diff --git a/INSTALL.swift b/INSTALL.swift
index 12e7372509601d74cbe8252cba3767c71ed0bc39..bafa8b7c236dd8f7a8d0c97b79b444de4e727e32 100644
--- a/INSTALL.swift
+++ b/INSTALL.swift
@@ -99,7 +99,7 @@ before you can build it.
- HDF5:
- A HDF5 library (v. 1.8.x or higher) is required to read and
+ A HDF5 library (v. 1.10.x or higher) is required to read and
write particle data. One of the commands "h5cc" or "h5pcc"
should be available. If "h5pcc" is located then a parallel
HDF5 built for the version of MPI located should be
diff --git a/doc/RTD/source/GettingStarted/compiling_code.rst b/doc/RTD/source/GettingStarted/compiling_code.rst
index 26a3b940888ba9103180e920ab0f623ad97bf3cc..9498fe90392b1420b2172bfa35b3febfd40a9874 100644
--- a/doc/RTD/source/GettingStarted/compiling_code.rst
+++ b/doc/RTD/source/GettingStarted/compiling_code.rst
@@ -31,10 +31,10 @@ To compile SWIFT, you will need the following libraries:
HDF5
~~~~
-Version 1.8.x or higher is required. Input and output files are stored as HDF5
+Version 1.10.x or higher is required. Input and output files are stored as HDF5
and are compatible with the existing GADGET-2 specification. Please consider
using a build of parallel-HDF5, as SWIFT can leverage this when writing and
-reading snapshots. We recommend using HDF5 > 1.10.x as this is *vastly superior*
+reading snapshots. We recommend using HDF5 >= 1.12.x as this is *vastly superior*
in parallel.
HDF5 is widely available through system package managers.
diff --git a/doc/onboardingGuide/source/dependencies.rst b/doc/onboardingGuide/source/dependencies.rst
index 217e02d7c0b12e4b8a499b2ac01e3c5e6ba27593..33d64eaa3ca476ed180a13cad0ac92b0ad5992de 100644
--- a/doc/onboardingGuide/source/dependencies.rst
+++ b/doc/onboardingGuide/source/dependencies.rst
@@ -8,9 +8,9 @@ To compile SWIFT, you will need the following libraries:
HDF5
~~~~
-Version 1.8.x or higher is required. Input and output files are stored as HDF5
+Version 1.10.x or higher is required. Input and output files are stored as HDF5
and are compatible with the GADGET-2 specification. A parallel-HDF5 build
-and HDF5 > 1.10.x is recommended when running over MPI.
+and HDF5 >= 1.12.x is recommended when running over MPI.
MPI
~~~
diff --git a/src/common_io.h b/src/common_io.h
index 3e66e574d636ead198e2b82b8eea48051e262bac..69a89fdf285332d26abe233714c36cb066649bab 100644
--- a/src/common_io.h
+++ b/src/common_io.h
@@ -31,6 +31,8 @@
#define PARTICLE_GROUP_BUFFER_SIZE 50
#define FILENAME_BUFFER_SIZE 150
#define IO_BUFFER_ALIGNMENT 1024
+#define HDF5_LOWEST_FILE_FORMAT_VERSION H5F_LIBVER_V18
+#define HDF5_HIGHEST_FILE_FORMAT_VERSION H5F_LIBVER_LATEST
/* Avoid cyclic inclusion problems */
struct cell;
diff --git a/src/distributed_io.c b/src/distributed_io.c
index 483eeb1631092f01d554ad5f6dc9f22a0b24b223..2634111d29792953867317a742e13e06633d1dfc 100644
--- a/src/distributed_io.c
+++ b/src/distributed_io.c
@@ -508,8 +508,14 @@ void write_virtual_file(struct engine* e, const char* fileName_base,
* specific output */
xmf_write_outputheader(xmfFile, fileName, e->time);
+ /* Set the minimal API version to avoid issues with advanced features */
+ hid_t h_props = H5Pcreate(H5P_FILE_ACCESS);
+ herr_t err = H5Pset_libver_bounds(h_props, HDF5_LOWEST_FILE_FORMAT_VERSION,
+ HDF5_HIGHEST_FILE_FORMAT_VERSION);
+ if (err < 0) error("Error setting the hdf5 API version");
+
/* Open HDF5 file with the chosen parameters */
- hid_t h_file = H5Fcreate(fileName, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
+ hid_t h_file = H5Fcreate(fileName, H5F_ACC_TRUNC, H5P_DEFAULT, h_props);
if (h_file < 0) error("Error while opening file '%s'.", fileName);
/* Open header to write simulation properties */
@@ -741,8 +747,9 @@ void write_virtual_file(struct engine* e, const char* fileName_base,
/* Write LXMF file descriptor */
xmf_write_outputfooter(xmfFile, e->snapshot_output_count, e->time);
- /* Close the file for now */
+ /* Close the file */
H5Fclose(h_file);
+ H5Pclose(h_props);
#else
error(
@@ -1002,9 +1009,15 @@ void write_output_distributed(struct engine* e,
}
}
+ /* Set the minimal API version to avoid issues with advanced features */
+ hid_t h_props = H5Pcreate(H5P_FILE_ACCESS);
+ herr_t err = H5Pset_libver_bounds(h_props, HDF5_LOWEST_FILE_FORMAT_VERSION,
+ HDF5_HIGHEST_FILE_FORMAT_VERSION);
+ if (err < 0) error("Error setting the hdf5 API version");
+
/* Open file */
/* message("Opening file '%s'.", fileName); */
- h_file = H5Fcreate(fileName, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
+ h_file = H5Fcreate(fileName, H5F_ACC_TRUNC, H5P_DEFAULT, h_props);
if (h_file < 0) error("Error while opening file '%s'.", fileName);
/* Open header to write simulation properties */
@@ -1490,6 +1503,7 @@ void write_output_distributed(struct engine* e,
/* Close file */
H5Fclose(h_file);
+ H5Pclose(h_props);
#if H5_VERSION_GE(1, 10, 0)
@@ -1512,8 +1526,13 @@ void write_output_distributed(struct engine* e,
char fileName_virtual[1030];
sprintf(fileName_virtual, "%s.hdf5", fileName_base);
+ h_props = H5Pcreate(H5P_FILE_ACCESS);
+ err = H5Pset_libver_bounds(h_props, HDF5_LOWEST_FILE_FORMAT_VERSION,
+ HDF5_HIGHEST_FILE_FORMAT_VERSION);
+ if (err < 0) error("Error setting the hdf5 API version");
+
/* Open the snapshot on rank 0 */
- h_file_cells = H5Fopen(fileName_virtual, H5F_ACC_RDWR, H5P_DEFAULT);
+ h_file_cells = H5Fopen(fileName_virtual, H5F_ACC_RDWR, h_props);
if (h_file_cells < 0)
error("Error while opening file '%s' on rank %d.", fileName_virtual,
mpi_rank);
@@ -1541,6 +1560,7 @@ void write_output_distributed(struct engine* e,
if (mpi_rank == 0) {
H5Gclose(h_grp_cells);
H5Fclose(h_file_cells);
+ H5Pclose(h_props);
}
#endif
diff --git a/src/fof_catalogue_io.c b/src/fof_catalogue_io.c
index 4b44724267f00f642358040be957bc36a2f56c36..e290341deb5d6af668c925ea413e66b984f49699 100644
--- a/src/fof_catalogue_io.c
+++ b/src/fof_catalogue_io.c
@@ -305,8 +305,14 @@ void write_fof_virtual_file(const struct fof_props* props,
sprintf(file_name_base, "%s/%s", subdir_name, base);
sprintf(file_name, "%s/%s.hdf5", subdir_name, base);
+ /* Set the minimal API version to avoid issues with advanced features */
+ hid_t h_props = H5Pcreate(H5P_FILE_ACCESS);
+ herr_t err = H5Pset_libver_bounds(h_props, HDF5_LOWEST_FILE_FORMAT_VERSION,
+ HDF5_HIGHEST_FILE_FORMAT_VERSION);
+ if (err < 0) error("Error setting the hdf5 API version");
+
/* Open HDF5 file with the chosen parameters */
- hid_t h_file = H5Fcreate(file_name, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
+ hid_t h_file = H5Fcreate(file_name, H5F_ACC_TRUNC, H5P_DEFAULT, h_props);
if (h_file < 0) error("Error while opening file '%s'.", file_name);
/* Start by writing the header */
@@ -356,6 +362,7 @@ void write_fof_virtual_file(const struct fof_props* props,
/* Close everything */
H5Gclose(h_grp);
H5Fclose(h_file);
+ H5Pclose(h_props);
#endif
}
@@ -533,7 +540,13 @@ void write_fof_hdf5_catalogue(const struct fof_props* props,
e->snapshot_output_count);
#endif
- hid_t h_file = H5Fcreate(file_name, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
+ /* Set the minimal API version to avoid issues with advanced features */
+ hid_t h_props = H5Pcreate(H5P_FILE_ACCESS);
+ herr_t err = H5Pset_libver_bounds(h_props, HDF5_LOWEST_FILE_FORMAT_VERSION,
+ HDF5_HIGHEST_FILE_FORMAT_VERSION);
+ if (err < 0) error("Error setting the hdf5 API version");
+
+ hid_t h_file = H5Fcreate(file_name, H5F_ACC_TRUNC, H5P_DEFAULT, h_props);
if (h_file < 0) error("Error while opening file '%s'.", file_name);
/* Compute the number of groups */
@@ -593,6 +606,7 @@ void write_fof_hdf5_catalogue(const struct fof_props* props,
/* Close everything */
H5Gclose(h_grp);
H5Fclose(h_file);
+ H5Pclose(h_props);
#ifdef WITH_MPI
#if H5_VERSION_GE(1, 10, 0)
diff --git a/src/lightcone/lightcone.c b/src/lightcone/lightcone.c
index d04076384afbbd52f7ed294c0e1d7494db9089b2..7a431ed83791dcac27079e66a2fb079be9141f78 100644
--- a/src/lightcone/lightcone.c
+++ b/src/lightcone/lightcone.c
@@ -864,7 +864,7 @@ void lightcone_flush_particle_buffers(struct lightcone_props *props, double a,
if ((types_to_flush > 0) || (end_file && props->file_needs_finalizing)) {
/* We have data to flush, so open or create the output file */
- hid_t file_id;
+ hid_t file_id, h_props;
char fname[FILENAME_BUFFER_SIZE];
if (props->start_new_file) {
@@ -873,8 +873,14 @@ void lightcone_flush_particle_buffers(struct lightcone_props *props, double a,
particle_file_name(fname, FILENAME_BUFFER_SIZE, props->subdir,
props->basename, props->current_file, engine_rank);
+ h_props = H5Pcreate(H5P_FILE_ACCESS);
+ herr_t err =
+ H5Pset_libver_bounds(h_props, HDF5_LOWEST_FILE_FORMAT_VERSION,
+ HDF5_HIGHEST_FILE_FORMAT_VERSION);
+ if (err < 0) error("Error setting the hdf5 API version");
+
/* Create the file */
- file_id = H5Fcreate(fname, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
+ file_id = H5Fcreate(fname, H5F_ACC_TRUNC, H5P_DEFAULT, h_props);
if (file_id < 0) error("Unable to create new lightcone file: %s", fname);
/* This new file has not been finalized yet */
@@ -924,10 +930,16 @@ void lightcone_flush_particle_buffers(struct lightcone_props *props, double a,
} else {
+ h_props = H5Pcreate(H5P_FILE_ACCESS);
+ herr_t err =
+ H5Pset_libver_bounds(h_props, HDF5_LOWEST_FILE_FORMAT_VERSION,
+ HDF5_HIGHEST_FILE_FORMAT_VERSION);
+ if (err < 0) error("Error setting the hdf5 API version");
+
/* Re-open an existing file */
particle_file_name(fname, FILENAME_BUFFER_SIZE, props->subdir,
props->basename, props->current_file, engine_rank);
- file_id = H5Fopen(fname, H5F_ACC_RDWR, H5P_DEFAULT);
+ file_id = H5Fopen(fname, H5F_ACC_RDWR, h_props);
if (file_id < 0)
error("Unable to open current lightcone file: %s", fname);
}
@@ -969,6 +981,7 @@ void lightcone_flush_particle_buffers(struct lightcone_props *props, double a,
/* We're done updating the output file */
H5Fclose(file_id);
+ H5Pclose(h_props);
}
/* If we need to start a new file next time, record this */
@@ -1101,6 +1114,12 @@ void lightcone_dump_completed_shells(struct lightcone_props *props,
/* Create the output file for this shell */
hid_t fapl_id = H5Pcreate(H5P_FILE_ACCESS);
+ /* Set the minimal API version to avoid issues with advanced features */
+ herr_t err =
+ H5Pset_libver_bounds(fapl_id, HDF5_LOWEST_FILE_FORMAT_VERSION,
+ HDF5_HIGHEST_FILE_FORMAT_VERSION);
+ if (err < 0) error("Error setting the hdf5 API version");
+
/* Set MPI collective mode, if necessary */
int collective = 0;
#ifdef WITH_MPI
@@ -1710,8 +1729,13 @@ void lightcone_write_index(struct lightcone_props *props,
check_snprintf(fname, FILENAME_BUFFER_SIZE, "%s/%s_index.hdf5",
props->subdir, props->basename);
+ hid_t h_props = H5Pcreate(H5P_FILE_ACCESS);
+ herr_t err = H5Pset_libver_bounds(h_props, HDF5_LOWEST_FILE_FORMAT_VERSION,
+ HDF5_HIGHEST_FILE_FORMAT_VERSION);
+ if (err < 0) error("Error setting the hdf5 API version");
+
/* Create the file */
- hid_t file_id = H5Fcreate(fname, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
+ hid_t file_id = H5Fcreate(fname, H5F_ACC_TRUNC, H5P_DEFAULT, h_props);
/* Write number of MPI ranks and number of files */
hid_t group_id =
@@ -1755,6 +1779,7 @@ void lightcone_write_index(struct lightcone_props *props,
H5Gclose(group_id);
H5Fclose(file_id);
+ H5Pclose(h_props);
}
free(current_file_on_rank);
diff --git a/src/line_of_sight.c b/src/line_of_sight.c
index 519aa09d89b58234fba501ea54dffd14008e5764..1a63a17954d67da46594e9563ebefe29a9f0e711 100644
--- a/src/line_of_sight.c
+++ b/src/line_of_sight.c
@@ -770,14 +770,21 @@ void do_line_of_sight(struct engine *e) {
#endif
/* Node 0 creates the HDF5 file. */
- hid_t h_file = -1, h_grp = -1;
+ hid_t h_file = -1, h_grp = -1, h_props = -1;
char fileName[256], groupName[200];
if (e->nodeID == 0) {
sprintf(fileName, "%s_%04i.hdf5", LOS_params->basename,
e->los_output_count);
if (verbose) message("Creating LOS file: %s", fileName);
- h_file = H5Fcreate(fileName, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
+
+ /* Set the minimal API version to avoid issues with advanced features */
+ h_props = H5Pcreate(H5P_FILE_ACCESS);
+ hid_t err = H5Pset_libver_bounds(h_props, HDF5_LOWEST_FILE_FORMAT_VERSION,
+ HDF5_HIGHEST_FILE_FORMAT_VERSION);
+ if (err < 0) error("Error setting the hdf5 API version");
+
+ h_file = H5Fcreate(fileName, H5F_ACC_TRUNC, H5P_DEFAULT, h_props);
if (h_file < 0) error("Error while opening file '%s'.", fileName);
}
@@ -1082,6 +1089,7 @@ void do_line_of_sight(struct engine *e) {
/* Close HDF5 file */
H5Fclose(h_file);
+ H5Pclose(h_props);
}
/* Up the LOS counter. */
diff --git a/src/parallel_io.c b/src/parallel_io.c
index 51b0dac1cb498f7d203c3d8555c4629ec3ea66f7..cf67c9fe9d775f7b6678aa684dc86572792e7435 100644
--- a/src/parallel_io.c
+++ b/src/parallel_io.c
@@ -1191,8 +1191,14 @@ void prepare_file(struct engine* e, const char* fileName,
/* Prepare the XMF file for the new entry */
xmfFile = xmf_prepare_file(xmfFileName);
+ /* Set the minimal API version to avoid issues with advanced features */
+ hid_t h_props = H5Pcreate(H5P_FILE_ACCESS);
+ herr_t err = H5Pset_libver_bounds(h_props, HDF5_LOWEST_FILE_FORMAT_VERSION,
+ HDF5_HIGHEST_FILE_FORMAT_VERSION);
+ if (err < 0) error("Error setting the hdf5 API version");
+
/* Open HDF5 file with the chosen parameters */
- hid_t h_file = H5Fcreate(fileName, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
+ hid_t h_file = H5Fcreate(fileName, H5F_ACC_TRUNC, H5P_DEFAULT, h_props);
if (h_file < 0) error("Error while opening file '%s'.", fileName);
/* Write the part of the XMF file corresponding to this
@@ -1430,6 +1436,7 @@ void prepare_file(struct engine* e, const char* fileName,
/* Close the file for now */
H5Fclose(h_file);
+ H5Pclose(h_props);
}
/**
@@ -1685,6 +1692,11 @@ void write_output_parallel(struct engine* e,
/* Prepare some file-access properties */
hid_t plist_id = H5Pcreate(H5P_FILE_ACCESS);
+ /* Set the minimal API version to avoid issues with advanced features */
+ herr_t err = H5Pset_libver_bounds(plist_id, HDF5_LOWEST_FILE_FORMAT_VERSION,
+ HDF5_HIGHEST_FILE_FORMAT_VERSION);
+ if (err < 0) error("Error setting the hdf5 API version");
+
/* Set some MPI-IO parameters */
// MPI_Info_set(info, "IBM_largeblock_io", "true");
MPI_Info_set(info, "romio_cb_write", "enable");
diff --git a/src/serial_io.c b/src/serial_io.c
index d6a3c9904a098a953ec1a5640b02da14a043c486..8e8cc9f5d0cc6a570022e4fc9874a62a5fe152dc 100644
--- a/src/serial_io.c
+++ b/src/serial_io.c
@@ -782,7 +782,14 @@ void read_ic_serial(char* fileName, const struct unit_system* internal_units,
/* Is it this rank's turn to read ? */
if (rank == mpi_rank) {
- h_file = H5Fopen(fileName, H5F_ACC_RDONLY, H5P_DEFAULT);
+ /* Set the minimal API version to avoid issues with advanced features */
+ hid_t h_props = H5Pcreate(H5P_FILE_ACCESS);
+ herr_t err =
+ H5Pset_libver_bounds(h_props, HDF5_LOWEST_FILE_FORMAT_VERSION,
+ HDF5_HIGHEST_FILE_FORMAT_VERSION);
+ if (err < 0) error("Error setting the hdf5 API version");
+
+ h_file = H5Fopen(fileName, H5F_ACC_RDONLY, h_props);
if (h_file < 0)
error("Error while opening file '%s' on rank %d.", fileName, mpi_rank);
@@ -889,6 +896,7 @@ void read_ic_serial(char* fileName, const struct unit_system* internal_units,
/* Close file */
H5Fclose(h_file);
+ H5Pclose(h_props);
}
/* Wait for the read of the reading to complete */
@@ -1165,9 +1173,15 @@ void write_output_serial(struct engine* e,
/* Write the part corresponding to this specific output */
xmf_write_outputheader(xmfFile, fileName, e->time);
+ /* Set the minimal API version to avoid issues with advanced features */
+ hid_t h_props = H5Pcreate(H5P_FILE_ACCESS);
+ herr_t err = H5Pset_libver_bounds(h_props, HDF5_LOWEST_FILE_FORMAT_VERSION,
+ HDF5_HIGHEST_FILE_FORMAT_VERSION);
+ if (err < 0) error("Error setting the hdf5 API version");
+
/* Open file */
/* message("Opening file '%s'.", fileName); */
- h_file = H5Fcreate(fileName, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
+ h_file = H5Fcreate(fileName, H5F_ACC_TRUNC, H5P_DEFAULT, h_props);
if (h_file < 0) error("Error while opening file '%s'.", fileName);
/* Open header to write simulation properties */
@@ -1307,14 +1321,21 @@ void write_output_serial(struct engine* e,
/* Close file */
H5Fclose(h_file);
+ H5Pclose(h_props);
}
/* Now write the top-level cell structure */
- hid_t h_file_cells = 0, h_grp_cells = 0;
+ hid_t h_file_cells = 0, h_grp_cells = 0, h_props_cells = 0;
if (mpi_rank == 0) {
+ /* Set the minimal API version to avoid issues with advanced features */
+ h_props_cells = H5Pcreate(H5P_FILE_ACCESS);
+ herr_t err = H5Pset_libver_bounds(h_props, HDF5_LOWEST_FILE_FORMAT_VERSION,
+ HDF5_HIGHEST_FILE_FORMAT_VERSION);
+ if (err < 0) error("Error setting the hdf5 API version");
+
/* Open the snapshot on rank 0 */
- h_file_cells = H5Fopen(fileName, H5F_ACC_RDWR, H5P_DEFAULT);
+ h_file_cells = H5Fopen(fileName, H5F_ACC_RDWR, h_props_cells);
if (h_file_cells < 0)
error("Error while opening file '%s' on rank %d.", fileName, mpi_rank);
@@ -1343,7 +1364,14 @@ void write_output_serial(struct engine* e,
/* Is it this rank's turn to write ? */
if (rank == mpi_rank) {
- h_file = H5Fopen(fileName, H5F_ACC_RDWR, H5P_DEFAULT);
+ /* Set the minimal API version to avoid issues with advanced features */
+ hid_t h_props = H5Pcreate(H5P_FILE_ACCESS);
+ herr_t err =
+ H5Pset_libver_bounds(h_props, HDF5_LOWEST_FILE_FORMAT_VERSION,
+ HDF5_HIGHEST_FILE_FORMAT_VERSION);
+ if (err < 0) error("Error setting the hdf5 API version");
+
+ h_file = H5Fopen(fileName, H5F_ACC_RDWR, h_props);
if (h_file < 0)
error("Error while opening file '%s' on rank %d.", fileName, mpi_rank);
@@ -1706,6 +1734,7 @@ void write_output_serial(struct engine* e,
/* Close file */
H5Fclose(h_file);
+ H5Pclose(h_props);
}
/* Wait for the read of the reading to complete */
diff --git a/src/single_io.c b/src/single_io.c
index c63be580b02106b0b9d21a70ae9a592e63ed2c89..5ea174ae970026669d0109ab93e1db3c835712b9 100644
--- a/src/single_io.c
+++ b/src/single_io.c
@@ -990,9 +990,15 @@ void write_output_single(struct engine* e,
};
+ /* Set the minimal API version to avoid issues with advanced features */
+ hid_t h_props = H5Pcreate(H5P_FILE_ACCESS);
+ herr_t err = H5Pset_libver_bounds(h_props, HDF5_LOWEST_FILE_FORMAT_VERSION,
+ HDF5_HIGHEST_FILE_FORMAT_VERSION);
+ if (err < 0) error("Error setting the hdf5 API version");
+
/* Open file */
/* message("Opening file '%s'.", fileName); */
- h_file = H5Fcreate(fileName, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
+ h_file = H5Fcreate(fileName, H5F_ACC_TRUNC, H5P_DEFAULT, h_props);
if (h_file < 0) error("Error while opening file '%s'.", fileName);
/* Open header to write simulation properties */
@@ -1481,6 +1487,7 @@ void write_output_single(struct engine* e,
/* Close file */
H5Fclose(h_file);
+ H5Pclose(h_props);
e->snapshot_output_count++;
if (e->snapshot_invoke_stf) e->stf_output_count++;