diff --git a/examples/main.c b/examples/main.c
index 2b33a12eb8737b3dfb7ef35c0cdc10df5ab5ac82..672ab68328ad530bf1634b252e00e2e5d1c608e4 100644
--- a/examples/main.c
+++ b/examples/main.c
@@ -362,8 +362,8 @@ int main(int argc, char *argv[]) {
if (myrank == 0) clocks_gettime(&tic);
#if defined(WITH_MPI)
#if defined(HAVE_PARALLEL_HDF5)
- read_ic_parallel(ICfileName, dim, &parts, &Ngas, &periodic, myrank, nr_nodes,
- MPI_COMM_WORLD, MPI_INFO_NULL);
+ read_ic_parallel(ICfileName, dim, &parts, &gparts, &Ngas, &Ngpart, &periodic,
+ myrank, nr_nodes, MPI_COMM_WORLD, MPI_INFO_NULL);
#else
read_ic_serial(ICfileName, dim, &parts, &gparts, &Ngas, &Ngpart, &periodic,
myrank, nr_nodes, MPI_COMM_WORLD, MPI_INFO_NULL);
diff --git a/src/parallel_io.c b/src/parallel_io.c
index cffa99a0fd75566ec3e850076d15e104504eeb40..aafce0a4fbf39537604e652e70eb324865d61660 100644
--- a/src/parallel_io.c
+++ b/src/parallel_io.c
@@ -178,9 +178,10 @@ void readArrayBackEnd(hid_t grp, char* name, enum DATA_TYPE type, int N,
*
* Calls #error() if an error occurs.
*/
-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,
+void writeArrayBackEnd(hid_t grp, char* fileName, FILE* xmfFile,
+ char* partTypeGroupName, char* name, enum DATA_TYPE type,
+ int N, int dim, long long N_total, int mpi_rank,
+ long long offset, char* part_c, size_t partSize,
struct UnitSystem* us,
enum UnitConversionFactor convFactor) {
hid_t h_data = 0, h_err = 0, h_memspace = 0, h_filespace = 0, h_plist_id = 0;
@@ -189,7 +190,6 @@ 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;
char buffer[150];
@@ -269,7 +269,7 @@ void writeArrayBackEnd(hid_t grp, char* fileName, FILE* xmfFile, char* name,
}
/* Write XMF description for this data set */
- if (mpi_rank == 0) writeXMFline(xmfFile, fileName, name, N_total, dim, type);
+ if (mpi_rank == 0) writeXMFline(xmfFile, fileName, partTypeGroupName, name, N_total, dim, type);
/* Write unit conversion factors for this data set */
conversionString(buffer, us, convFactor);
@@ -328,14 +328,18 @@ void writeArrayBackEnd(hid_t grp, char* fileName, FILE* xmfFile, char* name,
* @param convFactor The UnitConversionFactor for this array
*
*/
-#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)
+#define writeArray(grp, fileName, xmfFile, partTypeGroupName, name, type, N, \
+ dim, part, N_total, mpi_rank, offset, field, us, \
+ convFactor) \
+ writeArrayBackEnd(grp, fileName, xmfFile, partTypeGroupName, name, type, N, \
+ dim, N_total, 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) in parallel
@@ -357,16 +361,17 @@ void writeArrayBackEnd(hid_t grp, char* fileName, FILE* xmfFile, char* name,
*
*/
void read_ic_parallel(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;
+ /* GADGET has only cubic boxes (in cosmological mode) */
+ double boxSize[3] = {0.0, -1.0, -1.0};
+ 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};
/* Open file */
/* message("Opening file '%s' as IC.", fileName); */
@@ -398,8 +403,10 @@ void read_ic_parallel(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];
@@ -408,38 +415,85 @@ void read_ic_parallel(char* fileName, double dim[3], struct part** parts,
/* N_total, (periodic ? "": "non-"), dim[0], dim[1], dim[2]); */
/* 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];
+ }
/* Close header */
H5Gclose(h_grp);
- /* 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.)); */
- /* 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.\n");
+ /* 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 (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_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);
+ }
- /* Read particle fields into the particle structure */
- hydro_read_particles(h_grp, *N, N_total, offset, *parts);
+ /* Prepare the DM particles */
+ prepare_dm_gparts(*gparts, Ndm);
- /* Close particle group */
- H5Gclose(h_grp);
+ /* Now duplicate the hydro particle into gparts */
+ duplicate_hydro_gparts(*parts, *gparts, *Ngas, Ndm);
+
+ /* message("Done Reading particles..."); */
/* Close property handler */
H5Pclose(h_plist_id);
/* Close file */
H5Fclose(h_file);
-
- /* message("Done Reading particles..."); */
}
/**
@@ -459,23 +513,27 @@ void read_ic_parallel(char* fileName, double dim[3], struct part** parts,
void write_output_parallel(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;
- unsigned int numParticles[6] = {N, 0};
- unsigned 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;
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);
/* First time, we need to create the XMF file */
if (outputCount == 0 && mpi_rank == 0) createXMFfile();
@@ -492,20 +550,21 @@ void write_output_parallel(struct engine* e, struct UnitSystem* us,
}
/* 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 */
/* Write the part of the XMF file corresponding to this specific output */
- if (mpi_rank == 0) writeXMFheader(xmfFile, N_total, fileName, e->time);
+ if (mpi_rank == 0) writeXMFoutputheader(xmfFile, fileName, e->time);
/* Open header to write simulation properties */
/* message("Writing runtime parameters..."); */
@@ -523,27 +582,36 @@ void write_output_parallel(struct engine* e, struct UnitSystem* us,
/* 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 */
writeAttribute(h_grp, "BoxSize", DOUBLE, e->s->dim, 3);
- writeAttribute(h_grp, "NumPart_ThisFile", UINT, numParticles, 6);
double dblTime = e->time;
writeAttribute(h_grp, "Time", DOUBLE, &dblTime, 1);
-
+
/* GADGET-2 legacy values */
- numParticles[0] = (unsigned int)N_total;
- 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 */
H5Gclose(h_grp);
-
+
/* Print the code version */
writeCodeDescription(h_file);
@@ -556,30 +624,78 @@ void write_output_parallel(struct engine* e, struct UnitSystem* us,
/* 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");
-
- /* 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;
+
+ /* Add the global information for that particle type to the XMF meta-file */
+ if (mpi_rank == 0)
+ writeXMFgroupheader(xmfFile, fileName, N_total[ptype], 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 opening particle group %s.", partTypeGroupName);
+ }
+
+ /* Read particle fields into the particle structure */
+ switch (ptype) {
+
+ case GAS:
+ hydro_write_particles(h_grp, fileName, partTypeGroupName, 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, partTypeGroupName,
+ 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 this particle group in the XMF file as well */
+ if (mpi_rank == 0)
+ writeXMFgroupfooter(xmfFile, ptype);
+ }
+
/* Write LXMF file descriptor */
- if (mpi_rank == 0) writeXMFfooter(xmfFile);
-
+ if (mpi_rank == 0) writeXMFoutputfooter(xmfFile, outputCount, e->time);
+
/* message("Done writing particles..."); */
-
+
/* Close property descriptor */
H5Pclose(plist_id);
-
+
/* Close file */
H5Fclose(h_file);
-
+
++outputCount;
}
diff --git a/src/parallel_io.h b/src/parallel_io.h
index a0589944ec845c712abde1e64e305980748db0e7..09d6574309646d33416670e4c726cc7da0321a2e 100644
--- a/src/parallel_io.h
+++ b/src/parallel_io.h
@@ -32,8 +32,9 @@
#if defined(HAVE_HDF5) && defined(WITH_MPI) && defined(HAVE_PARALLEL_HDF5)
void read_ic_parallel(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_parallel(struct engine* e, struct UnitSystem* us,
int mpi_rank, int mpi_size, MPI_Comm comm,