diff --git a/examples/main.c b/examples/main.c
index c88f92a07a747c327692b5e0fbbc7dc07b93ac0c..2b33a12eb8737b3dfb7ef35c0cdc10df5ab5ac82 100644
--- a/examples/main.c
+++ b/examples/main.c
@@ -1,3 +1,4 @@
+
/*******************************************************************************
* This file is part of SWIFT.
* Copyright (c) 2012 Pedro Gonnet (pedro.gonnet@durham.ac.uk),
@@ -79,7 +80,9 @@ int main(int argc, char *argv[]) {
int nr_nodes = 1, myrank = 0;
FILE *file_thread;
int with_outputs = 1;
- int verbose = 0, talking;
+ int with_gravity = 0;
+ int engine_policies = 0;
+ int verbose = 0, talking = 0;
unsigned long long cpufreq = 0;
#ifdef WITH_MPI
@@ -97,8 +100,11 @@ int main(int argc, char *argv[]) {
#endif
#endif
-/* Choke on FP-exceptions. */
-// feenableexcept( FE_DIVBYZERO | FE_INVALID | FE_OVERFLOW );
+ /* Choke on FP-exceptions. */
+ // feenableexcept( FE_DIVBYZERO | FE_INVALID | FE_OVERFLOW );
+
+ /* Initialize CPU frequency, this also starts time. */
+ clocks_set_cpufreq(cpufreq);
#ifdef WITH_MPI
/* Start by initializing MPI. */
@@ -128,9 +134,6 @@ int main(int argc, char *argv[]) {
&initial_partition.grid[1], &initial_partition.grid[0]);
#endif
- /* Initialize CPU frequency, this also starts time. */
- clocks_set_cpufreq(cpufreq);
-
/* Greeting message */
if (myrank == 0) greetings();
@@ -156,7 +159,7 @@ int main(int argc, char *argv[]) {
bzero(&s, sizeof(struct space));
/* Parse the options */
- while ((c = getopt(argc, argv, "a:c:d:e:f:h:m:oP:q:R:s:t:v:w:y:z:")) != -1)
+ while ((c = getopt(argc, argv, "a:c:d:e:f:gh:m:oP:q:R:s:t:v:w:y:z:")) != -1)
switch (c) {
case 'a':
if (sscanf(optarg, "%lf", &scaling) != 1)
@@ -185,6 +188,9 @@ int main(int argc, char *argv[]) {
case 'f':
if (!strcpy(ICfileName, optarg)) error("Error parsing IC file name.");
break;
+ case 'g':
+ with_gravity = 1;
+ break;
case 'h':
if (sscanf(optarg, "%llu", &cpufreq) != 1)
error("Error parsing CPU frequency.");
@@ -359,8 +365,8 @@ int main(int argc, char *argv[]) {
read_ic_parallel(ICfileName, dim, &parts, &Ngas, &periodic, myrank, nr_nodes,
MPI_COMM_WORLD, MPI_INFO_NULL);
#else
- read_ic_serial(ICfileName, dim, &parts, &Ngas, &periodic, myrank, nr_nodes,
- MPI_COMM_WORLD, MPI_INFO_NULL);
+ read_ic_serial(ICfileName, dim, &parts, &gparts, &Ngas, &Ngpart, &periodic,
+ myrank, nr_nodes, MPI_COMM_WORLD, MPI_INFO_NULL);
#endif
#else
read_ic_single(ICfileName, dim, &parts, &gparts, &Ngas, &Ngpart, &periodic);
@@ -376,6 +382,7 @@ int main(int argc, char *argv[]) {
#if defined(WITH_MPI)
long long N_long[2] = {Ngas, Ngpart};
MPI_Reduce(&N_long, &N_total, 2, MPI_LONG_LONG, MPI_SUM, 0, MPI_COMM_WORLD);
+ N_total[1] -= N_total[0];
if (myrank == 0)
message("Read %lld gas particles and %lld DM particles from the ICs",
N_total[0], N_total[1]);
@@ -383,9 +390,34 @@ int main(int argc, char *argv[]) {
N_total[0] = Ngas;
N_total[1] = Ngpart - Ngas;
message("Read %lld gas particles and %lld DM particles from the ICs",
- N_total[0], N_total[1]);
+ N_total[0], N_total[1]);
#endif
+ /* MATTHIEU: Temporary fix to preserve master */
+ if (!with_gravity) {
+ free(gparts);
+ for(size_t k = 0; k < Ngas; ++k)
+ parts[k].gpart = NULL;
+ Ngpart = 0;
+#if defined(WITH_MPI)
+ N_long[0] = Ngas;
+ N_long[1] = Ngpart;
+ MPI_Reduce(&N_long, &N_total, 2, MPI_LONG_LONG, MPI_SUM, 0, MPI_COMM_WORLD);
+ if (myrank == 0)
+ message(
+ "AFTER FIX: Read %lld gas particles and %lld DM particles from the "
+ "ICs",
+ N_total[0], N_total[1]);
+#else
+ N_total[0] = Ngas;
+ N_total[1] = Ngpart;
+ message(
+ "AFTER FIX: Read %lld gas particles and %lld DM particles from the ICs",
+ N_total[0], N_total[1]);
+#endif
+ }
+ /* MATTHIEU: End temporary fix */
+
/* Apply h scaling */
if (scaling != 1.0)
for (size_t k = 0; k < Ngas; k++) parts[k].h *= scaling;
@@ -448,12 +480,15 @@ int main(int argc, char *argv[]) {
message("nr of cells at depth %i is %i.", data[0], data[1]);
}
+ /* Construct the engine policy */
+ engine_policies = ENGINE_POLICY | engine_policy_steal | engine_policy_hydro;
+ if (with_gravity) engine_policies |= engine_policy_external_gravity;
+
/* Initialize the engine with this space. */
if (myrank == 0) clocks_gettime(&tic);
if (myrank == 0) message("nr_nodes is %i.", nr_nodes);
engine_init(&e, &s, dt_max, nr_threads, nr_queues, nr_nodes, myrank,
- ENGINE_POLICY | engine_policy_steal | engine_policy_hydro, 0,
- time_end, dt_min, dt_max, talking);
+ engine_policies, 0, time_end, dt_min, dt_max, talking);
if (myrank == 0 && verbose) {
clocks_gettime(&toc);
message("engine_init took %.3f %s.", clocks_diff(&tic, &toc),
diff --git a/src/common_io.c b/src/common_io.c
index f6a4803333581b69671e3adc223b46122ec5364c..4be334ccd602c7b0c450f5dbe4aedd9155b35ff1 100644
--- a/src/common_io.c
+++ b/src/common_io.c
@@ -489,7 +489,8 @@ void prepare_dm_gparts(struct gpart* gparts, size_t Ndm) {
for (size_t i = 0; i < Ndm; ++i) {
/* 0 or negative ids are not allowed */
- if (gparts[i].id <= 0) error("0 or negative ID for DM particle");
+ if (gparts[i].id <= 0)
+ error("0 or negative ID for DM particle %zd: ID=%lld", i, gparts[i].id);
gparts[i].id = -gparts[i].id;
}
diff --git a/src/common_io.h b/src/common_io.h
index 2623a03f9a25ce0e650dde4f698da6eb49177e26..426fa6a01ec87a4413eceaaeb0d0880cbef8a214 100644
--- a/src/common_io.h
+++ b/src/common_io.h
@@ -70,6 +70,9 @@ enum PARTICLE_TYPE {
NUM_PARTICLE_TYPES
};
+#define FILENAME_BUFFER_SIZE 150
+#define PARTICLE_GROUP_BUFFER_SIZE 20
+
hid_t hdf5Type(enum DATA_TYPE type);
size_t sizeOfType(enum DATA_TYPE type);
diff --git a/src/engine.c b/src/engine.c
index 5a89555c988fc5d4f5456e75b6fab67f03469fe6..d5c748d9daea6f34fedb35563ed3a0ec611490d3 100644
--- a/src/engine.c
+++ b/src/engine.c
@@ -2014,6 +2014,7 @@ void engine_init(struct engine *e, struct space *s, float dt, int nr_threads,
e->dt_max = dt_max;
e->file_stats = NULL;
e->verbose = verbose;
+ e->count_step = 0;
e->wallclock_time = 0.f;
engine_rank = nodeID;
diff --git a/src/gravity/Default/gravity_part.h b/src/gravity/Default/gravity_part.h
index 7ce7b81892582f2a90f7dd07f7f244c0d4ed8afb..aaaab2055d8ce05d77a37d3f40e096bd91d87926 100644
--- a/src/gravity/Default/gravity_part.h
+++ b/src/gravity/Default/gravity_part.h
@@ -50,4 +50,4 @@ struct gpart {
struct part* part;
};
-} __attribute__((aligned(part_align)));
+} __attribute__((aligned(gpart_align)));
diff --git a/src/serial_io.c b/src/serial_io.c
index 8e63db5cfad3a3b50fc7e350bbac6ce09708230a..3fb1a1d1b743e48be4e8e6d81413c28e8034b870 100644
--- a/src/serial_io.c
+++ b/src/serial_io.c
@@ -68,7 +68,8 @@
*/
void readArrayBackEnd(hid_t grp, char* name, enum DATA_TYPE type, int N,
int dim, long long N_total, long long offset,
- char* part_c, enum DATA_IMPORTANCE importance) {
+ char* part_c, size_t partSize,
+ enum DATA_IMPORTANCE importance) {
hid_t h_data = 0, h_err = 0, h_type = 0, h_memspace = 0, h_filespace = 0;
hsize_t shape[2], offsets[2];
htri_t exist = 0;
@@ -76,7 +77,6 @@ void readArrayBackEnd(hid_t grp, char* name, enum DATA_TYPE type, int N,
int i = 0, rank = 0;
const size_t typeSize = sizeOfType(type);
const size_t copySize = typeSize * dim;
- const size_t partSize = sizeof(struct part);
char* temp_c = 0;
/* Check whether the dataspace exists or not */
@@ -270,7 +270,7 @@ void prepareArray(hid_t grp, char* fileName, FILE* xmfFile, char* name,
void writeArrayBackEnd(hid_t grp, char* fileName, FILE* xmfFile, char* name,
enum DATA_TYPE type, int N, int dim, long long N_total,
int mpi_rank, long long offset, char* part_c,
- struct UnitSystem* us,
+ size_t partSize, struct UnitSystem* us,
enum UnitConversionFactor convFactor) {
hid_t h_data = 0, h_err = 0, h_memspace = 0, h_filespace = 0;
@@ -279,7 +279,6 @@ void writeArrayBackEnd(hid_t grp, char* fileName, FILE* xmfFile, char* name,
int i = 0, rank = 0;
const size_t typeSize = sizeOfType(type);
const size_t copySize = typeSize * dim;
- const size_t partSize = sizeof(struct part);
char* temp_c = 0;
/* message("Writing '%s' array...", name); */
@@ -362,7 +361,7 @@ void writeArrayBackEnd(hid_t grp, char* fileName, FILE* xmfFile, char* name,
#define readArray(grp, name, type, N, dim, part, N_total, offset, field, \
importance) \
readArrayBackEnd(grp, name, type, N, dim, N_total, offset, \
- (char*)(&(part[0]).field), importance)
+ (char*)(&(part[0]).field), sizeof(part[0]), importance)
/**
* @brief A helper macro to call the readArrayBackEnd function more easily.
@@ -385,20 +384,28 @@ void writeArrayBackEnd(hid_t grp, char* fileName, FILE* xmfFile, char* name,
#define writeArray(grp, fileName, xmfFile, name, type, N, dim, part, N_total, \
mpi_rank, offset, field, us, convFactor) \
writeArrayBackEnd(grp, fileName, xmfFile, name, type, N, dim, N_total, \
- mpi_rank, offset, (char*)(&(part[0]).field), us, \
- convFactor)
+ mpi_rank, offset, (char*)(&(part[0]).field), \
+ sizeof(part[0]), us, convFactor)
/* Import the right hydro definition */
#include "hydro_io.h"
+/* Import the right gravity definition */
+#include "gravity_io.h"
/**
* @brief Reads an HDF5 initial condition file (GADGET-3 type)
*
* @param fileName The file to read.
* @param dim (output) The dimension of the volume read from the file.
- * @param parts (output) The array of #part read from the file.
- * @param N (output) The number of particles read from the file.
+ * @param parts (output) The array of #part (gas particles) read from the file.
+ * @param gparts (output) The array of #gpart read from the file.
+ * @param Ngas (output) The number of #part read from the file on that node.
+ * @param Ngparts (output) The number of #gpart read from the file on that node.
* @param periodic (output) 1 if the volume is periodic, 0 if not.
+ * @param mpi_rank The MPI rank of this node
+ * @param mpi_size The number of MPI ranks
+ * @param comm The MPI communicator
+ * @param info The MPI information object
*
* Opens the HDF5 file fileName and reads the particles contained
* in the parts array. N is the returned number of particles found
@@ -411,17 +418,18 @@ void writeArrayBackEnd(hid_t grp, char* fileName, FILE* xmfFile, char* name,
*
*/
void read_ic_serial(char* fileName, double dim[3], struct part** parts,
- size_t* N, int* periodic, int mpi_rank, int mpi_size,
- MPI_Comm comm, MPI_Info info) {
+ struct gpart** gparts, size_t* Ngas, size_t* Ngparts,
+ int* periodic, int mpi_rank, int mpi_size, MPI_Comm comm,
+ MPI_Info info) {
hid_t h_file = 0, h_grp = 0;
- double boxSize[3] = {0.0, -1.0, -1.0};
/* GADGET has only cubic boxes (in cosmological mode) */
- int numParticles[6] = {0};
- /* GADGET has 6 particle types. We only keep the type 0*/
- int numParticles_highWord[6] = {0};
- long long offset = 0;
- long long N_total = 0;
- int rank;
+ 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[NUM_PARTICLE_TYPES] = {0};
+ int numParticles_highWord[NUM_PARTICLE_TYPES] = {0};
+ size_t N[NUM_PARTICLE_TYPES] = {0};
+ long long N_total[NUM_PARTICLE_TYPES] = {0};
+ long long offset[NUM_PARTICLE_TYPES] = {0};
/* First read some information about the content */
if (mpi_rank == 0) {
@@ -453,8 +461,10 @@ void read_ic_serial(char* fileName, double dim[3], struct part** parts,
readAttribute(h_grp, "NumPart_Total", UINT, numParticles);
readAttribute(h_grp, "NumPart_Total_HighWord", UINT, numParticles_highWord);
- N_total = ((long long)numParticles[0]) +
- ((long long)numParticles_highWord[0] << 32);
+ for (int ptype = 0; ptype < NUM_PARTICLE_TYPES; ++ptype)
+ N_total[ptype] = ((long long)numParticles[ptype]) +
+ ((long long)numParticles_highWord[ptype] << 32);
+
dim[0] = boxSize[0];
dim[1] = (boxSize[1] < 0) ? boxSize[0] : boxSize[1];
dim[2] = (boxSize[2] < 0) ? boxSize[0] : boxSize[2];
@@ -474,22 +484,38 @@ void read_ic_serial(char* fileName, double dim[3], struct part** parts,
/* Now need to broadcast that information to all ranks. */
MPI_Bcast(periodic, 1, MPI_INT, 0, comm);
- MPI_Bcast(&N_total, 1, MPI_LONG_LONG, 0, comm);
+ MPI_Bcast(&N_total, NUM_PARTICLE_TYPES, MPI_LONG_LONG, 0, comm);
MPI_Bcast(dim, 3, MPI_DOUBLE, 0, comm);
/* Divide the particles among the tasks. */
- offset = mpi_rank * N_total / mpi_size;
- *N = (mpi_rank + 1) * N_total / mpi_size - offset;
+ for (int ptype = 0; ptype < NUM_PARTICLE_TYPES; ++ptype) {
+ offset[ptype] = mpi_rank * N_total[ptype] / mpi_size;
+ N[ptype] = (mpi_rank + 1) * N_total[ptype] / mpi_size - offset[ptype];
+ }
- /* Allocate memory to store particles */
- if (posix_memalign((void*)parts, part_align, (*N) * sizeof(struct part)) != 0)
+ /* Allocate memory to store SPH particles */
+ *Ngas = N[0];
+ if (posix_memalign((void*)parts, part_align, (*Ngas) * sizeof(struct part)) !=
+ 0)
error("Error while allocating memory for particles");
- bzero(*parts, *N * sizeof(struct part));
+ bzero(*parts, *Ngas * sizeof(struct part));
+
+ /* Allocate memory to store all particles */
+ const size_t Ndm = N[1];
+ *Ngparts = N[1] + N[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); */
+
/* Now loop over ranks and read the data */
- for (rank = 0; rank < mpi_size; ++rank) {
+ for (int rank = 0; rank < mpi_size; ++rank) {
/* Is it this rank's turn to read ? */
if (rank == mpi_rank) {
@@ -498,17 +524,41 @@ void read_ic_serial(char* fileName, double dim[3], struct part** parts,
if (h_file < 0)
error("Error while opening file '%s' on rank %d.", fileName, mpi_rank);
- /* Open SPH particles group */
- /* message("Reading particle arrays..."); */
- h_grp = H5Gopen(h_file, "/PartType0", H5P_DEFAULT);
- if (h_grp < 0)
- error("Error while opening particle group on rank %d.\n", mpi_rank);
+ /* Loop over all particle types */
+ for (int ptype = 0; ptype < NUM_PARTICLE_TYPES; ptype++) {
- /* Read particle fields into the particle structure */
- hydro_read_particles(h_grp, *N, N_total, offset, *parts);
+ /* Don't do anything if no particle of this kind */
+ if (N[ptype] == 0) continue;
- /* Close particle group */
- H5Gclose(h_grp);
+ /* 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);
+ }
+
+ /* Read particle fields into the particle structure */
+ switch (ptype) {
+
+ case GAS:
+ hydro_read_particles(h_grp, N[ptype], N_total[ptype], offset[ptype],
+ *parts);
+ break;
+
+ case DM:
+ darkmatter_read_particles(h_grp, N[ptype], N_total[ptype],
+ offset[ptype], *gparts);
+ break;
+
+ default:
+ error("Particle Type %d not yet supported. Aborting", ptype);
+ }
+
+ /* Close particle group */
+ H5Gclose(h_grp);
+ }
/* Close file */
H5Fclose(h_file);
@@ -518,6 +568,12 @@ void read_ic_serial(char* fileName, double dim[3], struct part** parts,
MPI_Barrier(comm);
}
+ /* Prepare the DM particles */
+ prepare_dm_gparts(*gparts, Ndm);
+
+ /* Now duplicate the hydro particle into gparts */
+ duplicate_hydro_gparts(*parts, *gparts, *Ngas, Ndm);
+
/* message("Done Reading particles..."); */
}
@@ -525,7 +581,11 @@ void read_ic_serial(char* fileName, double dim[3], struct part** parts,
* @brief Writes an HDF5 output file (GADGET-3 type) with its XMF descriptor
*
* @param e The engine containing all the system.
- * @param us The UnitSystem used for the conversion of units in the output
+ * @param us The UnitSystem used for the conversion of units in the output.
+ * @param mpi_rank The MPI rank of this node.
+ * @param mpi_size The number of MPI ranks.
+ * @param comm The MPI communicator.
+ * @param info The MPI information object
*
* Creates an HDF5 output file and writes the particles contained
* in the engine. If such a file already exists, it is erased and replaced
@@ -538,35 +598,40 @@ void read_ic_serial(char* fileName, double dim[3], struct part** parts,
void write_output_serial(struct engine* e, struct UnitSystem* us, int mpi_rank,
int mpi_size, MPI_Comm comm, MPI_Info info) {
hid_t h_file = 0, h_grp = 0, h_grpsph = 0;
- int N = e->s->nr_parts;
+ const size_t Ngas = e->s->nr_parts;
+ const size_t Ntot = e->s->nr_gparts;
int periodic = e->s->periodic;
- int numParticles[6] = {N, 0};
- int numParticlesHighWord[6] = {0};
- unsigned int flagEntropy[6] = {0};
- long long N_total = 0, offset = 0;
- double offset_d = 0., N_d = 0., N_total_d = 0.;
int numFiles = 1;
- int rank = 0;
struct part* parts = e->s->parts;
- FILE* xmfFile = 0;
+ struct gpart* gparts = e->s->gparts;
+ struct gpart* dmparts = NULL;
static int outputCount = 0;
+ FILE* xmfFile = 0;
+ /* Number of particles of each type */
+ //const size_t Ndm = Ntot - Ngas;
+
+ /* MATTHIEU: Temporary fix to preserve master */
+ const size_t Ndm = Ntot > 0 ? Ntot - Ngas: 0;
+ /* MATTHIEU: End temporary fix */
+
/* File name */
- char fileName[200];
- sprintf(fileName, "output_%03i.hdf5", outputCount);
+ char fileName[FILENAME_BUFFER_SIZE];
+ snprintf(fileName, FILENAME_BUFFER_SIZE, "output_%03i.hdf5", outputCount);
/* Compute offset in the file and total number of particles */
- /* Done using double to allow for up to 2^50=10^15 particles */
- N_d = (double)N;
- MPI_Exscan(&N_d, &offset_d, 1, MPI_DOUBLE, MPI_SUM, comm);
- N_total_d = offset_d + N_d;
- MPI_Bcast(&N_total_d, 1, MPI_DOUBLE, mpi_size - 1, comm);
- if (N_total_d > 1.e15)
- error(
- "Error while computing the offset for parallel output: Simulation has "
- "more than 10^15 particles.\n");
- N_total = (long long)N_total_d;
- offset = (long long)offset_d;
+ size_t N[NUM_PARTICLE_TYPES] = {Ngas, Ndm, 0};
+ long long N_total[NUM_PARTICLE_TYPES] = {0};
+ long long offset[NUM_PARTICLE_TYPES] = {0};
+ MPI_Exscan(&N, &offset, NUM_PARTICLE_TYPES, MPI_LONG_LONG, MPI_SUM, comm);
+ for (int ptype = 0; ptype < NUM_PARTICLE_TYPES; ++ptype)
+ N_total[ptype] = offset[ptype] + N[ptype];
+
+ /* The last rank now has the correct N_total. Let's broadcast from there */
+ MPI_Bcast(&N_total, 6, MPI_LONG_LONG, mpi_size - 1, comm);
+
+ /* Now everybody konws its offset and the total number of particles of each
+ * type */
/* Do common stuff first */
if (mpi_rank == 0) {
@@ -578,7 +643,7 @@ void write_output_serial(struct engine* e, struct UnitSystem* us, int mpi_rank,
xmfFile = prepareXMFfile();
/* Write the part corresponding to this specific output */
- writeXMFheader(xmfFile, N_total, fileName, e->time);
+ // writeXMFheader(xmfFile, N_total, fileName, e->time);
/* Open file */
/* message("Opening file '%s'.", fileName); */
@@ -610,15 +675,24 @@ void write_output_serial(struct engine* e, struct UnitSystem* us, int mpi_rank,
writeAttribute(h_grp, "Time", DOUBLE, &dblTime, 1);
/* GADGET-2 legacy values */
- numParticles[0] = (unsigned int)N_total;
- writeAttribute(h_grp, "NumPart_ThisFile", UINT, numParticles, 6);
- writeAttribute(h_grp, "NumPart_Total", UINT, numParticles, 6);
- numParticlesHighWord[0] = (unsigned int)(N_total >> 32);
+ /* Number of particles of each type */
+ unsigned int numParticles[NUM_PARTICLE_TYPES] = {0};
+ unsigned int numParticlesHighWord[NUM_PARTICLE_TYPES] = {0};
+ for (int ptype = 0; ptype < NUM_PARTICLE_TYPES; ++ptype) {
+ numParticles[ptype] = (unsigned int)N_total[ptype];
+ numParticlesHighWord[ptype] = (unsigned int)(N_total[ptype] >> 32);
+ }
+ writeAttribute(h_grp, "NumPart_ThisFile", LONGLONG, N_total,
+ NUM_PARTICLE_TYPES);
+ writeAttribute(h_grp, "NumPart_Total", UINT, numParticles,
+ NUM_PARTICLE_TYPES);
writeAttribute(h_grp, "NumPart_Total_HighWord", UINT, numParticlesHighWord,
- 6);
+ NUM_PARTICLE_TYPES);
double MassTable[6] = {0., 0., 0., 0., 0., 0.};
- writeAttribute(h_grp, "MassTable", DOUBLE, MassTable, 6);
- writeAttribute(h_grp, "Flag_Entropy_ICs", UINT, flagEntropy, 6);
+ writeAttribute(h_grp, "MassTable", DOUBLE, MassTable, NUM_PARTICLE_TYPES);
+ unsigned int flagEntropy[NUM_PARTICLE_TYPES] = {0};
+ writeAttribute(h_grp, "Flag_Entropy_ICs", UINT, flagEntropy,
+ NUM_PARTICLE_TYPES);
writeAttribute(h_grp, "NumFilesPerSnapshot", INT, &numFiles, 1);
/* Close header */
@@ -636,21 +710,32 @@ void write_output_serial(struct engine* e, struct UnitSystem* us, int mpi_rank,
/* Print the system of Units */
writeUnitSystem(h_file, us);
- /* Create SPH particles group */
- /* message("Writing particle arrays..."); */
- h_grp =
- H5Gcreate(h_file, "/PartType0", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
- if (h_grp < 0) error("Error while creating particle group.\n");
+ /* Loop over all particle types */
+ for (int ptype = 0; ptype < NUM_PARTICLE_TYPES; ptype++) {
- /* Close particle group */
- H5Gclose(h_grp);
+ /* Don't do anything if no particle of this kind */
+ if (N_total[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 = H5Gcreate(h_file, partTypeGroupName, H5P_DEFAULT, H5P_DEFAULT,
+ H5P_DEFAULT);
+ if (h_grp < 0) {
+ error("Error while creating particle group.\n");
+ }
+
+ /* Close particle group */
+ H5Gclose(h_grp);
+ }
/* Close file */
H5Fclose(h_file);
}
/* Now loop over ranks and write the data */
- for (rank = 0; rank < mpi_size; ++rank) {
+ for (int rank = 0; rank < mpi_size; ++rank) {
/* Is it this rank's turn to write ? */
if (rank == mpi_rank) {
@@ -659,18 +744,57 @@ void write_output_serial(struct engine* e, struct UnitSystem* us, int mpi_rank,
if (h_file < 0)
error("Error while opening file '%s' on rank %d.", fileName, mpi_rank);
- /* Open SPH particles group */
- /* message("Reading particle arrays..."); */
- h_grp = H5Gopen(h_file, "/PartType0", H5P_DEFAULT);
- if (h_grp < 0)
- error("Error while opening particle group on rank %d.\n", mpi_rank);
-
- /* Write particle fields from the particle structure */
- hydro_write_particles(h_grp, fileName, xmfFile, N, N_total, mpi_rank,
- offset, parts, us);
-
- /* Close particle group */
- H5Gclose(h_grp);
+ /* Loop over all particle types */
+ for (int ptype = 0; ptype < NUM_PARTICLE_TYPES; ptype++) {
+
+ /* Don't do anything if no particle of this kind */
+ if (N_total[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);
+ }
+
+ /* Read particle fields into the particle structure */
+ switch (ptype) {
+
+ case GAS:
+ hydro_write_particles(h_grp, fileName, xmfFile, N[ptype],
+ N_total[ptype], mpi_rank, offset[ptype],
+ parts, us);
+
+ break;
+
+ case DM:
+ /* 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 */
+ collect_dm_gparts(gparts, Ntot, dmparts, Ndm);
+
+ /* Write DM particles */
+ darkmatter_write_particles(h_grp, fileName, xmfFile, N[ptype],
+ N_total[ptype], mpi_rank, offset[ptype],
+ dmparts, us);
+
+ /* Free temporary array */
+ free(dmparts);
+ break;
+
+ default:
+ error("Particle Type %d not yet supported. Aborting", ptype);
+ }
+
+ /* Close particle group */
+ H5Gclose(h_grp);
+ }
/* Close file */
H5Fclose(h_file);
diff --git a/src/serial_io.h b/src/serial_io.h
index 95f09f5977a97a359e978db7a1b71b02030d6a14..5a34d420cfabd88d4147e3f3630e0efe89951c41 100644
--- a/src/serial_io.h
+++ b/src/serial_io.h
@@ -32,8 +32,9 @@
#if defined(HAVE_HDF5) && defined(WITH_MPI) && !defined(HAVE_PARALLEL_HDF5)
void read_ic_serial(char* fileName, double dim[3], struct part** parts,
- size_t* N, int* periodic, int mpi_rank, int mpi_size,
- MPI_Comm comm, MPI_Info info);
+ struct gpart** gparts, size_t* Ngas, size_t* Ngparts,
+ int* periodic, int mpi_rank, int mpi_size, MPI_Comm comm,
+ MPI_Info info);
void write_output_serial(struct engine* e, struct UnitSystem* us, int mpi_rank,
int mpi_size, MPI_Comm comm, MPI_Info info);
diff --git a/src/single_io.c b/src/single_io.c
index 59686a68b5d9e5ea41267ba7b3aad9391862fae4..54ace5c4e369cd6b9a02d44f8a8f03ef6cbadd5f 100644
--- a/src/single_io.c
+++ b/src/single_io.c
@@ -39,9 +39,6 @@
#include "common_io.h"
#include "error.h"
-#define FILENAME_BUFFER_SIZE 150
-#define PARTICLE_GROUP_BUFFER_SIZE 20
-
/*-----------------------------------------------------------------------------
* Routines reading an IC file
*-----------------------------------------------------------------------------*/
@@ -66,14 +63,14 @@
* Calls #error() if an error occurs.
*/
void readArrayBackEnd(hid_t grp, char* name, enum DATA_TYPE type, int N,
- int dim, char* part_c, enum DATA_IMPORTANCE importance) {
+ int dim, char* part_c, size_t partSize,
+ enum DATA_IMPORTANCE importance) {
hid_t h_data = 0, h_err = 0, h_type = 0;
htri_t exist = 0;
void* temp;
int i = 0;
const size_t typeSize = sizeOfType(type);
const size_t copySize = typeSize * dim;
- const size_t partSize = sizeof(struct part);
char* temp_c = 0;
/* Check whether the dataspace exists or not */
@@ -158,14 +155,13 @@ void readArrayBackEnd(hid_t grp, char* name, enum DATA_TYPE type, int N,
*/
void writeArrayBackEnd(hid_t grp, char* fileName, FILE* xmfFile, char* name,
enum DATA_TYPE type, int N, int dim, char* part_c,
- struct UnitSystem* us,
+ size_t partSize, struct UnitSystem* us,
enum UnitConversionFactor convFactor) {
hid_t h_data = 0, h_err = 0, h_space = 0, h_prop = 0;
void* temp = 0;
int i = 0, rank = 0;
const size_t typeSize = sizeOfType(type);
const size_t copySize = typeSize * dim;
- const size_t partSize = sizeof(struct part);
char* temp_c = 0;
hsize_t shape[2];
hsize_t chunk_shape[2];
@@ -204,7 +200,7 @@ void writeArrayBackEnd(hid_t grp, char* fileName, FILE* xmfFile, char* name,
/* Make sure the chunks are not larger than the dataset */
if (chunk_shape[0] > N) chunk_shape[0] = N;
-
+
/* Change shape of data space */
h_err = H5Sset_extent_simple(h_space, rank, shape, NULL);
if (h_err < 0) {
@@ -276,7 +272,7 @@ void writeArrayBackEnd(hid_t grp, char* fileName, FILE* xmfFile, char* name,
#define readArray(grp, name, type, N, dim, part, N_total, offset, field, \
importance) \
readArrayBackEnd(grp, name, type, N, dim, (char*)(&(part[0]).field), \
- importance)
+ sizeof(part[0]), importance)
/**
* @brief A helper macro to call the readArrayBackEnd function more easily.
@@ -301,7 +297,8 @@ void writeArrayBackEnd(hid_t grp, char* fileName, FILE* xmfFile, char* name,
#define writeArray(grp, fileName, xmfFile, name, type, N, dim, part, N_total, \
mpi_rank, offset, field, us, convFactor) \
writeArrayBackEnd(grp, fileName, xmfFile, name, type, N, dim, \
- (char*)(&(part[0]).field), us, convFactor)
+ (char*)(&(part[0]).field), sizeof(part[0]), us, \
+ convFactor)
/* Import the right hydro definition */
#include "hydro_io.h"
@@ -314,9 +311,9 @@ void writeArrayBackEnd(hid_t grp, char* fileName, FILE* xmfFile, char* name,
* @param fileName The file to read.
* @param dim (output) The dimension of the volume.
* @param parts (output) Array of Gas particles.
- * @param gparts (output) Array of DM particles.
+ * @param gparts (output) Array of #gpart particles.
* @param Ngas (output) number of Gas particles read.
- * @param Ngparts (output) The number of DM particles read.
+ * @param Ngparts (output) The number of #gpart read.
* @param periodic (output) 1 if the volume is periodic, 0 if not.
*
* Opens the HDF5 file fileName and reads the particles contained
@@ -337,6 +334,8 @@ void read_ic_single(char* fileName, double dim[3], struct part** parts,
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[NUM_PARTICLE_TYPES] = {0};
+ int numParticles_highWord[NUM_PARTICLE_TYPES] = {0};
+ size_t N[NUM_PARTICLE_TYPES] = {0};
size_t Ndm;
/* Open file */
@@ -365,9 +364,12 @@ void read_ic_single(char* fileName, double dim[3], struct part** parts,
/* Read the relevant information and print status */
readAttribute(h_grp, "BoxSize", DOUBLE, boxSize);
readAttribute(h_grp, "NumPart_Total", UINT, numParticles);
+ readAttribute(h_grp, "NumPart_Total_HighWord", UINT, numParticles_highWord);
+
+ for (int ptype = 0; ptype < NUM_PARTICLE_TYPES; ++ptype)
+ N[ptype] = ((long long)numParticles[ptype]) +
+ ((long long)numParticles_highWord[ptype] << 32);
- *Ngas = numParticles[0];
- Ndm = numParticles[1];
dim[0] = boxSize[0];
dim[1] = (boxSize[1] < 0) ? boxSize[0] : boxSize[1];
dim[2] = (boxSize[2] < 0) ? boxSize[0] : boxSize[2];
@@ -378,16 +380,16 @@ void read_ic_single(char* fileName, double dim[3], struct part** parts,
/* Close header */
H5Gclose(h_grp);
- /* Total number of particles */
- *Ngparts = *Ngas + Ndm;
-
/* Allocate memory to store SPH particles */
+ *Ngas = N[0];
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 all particles */
+ Ndm = N[1];
+ *Ngparts = N[1] + N[0];
if (posix_memalign((void*)gparts, gpart_align,
*Ngparts * sizeof(struct gpart)) != 0)
error("Error while allocating memory for gravity particles");
@@ -396,16 +398,14 @@ void read_ic_single(char* fileName, double dim[3], struct part** parts,
/* message("Allocated %8.2f MB for particles.", *N * sizeof(struct part) /
* (1024.*1024.)); */
- /* Open SPH particles group */
- /* message("Reading particle arrays..."); */
- message("BoxSize = %lf", dim[0]);
- message("NumPart = [%zd, %zd] Total = %zd", *Ngas, Ndm, *Ngparts);
+ /* message("BoxSize = %lf", dim[0]); */
+ /* message("NumPart = [%zd, %zd] Total = %zd", *Ngas, Ndm, *Ngparts); */
/* Loop over all particle types */
for (int ptype = 0; ptype < NUM_PARTICLE_TYPES; ptype++) {
/* Don't do anything if no particle of this kind */
- if (numParticles[ptype] == 0) continue;
+ if (N[ptype] == 0) continue;
/* Open the particle group in the file */
char partTypeGroupName[PARTICLE_GROUP_BUFFER_SIZE];
@@ -476,10 +476,13 @@ void write_output_single(struct engine* e, struct UnitSystem* us) {
static int outputCount = 0;
/* Number of particles of each type */
- const size_t Ndm = Ntot - Ngas;
- int numParticles[NUM_PARTICLE_TYPES] = /* Gadget-2 convention here */
- {Ngas, Ndm, 0}; /* Could use size_t instead */
- int numParticlesHighWord[NUM_PARTICLE_TYPES] = {0};
+ //const size_t Ndm = Ntot - Ngas;
+
+ /* MATTHIEU: Temporary fix to preserve master */
+ const size_t Ndm = Ntot > 0 ? Ntot - Ngas: 0;
+ /* MATTHIEU: End temporary fix */
+
+ long long N_total[NUM_PARTICLE_TYPES] = {Ngas, Ndm, 0};
/* File name */
char fileName[FILENAME_BUFFER_SIZE];
@@ -521,19 +524,27 @@ void write_output_single(struct engine* e, struct UnitSystem* us) {
/* Print the relevant information and print status */
writeAttribute(h_grp, "BoxSize", DOUBLE, e->s->dim, 3);
- writeAttribute(h_grp, "NumPart_ThisFile", UINT, numParticles,
- NUM_PARTICLE_TYPES);
double dblTime = e->time;
writeAttribute(h_grp, "Time", DOUBLE, &dblTime, 1);
/* GADGET-2 legacy values */
+ /* Number of particles of each type */
+ unsigned int numParticles[NUM_PARTICLE_TYPES] = {0};
+ unsigned int numParticlesHighWord[NUM_PARTICLE_TYPES] = {0};
+ for (int ptype = 0; ptype < NUM_PARTICLE_TYPES; ++ptype) {
+ numParticles[ptype] = (unsigned int)N_total[ptype];
+ numParticlesHighWord[ptype] = (unsigned int)(N_total[ptype] >> 32);
+ }
+ writeAttribute(h_grp, "NumPart_ThisFile", LONGLONG, N_total,
+ NUM_PARTICLE_TYPES);
writeAttribute(h_grp, "NumPart_Total", UINT, numParticles,
NUM_PARTICLE_TYPES);
writeAttribute(h_grp, "NumPart_Total_HighWord", UINT, numParticlesHighWord,
NUM_PARTICLE_TYPES);
- double MassTable[NUM_PARTICLE_TYPES] = {0., 0., 0., 0., 0., 0.};
+ double MassTable[NUM_PARTICLE_TYPES] = {0};
writeAttribute(h_grp, "MassTable", DOUBLE, MassTable, NUM_PARTICLE_TYPES);
- writeAttribute(h_grp, "Flag_Entropy_ICs", UINT, numParticlesHighWord,
+ unsigned int flagEntropy[NUM_PARTICLE_TYPES] = {0};
+ writeAttribute(h_grp, "Flag_Entropy_ICs", UINT, flagEntropy,
NUM_PARTICLE_TYPES);
writeAttribute(h_grp, "NumFilesPerSnapshot", INT, &numFiles, 1);