diff --git a/src/engine.c b/src/engine.c
index 87f34ac765cfb09e5f34ac3e9d203285670cff23..9e4cbf59fd592552b670b32723dde7d136b71dd3 100644
--- a/src/engine.c
+++ b/src/engine.c
@@ -5628,9 +5628,8 @@ void engine_check_for_dumps(struct engine *e) {
engine_print_stats(e);
#ifdef WITH_LOGGER
engine_dump_index(e);
-#else
- engine_dump_snapshot(e);
#endif
+ engine_dump_snapshot(e);
} else if (e->ti_next_stats < e->ti_next_snapshot) {
@@ -5662,9 +5661,8 @@ void engine_check_for_dumps(struct engine *e) {
/* Dump snapshot */
#ifdef WITH_LOGGER
engine_dump_index(e);
-#else
- engine_dump_snapshot(e);
#endif
+ engine_dump_snapshot(e);
} else if (e->ti_next_stats > e->ti_next_snapshot) {
@@ -5684,9 +5682,8 @@ void engine_check_for_dumps(struct engine *e) {
/* Dump snapshot */
#ifdef WITH_LOGGER
engine_dump_index(e);
-#else
- engine_dump_snapshot(e);
#endif
+ engine_dump_snapshot(e);
/* Let's fake that we are at the stats dump time */
e->ti_current = e->ti_next_stats;
@@ -5723,9 +5720,8 @@ void engine_check_for_dumps(struct engine *e) {
/* Dump... */
#ifdef WITH_LOGGER
engine_dump_index(e);
-#else
- engine_dump_snapshot(e);
#endif
+ engine_dump_snapshot(e);
/* ... and find the next output time */
engine_compute_next_snapshot_time(e);
diff --git a/src/engine.h b/src/engine.h
index 7dc3860097f3daaad3a2541fca9097eccf7b276a..dd2fc89b6944d53802164f958ae263f68ae9247a 100644
--- a/src/engine.h
+++ b/src/engine.h
@@ -326,7 +326,7 @@ struct engine {
size_t logger_time_offset;
/* Size of the dump file */
- size_t logger_size;
+ size_t logger_buffer_size;
#endif
/* Need to dump a snapshot ? */
diff --git a/src/logger.c b/src/logger.c
index d1e79ad3d479c2dd00058ecb9becfefd731c3a45..00a11a0012dbdc6c1a0d7b6a4b406116891bd73e 100644
--- a/src/logger.c
+++ b/src/logger.c
@@ -61,7 +61,7 @@ const unsigned int logger_data_size[logger_data_count] = {
*
* @return updated buff
*/
-__attribute__((always_inline)) INLINE static char *logger_write_chunk_header(char *buff, const unsigned int *mask, const size_t *offset, const size_t offset_new) {
+char *logger_write_chunk_header(char *buff, const unsigned int *mask, const size_t *offset, const size_t offset_new) {
memcpy(buff, mask, logger_size_mask);
buff += logger_size_mask;
@@ -129,7 +129,7 @@ void logger_write_general_data(struct dump *d, struct logger_const *log, size_t
*
* @return The size of the logger message in bytes.
*/
-int logger_size(unsigned int mask) {
+int logger_compute_chunk_size(unsigned int mask) {
/* Start with 8 bytes for the header. */
int size = 8;
@@ -208,7 +208,7 @@ void logger_log_part(const struct part *p, const unsigned int mask, size_t *offs
error("You should not log particles as timestamps.");
/* Start by computing the size of the message. */
- const int size = logger_buffer_size(mask);
+ const int size = logger_compute_chunk_size(mask);
/* Allocate a chunk of memory in the dump of the right size. */
size_t offset_new;
@@ -289,7 +289,7 @@ void logger_log_gpart(const struct gpart *p, const unsigned int mask, size_t *of
error("Can't log SPH quantities for gparts.");
/* Start by computing the size of the message. */
- const int size = logger_buffer_size(mask);
+ const int size = logger_compute_chunk_size(mask);
/* Allocate a chunk of memory in the dump of the right size. */
size_t offset_new;
@@ -338,7 +338,7 @@ void logger_log_gpart(const struct gpart *p, const unsigned int mask, size_t *of
void logger_log_timestamp(integertime_t timestamp, size_t *offset,
struct dump *dump) {
/* Start by computing the size of the message. */
- const int size = logger_buffer_size(logger_mask_timestamp);
+ const int size = logger_compute_chunk_size(logger_mask_timestamp);
/* Allocate a chunk of memory in the dump of the right size. */
size_t offset_new;
diff --git a/src/logger.h b/src/logger.h
index f81a833d505fd3970b0210ab955b94beb4e7034f..ecdc617643e2e7c271e135bf6cbf901a430c9a69 100644
--- a/src/logger.h
+++ b/src/logger.h
@@ -119,7 +119,7 @@ enum logger_datatype {
extern const unsigned int logger_data_size[];
/* Function prototypes. */
-int logger_size(unsigned int mask);
+int logger_compute_chunk_size(unsigned int mask);
void logger_log_all(struct part *p,
const long long Np, struct dump *dump);
void logger_log_part(const struct part *p, const unsigned int mask, size_t *offset,
@@ -135,7 +135,7 @@ int logger_read_timestamp(unsigned long long int *t, size_t *offset,
void logger_write_file_header(struct dump *dump, struct engine* e);
void logger_const_init(struct logger_const* log_const);
void logger_const_free(struct logger_const* log_const);
-void logger_ensure_size(size_t total_nr_parts, size_t logger_size);
+void logger_ensure_size(size_t total_nr_parts, size_t logger_buffer_size);
#endif /* WITH_LOGGER */
diff --git a/src/logger_io.c b/src/logger_io.c
index 7b9b0500eb0f738ab43a9782cfb9a5e188e4d71c..e877e7533091f41668b2fc02dd2f05d74ae127fe 100644
--- a/src/logger_io.c
+++ b/src/logger_io.c
@@ -21,7 +21,7 @@
/* Config parameters. */
#include "../config.h"
-#if defined(HAVE_HDF5) && !defined(WITH_MPI) && defined(WITH_LOGGER)
+#ifdef WITH_LOGGER
/* Some standard headers. */
#include <hdf5.h>
@@ -47,771 +47,14 @@
#include "hydro_properties.h"
#include "io_properties.h"
#include "kernel_hydro.h"
+#include "parallel_io.h"
#include "part.h"
+#include "serial_io.h"
+#include "single_io.h"
#include "stars_io.h"
#include "units.h"
#include "xmf.h"
-/*-----------------------------------------------------------------------------
- * Routines reading an IC file
- *-----------------------------------------------------------------------------*/
-
-/**
- * @brief Reads a data array from a given HDF5 group.
- *
- * @param h_grp The group from which to read.
- * @param prop The #io_props of the field to read
- * @param N The number of particles.
- * @param internal_units The #unit_system used internally
- * @param ic_units The #unit_system used in the ICs
- *
- * @todo A better version using HDF5 hyper-slabs to read the file directly into
- * the part array will be written once the structures have been stabilized.
- */
-void readArray(hid_t h_grp, const struct io_props prop, size_t N,
- const struct unit_system* internal_units,
- const struct unit_system* ic_units) {
-
- const size_t typeSize = io_sizeof_type(prop.type);
- const size_t copySize = typeSize * prop.dimension;
- const size_t num_elements = N * prop.dimension;
-
- /* Check whether the dataspace exists or not */
- const htri_t exist = H5Lexists(h_grp, prop.name, 0);
- if (exist < 0) {
- error("Error while checking the existence of data set '%s'.", prop.name);
- } else if (exist == 0) {
- if (prop.importance == COMPULSORY) {
- error("Compulsory data set '%s' not present in the file.", prop.name);
- } else {
- /* message("Optional data set '%s' not present. Zeroing this particle
- * prop...", name); */
-
- for (size_t i = 0; i < N; ++i)
- memset(prop.field + i * prop.partSize, 0, copySize);
-
- return;
- }
- }
-
- /* message("Reading %s '%s' array...", */
- /* prop.importance == COMPULSORY ? "compulsory" : "optional ", */
- /* prop.name); */
-
- /* Open data space */
- const hid_t h_data = H5Dopen(h_grp, prop.name, H5P_DEFAULT);
- if (h_data < 0) {
- error("Error while opening data space '%s'.", prop.name);
- }
-
- /* Check data type */
- const hid_t h_type = H5Dget_type(h_data);
- if (h_type < 0) error("Unable to retrieve data type from the file");
- // if (!H5Tequal(h_type, hdf5_type(type)))
- // error("Non-matching types between the code and the file");
-
- /* Allocate temporary buffer */
- void* temp = malloc(num_elements * typeSize);
- if (temp == NULL) error("Unable to allocate memory for temporary buffer");
-
- /* Read HDF5 dataspace in temporary buffer */
- /* Dirty version that happens to work for vectors but should be improved */
- /* Using HDF5 dataspaces would be better */
- const hid_t h_err = H5Dread(h_data, io_hdf5_type(prop.type), H5S_ALL, H5S_ALL,
- H5P_DEFAULT, temp);
- if (h_err < 0) {
- error("Error while reading data array '%s'.", prop.name);
- }
-
- /* Unit conversion if necessary */
- const double factor =
- units_conversion_factor(ic_units, internal_units, prop.units);
- if (factor != 1. && exist != 0) {
-
- /* message("Converting ! factor=%e", factor); */
-
- if (io_is_double_precision(prop.type)) {
- double* temp_d = temp;
- for (size_t i = 0; i < num_elements; ++i) temp_d[i] *= factor;
- } else {
- float* temp_f = temp;
- for (size_t i = 0; i < num_elements; ++i) temp_f[i] *= factor;
- }
- }
-
- /* Copy temporary buffer to particle data */
- char* temp_c = temp;
- for (size_t i = 0; i < N; ++i)
- memcpy(prop.field + i * prop.partSize, &temp_c[i * copySize], copySize);
-
- /* Free and close everything */
- free(temp);
- H5Tclose(h_type);
- H5Dclose(h_data);
-}
-
-/*-----------------------------------------------------------------------------
- * Routines writing an output file
- *-----------------------------------------------------------------------------*/
-
-/**
- * @brief Writes a data array in given HDF5 group.
- *
- * @param e The #engine we are writing from.
- * @param grp The group in which to write.
- * @param fileName The name of the file in which the data is written
- * @param xmfFile The FILE used to write the XMF description
- * @param partTypeGroupName The name of the group containing the particles in
- * the HDF5 file.
- * @param props The #io_props of the field to read
- * @param N The number of particles to write.
- * @param internal_units The #unit_system used internally
- * @param snapshot_units The #unit_system used in the snapshots
- *
- * @todo A better version using HDF5 hyper-slabs to write the file directly from
- * the part array will be written once the structures have been stabilized.
- */
-void writeArray(const struct engine* e, hid_t grp, char* fileName,
- FILE* xmfFile, char* partTypeGroupName,
- const struct io_props props, size_t N,
- const struct unit_system* internal_units,
- const struct unit_system* snapshot_units) {
-
- const size_t typeSize = io_sizeof_type(props.type);
- const size_t num_elements = N * props.dimension;
-
- /* message("Writing '%s' array...", props.name); */
-
- /* Allocate temporary buffer */
- void* temp = NULL;
- if (posix_memalign((void**)&temp, IO_BUFFER_ALIGNMENT,
- num_elements * typeSize) != 0)
- error("Unable to allocate temporary i/o buffer");
-
- /* Copy the particle data to the temporary buffer */
- io_copy_temp_buffer(temp, e, props, N, internal_units, snapshot_units);
-
- /* Create data space */
- const hid_t h_space = H5Screate(H5S_SIMPLE);
- int rank;
- hsize_t shape[2];
- hsize_t chunk_shape[2];
- if (h_space < 0) {
- error("Error while creating data space for field '%s'.", props.name);
- }
-
- if (props.dimension > 1) {
- rank = 2;
- shape[0] = N;
- shape[1] = props.dimension;
- chunk_shape[0] = 1 << 16; /* Just a guess...*/
- chunk_shape[1] = props.dimension;
- } else {
- rank = 1;
- shape[0] = N;
- shape[1] = 0;
- chunk_shape[0] = 1 << 16; /* Just a guess...*/
- chunk_shape[1] = 0;
- }
-
- /* Make sure the chunks are not larger than the dataset */
- if (chunk_shape[0] > N) chunk_shape[0] = N;
-
- /* Change shape of data space */
- hid_t h_err = H5Sset_extent_simple(h_space, rank, shape, NULL);
- if (h_err < 0) {
- error("Error while changing data space shape for field '%s'.", props.name);
- }
-
- /* Dataset properties */
- const hid_t h_prop = H5Pcreate(H5P_DATASET_CREATE);
-
- /* Set chunk size */
- h_err = H5Pset_chunk(h_prop, rank, chunk_shape);
- if (h_err < 0) {
- error("Error while setting chunk size (%llu, %llu) for field '%s'.",
- chunk_shape[0], chunk_shape[1], props.name);
- }
-
- /* Impose data compression */
- if (e->snapshotCompression > 0) {
- h_err = H5Pset_deflate(h_prop, e->snapshotCompression);
- if (h_err < 0) {
- error("Error while setting compression options for field '%s'.",
- props.name);
- }
- }
-
- /* Create dataset */
- const hid_t h_data = H5Dcreate(grp, props.name, io_hdf5_type(props.type),
- h_space, H5P_DEFAULT, h_prop, H5P_DEFAULT);
- if (h_data < 0) {
- error("Error while creating dataspace '%s'.", props.name);
- }
-
- /* Write temporary buffer to HDF5 dataspace */
- h_err = H5Dwrite(h_data, io_hdf5_type(props.type), h_space, H5S_ALL,
- H5P_DEFAULT, temp);
- if (h_err < 0) {
- error("Error while writing data array '%s'.", props.name);
- }
-
- /* Write XMF description for this data set */
- if (xmfFile != NULL)
- xmf_write_line(xmfFile, fileName, partTypeGroupName, props.name, N,
- props.dimension, props.type);
-
- /* Write unit conversion factors for this data set */
- char buffer[FIELD_BUFFER_SIZE];
- units_cgs_conversion_string(buffer, snapshot_units, props.units);
- io_write_attribute_d(
- h_data, "CGS conversion factor",
- units_cgs_conversion_factor(snapshot_units, props.units));
- io_write_attribute_f(h_data, "h-scale exponent",
- units_h_factor(snapshot_units, props.units));
- io_write_attribute_f(h_data, "a-scale exponent",
- units_a_factor(snapshot_units, props.units));
- io_write_attribute_s(h_data, "Conversion factor", buffer);
-
- /* Free and close everything */
- free(temp);
- H5Pclose(h_prop);
- H5Dclose(h_data);
- H5Sclose(h_space);
-}
-
-/**
- * @brief Reads an HDF5 initial condition file (GADGET-3 type)
- *
- * @param fileName The file to read.
- * @param internal_units The system units used internally
- * @param dim (output) The dimension of the volume.
- * @param parts (output) Array of #part particles.
- * @param gparts (output) Array of #gpart particles.
- * @param sparts (output) Array of #spart particles.
- * @param Ngas (output) number of Gas particles read.
- * @param Ngparts (output) The number of #gpart read.
- * @param Nstars (output) The number of #spart read.
- * @param periodic (output) 1 if the volume is periodic, 0 if not.
- * @param flag_entropy (output) 1 if the ICs contained Entropy in the
- * InternalEnergy field
- * @param with_hydro Are we reading gas particles ?
- * @param with_gravity Are we reading/creating #gpart arrays ?
- * @param with_stars Are we reading star particles ?
- * @param dry_run If 1, don't read the particle. Only allocates the arrays.
- *
- * Opens the HDF5 file fileName and reads the particles contained
- * in the parts array. N is the returned number of particles found
- * in the file.
- *
- * @warning Can not read snapshot distributed over more than 1 file !!!
- * @todo Read snapshots distributed in more than one file.
- *
- */
-void read_ic_single(char* fileName, const struct unit_system* internal_units,
- double dim[3], struct part** parts, struct gpart** gparts,
- struct spart** sparts, size_t* Ngas, size_t* Ngparts,
- size_t* Nstars, int* periodic, int* flag_entropy,
- int with_hydro, int with_gravity, int with_stars,
- int n_threads, int dry_run) {
-
- hid_t h_file = 0, h_grp = 0;
- /* GADGET has only cubic boxes (in cosmological mode) */
- double boxSize[3] = {0.0, -1.0, -1.0};
- /* GADGET has 6 particle types. We only keep the type 0 & 1 for now...*/
- int numParticles[swift_type_count] = {0};
- int numParticles_highWord[swift_type_count] = {0};
- size_t N[swift_type_count] = {0};
- int dimension = 3; /* Assume 3D if nothing is specified */
- size_t Ndm = 0;
-
- /* Open file */
- /* message("Opening file '%s' as IC.", fileName); */
- h_file = H5Fopen(fileName, H5F_ACC_RDONLY, H5P_DEFAULT);
- if (h_file < 0) {
- error("Error while opening file '%s'.", fileName);
- }
-
- /* Open header to read simulation properties */
- /* message("Reading runtime parameters..."); */
- h_grp = H5Gopen(h_file, "/RuntimePars", H5P_DEFAULT);
- if (h_grp < 0) error("Error while opening runtime parameters\n");
-
- /* Read the relevant information */
- io_read_attribute(h_grp, "PeriodicBoundariesOn", INT, periodic);
-
- /* Close runtime parameters */
- H5Gclose(h_grp);
-
- /* Open header to read simulation properties */
- /* message("Reading file header..."); */
- h_grp = H5Gopen(h_file, "/Header", H5P_DEFAULT);
- if (h_grp < 0) error("Error while opening file header\n");
-
- /* Check the dimensionality of the ICs (if the info exists) */
- const hid_t hid_dim = H5Aexists(h_grp, "Dimension");
- if (hid_dim < 0)
- error("Error while testing existance of 'Dimension' attribute");
- if (hid_dim > 0) io_read_attribute(h_grp, "Dimension", INT, &dimension);
- if (dimension != hydro_dimension)
- error("ICs dimensionality (%dD) does not match code dimensionality (%dD)",
- dimension, (int)hydro_dimension);
-
- /* Read the relevant information and print status */
- int flag_entropy_temp[6];
- io_read_attribute(h_grp, "Flag_Entropy_ICs", INT, flag_entropy_temp);
- *flag_entropy = flag_entropy_temp[0];
- io_read_attribute(h_grp, "BoxSize", DOUBLE, boxSize);
- io_read_attribute(h_grp, "NumPart_Total", UINT, numParticles);
- io_read_attribute(h_grp, "NumPart_Total_HighWord", UINT,
- numParticles_highWord);
-
- for (int ptype = 0; ptype < swift_type_count; ++ptype)
- N[ptype] = ((long long)numParticles[ptype]) +
- ((long long)numParticles_highWord[ptype] << 32);
-
- /* Get the box size if not cubic */
- dim[0] = boxSize[0];
- dim[1] = (boxSize[1] < 0) ? boxSize[0] : boxSize[1];
- dim[2] = (boxSize[2] < 0) ? boxSize[0] : boxSize[2];
-
- /* Change box size in the 1D and 2D case */
- if (hydro_dimension == 2)
- dim[2] = min(dim[0], dim[1]);
- else if (hydro_dimension == 1)
- dim[2] = dim[1] = dim[0];
-
- /* message("Found %d particles in a %speriodic box of size [%f %f %f].", */
- /* *N, (periodic ? "": "non-"), dim[0], dim[1], dim[2]); */
-
- /* Close header */
- H5Gclose(h_grp);
-
- /* Read the unit system used in the ICs */
- struct unit_system* ic_units = malloc(sizeof(struct unit_system));
- if (ic_units == NULL) error("Unable to allocate memory for IC unit system");
- io_read_unit_system(h_file, ic_units, 0);
-
- /* Tell the user if a conversion will be needed */
- if (units_are_equal(ic_units, internal_units)) {
-
- message("IC and internal units match. No conversion needed.");
-
- } else {
-
- message("Conversion needed from:");
- message("(ICs) Unit system: U_M = %e g.", ic_units->UnitMass_in_cgs);
- message("(ICs) Unit system: U_L = %e cm.",
- ic_units->UnitLength_in_cgs);
- message("(ICs) Unit system: U_t = %e s.", ic_units->UnitTime_in_cgs);
- message("(ICs) Unit system: U_I = %e A.",
- ic_units->UnitCurrent_in_cgs);
- message("(ICs) Unit system: U_T = %e K.",
- ic_units->UnitTemperature_in_cgs);
- message("to:");
- message("(internal) Unit system: U_M = %e g.",
- internal_units->UnitMass_in_cgs);
- message("(internal) Unit system: U_L = %e cm.",
- internal_units->UnitLength_in_cgs);
- message("(internal) Unit system: U_t = %e s.",
- internal_units->UnitTime_in_cgs);
- message("(internal) Unit system: U_I = %e A.",
- internal_units->UnitCurrent_in_cgs);
- message("(internal) Unit system: U_T = %e K.",
- internal_units->UnitTemperature_in_cgs);
- }
-
- /* Convert the dimensions of the box */
- for (int j = 0; j < 3; j++)
- dim[j] *=
- units_conversion_factor(ic_units, internal_units, UNIT_CONV_LENGTH);
-
- /* Allocate memory to store SPH particles */
- if (with_hydro) {
- *Ngas = N[swift_type_gas];
- if (posix_memalign((void*)parts, part_align, *Ngas * sizeof(struct part)) !=
- 0)
- error("Error while allocating memory for SPH particles");
- bzero(*parts, *Ngas * sizeof(struct part));
- }
-
- /* Allocate memory to store star particles */
- if (with_stars) {
- *Nstars = N[swift_type_star];
- if (posix_memalign((void*)sparts, spart_align,
- *Nstars * sizeof(struct spart)) != 0)
- error("Error while allocating memory for star particles");
- bzero(*sparts, *Nstars * sizeof(struct spart));
- }
-
- /* Allocate memory to store all gravity particles */
- if (with_gravity) {
- Ndm = N[swift_type_dark_matter];
- *Ngparts = (with_hydro ? N[swift_type_gas] : 0) +
- N[swift_type_dark_matter] +
- (with_stars ? N[swift_type_star] : 0);
- if (posix_memalign((void*)gparts, gpart_align,
- *Ngparts * sizeof(struct gpart)) != 0)
- error("Error while allocating memory for gravity particles");
- bzero(*gparts, *Ngparts * sizeof(struct gpart));
- }
-
- /* message("Allocated %8.2f MB for particles.", *N * sizeof(struct part) /
- * (1024.*1024.)); */
-
- /* message("BoxSize = %lf", dim[0]); */
- /* message("NumPart = [%zd, %zd] Total = %zd", *Ngas, Ndm, *Ngparts); */
-
- /* Loop over all particle types */
- for (int ptype = 0; ptype < swift_type_count; ptype++) {
-
- /* Don't do anything if no particle of this kind */
- if (N[ptype] == 0) continue;
-
- /* Open the particle group in the file */
- char partTypeGroupName[PARTICLE_GROUP_BUFFER_SIZE];
- snprintf(partTypeGroupName, PARTICLE_GROUP_BUFFER_SIZE, "/PartType%d",
- ptype);
- h_grp = H5Gopen(h_file, partTypeGroupName, H5P_DEFAULT);
- if (h_grp < 0) {
- error("Error while opening particle group %s.", partTypeGroupName);
- }
-
- int num_fields = 0;
- struct io_props list[100];
- size_t Nparticles = 0;
-
- /* Read particle fields into the structure */
- switch (ptype) {
-
- case swift_type_gas:
- if (with_hydro) {
- Nparticles = *Ngas;
- hydro_read_particles(*parts, list, &num_fields);
- num_fields += chemistry_read_particles(*parts, list + num_fields);
- }
- break;
-
- case swift_type_dark_matter:
- if (with_gravity) {
- Nparticles = Ndm;
- darkmatter_read_particles(*gparts, list, &num_fields);
- }
- break;
-
- case swift_type_star:
- if (with_stars) {
- Nparticles = *Nstars;
- star_read_particles(*sparts, list, &num_fields);
- }
- break;
-
- default:
- message("Particle Type %d not yet supported. Particles ignored", ptype);
- }
-
- /* Read everything */
- if (!dry_run)
- for (int i = 0; i < num_fields; ++i)
- readArray(h_grp, list[i], Nparticles, internal_units, ic_units);
-
- /* Close particle group */
- H5Gclose(h_grp);
- }
-
- /* Duplicate the parts for gravity */
- if (!dry_run && with_gravity) {
-
- /* Let's initialise a bit of thread parallelism here */
- struct threadpool tp;
- threadpool_init(&tp, n_threads);
-
- /* Prepare the DM particles */
- io_prepare_dm_gparts(&tp, *gparts, Ndm);
-
- /* Duplicate the hydro particles into gparts */
- if (with_hydro) io_duplicate_hydro_gparts(&tp, *parts, *gparts, *Ngas, Ndm);
-
- /* Duplicate the star particles into gparts */
- if (with_stars)
- io_duplicate_star_gparts(&tp, *sparts, *gparts, *Nstars, Ndm + *Ngas);
-
- threadpool_clean(&tp);
- }
-
- /* message("Done Reading particles..."); */
-
- /* Clean up */
- free(ic_units);
-
- /* Close file */
- H5Fclose(h_file);
-}
-
-/**
- * @brief Writes an HDF5 output file (GADGET-3 type) with its XMF descriptor
- *
- * @param e The engine containing all the system.
- * @param baseName The common part of the snapshot file name.
- * @param internal_units The #unit_system used internally
- * @param snapshot_units The #unit_system used in the snapshots
- *
- * Creates an HDF5 output file and writes the particles contained
- * in the engine. If such a file already exists, it is erased and replaced
- * by the new one.
- * The companion XMF file is also updated accordingly.
- *
- * Calls #error() if an error occurs.
- *
- */
-void write_output_single(struct engine* e, const char* baseName,
- const struct unit_system* internal_units,
- const struct unit_system* snapshot_units) {
-
- hid_t h_file = 0, h_grp = 0;
- const size_t Ngas = e->s->nr_parts;
- const size_t Nstars = e->s->nr_sparts;
- const size_t Ntot = e->s->nr_gparts;
- int periodic = e->s->periodic;
- int numFiles = 1;
- struct part* parts = e->s->parts;
- struct gpart* gparts = e->s->gparts;
- struct gpart* dmparts = NULL;
- struct spart* sparts = e->s->sparts;
- static int outputCount = 0;
-
- /* Number of unassociated gparts */
- const size_t Ndm = Ntot > 0 ? Ntot - (Ngas + Nstars) : 0;
-
- long long N_total[swift_type_count] = {Ngas, Ndm, 0, 0, Nstars, 0};
-
- /* File name */
- char fileName[FILENAME_BUFFER_SIZE];
- snprintf(fileName, FILENAME_BUFFER_SIZE, "%s_%04i.hdf5", baseName,
- outputCount);
-
- /* First time, we need to create the XMF file */
- if (outputCount == 0) xmf_create_file(baseName);
-
- /* Prepare the XMF file for the new entry */
- FILE* xmfFile = 0;
- xmfFile = xmf_prepare_file(baseName);
-
- /* Write the part corresponding to this specific output */
- xmf_write_outputheader(xmfFile, fileName, e->time);
-
- /* Open file */
- /* message("Opening file '%s'.", fileName); */
- h_file = H5Fcreate(fileName, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
- if (h_file < 0) {
- error("Error while opening file '%s'.", fileName);
- }
-
- /* Open header to write simulation properties */
- /* message("Writing runtime parameters..."); */
- h_grp =
- H5Gcreate(h_file, "/RuntimePars", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
- if (h_grp < 0) error("Error while creating runtime parameters group\n");
-
- /* Write the relevant information */
- io_write_attribute(h_grp, "PeriodicBoundariesOn", INT, &periodic, 1);
- int index = 0;
- io_write_attribute(h_grp, "IsIndexFile", INT, &index, 1);
-
- /* Close runtime parameters */
- H5Gclose(h_grp);
-
- /* Open header to write simulation properties */
- /* message("Writing file header..."); */
- h_grp = H5Gcreate(h_file, "/Header", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
- if (h_grp < 0) error("Error while creating file header\n");
-
- /* Print the relevant information and print status */
- io_write_attribute(h_grp, "BoxSize", DOUBLE, e->s->dim, 3);
- double dblTime = e->time;
- io_write_attribute(h_grp, "Time", DOUBLE, &dblTime, 1);
- int dimension = (int)hydro_dimension;
- io_write_attribute(h_grp, "Dimension", INT, &dimension, 1);
-
- /* GADGET-2 legacy values */
- /* Number of particles of each type */
- unsigned int numParticles[swift_type_count] = {0};
- unsigned int numParticlesHighWord[swift_type_count] = {0};
- for (int ptype = 0; ptype < swift_type_count; ++ptype) {
- numParticles[ptype] = (unsigned int)N_total[ptype];
- numParticlesHighWord[ptype] = (unsigned int)(N_total[ptype] >> 32);
- }
- io_write_attribute(h_grp, "NumPart_ThisFile", LONGLONG, N_total,
- swift_type_count);
- io_write_attribute(h_grp, "NumPart_Total", UINT, numParticles,
- swift_type_count);
- io_write_attribute(h_grp, "NumPart_Total_HighWord", UINT,
- numParticlesHighWord, swift_type_count);
- double MassTable[swift_type_count] = {0};
- io_write_attribute(h_grp, "MassTable", DOUBLE, MassTable, swift_type_count);
- unsigned int flagEntropy[swift_type_count] = {0};
- flagEntropy[0] = writeEntropyFlag();
- io_write_attribute(h_grp, "Flag_Entropy_ICs", UINT, flagEntropy,
- swift_type_count);
- io_write_attribute(h_grp, "NumFilesPerSnapshot", INT, &numFiles, 1);
-
- /* Close header */
- H5Gclose(h_grp);
-
- /* Print the code version */
- io_write_code_description(h_file);
-
- /* Print the SPH parameters */
- if (e->policy & engine_policy_hydro) {
- h_grp = H5Gcreate(h_file, "/HydroScheme", H5P_DEFAULT, H5P_DEFAULT,
- H5P_DEFAULT);
- if (h_grp < 0) error("Error while creating SPH group");
- hydro_props_print_snapshot(h_grp, e->hydro_properties);
- hydro_write_flavour(h_grp);
- H5Gclose(h_grp);
- }
-
- /* Print the gravity parameters */
- if (e->policy & engine_policy_self_gravity) {
- h_grp = H5Gcreate(h_file, "/GravityScheme", H5P_DEFAULT, H5P_DEFAULT,
- H5P_DEFAULT);
- if (h_grp < 0) error("Error while creating gravity group");
- gravity_props_print_snapshot(h_grp, e->gravity_properties);
- H5Gclose(h_grp);
- }
-
- /* Print the runtime parameters */
- h_grp =
- H5Gcreate(h_file, "/Parameters", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
- if (h_grp < 0) error("Error while creating parameters group");
- parser_write_params_to_hdf5(e->parameter_file, h_grp);
- H5Gclose(h_grp);
-
- /* Print the system of Units used in the spashot */
- io_write_unit_system(h_file, snapshot_units, "Units");
-
- /* Print the system of Units used internally */
- io_write_unit_system(h_file, internal_units, "InternalCodeUnits");
-
- /* Tell the user if a conversion will be needed */
- if (e->verbose) {
- if (units_are_equal(snapshot_units, internal_units)) {
-
- message("Snapshot and internal units match. No conversion needed.");
-
- } else {
-
- message("Conversion needed from:");
- message("(Snapshot) Unit system: U_M = %e g.",
- snapshot_units->UnitMass_in_cgs);
- message("(Snapshot) Unit system: U_L = %e cm.",
- snapshot_units->UnitLength_in_cgs);
- message("(Snapshot) Unit system: U_t = %e s.",
- snapshot_units->UnitTime_in_cgs);
- message("(Snapshot) Unit system: U_I = %e A.",
- snapshot_units->UnitCurrent_in_cgs);
- message("(Snapshot) Unit system: U_T = %e K.",
- snapshot_units->UnitTemperature_in_cgs);
- message("to:");
- message("(internal) Unit system: U_M = %e g.",
- internal_units->UnitMass_in_cgs);
- message("(internal) Unit system: U_L = %e cm.",
- internal_units->UnitLength_in_cgs);
- message("(internal) Unit system: U_t = %e s.",
- internal_units->UnitTime_in_cgs);
- message("(internal) Unit system: U_I = %e A.",
- internal_units->UnitCurrent_in_cgs);
- message("(internal) Unit system: U_T = %e K.",
- internal_units->UnitTemperature_in_cgs);
- }
- }
-
- /* Loop over all particle types */
- for (int ptype = 0; ptype < swift_type_count; ptype++) {
-
- /* Don't do anything if no particle of this kind */
- if (numParticles[ptype] == 0) continue;
-
- /* Add the global information for that particle type to the XMF meta-file */
- xmf_write_groupheader(xmfFile, fileName, numParticles[ptype],
- (enum part_type)ptype);
-
- /* Open the particle group in the file */
- char partTypeGroupName[PARTICLE_GROUP_BUFFER_SIZE];
- snprintf(partTypeGroupName, PARTICLE_GROUP_BUFFER_SIZE, "/PartType%d",
- ptype);
- h_grp = H5Gcreate(h_file, partTypeGroupName, H5P_DEFAULT, H5P_DEFAULT,
- H5P_DEFAULT);
- if (h_grp < 0) {
- error("Error while creating particle group.\n");
- }
-
- int num_fields = 0;
- struct io_props list[100];
- size_t N = 0;
-
- /* Write particle fields from the particle structure */
- switch (ptype) {
-
- case swift_type_gas:
- N = Ngas;
- hydro_write_particles(parts, list, &num_fields);
- break;
-
- case swift_type_dark_matter:
- /* Allocate temporary array */
- if (posix_memalign((void*)&dmparts, gpart_align,
- Ndm * sizeof(struct gpart)) != 0)
- error("Error while allocating temporart memory for DM particles");
- bzero(dmparts, Ndm * sizeof(struct gpart));
-
- /* Collect the DM particles from gpart */
- io_collect_dm_gparts(gparts, Ntot, dmparts, Ndm);
-
- /* Write DM particles */
- N = Ndm;
- darkmatter_write_particles(dmparts, list, &num_fields);
- break;
-
- case swift_type_star:
- N = Nstars;
- star_write_particles(sparts, list, &num_fields);
- break;
-
- default:
- error("Particle Type %d not yet supported. Aborting", ptype);
- }
-
- /* Write everything */
- for (int i = 0; i < num_fields; ++i)
- writeArray(e, h_grp, fileName, xmfFile, partTypeGroupName, list[i], N,
- internal_units, snapshot_units);
-
- /* Free temporary array */
- if (dmparts) {
- free(dmparts);
- dmparts = NULL;
- }
-
- /* Close particle group */
- H5Gclose(h_grp);
-
- /* Close this particle group in the XMF file as well */
- xmf_write_groupfooter(xmfFile, (enum part_type)ptype);
- }
-
- /* Write LXMF file descriptor */
- xmf_write_outputfooter(xmfFile, outputCount, e->time);
-
- /* message("Done writing particles..."); */
-
- /* Close file */
- H5Fclose(h_file);
-
- ++outputCount;
-}
-
-
/**
* @brief Writes an HDF5 index file
*
diff --git a/src/logger_io.h b/src/logger_io.h
index c4f245395f38c235c1f1249272c835658a486a7c..208166ac6d6f2e883f3006659a6d3de08908c593 100644
--- a/src/logger_io.h
+++ b/src/logger_io.h
@@ -22,7 +22,7 @@
/* Config parameters. */
#include "../config.h"
-#if defined(HAVE_HDF5) && !defined(WITH_MPI) && defined(WITH_LOGGER)
+#ifdef WITH_LOGGER
/* Includes. */
#include "engine.h"
diff --git a/src/parallel_io.c b/src/parallel_io.c
index 44149480b572ec41c4c85b6957156a8ae75757ba..e1a9d2c068040192654a560508b0ede7544f1b3e 100644
--- a/src/parallel_io.c
+++ b/src/parallel_io.c
@@ -21,7 +21,7 @@
/* Config parameters. */
#include "../config.h"
-#if defined(HAVE_HDF5) && defined(WITH_MPI) && defined(HAVE_PARALLEL_HDF5) && !defined(WITH_LOGGER)
+#if defined(HAVE_HDF5) && defined(WITH_MPI) && defined(HAVE_PARALLEL_HDF5)
/* Some standard headers. */
#include <hdf5.h>
diff --git a/src/parallel_io.h b/src/parallel_io.h
index 1805d9c4a99fdf3bb55959fbb238aeffbee18615..2de83265f3ff964ae4808da14a8db6aff635cd3c 100644
--- a/src/parallel_io.h
+++ b/src/parallel_io.h
@@ -46,6 +46,13 @@ void write_output_parallel(struct engine* e, const char* baseName,
const struct unit_system* snapshot_units,
int mpi_rank, int mpi_size, MPI_Comm comm,
MPI_Info info);
+
+void writeArray(struct engine* e, hid_t grp, char* fileName, FILE* xmfFile,
+ char* partTypeGroupName, struct io_props props, size_t N,
+ long long N_total, int mpi_rank, long long offset,
+ const struct unit_system* internal_units,
+ const struct unit_system* snapshot_units);
+
#endif
#endif /* SWIFT_PARALLEL_IO_H */
diff --git a/src/serial_io.c b/src/serial_io.c
index 042c60cba129db374565782585821b605f9f3f20..8e63f9b72ebe0df5881b1dbf6b43631f9ed79a0e 100644
--- a/src/serial_io.c
+++ b/src/serial_io.c
@@ -21,7 +21,7 @@
/* Config parameters. */
#include "../config.h"
-#if defined(HAVE_HDF5) && defined(WITH_MPI) && !defined(HAVE_PARALLEL_HDF5) && !defined(WITH_LOGGER)
+#if defined(HAVE_HDF5) && defined(WITH_MPI) && !defined(HAVE_PARALLEL_HDF5)
/* Some standard headers. */
#include <hdf5.h>
diff --git a/src/serial_io.h b/src/serial_io.h
index f6280085e2ac294301017768126eec8c8f2c3d0e..d46e9687546d93af9c99339cdbe1d7dd72c87116 100644
--- a/src/serial_io.h
+++ b/src/serial_io.h
@@ -48,6 +48,12 @@ void write_output_serial(struct engine* e, const char* baseName,
const struct unit_system* snapshot_units, int mpi_rank,
int mpi_size, MPI_Comm comm, MPI_Info info);
+void writeArray(const struct engine* e, hid_t grp, char* fileName,
+ FILE* xmfFile, char* partTypeGroupName,
+ const struct io_props props, size_t N, long long N_total,
+ int mpi_rank, long long offset,
+ const struct unit_system* internal_units,
+ const struct unit_system* snapshot_units);
#endif
#endif /* SWIFT_SERIAL_IO_H */
diff --git a/src/single_io.c b/src/single_io.c
index a8d208b267384a9eb9ce59a5f17644828bd31d2c..d3c46a58bd375a7412774c36e86ce2b36173f333 100644
--- a/src/single_io.c
+++ b/src/single_io.c
@@ -21,7 +21,7 @@
/* Config parameters. */
#include "../config.h"
-#if defined(HAVE_HDF5) && !defined(WITH_MPI) && !defined(WITH_LOGGER)
+#if defined(HAVE_HDF5) && !defined(WITH_MPI)
/* Some standard headers. */
#include <hdf5.h>
diff --git a/src/single_io.h b/src/single_io.h
index aef5d1c8b667d4694981031cb691bbceb249950c..390a3aac149a9ab1c31cc24769c1d7a8d17e48e2 100644
--- a/src/single_io.h
+++ b/src/single_io.h
@@ -26,6 +26,7 @@
/* Includes. */
#include "engine.h"
+#include "io_properties.h"
#include "part.h"
#include "units.h"
@@ -46,6 +47,10 @@ void write_index_single(struct engine* e, const char* baseName,
const struct unit_system* internal_units,
const struct unit_system* snapshot_units);
-#endif /* HAVE_HDF5 && !WITH_MPI */
+void writeArray(const struct engine* e, hid_t grp, char* fileName,
+ FILE* xmfFile, char* partTypeGroupName,
+ const struct io_props props, size_t N,
+ const struct unit_system* internal_units,
+ const struct unit_system* snapshot_units);
#endif /* SWIFT_SINGLE_IO_H */