Clean logger code

src/dump.c

@@ -85,13 +85,8 @@ void dump_ensure(struct dump *d, size_t size) {
   /* Re-map starting at the end of the file. */
   if ((d->data = mmap(NULL, d->size, PROT_WRITE, MAP_SHARED, d->fd,
                       d->file_offset)) == MAP_FAILED) {
-    size_t mega = 1e6;
-    if (d->size > mega)
-      error("Failed to allocate map of size %zi Mbytes (%s).", d->size / mega,
-	    strerror(errno));
-    else
-      error("Failed to allocate map of size %zi bytes (%s).", d->size,
-	    strerror(errno));
+    error("Failed to allocate map of size %zi bytes (%s).", d->size,
+	  strerror(errno));
   }
 }
 

src/gravity/Default/gravity.h

@@ -22,11 +22,13 @@
 
 #include <float.h>
 
+/* Local includes. */
 #include "cosmology.h"
 #include "gravity_properties.h"
 #include "kernel_gravity.h"
 #include "minmax.h"
 
+
 /**
  * @brief Returns the mass of a particle
  *
@@ -228,11 +230,6 @@ __attribute__((always_inline)) INLINE static void gravity_first_init_gpart(
   gp->time_bin = 0;
 
   gravity_init_gpart(gp);
-
-#ifdef WITH_LOGGER
-  gp->last_output = SHRT_MAX;
-  gp->last_offset = 0;
-#endif
 }
 
 #endif /* SWIFT_DEFAULT_GRAVITY_H */

src/gravity/Default/gravity_io.h

@@ -117,32 +117,4 @@ INLINE static void darkmatter_write_particles(const struct gpart* gparts,
                                  UNIT_CONV_NO_UNITS, gparts, id_or_neg_offset);
 }
 
-
-/**
- * @brief Specifies which g-particle fields to write to a dataset
- *
- * @param gparts The g-particle array.
- * @param list The list of i/o properties to write.
- * @param num_fields The number of i/o fields to write.
- * 
- * In this version, we only want the ids and the offset.
- */
-void darkmatter_write_index(struct gpart* gparts, struct io_props* list,
-			    int* num_fields) {
-
-#ifdef WITH_LOGGER
-  /* Say how much we want to read */
-  *num_fields = 2;
-
-  /* List what we want to read */
-  list[0] = io_make_output_field("ParticleIDs", ULONGLONG, 1,
-                                 UNIT_CONV_NO_UNITS, gparts, id_or_neg_offset);
-
-  list[1] = io_make_output_field("Offset", ULONGLONG, 1,
-                                 UNIT_CONV_NO_UNITS, gparts, last_offset);
-#else
-  error("Cannot write index without logger");
-#endif
-}
-
 #endif /* SWIFT_DEFAULT_GRAVITY_IO_H */

src/gravity/Default/gravity_part.h

@@ -75,14 +75,6 @@ struct gpart {
   double potential_exact;
 #endif
 
-#ifdef WITH_LOGGER
-  /* Number of time step since last output */
-  short int last_output;
-  
-  /* offset at last writing */
-  size_t last_offset;
-#endif
-
 } SWIFT_STRUCT_ALIGN;
 
 #endif /* SWIFT_DEFAULT_GRAVITY_PART_H */

src/hydro/Gadget2/hydro.h

@@ -35,6 +35,7 @@
 #include "approx_math.h"
 #include "cosmology.h"
 #include "dimension.h"
+#include "engine.h"
 #include "equation_of_state.h"
 #include "hydro_properties.h"
 #include "hydro_space.h"
@@ -777,4 +778,19 @@ hydro_set_init_internal_energy(struct part *p, float u_init) {
   p->entropy = u_init;
 }
 
+#ifdef WITH_LOGGER
+/**
+ * @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);  
+}
+#endif
+
 #endif /* SWIFT_GADGET2_HYDRO_H */

src/logger.c

@@ -51,6 +51,36 @@ const unsigned int logger_data_size[logger_data_count] = {
   1,
 };
 
+/**
+ * @brief write chunk header
+ *
+ * @param buff The writing buffer
+ * @param mask The mask to write
+ * @param offset The old offset
+ * @param offset_new The new offset
+ *
+ * @return updated buff
+ */
+__attribute__((always_inline)) INLINE static char *logger_write_chunk_header(char *buff, const unsigned int *mask, const size_t *offset, const size_t offset_new) {
+  memcpy(buff, mask, logger_size_mask);
+  buff += logger_size_mask;
+  
+  size_t diff_offset = offset_new - *offset;
+  memcpy(buff, &diff_offset, logger_size_offset);
+  buff += logger_size_offset;
+
+  return buff;
+}
+
+
+/**
+ * @brief write a data to the file
+ *
+ * @param d #dump file
+ * @param offset offset at which to write
+ * @param size number of bytes to write
+ * @param p pointer to the data
+ */
 void logger_write_data(struct dump *d, size_t *offset, const size_t size, void *const p)
 {
   char *buff = dump_get(d, size, offset);
@@ -58,7 +88,16 @@ void logger_write_data(struct dump *d, size_t *offset, const size_t size, void *
 }
 
 /**
- * WARNING: name should be at max of size log->name
+ * @brief write a general data to the file
+ *
+ * write data in the following order: name, data type, data
+ *
+ * @param d #dump file
+ * @param log #logger_const file format informations
+ * @param offset offset at which to write (moved by the data size)
+ * @param p pointer to the data
+ * @param name data name (should be smaller than log->name)
+ * @param data_type #logger_datatype to write
  */
 void logger_write_general_data(struct dump *d, struct logger_const *log, size_t *offset,
 			       void *p, char* name, size_t data_type)
@@ -271,11 +310,15 @@ void logger_log_gpart(struct gpart *p, unsigned int mask, size_t *offset,
   *offset = offset_new;
 }
 
+/**
+ * @brief write a timestamp
+ *
+ * @param timestamp time to write
+ * @param offset In: previous offset, out: offset of this chunk
+ * @param dump #dump file
+ */
 void logger_log_timestamp(integertime_t timestamp, size_t *offset,
                           struct dump *dump) {
-#ifdef SWIFT_DEBUG_CHECKS
-  message("writing timestamp: %llu", timestamp);
-#endif
   /* Start by computing the size of the message. */
   const int size = logger_size(logger_mask_timestamp);
 
@@ -295,6 +338,12 @@ void logger_log_timestamp(integertime_t timestamp, size_t *offset,
 }
 
 
+/**
+ * @brief ensure that the input parameter logger size is large enough
+ *
+ * @param total_nr_nparts total number of particle
+ * @param logger_size requested file size upate
+ */
 void logger_ensure_size(size_t total_nr_parts, size_t logger_size) {
   size_t limit, i;
   struct logger_const log_const;
@@ -304,7 +353,8 @@ void logger_ensure_size(size_t total_nr_parts, size_t logger_size) {
   limit = log_const.offset + log_const.mask;
 
   for(i=0; i < log_const.nber_mask; i++) {
-    limit += log_const.masks_size[i];
+    if (log_const.masks[i] != logger_mask_timestamp)
+      limit += log_const.masks_size[i];
   }
 
   limit *= total_nr_parts;
@@ -397,6 +447,11 @@ void logger_write_file_header(struct dump *dump, struct engine *e) {
   free(name);
 }
 
+/**
+ * @brief initialize the #logger_const with the format informations
+ *
+ * @param log_const #logger_const to initialize
+ */
 void logger_const_init(struct logger_const* log_const) {
   log_const->name = 20;
   log_const->offset = 7;
@@ -471,6 +526,11 @@ void logger_const_init(struct logger_const* log_const) {
 
 }
 
+/**
+ * @brief free the memory allocated when initializing the #logger_const
+ *
+ * @param log_const #logger_const to clean
+ */
 void logger_const_free(struct logger_const* log_const) {
   free(log_const->masks);
   free(log_const->masks_name);

src/logger.h

@@ -78,16 +78,19 @@ struct dump;
 #define logger_mask_consts 64
 #define logger_mask_timestamp 128
 
+#define logger_size_mask 1 // size of the mask
+#define logger_size_offset 7 // size of the offset
+
 /* header constants
  * Thoses are definitions from the format and therefore should not be changed!
  * Size in bytes
  */
 #define LOGGER_VERSION_SIZE 20 // size of the version message
-#define LOGGER_NAME_SIZE 2 // size of the labels size
-#define LOGGER_MASK_SIZE 1 // size of the masks size
-#define LOGGER_NBER_SIZE 1 // size of the number of elements size
+#define LOGGER_NAME_SIZE 2 // size of the labels size information
+#define LOGGER_MASK_SIZE 1 // size of the masks size information
+#define LOGGER_NBER_SIZE 1 // size of the number of elements information
 #define LOGGER_OFFSET_SIZE 1// size of the offset size information
-#define LOGGER_DATATYPE_SIZE 1
+#define LOGGER_DATATYPE_SIZE 1 // size of the data type information
 
 extern char LOGGER_VERSION[LOGGER_VERSION_SIZE];
 
@@ -132,66 +135,6 @@ void logger_const_init(struct logger_const* log_const);
 void logger_const_free(struct logger_const* log_const);
 void logger_ensure_size(size_t total_nr_parts, size_t logger_size);
 
-/**
- * @brief write chunk header
- *
- * @param buff The writing buffer
- * @param maks The mask to write
- * @param offset The old offset
- * @param offset_new The new offset
- *
- * @return updated buff
- */
-__attribute__((always_inline)) INLINE static char *logger_write_chunk_header(char *buff, const unsigned int *mask, const size_t *offset, const size_t offset_new) {
-  memcpy(buff, mask, 1);
-  buff += 1;
-  
-  size_t diff_offset = offset_new - *offset;
-  memcpy(buff, &diff_offset, 7);
-  buff += 7;
-
-  return 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 /* WITH_LOGGER */
 
 #endif /* SWIFT_LOGGER_H */

src/logger_io.c

@@ -838,7 +838,7 @@ void write_index_single(struct engine* e, const char* baseName,
   int periodic = e->s->periodic;
   int numFiles = 1;
   struct part* parts = e->s->parts;
-  struct gpart* gparts = e->s->gparts;
+  //struct gpart* gparts = e->s->gparts;
   struct gpart* dmparts = NULL;
   //struct spart* sparts = e->s->sparts;
   static int outputCount = 0;
@@ -1009,20 +1009,9 @@ void write_index_single(struct engine* e, const char* baseName,
         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;
-
+	error("TODO");
+	break;
+	  
       case swift_type_star:
         N = Nstars;
 	error("TODO");

src/runner.c

@@ -2710,9 +2710,7 @@ void runner_do_logger(struct runner *r, struct cell *c, int timer) {
   const struct engine *e = r->e;
   struct part *restrict parts = c->parts;
   struct xpart *restrict xparts = c->xparts;
-  struct gpart *restrict gparts = c->gparts;
   const int count = c->count;
-  const int gcount = c->gcount;
 
   /* Anything to do here? */
   if (!cell_is_starting_hydro(c, e) && !cell_is_starting_gravity(c, e))
@@ -2751,32 +2749,6 @@ void runner_do_logger(struct runner *r, struct cell *c, int timer) {
       }
     }
 
-    /* Loop over the gparts in this cell. */
-    for (int k = 0; k < gcount; k++) {
-
-      /* Get a handle on the part. */
-      struct gpart *restrict gp = &gparts[k];
-
-      /* If particle needs to be kicked */
-      if (gpart_is_starting(gp, e)) {
-
-	if (gpart_should_write(gp, e))
-	  {
-	    /* Write particle */
-	    logger_log_gpart(gp, logger_mask_x | logger_mask_v | logger_mask_a |
-			     logger_mask_h | logger_mask_consts,
-			     &gp->last_offset, e->logger_dump);
-	    /* Set counter back to zero */
-	    gp->last_output = 0;
-	  }
-	else
-	  {
-	    /* Update counter */
-	    gp->last_output += 1;
-	  }
-      }
-    }
-
   }
   if (timer) TIMER_TOC(timer_logger);
 

src/stars/Default/stars_part.h

@@ -62,9 +62,6 @@ struct spart {
 
   } density;
 
-  /* Number of time step since last output */
-  short int last_output;
-    
 #ifdef SWIFT_DEBUG_CHECKS
 
   /* Time of the last drift */