Prepared files and infrastructure for i/o using MPI but not parallel-hdf5.

Former-commit-id: 58b8fad089635e8318f45b7ef7acc6e368eb23f0

src/single_io.c

+/*******************************************************************************
+ * This file is part of SWIFT.
+ * Coypright (c) 2012 Pedro Gonnet (pedro.gonnet@durham.ac.uk),
+ *                    Matthieu Schaller (matthieu.schaller@durham.ac.uk).
+ * 
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published
+ * by the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ * 
+ ******************************************************************************/
+
+/* Config parameters. */
+#include "../config.h"
+
+#if defined(HAVE_HDF5) && !defined(WITH_MPI)
+
+
+/* Some standard headers. */
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <stddef.h>
+#include <hdf5.h>
+#include <math.h>
+
+#include "const.h"
+#include "cycle.h"
+#include "lock.h"
+#include "task.h"
+#include "part.h"
+#include "space.h"
+#include "scheduler.h"
+#include "engine.h"
+#include "error.h"
+#include "kernel.h"
+#include "common_io.h"
+
+
+
+/*-----------------------------------------------------------------------------
+ * Routines reading an IC file
+ *-----------------------------------------------------------------------------*/
+
+/**
+ * @brief Reads a data array from a given HDF5 group.
+ *
+ * @param grp The group from which to read.
+ * @param name The name of the array to read.
+ * @param type The #DATA_TYPE of the attribute.
+ * @param N The number of particles.
+ * @param dim The dimension of the data (1 for scalar, 3 for vector)
+ * @param part_c A (char*) pointer on the first occurence of the field of interest in the parts array
+ * @param importance If COMPULSORY, the data must be present in the IC file. If OPTIONAL, the array will be zeroed when the data is not present.
+ *
+ * @todo A better version using HDF5 hyperslabs to read the file directly into the part array 
+ * will be written once the strucutres have been stabilized.
+ *  
+ * 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)
+{
+  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 */
+  exist = H5Lexists(grp, name, 0);
+  if(exist < 0)
+    {
+      error( "Error while checking the existence of data set '%s'." , name );
+    }
+  else if(exist == 0)
+    {
+      if(importance == COMPULSORY)
+	{
+	  error( "Compulsory data set '%s' not present in the file." , name );
+	}
+      else
+	{
+	  /* message("Optional data set '%s' not present. Zeroing this particle field...", name);	   */
+	  
+	  for(i=0; i<N; ++i)
+	    memset(part_c+i*partSize, 0, copySize);
+	  
+	  return;
+	}
+   }
+
+  /* message( "Reading %s '%s' array...", importance == COMPULSORY ? "compulsory": "optional  ", name); */
+
+  /* Open data space */
+  h_data = H5Dopen1(grp, name);
+  if(h_data < 0)
+    {
+      error( "Error while opening data space '%s'." , name );
+    }
+
+  /* Check data type */
+  h_type = H5Dget_type(h_data);
+  if(h_type < 0)
+    error("Unable to retrieve data type from the file");
+  if(!H5Tequal(h_type, hdf5Type(type)))
+    error("Non-matching types between the code and the file");
+  
+  /* Allocate temporary buffer */
+  temp = malloc(N * dim * sizeOfType(type));
+  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 */
+  h_err = H5Dread(h_data, hdf5Type(type), H5S_ALL, H5S_ALL, H5P_DEFAULT, temp);
+  if(h_err < 0)
+    {
+      error( "Error while reading data array '%s'." , name );
+    }
+
+  /* Copy temporary buffer to particle data */
+  temp_c = temp;
+  for(i=0; i<N; ++i)
+    memcpy(part_c+i*partSize, &temp_c[i*copySize], copySize);
+  
+  /* Free and close everything */
+  free(temp);
+  H5Tclose(h_type);
+  H5Dclose(h_data);
+}
+
+/**
+ * @brief A helper macro to call the readArrayBackEnd function more easily.
+ *
+ * @param grp The group from which to read.
+ * @param name The name of the array to read.
+ * @param type The #DATA_TYPE of the attribute.
+ * @param N The number of particles.
+ * @param dim The dimension of the data (1 for scalar, 3 for vector)
+ * @param part The array of particles to fill
+ * @param field The name of the field (C code name as defined in part.h) to fill
+ * @param importance Is the data compulsory or not
+ *
+ */
+#define readArray(grp, name, type, N, dim, part, field, importance) readArrayBackEnd(grp, name, type, N, dim, (char*)(&(part[0]).field), importance)
+
+/**
+ * @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 periodic (output) 1 if the volume is periodic, 0 if not.
+ *
+ * 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 snaphsots distributed in more than one file.
+ *
+ * Calls #error() if an error occurs.
+ *
+ */
+void read_ic_single ( char* fileName, double dim[3], struct part **parts,  int* N, int* periodic)
+{
+  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*/
+
+  /* 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 = H5Gopen1(h_file, "/RuntimePars");
+  if(h_grp < 0)
+    error("Error while opening runtime parameters\n");
+
+  /* Read the relevant information */
+  readAttribute(h_grp, "PeriodicBoundariesOn", INT, periodic);
+
+  /* Close runtime parameters */
+  H5Gclose(h_grp);
+  
+  /* Open header to read simulation properties */
+  /* message("Reading file header..."); */
+  h_grp = H5Gopen1(h_file, "/Header");
+  if(h_grp < 0)
+    error("Error while opening file header\n");
+    
+  /* Read the relevant information and print status */
+  readAttribute(h_grp, "BoxSize", DOUBLE, boxSize);
+  readAttribute(h_grp, "NumPart_Total", UINT, numParticles);
+
+  *N = numParticles[0];
+  dim[0] = boxSize[0];
+  dim[1] = ( boxSize[1] < 0 ) ? boxSize[0] : boxSize[1];
+  dim[2] = ( boxSize[2] < 0 ) ? boxSize[0] : boxSize[2];
+
+  /* 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);
+
+  /* Allocate memory to store particles */
+  if(posix_memalign( (void*)parts , part_align , *N * sizeof(struct part)) != 0)
+    error("Error while allocating memory for particles");
+  bzero( *parts , *N * sizeof(struct part) );
+
+  /* message("Allocated %8.2f MB for particles.", *N * sizeof(struct part) / (1024.*1024.)); */
+		  
+  /* Open SPH particles group */
+  /* message("Reading particle arrays..."); */
+  h_grp = H5Gopen1(h_file, "/PartType0");
+  if(h_grp < 0)
+    error( "Error while opening particle group.\n");
+
+  /* Read arrays */
+  readArray(h_grp, "Coordinates", DOUBLE, *N, 3, *parts, x, COMPULSORY);
+  readArray(h_grp, "Velocities", FLOAT, *N, 3, *parts, v, COMPULSORY);
+  readArray(h_grp, "Masses", FLOAT, *N, 1, *parts, mass, COMPULSORY);
+  readArray(h_grp, "SmoothingLength", FLOAT, *N, 1, *parts, h, COMPULSORY);
+  readArray(h_grp, "InternalEnergy", FLOAT, *N, 1, *parts, u, COMPULSORY);
+  readArray(h_grp, "ParticleIDs", ULONGLONG, *N, 1, *parts, id, COMPULSORY);
+  readArray(h_grp, "TimeStep", FLOAT, *N, 1, *parts, dt, OPTIONAL);
+  readArray(h_grp, "Acceleration", FLOAT, *N, 3, *parts, a, OPTIONAL);
+  readArray(h_grp, "Density", FLOAT, *N, 1, *parts, rho, OPTIONAL );
+
+  /* Close particle group */
+  H5Gclose(h_grp);
+
+  /* message("Done Reading particles..."); */
+
+  /* Close file */
+  H5Fclose(h_file);
+}
+
+
+/*-----------------------------------------------------------------------------
+ * Routines writing an output file
+ *-----------------------------------------------------------------------------*/
+
+/**
+ * @brief Writes a data array in given HDF5 group.
+ *
+ * @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 name The name of the array to write.
+ * @param type The #DATA_TYPE of the array.
+ * @param N The number of particles to write.
+ * @param dim The dimension of the data (1 for scalar, 3 for vector)
+ * @param part_c A (char*) pointer on the first occurence of the field of interest in the parts array
+ * @param us The UnitSystem currently in use
+ * @param convFactor The UnitConversionFactor for this array
+ *
+ * @todo A better version using HDF5 hyperslabs to write the file directly from the part array
+ * will be written once the strucutres have been stabilized.
+ *
+ * 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, char* part_c, struct UnitSystem* us, enum UnitConversionFactor convFactor)
+{
+  hid_t h_data=0, h_err=0, h_space=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];
+  char buffer[150];
+
+  /* message("Writing '%s' array...", name); */
+
+  /* Allocate temporary buffer */
+  temp = malloc(N * dim * sizeOfType(type));
+  if(temp == NULL)
+    error("Unable to allocate memory for temporary buffer");
+
+  /* Copy particle data to temporary buffer */
+  temp_c = temp;
+  for(i=0; i<N; ++i)
+    memcpy(&temp_c[i*copySize], part_c+i*partSize, copySize);
+
+  /* Create data space */
+  h_space = H5Screate(H5S_SIMPLE);
+  if(h_space < 0)
+    {
+      error( "Error while creating data space for field '%s'." , name );
+    }
+  
+  if(dim > 1)
+    {
+      rank = 2;
+      shape[0] = N; shape[1] = dim;
+    }
+  else
+    {
+      rank = 1;
+      shape[0] = N; shape[1] = 0;
+    }
+  
+  /* Change shape of data space */
+  h_err = H5Sset_extent_simple(h_space, rank, shape, NULL);
+  if(h_err < 0)
+    {
+      error( "Error while changing data space shape for field '%s'." , name );
+    }
+  
+  /* Create dataset */
+  h_data = H5Dcreate1(grp, name, hdf5Type(type), h_space, H5P_DEFAULT);
+  if(h_data < 0)
+    {
+      error( "Error while creating dataspace '%s'." , name );
+    }
+  
+  /* Write temporary buffer to HDF5 dataspace */
+  h_err = H5Dwrite(h_data, hdf5Type(type), h_space, H5S_ALL, H5P_DEFAULT, temp);
+  if(h_err < 0)
+    {
+      error( "Error while writing data array '%s'." , name );
+    }
+
+  /* Write XMF description for this data set */
+  writeXMFline(xmfFile, fileName, name, N, dim, type);
+
+  /* Write unit conversion factors for this data set */
+  conversionString( buffer, us, convFactor );
+  writeAttribute_d( h_data, "CGS conversion factor", conversionFactor( us, convFactor ) );
+  writeAttribute_f( h_data, "h-scale exponant", hFactor( us, convFactor ) );
+  writeAttribute_f( h_data, "a-scale exponant", aFactor( us, convFactor ) );
+  writeAttribute_s( h_data, "Conversion factor", buffer );
+  
+  /* Free and close everything */
+  free(temp);
+  H5Dclose(h_data);
+  H5Sclose(h_space);
+}
+
+/**
+ * @brief A helper macro to call the readArrayBackEnd function more easily.
+ *
+ * @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 name The name of the array to write.
+ * @param type The #DATA_TYPE of the array.
+ * @param N The number of particles to write.
+ * @param dim The dimension of the data (1 for scalar, 3 for vector)
+ * @param part A (char*) pointer on the first occurence of the field of interest in the parts array
+ * @param field The name (code name) of the field to read from.
+ * @param us The UnitSystem currently in use
+ * @param convFactor The UnitConversionFactor for this array
+ *
+ */
+#define writeArray(grp, fileName, xmfFile, name, type, N, dim, part, field, us, convFactor) writeArrayBackEnd(grp, fileName, xmfFile, name, type, N, dim, (char*)(&(part[0]).field), us, convFactor)
+
+/**
+ * @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
+ *
+ * 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, struct UnitSystem* us)
+{
+  
+  hid_t h_file=0, h_grp=0;
+  int N = e->s->nr_parts;
+  int periodic = e->s->periodic;
+  int numParticles[6]={N,0};
+  int numParticlesHighWord[6]={0};
+  int numFiles = 1;
+  struct part* parts = e->s->parts;
+  FILE* xmfFile = 0;
+  static int outputCount = 0;
+  
+  /* File name */
+  char fileName[200];
+  sprintf(fileName, "output_%03i.hdf5", outputCount);
+
+  /* First time, we need to create the XMF file */
+  if(outputCount == 0)
+    createXMFfile();
+  
+  /* Prepare the XMF file for the new entry */
+  xmfFile = prepareXMFfile();
+
+  /* Write the part corresponding to this specific output */
+  writeXMFheader(xmfFile, N, 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 = H5Gcreate1(h_file, "/RuntimePars", 0);
+  if(h_grp < 0)
+    error("Error while creating runtime parameters group\n");
+
+  /* Write the relevant information */
+  writeAttribute(h_grp, "PeriodicBoundariesOn", INT, &periodic, 1);
+
+  /* Close runtime parameters */
+  H5Gclose(h_grp);
+  
+  /* Open header to write simulation properties */
+  /* message("Writing file header..."); */
+  h_grp = H5Gcreate1(h_file, "/Header", 0);
+  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);
+  writeAttribute(h_grp, "Time", DOUBLE, &e->time, 1);
+
+  /* GADGET-2 legacy values */
+  writeAttribute(h_grp, "NumPart_Total", UINT, numParticles, 6);
+  writeAttribute(h_grp, "NumPart_Total_HighWord", UINT, numParticlesHighWord, 6);
+  double MassTable[6] = {0., 0., 0., 0., 0., 0.};
+  writeAttribute(h_grp, "MassTable", DOUBLE, MassTable, 6);
+  writeAttribute(h_grp, "Flag_Entropy_ICs", UINT, numParticlesHighWord, 6);
+  writeAttribute(h_grp, "NumFilesPerSnapshot", INT, &numFiles, 1);
+
+  /* Close header */
+  H5Gclose(h_grp);
+
+  /* Print the SPH parameters */
+  writeSPHflavour(h_file);
+
+  /* Print the system of Units */
+  writeUnitSystem(h_file, us);
+		  
+  /* Create SPH particles group */
+  /* message("Writing particle arrays..."); */
+  h_grp = H5Gcreate1(h_file, "/PartType0", 0);
+  if(h_grp < 0)
+    error( "Error while creating particle group.\n");
+
+  /* Write arrays */
+  writeArray(h_grp, fileName, xmfFile, "Coordinates", DOUBLE, N, 3, parts, x, us, UNIT_CONV_LENGTH);
+  writeArray(h_grp, fileName, xmfFile, "Velocities", FLOAT, N, 3, parts, v, us, UNIT_CONV_SPEED);
+  writeArray(h_grp, fileName, xmfFile, "Masses", FLOAT, N, 1, parts, mass, us, UNIT_CONV_MASS);
+  writeArray(h_grp, fileName, xmfFile, "SmoothingLength", FLOAT, N, 1, parts, h, us, UNIT_CONV_LENGTH);
+  writeArray(h_grp, fileName, xmfFile, "InternalEnergy", FLOAT, N, 1, parts, u, us, UNIT_CONV_ENERGY_PER_UNIT_MASS);
+  writeArray(h_grp, fileName, xmfFile, "ParticleIDs", ULONGLONG, N, 1, parts, id, us, UNIT_CONV_NO_UNITS);
+  writeArray(h_grp, fileName, xmfFile, "TimeStep", FLOAT, N, 1, parts, dt, us, UNIT_CONV_TIME);
+  writeArray(h_grp, fileName, xmfFile, "Acceleration", FLOAT, N, 3, parts, a, us, UNIT_CONV_ACCELERATION);
+  writeArray(h_grp, fileName, xmfFile, "Density", FLOAT, N, 1, parts, rho, us, UNIT_CONV_DENSITY);
+
+  /* Close particle group */
+  H5Gclose(h_grp);
+
+  /* Write LXMF file descriptor */
+  writeXMFfooter(xmfFile);
+
+  /* message("Done writing particles..."); */
+
+  /* Close file */
+  H5Fclose(h_file);
+
+  ++outputCount;
+}
+
+
+#endif  /* HAVE_HDF5 */
+
+

src/single_io.h

+/*******************************************************************************
+ * This file is part of SWIFT.
+ * Coypright (c) 2012 Matthieu Schaller (matthieu.schaller@durham.ac.uk).
+ * 
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published
+ * by the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ * 
+ ******************************************************************************/
+
+
+#if defined(HAVE_HDF5) && !defined(WITH_MPI)
+
+void read_ic_single ( char* fileName, double dim[3], struct part **parts,  int* N, int* periodic);
+
+void write_output_single ( struct engine* e, struct UnitSystem* us );
+
+#endif
+