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Support SWMR in HDF5 #1448

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Support SWMR in HDF5 #1448

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633182a
Initial implementation
eivindlm Jul 10, 2019
757207f
Move up call to flush
eivindlm Jul 31, 2019
ba9362a
Merge branch 'master' into hdf5_swmr
eivindlm Jul 31, 2019
932d6e0
Expand test
eivindlm Jul 31, 2019
f0f3543
Add flag H5F_ACC_SWMR_WRITE to H5Fcreate if we do not have H5P_set_li…
eivindlm Jul 31, 2019
cd4cd05
Protect usage of swmr by ifdefs
eivindlm Aug 6, 2019
9a4e0b5
Merge branch 'master' into hdf5_swmr
eivindlm Aug 6, 2019
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9 changes: 9 additions & 0 deletions CMakeLists.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -496,6 +496,8 @@ IF(ENABLE_HDF4)
ENDIF()
ENDIF()

OPTION(ENABLE_HDF5_SWMR "Support SWMR in HDF5. This requires HDF version 1.10 or later" OFF)

# Option to Build DLL
IF(WIN32)
OPTION(ENABLE_DLL "Build a Windows DLL." ${BUILD_SHARED_LIBS})
Expand Down Expand Up @@ -629,6 +631,10 @@ IF(USE_HDF5 OR ENABLE_NETCDF_4)
# Assert HDF5 version meets minimum required version.
##
SET(HDF5_VERSION_REQUIRED 1.8.10)
IF(ENABLE_HDF5_SWMR_SUPPORT)
SET(HDF5_VERSION_REQUIRED 1.10)
MESSAGE(STATUS "HDF5 SWMR is enabled. This implies that HDF5 version at least ${HDF5_VERSION_REQUIRED} is required.")
ENDIF()

IF(HDF5_VERSION_STRING AND NOT HDF5_VERSION)
SET(HDF5_VERSION ${HDF5_VERSION_STRING})
Expand All @@ -642,6 +648,9 @@ IF(USE_HDF5 OR ENABLE_NETCDF_4)
"netCDF requires at least HDF5 ${HDF5_VERSION_REQUIRED}. Found ${HDF5_VERSION}.")
ELSE()
MESSAGE(STATUS "Found HDF5 libraries version ${HDF5_VERSION}")
IF(ENABLE_HDF5_SWMR_SUPPORT)
ADD_DEFINITIONS(-DHDF5_HAS_SWMR)
ENDIF()
ENDIF()
ENDIF()

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1 change: 1 addition & 0 deletions include/netcdf.h
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Expand Up @@ -159,6 +159,7 @@ Use this in mode flags for both nc_create() and nc_open(). */

#define NC_PERSIST 0x4000 /**< Save diskless contents to disk. Mode flag for nc_open() or nc_create() */
#define NC_INMEMORY 0x8000 /**< Read from memory. Mode flag for nc_open() or nc_create() */
#define NC_HDF5_SWMR 0x2000 /** Reuse deprecated MPIIO flag for SWMR **/

#define NC_MAX_MAGIC_NUMBER_LEN 8 /**< Max len of user-defined format magic number. */

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35 changes: 31 additions & 4 deletions libhdf5/hdf5create.c
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Expand Up @@ -51,6 +51,10 @@ nc4_create_file(const char *path, int cmode, size_t initialsz,
NC_HDF5_FILE_INFO_T *hdf5_info;
NC_HDF5_GRP_INFO_T *hdf5_grp;

#ifdef HAVE_H5PSET_LIBVER_BOUNDS
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Do we ever not have H5PSET_LIBVER_BOUNDS?

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It was introduced in HDF5-1.8.0

H5F_libver_t low, high;
#endif

#ifdef USE_PARALLEL4
NC_MPI_INFO *mpiinfo = NULL;
MPI_Comm comm;
Expand Down Expand Up @@ -105,6 +109,13 @@ nc4_create_file(const char *path, int cmode, size_t initialsz,
else
flags = H5F_ACC_TRUNC;

#ifdef HDF5_HAS_SWMR
#ifndef HAVE_H5PSET_LIBVER_BOUNDS
if (cmode & NC_HDF5_SWMR)
flags |= H5F_ACC_SWMR_WRITE;
#endif
#endif

/* If this file already exists, and NC_NOCLOBBER is specified,
return an error (unless diskless|inmemory) */
if (!nc4_info->mem.diskless && !nc4_info->mem.inmemory) {
Expand Down Expand Up @@ -158,12 +169,20 @@ nc4_create_file(const char *path, int cmode, size_t initialsz,

#ifdef HAVE_H5PSET_LIBVER_BOUNDS
#if H5_VERSION_GE(1,10,2)
if (H5Pset_libver_bounds(fapl_id, H5F_LIBVER_EARLIEST, H5F_LIBVER_V18) < 0)
low = H5F_LIBVER_EARLIEST;
high = H5F_LIBVER_V18;
#ifdef HDF5_HAS_SWMR
if ((cmode & NC_HDF5_SWMR)) {
low = H5F_LIBVER_LATEST;
high = H5F_LIBVER_LATEST;
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Will this create files that are unreadable by older versions of HDF5?

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Note that H5F_LIBVER_V18 was introduced in 1.10.2 so maybe the HAVE_H5PSET_LIBVER_BOUNDS is checking for that version and not for existance of H5Pset_libver_bounds

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I think that the files will be unreadable with 1.8.X clients. Here is a blurb from 1.10.2 release notes:

When it is used in application linked with HDF5 1.10.0, it will enable new chunk indexing for Single Writer/Multiple Reader (SWMR) access and Virtual Dataset storage.

What does this change mean to an HDF5 application?
When an HDF5 application linked with HDF5 1.10.2 specifies H5F_LIBVER_LATEST as a value for the “high” parameter, the application may produce files that are not compatible with the HDF5 1.8.* file format. For example, new chunk indexing will be used that was not known to HDF5 1.8.. This means that an application linked with HDF5 1.8. libraries may not be able to read such files.

When an HDF5 application linked with HDF5 1.10.2 specifies H5F_LIBVER_V18 as a value for the “high” parameter, the application will produce files fully compatible with HDF5 1.8., meaning that any application linked with the HDF5 1.8. libraries will be able to read such files.

}
#endif /* HDF5_HAS_SWMR */
#else
if (H5Pset_libver_bounds(fapl_id, H5F_LIBVER_EARLIEST,
H5F_LIBVER_LATEST) < 0)
low = H5F_LIBVER_EARLIEST;
high = H5F_LIBVER_LATEST;
#endif
BAIL(NC_EHDFERR);
if (H5Pset_libver_bounds(fapl_id, low, high) < 0)
BAIL(NC_EHDFERR);
#endif

/* Create the property list. */
Expand Down Expand Up @@ -238,6 +257,14 @@ nc4_create_file(const char *path, int cmode, size_t initialsz,
if ((retval = NC4_new_provenance(nc4_info)))
BAIL(retval);

#ifdef HDF5_HAS_SWMR
if ((cmode & NC_HDF5_SWMR)) {
/* Prepare for single writer multiple readers */
if ((retval = H5Fstart_swmr_write(hdf5_info->hdfid)))
BAIL(retval);
}
#endif

return NC_NOERR;

exit: /*failure exit*/
Expand Down
20 changes: 19 additions & 1 deletion libhdf5/hdf5open.c
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Expand Up @@ -658,7 +658,16 @@ nc4_open_file(const char *path, int mode, void* parameters, int ncid)
assert(nc && nc->model->impl == NC_FORMATX_NC4);

/* Determine the HDF5 open flag to use. */
flags = (mode & NC_WRITE) ? H5F_ACC_RDWR : H5F_ACC_RDONLY;
if((mode & NC_WRITE)) {
flags = H5F_ACC_RDWR;
} else {
flags = H5F_ACC_RDONLY;
#ifdef HDF5_HAS_SWMR
if((mode & NC_HDF5_SWMR)) {
flags |= H5F_ACC_SWMR_READ;
}
#endif
}

/* Add necessary structs to hold netcdf-4 file data. */
if ((retval = nc4_nc4f_list_add(nc, path, mode)))
Expand Down Expand Up @@ -835,6 +844,15 @@ nc4_open_file(const char *path, int mode, void* parameters, int ncid)
if (H5Pclose(fapl_id) < 0)
BAIL(NC_EHDFERR);

#ifdef HDF5_HAS_SWMR
/* Prepare for single writer multiple reader. */
if (mode & NC_WRITE && mode & NC_HDF5_SWMR) {
if ((retval = H5Fstart_swmr_write(h5->hdfid))) {
BAIL(retval);
}
}
#endif

return NC_NOERR;

exit:
Expand Down
7 changes: 7 additions & 0 deletions libhdf5/hdf5var.c
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Expand Up @@ -1736,6 +1736,12 @@ NC4_put_vars(int ncid, int varid, const size_t *startp, const size_t *countp,
mem_spaceid, file_spaceid, xfer_plistid, bufr) < 0)
BAIL(NC_EHDFERR);

#ifdef HDF5_HAS_SWMR
/* Flush data for SWMR */
if (H5Dflush(hdf5_var->hdf_datasetid) < 0)
BAIL(NC_EHDFERR);
#endif

/* Remember that we have written to this var so that Fill Value
* can't be set for it. */
if (!var->written_to)
Expand Down Expand Up @@ -1764,6 +1770,7 @@ NC4_put_vars(int ncid, int varid, const size_t *startp, const size_t *countp,
return retval;
if (range_error)
return NC_ERANGE;

return NC_NOERR;
}

Expand Down
73 changes: 73 additions & 0 deletions nc_test4/tst_files.c
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Expand Up @@ -292,6 +292,79 @@ main(int argc, char **argv)
if (nc_close(ncid)) ERR;
}
SUMMARIZE_ERR;
#ifdef HDF5_HAS_SWMR
printf("*** testing HDF5 SWMR...");
{
#define DATA_LEN 3

int ncid, ncid2, varid, dimids[2];
size_t time_len, beam_len;
int i;
int values[DATA_LEN];
size_t start[2] = {0,0}, count[2] = {1, DATA_LEN};

/* Initialize some phony data. */
for (i = 0; i < DATA_LEN; i++)
values[i] = DATA_LEN*2 - i;

/* Create a file in SWMR mode for writing, create structure and close. */
if (nc_create(FILE_NAME, NC_NETCDF4|NC_HDF5_SWMR, &ncid)) ERR;
if (nc_def_dim(ncid, "time", NC_UNLIMITED, &dimids[0])) ERR;
if (nc_def_dim(ncid, "beam", NC_UNLIMITED, &dimids[1])) ERR;
if (nc_def_var(ncid, "depth", NC_INT, 2, dimids, &varid)) ERR;
if (nc_close(ncid)) ERR;

/* Open the file for SWMR reading and close. */
if (nc_open(FILE_NAME, NC_HDF5_SWMR, &ncid)) ERR;
if (nc_close(ncid)) ERR;

/* Open the file for SWMR writing, append data, and close. */
if (nc_open(FILE_NAME, NC_WRITE|NC_HDF5_SWMR, &ncid)) ERR;
if (nc_inq_varid(ncid, "depth", &varid)) ERR;
if (nc_put_vara_int(ncid, varid, start, count, values)) ERR;
if (nc_inq_dimlen(ncid, dimids[0], &time_len)) ERR;
if (time_len != 1) ERR;
if (nc_inq_dimlen(ncid, dimids[1], &beam_len)) ERR;
if (beam_len != DATA_LEN) ERR;
if (nc_close(ncid)) ERR;

/* Open the file for SWMR reading, verify data, and close. */
if (nc_open(FILE_NAME, NC_HDF5_SWMR, &ncid)) ERR;
if (nc_inq_varid(ncid, "depth", &varid)) ERR;
if (nc_put_vara_int(ncid, varid, start, count, values) == 0) ERR; // Writing should fail
if (nc_inq_dimlen(ncid, dimids[0], &time_len)) ERR;
if (time_len != 1) ERR;
if (nc_inq_dimlen(ncid, dimids[1], &beam_len)) ERR;
if (beam_len != DATA_LEN) ERR;
if (nc_close(ncid)) ERR;

/* Append data to the file from one writer (ncid1) and verify from a reader (ncid2) */
if (nc_open(FILE_NAME, NC_WRITE|NC_HDF5_SWMR, &ncid)) ERR;
if (nc_open(FILE_NAME, NC_HDF5_SWMR, &ncid2)) ERR;

// Verify length of time dimension == 1 in both reader and writer
if (nc_inq_dimlen(ncid, dimids[0], &time_len)) ERR;
if (time_len != 1) ERR;
if (nc_inq_dimlen(ncid2, dimids[0], &time_len)) ERR;
if (time_len != 1) ERR;

// Append data
start[0] = 1; start[1] = 0;
if (nc_inq_varid(ncid, "depth", &varid)) ERR;
if (nc_put_vara_int(ncid, varid, start, count, values)) ERR;

// Verify length of time dimension == 2 in both reader and writer
if (nc_inq_dimlen(ncid, dimids[0], &time_len)) ERR;
if (time_len != 2) ERR;
if (nc_inq_dimlen(ncid2, dimids[0], &time_len)) ERR;
if (time_len != 2) ERR;

if (nc_close(ncid)) ERR;
if (nc_close(ncid2)) ERR;

}
SUMMARIZE_ERR;
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Excellent test, thanks!

#endif /* HDF_HAS_SWMR */
printf("*** testing CLASSIC_MODEL flag with classic formats...");
{
int ncid;
Expand Down