE_SIZE || nelems != HDF5_DEFAULT_NELEMS ||
preemption != HDF5_DEFAULT_PREEMPTION) ERR;
if (nc_close(ncid)) ERR;
/* Open the file with sequential I/O and check cache settings
* on processor 0. Now, instead of being set to the HDF5
* defaults, the chunk settings are set to the netCDF
* defaults. */
if (!mpi_rank)
{
if (nc_open(FILE, 0, &ncid)) ERR;
if (nc4_hdf5_get_chunk_cache(ncid, &size, &nelems, &preemption)) ERR;
if (size != CHUNK_CACHE_SIZE || nelems != CHUNK_CACHE_NELEMS ||
preemption != CHUNK_CACHE_PREEMPTION) ERR;
if (nc_close(ncid)) ERR;
}
}
if (!mpi_rank)
SUMMARIZE_ERR;
#ifdef HAVE_H5Z_SZIP
#ifdef HDF5_SUPPORTS_PAR_FILTERS
#define SZIP_DIM_LEN 256
#define SZIP_DIM_NAME "Barrels"
#define SZIP_VAR_NAME "Best_Sligo_Rags"
#define SZIP_PIXELS_PER_BLOCK 32
if (!mpi_rank)
printf("*** testing szip compression with parallel I/O...");
{
int ncid, dimid, varid;
float *data;
float *data_in;
int elements_per_pe = SZIP_DIM_LEN/mpi_size;
size_t start[NDIMS1], count[NDIMS1];
int i;
/* Create test data. */
if (!(data = malloc(elements_per_pe * sizeof(float)))) ERR;
for (i = 0; i < elements_per_pe; i++)
data[i] = mpi_rank + i * 0.1;
/* Crate a file with a scalar NC_BYTE value. */
if (nc_create_par(FILE, NC_NETCDF4, MPI_COMM_WORLD, MPI_INFO_NULL,
&ncid)) ERR;
if (nc_def_dim(ncid, SZIP_DIM_NAME, SZIP_DIM_LEN, &dimid)) ERR;
if (nc_def_var(ncid, SZIP_VAR_NAME, NC_FLOAT, NDIMS1, &dimid, &varid)) ERR;
if (nc_def_var_szip(ncid, varid, H5_SZIP_NN_OPTION_MASK,
SZIP_PIXELS_PER_BLOCK)) ERR;
if (nc_enddef(ncid)) ERR;
start[0] = mpi_rank * elements_per_pe;
count[0] = elements_per_pe;
if (nc_put_vara_float(ncid, varid, start, count, data)) ERR;
if (nc_close(ncid)) ERR;
/* Reopen the file and check. */
if (nc_open_par(FILE, 0, comm, info, &ncid)) ERR;
if (!(data_in = malloc(elements_per_pe * sizeof(float)))) ERR;
if (nc_get_vara_float(ncid, varid, start, count, data_in)) ERR;
if (nc_close(ncid)) ERR;
for (i = 0; i < elements_per_pe; i++)
if (data_in[i] != data[i]) ERR;
/* Release resources. */
free(data_in);
free(data);
}
if (!mpi_rank)
SUMMARIZE_ERR;
#endif /* HDF5_SUPPORTS_PAR_FILTERS */
#endif /* HAVE_H5Z_SZIP */
#ifdef HAVE_H5Z_SZIP
#ifdef HDF5_SUPPORTS_PAR_FILTERS
#define SZIP_DIM_LEN 256
#define SZIP_DIM_NAME "Barrels"
#define SZIP_VAR_NAME "Best_Sligo_Rags"
#define SZIP_PIXELS_PER_BLOCK 32
if (!mpi_rank)
printf("*** testing szip compression with parallel I/O...");
{
int ncid, dimid, varid;
float *data;
float *data_in;
int elements_per_pe = SZIP_DIM_LEN/mpi_size;
size_t start[NDIMS1], count[NDIMS1];
int i;
/* Create test data. */
if (!(data = malloc(elements_per_pe * sizeof(float)))) ERR;
for (i = 0; i < elements_per_pe; i++)
data[i] = mpi_rank + i * 0.1;
/* Crate a file with a scalar NC_BYTE value. */
if (nc_create_par(FILE, NC_NETCDF4, MPI_COMM_WORLD, MPI_INFO_NULL,
&ncid)) ERR;
if (nc_def_dim(ncid, SZIP_DIM_NAME, SZIP_DIM_LEN, &dimid)) ERR;
if (nc_def_var(ncid, SZIP_VAR_NAME, NC_FLOAT, NDIMS1, &dimid, &varid)) ERR;
if (nc_def_var_szip(ncid, varid, NC_SZIP_NN, SZIP_PIXELS_PER_BLOCK)) ERR;
if (nc_enddef(ncid)) ERR;
start[0] = mpi_rank * elements_per_pe;
count[0] = elements_per_pe;
if (nc_put_vara_float(ncid, varid, start, count, data));
if (nc_close(ncid)) ERR;
/* Reopen the file and check. */
if (nc_open_par(FILE, 0, comm, info, &ncid)) ERR;
if (!(data_in = malloc(elements_per_pe * sizeof(float)))) ERR;
if (nc_get_vara_float(ncid, varid, start, count, data_in));
if (nc_close(ncid)) ERR;
for (i = 0; i < elements_per_pe; i++)
if (data_in[i] != data[i]) ERR;
/* Release resources. */
free(data_in);
free(data);
}
if (!mpi_rank)
SUMMARIZE_ERR;
#endif /* HDF5_SUPPORTS_PAR_FILTERS */
#endif /* HAVE_H5Z_SZIP */
/* Shut down MPI. */
MPI_Finalize();
if (!mpi_rank)
FINAL_RESULTS;
return 0;
}
Reference in New Issue View Git Blame Copy Permalink