Non periodic partitioning

The graph of cells that we currently use assumes that the space wraps at the boundaries. This is not true for non-periodic volumes and we have no work across those boundaries. These updates allow for that.

They also allow for vertex weights of zero, as non-periodic spaces can have many empty cells, which should not be considered to carry any work. This latter point is important as this allows empty cells to be gathered to a single node (more frequently anyway, having uniform weights seems not to disallow this effect), which reduces the area of the regions, reducing the number of proxies required (important for spaces with 256x256x256 cells, with a small number of active cells).

Fixes #540 (closed).

examples/main.c

@@ -242,12 +242,12 @@ int main(int argc, char *argv[]) {
                  handle_cmdparam, (intptr_t)&cmdps, 0),
       OPT_BOOLEAN('r', "restart", &restart, "Continue using restart files.",
                   NULL, 0, 0),
+      OPT_BOOLEAN('T', "timers", &with_verbose_timers,
+                  "Print timers every time-step.", NULL, 0, 0),
       OPT_INTEGER('t', "threads", &nr_threads,
                   "The number of threads to use on each MPI rank. Defaults to "
                   "1 if not specified.",
                   NULL, 0, 0),
-      OPT_INTEGER('T', "timers", &with_verbose_timers,
-                  "Print timers every time-step.", NULL, 0, 0),
       OPT_INTEGER('v', "verbose", &verbose,
                   "Run in verbose mode, in MPI mode 2 outputs from all ranks.",
                   NULL, 0, 0),