Split logger with hdf5 files

configure.ac

@@ -54,6 +54,19 @@ AX_COMPILER_VERSION
 #  Restrict support.
 AC_C_RESTRICT
 
+# logger
+AC_ARG_ENABLE([logger],
+	[AS_HELP_STRING([--enable-logger],
+		[enable the logger output format]
+	)],
+	[with_logger="${enableval}"],
+	[with_logger="no"]
+)
+
+if test "$with_logger" = "yes"; then
+   AC_DEFINE([WITH_LOGGER], 1, [logger enabled])
+fi
+
 # Interprocedural optimization support. Needs special handling for linking and
 # archiving as well as compilation with Intels, needs to be done before
 # libtool is configured (to use correct LD).
@@ -1609,6 +1622,7 @@ AC_MSG_RESULT([
    CPU profiler         : $have_profiler
    Pthread barriers     : $have_pthread_barrier
    VELOCIraptor enabled : $have_velociraptor
+   Logger               : $with_logger
 
    Hydro scheme       : $with_hydro
    Dimensionality     : $with_dimension

src/Makefile.am

@@ -48,7 +48,8 @@ include_HEADERS = space.h runner.h queue.h task.h lock.h cell.h part.h const.h \
     dump.h logger.h active.h timeline.h xmf.h gravity_properties.h gravity_derivatives.h \
     gravity_softened_derivatives.h vector_power.h collectgroup.h hydro_space.h sort_part.h \
     chemistry.h chemistry_io.h chemistry_struct.h cosmology.h restart.h space_getsid.h utilities.h \
-    mesh_gravity.h cbrt.h velociraptor_interface.h swift_velociraptor_part.h outputlist.h
+    mesh_gravity.h cbrt.h velociraptor_interface.h swift_velociraptor_part.h outputlist.h \
+    logger_io.h
 
 # Common source files
 AM_SOURCES = space.c runner.c queue.c task.c cell.c engine.c \
@@ -61,13 +62,14 @@ AM_SOURCES = space.c runner.c queue.c task.c cell.c engine.c \
     part_type.c xmf.c gravity_properties.c gravity.c \
     collectgroup.c hydro_space.c equation_of_state.c \
     chemistry.c cosmology.c restart.c mesh_gravity.c velociraptor_interface.c \
-    outputlist.c velociraptor_dummy.c
+    outputlist.c velociraptor_dummy.c logger_io.c
 
 # Include files for distribution, not installation.
 nobase_noinst_HEADERS = align.h approx_math.h atomic.h barrier.h cycle.h error.h inline.h kernel_hydro.h kernel_gravity.h \
 		 gravity_iact.h kernel_long_gravity.h vector.h cache.h runner_doiact.h runner_doiact_vec.h runner_doiact_grav.h  \
                  runner_doiact_nosort.h runner_doiact_stars.h units.h intrinsics.h minmax.h kick.h timestep.h drift.h \
 		 adiabatic_index.h io_properties.h dimension.h part_type.h periodic.h memswap.h dump.h logger.h sign.h \
+		 logger_io.h \
 		 gravity.h gravity_io.h gravity_cache.h \
 		 gravity/Default/gravity.h gravity/Default/gravity_iact.h gravity/Default/gravity_io.h \
 		 gravity/Default/gravity_debug.h gravity/Default/gravity_part.h  \

src/active.h

@@ -444,43 +444,4 @@ __attribute__((always_inline)) INLINE static int spart_is_starting(
   return (spart_bin <= max_active_bin);
 }
 
-/**
- * @brief Should this particle write its data now ?
- *
- * @param xp The #xpart.
- * @param e The #engine containing information about the current time.
- * @return 1 if the #part should write, 0 otherwise.
- */
-__attribute__((always_inline)) INLINE static int xpart_should_write(
-    const struct xpart *xp, const struct engine *e) {
-
-  return (xp->last_output > e->logger_max_steps);  
-}
-
-/**
- * @brief Should this particle write its data now ?
- *
- * @param p The #gpart.
- * @param e The #engine containing information about the current time.
- * @return 1 if the #gpart should write, 0 otherwise.
- */
-__attribute__((always_inline)) INLINE static int gpart_should_write(
-    const struct gpart *gp, const struct engine *e) {
-
-  return (gp->last_output > e->logger_max_steps);  
-}
-
-/**
- * @brief Should this particle write its data now ?
- *
- * @param p The #spart.
- * @param e The #engine containing information about the current time.
- * @return 1 if the #spart should write, 0 otherwise.
- */
-__attribute__((always_inline)) INLINE static int spart_should_write(
-    const struct spart *sp, const struct engine *e) {
-
-  return (sp->last_output > e->logger_max_steps);  
-}
-
 #endif /* SWIFT_ACTIVE_H */

src/engine.c

@@ -67,6 +67,7 @@
 #include "gravity.h"
 #include "gravity_cache.h"
 #include "hydro.h"
+#include "logger_io.h"
 #include "map.h"
 #include "memswap.h"
 #include "minmax.h"

src/logger.c

@@ -26,6 +26,7 @@
 #include <stdint.h>
 #include <stdlib.h>
 #include <string.h>
+#include <hdf5.h>
 
 /* This object's header. */
 #include "logger.h"
@@ -35,6 +36,8 @@
 #include "dump.h"
 #include "error.h"
 #include "part.h"
+#include "units.h"
+#include "engine.h"
 
 /**
  * @brief Compute the size of a message given its mask.

src/logger.h

@@ -21,6 +21,9 @@
 
 /* Includes. */
 #include "part.h"
+#include "units.h"
+#include "engine.h"
+#include "common_io.h"
 
 /* Forward declaration */
 struct dump;
@@ -86,4 +89,45 @@ int logger_read_gpart(struct gpart *p, size_t *offset, const char *buff);
 int logger_read_timestamp(unsigned long long int *t, size_t *offset,
                           const char *buff);
 
+
+
+/**
+ * @brief Should this particle write its data now ?
+ *
+ * @param xp The #xpart.
+ * @param e The #engine containing information about the current time.
+ * @return 1 if the #part should write, 0 otherwise.
+ */
+__attribute__((always_inline)) INLINE static int xpart_should_write(
+    const struct xpart *xp, const struct engine *e) {
+
+  return (xp->last_output > e->logger_max_steps);  
+}
+
+/**
+ * @brief Should this particle write its data now ?
+ *
+ * @param p The #gpart.
+ * @param e The #engine containing information about the current time.
+ * @return 1 if the #gpart should write, 0 otherwise.
+ */
+__attribute__((always_inline)) INLINE static int gpart_should_write(
+    const struct gpart *gp, const struct engine *e) {
+
+  return (gp->last_output > e->logger_max_steps);  
+}
+
+/**
+ * @brief Should this particle write its data now ?
+ *
+ * @param p The #spart.
+ * @param e The #engine containing information about the current time.
+ * @return 1 if the #spart should write, 0 otherwise.
+ */
+__attribute__((always_inline)) INLINE static int spart_should_write(
+    const struct spart *sp, const struct engine *e) {
+
+  return (sp->last_output > e->logger_max_steps);  
+}
+
 #endif /* SWIFT_LOGGER_H */

src/logger_io.h

+/*******************************************************************************
+ * This file is part of SWIFT.
+ * Copyright (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/>.
+ *
+ ******************************************************************************/
+#ifndef SWIFT_LOGGER_IO_H
+#define SWIFT_LOGGER_IO_H
+
+/* Config parameters. */
+#include "../config.h"
+
+#if defined(HAVE_HDF5) && !defined(WITH_MPI) && defined(WITH_LOGGER)
+
+/* Includes. */
+#include "engine.h"
+#include "part.h"
+#include "units.h"
+
+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* Ndm,
+                    size_t* Nstars, int* periodic, int* flag_entropy,
+                    int with_hydro, int with_gravity, int with_stars,
+                    int dry_run);
+
+void write_output_single(struct engine* e, const char* baseName,
+                         const struct unit_system* internal_units,
+                         const struct unit_system* snapshot_units);
+
+void write_index_single(struct engine* e, const char* baseName,
+			const struct unit_system* internal_units,
+			const struct unit_system* snapshot_units);
+#endif
+
+#endif /* SWIFT_LOGGER_IO_H */

src/parallel_io.c

@@ -21,7 +21,7 @@
 /* Config parameters. */
 #include "../config.h"
 
-#if defined(HAVE_HDF5) && defined(WITH_MPI) && defined(HAVE_PARALLEL_HDF5)
+#if defined(HAVE_HDF5) && defined(WITH_MPI) && defined(HAVE_PARALLEL_HDF5) && !defined(WITH_LOGGER)
 
 /* Some standard headers. */
 #include <hdf5.h>

src/serial_io.c

@@ -21,7 +21,7 @@
 /* Config parameters. */
 #include "../config.h"
 
-#if defined(HAVE_HDF5) && defined(WITH_MPI) && !defined(HAVE_PARALLEL_HDF5)
+#if defined(HAVE_HDF5) && defined(WITH_MPI) && !defined(HAVE_PARALLEL_HDF5) && !defined(WITH_LOGGER)
 
 /* Some standard headers. */
 #include <hdf5.h>

src/single_io.c

@@ -21,7 +21,7 @@
 /* Config parameters. */
 #include "../config.h"
 
-#if defined(HAVE_HDF5) && !defined(WITH_MPI)
+#if defined(HAVE_HDF5) && !defined(WITH_MPI) && !defined(WITH_LOGGER)
 
 /* Some standard headers. */
 #include <hdf5.h>
@@ -998,248 +998,4 @@ void write_output_single(struct engine* e, const char* baseName,
 }
 
 
-/**
- * @brief Writes an HDF5 index file
- *
- * @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 offset and id of particles contained
- * in the engine. If such a file already exists, it is erased and replaced
- * by the new one.
- *
- * Calls #error() if an error occurs.
- *
- */
-void write_index_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);
-
-  /* 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 = 1;
-  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);
-    writeSPHflavour(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;
-
-    /* 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_index(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_index(dmparts, list, &num_fields);
-        break;
-
-      case swift_type_star:
-        N = Nstars;
-	error("TODO");
-        //star_write_index(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, NULL, partTypeGroupName, list[i], N,
-                 internal_units, snapshot_units);
-
-    /* Free temporary array */
-    if (dmparts) {
-      free(dmparts);
-      dmparts = NULL;
-    }
-
-    /* Close particle group */
-    H5Gclose(h_grp);
-
-  }
-
-  /* message("Done writing particles..."); */
-
-  /* Close file */
-  H5Fclose(h_file);
-
-  ++outputCount;
-}
-
 #endif /* HAVE_HDF5 */

src/single_io.h

@@ -45,6 +45,7 @@ void write_output_single(struct engine* e, const char* baseName,
 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 */
 
 #endif /* SWIFT_SINGLE_IO_H */

src/swift.h

@@ -46,6 +46,7 @@
 #include "hydro_properties.h"
 #include "lock.h"
 #include "logger.h"
+#include "logger_io.h"
 #include "map.h"
 #include "mesh_gravity.h"
 #include "multipole.h"