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 */