Fixed memory leaks

CMakeLists.txt

@@ -371,7 +371,8 @@ if(MEMORYCHECK_COMMAND)
     add_custom_command(
       OUTPUT ${logfile}
       COMMAND ${CMAKE_COMMAND}
-        -E env PYTHONMALLOC=malloc ${MEMORYCHECK_COMMAND}
+        -E env PYTHONMALLOC=malloc DLITE_ATEXIT_FREE=
+        -- ${MEMORYCHECK_COMMAND}
         --leak-check=yes
         --show-leak-kinds=all
         --keep-debuginfo=yes

cmake/valgrind-python.supp

@@ -634,6 +634,29 @@
    fun:Py_BytesMain
 }
 
+{
+   Leak in numpy random_bit_generator (py311, alvis)
+   Memcheck:Leak
+   match-leak-kinds: definite
+   fun:calloc
+   obj:/usr/lib64/libgomp.so.1.0.0
+   obj:/usr/lib64/libgomp.so.1.0.0
+   obj:/usr/lib64/libgomp.so.1.0.0
+   fun:call_init
+   fun:call_init
+   fun:_dl_init
+   fun:_dl_catch_exception
+}
+
+{
+   Leak in pydantic initialisation (py311)
+   Memcheck:Leak
+   match-leak-kinds: definite
+   fun:realloc
+   ...
+   fun:PyInit__pydantic_core
+}
+
 
 # ------------------------------------
 # Python plugins

src/dlite-mapping.c

@@ -100,6 +100,14 @@ DLiteMapping *mapping_create_rec(const char *output_uri, Instances *inputs,
     }
     if (ignore) continue;
 
+    /*
+      FIXME: avoid memory leak
+      Implement dlite_mapping_plugin_free() and call it here.
+
+      Even better, implement caching in dlite_mapping_plugin_next()
+      such that it returns borrowed references to the api. Add a function
+      to clear the cache.
+    */
     if (!cheapest || cost < lowest_cost) {
       cheapest = api;
       lowest_cost = cost;

src/dlite-misc.c

@@ -465,6 +465,7 @@ int dlite_add_dll_path(void)
 /* Local state for this module. */
 typedef struct {
   int in_atexit;
+  int finalizing;
 } Locals;
 
 
@@ -496,7 +497,7 @@ static Locals *get_locals(void)
 static void _handle_atexit(void) {
 
   /* No extra finalisation is needed if we already are in an atexit handler */
-  if (dlite_globals_in_atexit()) return;
+  if (dlite_globals_in_atexit() && !getenv("DLITE_ATEXIT_FREE")) return;
 
   /* Mark that we are in an atexit handler */
   dlite_globals_set_atexit();
@@ -582,6 +583,11 @@ void dlite_init(void)
 void dlite_finalize(void)
 {
   Session *s = session_get_default();
+  Locals *locals = get_locals();
+
+  /* Ensure that we only finalize once. */
+  if (locals->finalizing) return;
+  locals->finalizing = 1;
 
   /* Don't free anything if we are in an atexit handler */
   if (dlite_globals_in_atexit() && !getenv("DLITE_ATEXIT_FREE")) return;

src/pyembed/dlite-python-storage.c

@@ -46,7 +46,7 @@ static void free_globals(void *globals)
   if (g->initialised) fu_paths_deinit(&g->paths);
 
   /* Do not call Py_DECREF if we are in an atexit handler */
-  if (!dlite_globals_in_atexit() || getenv("DLITE_ATEXIT_FREE")) {
+  if (!dlite_globals_in_atexit()) {
     Py_XDECREF(g->loaded_storages);
     g->loaded_storages = NULL;
   }

storages/json/dlite-json-storage.c

@@ -318,9 +318,12 @@ DLiteInstance *json_memload(const DLiteStoragePlugin *api,
                             const unsigned char *buf, size_t size,
                             const char *id, const char *options)
 {
+  DLiteInstance *inst;
   DLiteStorage *s = json_loader(api, NULL, buf, size, options);
-  DLiteInstance *inst = json_load(s, id);
+  if (!s) return NULL;
+  inst = json_load(s, id);
   json_close(s);
+  free(s);
   return inst;
 }