The parts of i/o common to the serial and parallel modes is now stored in a separate file.

The serial i/o now also outputs the units.



Former-commit-id: 541c149359cb0e1afd3e564ad19c218c1e69fcbd

examples/test.c

@@ -925,7 +925,7 @@ int main ( int argc , char *argv[] ) {
 #ifdef WITH_MPI
     write_output_parallel(&e, &us, myrank, nr_nodes, MPI_COMM_WORLD, MPI_INFO_NULL);
 #else
-    write_output(&e);
+    write_output(&e, &us);
 #endif
     message( "writing particle properties took %.3f ms." , ((double)(getticks() - tic)) / CPU_TPS * 1000 ); fflush(stdout);
     
@@ -974,7 +974,7 @@ int main ( int argc , char *argv[] ) {
 #ifdef WITH_MPI
              write_output_parallel(&e, &us, myrank, nr_nodes, MPI_COMM_WORLD, MPI_INFO_NULL);
 #else
-             write_output(&e);
+             write_output(&e, &us);
 #endif
           }
                 
@@ -1019,7 +1019,7 @@ int main ( int argc , char *argv[] ) {
 #ifdef WITH_MPI
 	write_output_parallel( &e, &us, myrank, nr_nodes, MPI_COMM_WORLD, MPI_INFO_NULL );
 #else
-	write_output( &e );
+	write_output( &e , &us );
 #endif
         
 #ifdef WITH_MPI

src/Makefile.am

@@ -38,11 +38,11 @@ endif
 
 # List required headers
 include_HEADERS = space.h runner.h queue.h task.h lock.h cell.h part.h const.h \
-    engine.h swift.h serial_io.h timers.h debug.h scheduler.h proxy.h parallel_io.h
+    engine.h swift.h serial_io.h timers.h debug.h scheduler.h proxy.h parallel_io.h common_io.h
 
 # Common source files
 AM_SOURCES = space.c runner.c queue.c task.c cell.c engine.c \
-    serial_io.c timers.c debug.c scheduler.c proxy.c parallel_io.c units.c
+    serial_io.c timers.c debug.c scheduler.c proxy.c parallel_io.c units.c common_io.c
     
 # Sources and flags for regular library
 libswiftsim_la_SOURCES = $(AM_SOURCES)

src/common_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)
+
+/* 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"
+
+
+
+/**
+ * @brief Converts a C data type to the HDF5 equivalent. 
+ *
+ * This function is a trivial wrapper around the HDF5 types but allows
+ * to change the exact storage types matching the code types in a transparent way.
+ */
+hid_t hdf5Type(enum DATA_TYPE type)
+{
+  switch(type)
+    {
+    case INT: return H5T_NATIVE_INT;
+    case UINT: return H5T_NATIVE_UINT;
+    case LONG: return H5T_NATIVE_LONG;
+    case ULONG: return H5T_NATIVE_ULONG;
+    case LONGLONG: return H5T_NATIVE_LLONG;
+    case ULONGLONG: return H5T_NATIVE_ULLONG;
+    case FLOAT: return H5T_NATIVE_FLOAT;
+    case DOUBLE: return H5T_NATIVE_DOUBLE;
+    case CHAR: return H5T_C_S1;
+    default: error("Unknown type"); return 0;
+    }
+}
+
+/**
+ * @brief Returns the memory size of the data type
+ */
+size_t sizeOfType(enum DATA_TYPE type)
+{
+  switch(type)
+    {
+    case INT: return sizeof(int);
+    case UINT: return sizeof(unsigned int);
+    case LONG: return sizeof(long);
+    case ULONG: return sizeof(unsigned long);
+    case LONGLONG: return sizeof(long long);
+    case ULONGLONG: return sizeof(unsigned long long);
+    case FLOAT: return sizeof(float);
+    case DOUBLE: return sizeof(double);
+    case CHAR: return sizeof(char);
+    default: error("Unknown type"); return 0;
+    }
+}
+
+
+
+/**
+ * @brief Reads an attribute from a given HDF5 group.
+ *
+ * @param grp The group from which to read.
+ * @param name The name of the attribute to read.
+ * @param type The #DATA_TYPE of the attribute.
+ * @param data (output) The attribute read from the HDF5 group.
+ *
+ * Calls #error() if an error occurs.
+ */
+void readAttribute(hid_t grp, char* name, enum DATA_TYPE type, void* data)
+{
+  hid_t h_attr=0, h_err=0;
+
+  h_attr = H5Aopen(grp, name, H5P_DEFAULT);
+  if(h_attr < 0)
+    {
+      error( "Error while opening attribute '%s'" , name );
+    }
+
+  h_err = H5Aread(h_attr, hdf5Type(type), data);
+  if(h_err < 0)
+    {
+      error( "Error while reading attribute '%s'" , name );
+    }
+
+  H5Aclose(h_attr);
+}
+
+/**
+ * @brief Write an attribute to a given HDF5 group.
+ *
+ * @param grp The group in which to write.
+ * @param name The name of the attribute to write.
+ * @param type The #DATA_TYPE of the attribute.
+ * @param data The attribute to write.
+ * @param num The number of elements to write
+ *
+ * Calls #error() if an error occurs.
+ */
+void writeAttribute(hid_t grp, char* name, enum DATA_TYPE type, void* data, int num)
+{
+  hid_t h_space=0, h_attr=0, h_err=0;
+  hsize_t dim[1]={num};
+
+  h_space = H5Screate(H5S_SIMPLE);
+  if(h_space < 0)
+    {
+      error( "Error while creating dataspace for attribute '%s'." , name );
+    }
+
+  h_err = H5Sset_extent_simple(h_space, 1, dim, NULL);
+  if(h_err < 0)
+    {
+      error( "Error while changing dataspace shape for attribute '%s'." , name );
+    }
+
+  h_attr = H5Acreate1(grp, name, hdf5Type(type), h_space, H5P_DEFAULT);
+  if(h_attr < 0)
+    {
+      error( "Error while creating attribute '%s'.", name );
+    }
+
+  h_err = H5Awrite(h_attr, hdf5Type(type), data);
+  if(h_err < 0)
+    {
+      error( "Error while reading attribute '%s'." , name );
+    }
+
+  H5Sclose(h_space);
+  H5Aclose(h_attr);
+}
+
+/**
+ * @brief Write a string as an attribute to a given HDF5 group.
+ *
+ * @param grp The group in which to write.
+ * @param name The name of the attribute to write.
+ * @param str The string to write.
+ * @param length The length of the string
+ *
+ * Calls #error() if an error occurs.
+ */
+void writeStringAttribute(hid_t grp, char* name, char* str, int length)
+{
+  hid_t h_space=0, h_attr=0, h_err=0, h_type=0;
+
+  h_space = H5Screate(H5S_SCALAR);
+  if(h_space < 0)
+    {
+      error( "Error while creating dataspace for attribute '%s'." , name );
+    }
+
+  h_type = H5Tcopy(H5T_C_S1);
+  if(h_type < 0)
+    {
+      error( "Error while copying datatype 'H5T_C_S1'." );
+    }
+
+  h_err = H5Tset_size(h_type, length);
+  if(h_err < 0)
+    {
+      error( "Error while resizing attribute tyep to '%i'." , length );
+    }
+
+  h_attr = H5Acreate1(grp, name, h_type, h_space, H5P_DEFAULT);
+  if(h_attr < 0)
+    {
+      error( "Error while creating attribute '%s'." , name );
+    }
+
+  h_err = H5Awrite(h_attr, h_type, str );
+  if(h_err < 0)
+    {
+      error( "Error while reading attribute '%s'." , name );
+    }
+
+  H5Tclose(h_type);
+  H5Sclose(h_space);
+  H5Aclose(h_attr);
+}
+
+/**
+ * @brief Writes a double value as an attribute
+ * @param grp The groupm in which to write
+ * @param name The name of the attribute
+ * @param data The value to write
+ */
+void writeAttribute_d(hid_t grp, char* name, double data)
+{
+  writeAttribute(grp, name, DOUBLE, &data, 1);
+}
+
+/**
+ * @brief Writes a float value as an attribute
+ * @param grp The groupm in which to write
+ * @param name The name of the attribute
+ * @param data The value to write
+ */
+void writeAttribute_f(hid_t grp, char* name, float data)
+{
+  writeAttribute(grp, name, FLOAT, &data, 1);
+}
+
+/**
+ * @brief Writes an int value as an attribute
+ * @param grp The groupm in which to write
+ * @param name The name of the attribute
+ * @param data The value to write
+ */
+
+void writeAttribute_i(hid_t grp, char* name, int data)
+{
+  writeAttribute(grp, name, INT, &data, 1);
+}
+
+/**
+ * @brief Writes a long value as an attribute
+ * @param grp The groupm in which to write
+ * @param name The name of the attribute
+ * @param data The value to write
+ */
+void writeAttribute_l(hid_t grp, char* name, long data)
+{
+  writeAttribute(grp, name, LONG, &data, 1);
+}
+
+/**
+ * @brief Writes a string value as an attribute
+ * @param grp The groupm in which to write
+ * @param name The name of the attribute
+ * @param str The string to write
+ */
+void writeAttribute_s(hid_t grp, char* name, char* str)
+{
+  writeStringAttribute(grp, name, str, strlen(str));
+}
+
+
+/* ------------------------------------------------------------------------------------------------ 
+ * This part writes the XMF file descriptor enabling a visualisation through ParaView
+ * ------------------------------------------------------------------------------------------------ */
+/**
+ * @brief Writes the current model of SPH to the file
+ * @param h_file The (opened) HDF5 file in which to write
+ */
+void writeSPHflavour(hid_t h_file)
+{
+  hid_t h_grpsph=0;
+
+  h_grpsph = H5Gcreate1(h_file, "/SPH", 0);
+  if(h_grpsph < 0)
+    error("Error while creating SPH group");
+
+  writeAttribute_f(h_grpsph, "Kernel eta", const_eta_kernel);
+  writeAttribute_f(h_grpsph, "Weighted N_ngb", kernel_nwneigh);
+  writeAttribute_f(h_grpsph, "Delta N_ngb", const_delta_nwneigh);
+  writeAttribute_f(h_grpsph, "Hydro gamma", const_hydro_gamma);
+
+#ifdef LEGACY_GADGET2_SPH
+  writeAttribute_s(h_grpsph, "Thermal Conductivity Model", "(No treatment) Legacy Gadget-2 as in Springel (2005)");  
+  writeAttribute_s(h_grpsph, "Viscosity Model", "Legacy Gadget-2 as in Springel (2005)");  
+  writeAttribute_f(h_grpsph, "Viscosity alpha", const_viscosity_alpha);  
+  writeAttribute_f(h_grpsph, "Viscosity beta", 3.f);  
+#else
+  writeAttribute_s(h_grpsph, "Thermal Conductivity Model", "Price (2008) without switch");  
+  writeAttribute_f(h_grpsph, "Thermal Conductivity alpha", const_conductivity_alpha);  
+  writeAttribute_s(h_grpsph, "Viscosity Model", "Morris & Monaghan (1997), Rosswog, Davies, Thielemann & Piran (2000) with additional Balsara (1995) switch");  
+  writeAttribute_f(h_grpsph, "Viscosity alpha_min", const_viscosity_alpha_min);  
+  writeAttribute_f(h_grpsph, "Viscosity alpha_max", const_viscosity_alpha_max);  
+  writeAttribute_f(h_grpsph, "Viscosity beta", 2.f);  
+  writeAttribute_f(h_grpsph, "Viscosity decay length", const_viscosity_length);  
+#endif
+
+  writeAttribute_f(h_grpsph, "CFL parameter", const_cfl);  
+  writeAttribute_f(h_grpsph, "Maximal ln(Delta h) change over dt", const_ln_max_h_change);  
+  writeAttribute_f(h_grpsph, "Maximal Delta h change over dt", exp(const_ln_max_h_change));  
+  writeAttribute_f(h_grpsph, "Maximal Delta u change over dt", const_max_u_change);  
+  writeAttribute_s(h_grpsph, "Kernel", kernel_name);
+
+  H5Gclose(h_grpsph);
+}
+
+/**
+ * @brief Writes the current Unit System
+ * @param h_file The (opened) HDF5 file in which to write
+ */
+void writeUnitSystem(hid_t h_file, struct UnitSystem* us)
+{
+  hid_t h_grpunit=0;
+
+  h_grpunit = H5Gcreate1(h_file, "/Units", 0);
+  if(h_grpunit < 0)
+    error("Error while creating Unit System group");
+
+  writeAttribute_d(h_grpunit, "Unit mass in cgs", getBaseUnit(us, UNIT_MASS));
+  writeAttribute_d(h_grpunit, "Unit length in cgs", getBaseUnit(us, UNIT_LENGTH));
+  writeAttribute_d(h_grpunit, "Unit time in cgs", getBaseUnit(us, UNIT_TIME));
+  writeAttribute_d(h_grpunit, "Unit current in cgs", getBaseUnit(us, UNIT_CURRENT));
+  writeAttribute_d(h_grpunit, "Unit temperature in cgs", getBaseUnit(us, UNIT_TEMPERATURE));  
+
+  H5Gclose(h_grpunit);
+}
+
+
+
+/**
+ * @brief Prepares the XMF file for the new entry
+ *
+ * Creates a temporary file on the disk in order to copy the right lines.
+ *
+ * @todo Use a proper XML library to avoid stupid copies.
+ */
+FILE* prepareXMFfile()
+{
+  char buffer[1024];
+
+  FILE* xmfFile = fopen("output.xmf", "r");
+  FILE* tempFile = fopen("output_temp.xmf", "w");
+
+  if(xmfFile == NULL)
+    error("Unable to open current XMF file.");
+
+  if(tempFile == NULL)
+    error("Unable to open temporary file.");
+
+
+  /* First we make a temporary copy of the XMF file and count the lines */
+  int counter = 0;
+  while (fgets(buffer, 1024, xmfFile) != NULL)
+    {
+      counter++;
+      fprintf(tempFile, "%s", buffer);
+    }
+  fclose(tempFile);
+  fclose(xmfFile);
+  
+  /* We then copy the XMF file back up to the closing lines */
+  xmfFile = fopen("output.xmf", "w");
+  tempFile = fopen("output_temp.xmf", "r");
+
+  if(xmfFile == NULL)
+    error("Unable to open current XMF file.");
+
+  if(tempFile == NULL)
+    error("Unable to open temporary file.");
+
+  int i = 0;
+  while (fgets(buffer, 1024, tempFile) != NULL && i < counter - 3)
+    {
+      i++;
+      fprintf(xmfFile, "%s", buffer);
+    }
+  fprintf(xmfFile, "\n");
+  fclose(tempFile);
+  remove("output_temp.xmf");
+ 
+  return xmfFile;
+}
+
+/**
+ * @brief Writes the begin of the XMF file
+ *
+ * @todo Exploit the XML nature of the XMF format to write a proper XML writer and simplify all the XMF-related stuff.
+ */
+void createXMFfile()
+{
+  FILE* xmfFile = fopen("output.xmf", "w");
+
+  fprintf(xmfFile, "<?xml version=\"1.0\" ?> \n");
+  fprintf(xmfFile, "<!DOCTYPE Xdmf SYSTEM \"Xdmf.dtd\" []> \n");
+  fprintf(xmfFile, "<Xdmf xmlns:xi=\"http://www.w3.org/2003/XInclude\" Version=\"2.1\">\n");
+  fprintf(xmfFile, "<Domain>\n");
+  fprintf(xmfFile, "<Grid Name=\"TimeSeries\" GridType=\"Collection\" CollectionType=\"Temporal\">\n\n");
+
+  fprintf(xmfFile, "</Grid>\n");
+  fprintf(xmfFile, "</Domain>\n");
+  fprintf(xmfFile, "</Xdmf>\n");
+
+  fclose(xmfFile);
+}
+
+
+/**
+ * @brief Writes the part of the XMF entry presenting the geometry of the snapshot
+ *
+ * @param xmfFile The file to write in.
+ * @param Nparts The number of particles.
+ * @param hdfFileName The name of the HDF5 file corresponding to this output.
+ * @param time The current simulation time.
+ */
+void writeXMFheader(FILE* xmfFile, long long Nparts, char* hdfFileName, float time)
+{
+  /* Write end of file */
+  
+  fprintf(xmfFile, "<Grid GridType=\"Collection\" CollectionType=\"Spatial\">\n");
+  fprintf(xmfFile, "<Time Type=\"Single\" Value=\"%f\"/>\n", time);
+  fprintf(xmfFile, "<Grid Name=\"Gas\" GridType=\"Uniform\">\n");
+  fprintf(xmfFile, "<Topology TopologyType=\"Polyvertex\" Dimensions=\"%lld\"/>\n", Nparts);
+  fprintf(xmfFile, "<Geometry GeometryType=\"XYZ\">\n");
+  fprintf(xmfFile, "<DataItem Dimensions=\"%lld 3\" NumberType=\"Double\" Precision=\"8\" Format=\"HDF\">%s:/PartType0/Coordinates</DataItem>\n", Nparts, hdfFileName);
+  fprintf(xmfFile, "</Geometry>");
+}
+
+
+/**
+ * @brief Writes the end of the XMF file (closes all open markups)
+ *
+ * @param xmfFile The file to write in.
+ */
+void writeXMFfooter(FILE* xmfFile)
+{
+  /* Write end of the section of this time step */
+  
+  fprintf(xmfFile, "\n</Grid>\n");
+  fprintf(xmfFile, "</Grid>\n");
+  fprintf(xmfFile, "\n</Grid>\n");
+  fprintf(xmfFile, "</Domain>\n");
+  fprintf(xmfFile, "</Xdmf>\n");
+  
+  fclose(xmfFile);
+}
+
+
+/**
+ * @brief Writes the lines corresponding to an array of the HDF5 output
+ *
+ * @param xmfFile The file in which to write
+ * @param fileName The name of the HDF5 file associated to this XMF descriptor.
+ * @param name The name of the array in the HDF5 file.
+ * @param N The number of particles.
+ * @param dim The dimension of the quantity (1 for scalars, 3 for vectors).
+ * @param type The type of the data to write.
+ *
+ * @todo Treat the types in a better way.
+ */
+void writeXMFline(FILE* xmfFile, char* fileName, char* name, long long N, int dim, enum DATA_TYPE type )
+{
+  fprintf(xmfFile, "<Attribute Name=\"%s\" AttributeType=\"%s\" Center=\"Node\">\n", name, dim == 1 ? "Scalar": "Vector");
+  if(dim == 1)
+    fprintf(xmfFile, "<DataItem Dimensions=\"%lld\" NumberType=\"Double\" Precision=\"%d\" Format=\"HDF\">%s:/PartType0/%s</DataItem>\n", N, type==FLOAT ? 4:8, fileName, name);
+  else
+    fprintf(xmfFile, "<DataItem Dimensions=\"%lld %d\" NumberType=\"Double\" Precision=\"%d\" Format=\"HDF\">%s:/PartType0/%s</DataItem>\n", N, dim, type==FLOAT ? 4:8, fileName, name);
+  fprintf(xmfFile, "</Attribute>\n");
+}
+
+
+#endif

src/common_io.h

+/*******************************************************************************
+ * 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"
+
+#include "units.h"
+
+#if defined(HAVE_HDF5)
+
+
+/**
+ * @brief The different types of data used in the GADGET IC files.
+ *
+ * (This is admittedly a poor substitute to C++ templates...)
+ */
+enum DATA_TYPE{INT, LONG, LONGLONG, UINT, ULONG, ULONGLONG, FLOAT, DOUBLE, CHAR};
+
+/**
+ * @brief The two sorts of data present in the GADGET IC files: compulsory to start a run or optional.
+ *
+ */
+enum DATA_IMPORTANCE{COMPULSORY=1, OPTIONAL=0};
+
+
+
+
+hid_t hdf5Type(enum DATA_TYPE type);
+size_t sizeOfType(enum DATA_TYPE type);
+
+void readAttribute(hid_t grp, char* name, enum DATA_TYPE type, void* data);
+
+void writeAttribute(hid_t grp, char* name, enum DATA_TYPE type, void* data, int num);
+
+void writeAttribute_d(hid_t grp, char* name, double data);
+void writeAttribute_f(hid_t grp, char* name, float data);
+void writeAttribute_i(hid_t grp, char* name, int data);
+void writeAttribute_l(hid_t grp, char* name, long data);
+void writeAttribute_s(hid_t grp, char* name, char* str);
+
+void createXMFfile();
+FILE* prepareXMFfile();
+void writeXMFfooter(FILE* xmfFile);
+void writeXMFheader(FILE* xmfFile, long long N, char* hdfFileName,  float time);
+void writeXMFline(FILE* xmfFile, char* fileName, char* name, long long N, int dim, enum DATA_TYPE type);
+
+
+/**
+ * @brief Writes the current model of SPH to the file
+ * @param h_file The (opened) HDF5 file in which to write
+ */
+void writeSPHflavour(hid_t h_file);
+
+/**
+ * @brief Writes the current Unit System
+ * @param h_file The (opened) HDF5 file in which to write
+ */
+void writeUnitSystem(hid_t h_file, struct UnitSystem* us);
+
+
+#endif

src/parallel_io.c

@@ -43,98 +43,7 @@
 #include "engine.h"
 #include "error.h"
 #include "kernel.h"
-#include "units.h"
-
-/**
- * @brief The different types of data used in the GADGET IC files.
- *
- * (This is admittedly a poor substitute to C++ templates...)
- */
-enum DATA_TYPE{INT, LONG, LONGLONG, UINT, ULONG, ULONGLONG, FLOAT, DOUBLE, CHAR};
-
-/**
- * @brief The two sorts of data present in the GADGET IC files: compulsory to start a run or optional.
- *
- */
-enum DATA_IMPORTANCE{COMPULSORY=1, OPTIONAL=0};
-
-/**
- * @brief Converts a C data type to the HDF5 equivalent. 
- *
- * This function is a trivial wrapper around the HDF5 types but allows
- * to change the exact storage types matching the code types in a transparent way.
- */
-static hid_t hdf5Type(enum DATA_TYPE type)
-{
-  switch(type)
-    {