Update cell graph

README

@@ -71,6 +71,8 @@ Parameters:
                                       from all ranks.
     -y, --task-dumps=<int>            Time-step frequency at which task analysis
                                       files and/or tasks are dumped.
+    --cell-dumps=<int>                Time-step frequency at which cell graphs 
+                                      are dumped. 
     -Y, --threadpool-dumps=<int>      Time-step frequency at which threadpool
                                       tasks are dumped.
 

README.md

@@ -122,6 +122,8 @@ Parameters:
                                       from all ranks.
     -y, --task-dumps=<int>            Time-step frequency at which task analysis
                                       files and/or tasks are dumped.
+    --cell-dumps=<int>                Time-step frequency at which cell graphs 
+                                      are dumped. 
     -Y, --threadpool-dumps=<int>      Time-step frequency at which threadpool
                                       tasks are dumped.
 

doc/RTD/source/AnalysisTools/index.rst

@@ -21,11 +21,13 @@ Cell graph
 ----------
 
 An interactive graph of the cells is available with the configuration option ``--enable-cell-graph``.
-During a run, SWIFT will generate a ``cell_hierarchy_*.csv`` file per MPI rank.
-The command ``tools/make_cell_hierarchy.sh cell_hierarchy_*.csv`` merges the files together and generates the file ``cell_hierarchy.html``
+During a run, SWIFT will generate a ``cell_hierarchy_*.csv`` file per MPI rank at the frequency given by the parameter ``--cell-dumps=n``.
+The command ``tools/make_cell_hierarchy.sh cell_hierarchy_0000_*.csv`` merges the files at time step 0 together and generates the file ``cell_hierarchy.html``
 that contains the graph and can be read with your favorite web browser.
 
-With chrome, you cannot access the files directly, you will need to either access them through an existing server (e.g. public http provided by your university)
+With most web browsers, you cannot access the files directly.
+If it is the case, the cells will never appear (but everything else should be fine).
+To solve this problem, you will need to either access them through an existing server (e.g. public http provided by your university)
 or install ``npm`` and then run the following commands
 
 .. code-block:: bash
@@ -34,6 +36,14 @@ or install ``npm`` and then run the following commands
    http-server .
 
 Now you can open the web page ``http://localhost:8080/cell_hierarchy.html``.
+When running a large simulation, the data loading may take a while (a few seconds for EAGLE_6).
+Your browser should not be hanging, but will seems to be idle.
+
+If you wish to add some information to the graph, you can do it by modifying the files ``src/space.c`` and ``tools/data/cell_hierarchy.html``.
+In the first one, you will need to modify the calls to ``fprintf`` in the functions ``space_write_cell_hierarchy`` and ``space_write_cell``.
+Here the code is simply writing CSV files containing all the required information about the cells.
+In the second one, you will need to find the function ``mouseover`` and add the field that you have created.
+You can also increase the size of the bubble through the style parameter ``height``.
 
 Memory usage reports
 --------------------

doc/RTD/source/CommandLineOptions/index.rst

@@ -65,5 +65,7 @@ can be found by typing ``./swift -h``::
                                       from all ranks.
     -y, --task-dumps=<int>            Time-step frequency at which task analysis
                                       files and/or tasks are dumped.
+    --cell-dumps=<int>                Time-step frequency at which cell graphs 
+                                      are dumped. 
     -Y, --threadpool-dumps=<int>      Time-step frequency at which threadpool
                                       tasks are dumped.

examples/main.c

@@ -148,6 +148,7 @@ int main(int argc, char *argv[]) {
   int with_aff = 0;
   int dry_run = 0;
   int dump_tasks = 0;
+  int dump_cells = 0;
   int dump_threadpool = 0;
   int nsteps = -2;
   int restart = 0;
@@ -263,6 +264,9 @@ int main(int argc, char *argv[]) {
       OPT_INTEGER('y', "task-dumps", &dump_tasks,
                   "Time-step frequency at which task graphs are dumped.", NULL,
                   0, 0),
+      OPT_INTEGER(0, "cell-dumps", &dump_cells,
+                  "Time-step frequency at which cell graphs are dumped.", NULL,
+                  0, 0),
       OPT_INTEGER('Y', "threadpool-dumps", &dump_threadpool,
                   "Time-step frequency at which threadpool tasks are dumped.",
                   NULL, 0, 0),
@@ -323,6 +327,16 @@ int main(int argc, char *argv[]) {
   }
 #endif
 
+#ifndef SWIFT_CELL_GRAPH
+  if (dump_cells) {
+    if (myrank == 0) {
+      error(
+          "complete cell dumps are only created when "
+          "configured with --enable-cell-graph.");
+    }
+  }
+#endif
+
 #ifndef SWIFT_DEBUG_THREADPOOL
   if (dump_threadpool) {
     printf(
@@ -1261,6 +1275,13 @@ int main(int argc, char *argv[]) {
       task_dump_stats(dumpfile, &e, /* header = */ 0, /* allranks = */ 1);
     }
 
+#ifdef SWIFT_CELL_GRAPH
+    /* Dump the cell data using the given frequency. */
+    if (dump_cells && (dump_cells == 1 || j % dump_cells == 1)) {
+      space_write_cell_hierarchy(e.s, j + 1);
+    }
+#endif
+
       /* Dump memory use report if collected. */
 #ifdef SWIFT_MEMUSE_REPORTS
     {

src/engine.c

@@ -3557,7 +3557,6 @@ void engine_init_particles(struct engine *e, int flag_entropy_ICs,
 #endif
 
   scheduler_write_dependencies(&e->sched, e->verbose);
-  space_write_cell_hierarchy(e->s);
   if (e->nodeID == 0) scheduler_write_task_level(&e->sched);
 
   /* Run the 0th time-step */

src/space.c

@@ -5670,14 +5670,15 @@ void space_write_cell(const struct space *s, FILE *f, const struct cell *c) {
  * @brief Write a csv file containing the cell hierarchy
  *
  * @param s The #space.
+ * @param j The file number.
  */
-void space_write_cell_hierarchy(const struct space *s) {
+void space_write_cell_hierarchy(const struct space *s, int j) {
 
 #ifdef SWIFT_CELL_GRAPH
 
   /* Open file */
   char filename[200];
-  sprintf(filename, "cell_hierarchy_%04i.csv", engine_rank);
+  sprintf(filename, "cell_hierarchy_%04i_%04i.csv", j, engine_rank);
   FILE *f = fopen(filename, "w");
   if (f == NULL) error("Error opening task level file.");
 

src/space.h

@@ -374,6 +374,6 @@ void space_free_foreign_parts(struct space *s);
 
 void space_struct_dump(struct space *s, FILE *stream);
 void space_struct_restore(struct space *s, FILE *stream);
-void space_write_cell_hierarchy(const struct space *s);
+void space_write_cell_hierarchy(const struct space *s, int j);
 
 #endif /* SWIFT_SPACE_H */

tools/make_cell_hierarchy.sh

@@ -9,7 +9,7 @@ then
    rm $csv_output
 fi
 
-for filename in ./cell_hierarchy_*.csv;
+for filename in $@;
 do
     cat $filename >> cell_hierarchy.csv
 done