Support deleting methods during precompilation for stdlib excision (#51641)

The problem with the `delete_method` in `__init__` approach is that we
invalidate the method-table,
after we have performed all of the caching work. A package dependent on
`Random`, will still see
the stub method in Base and thus when we delete the stub, we may
invalidate useful work.

Instead we delete the methods when Random is being loaded, thus a
dependent package only ever sees
the method table with all the methods in Random, and non of the stubs
methods.

The only invalidation that thus may happen are calls to `rand` and
`randn` without first doing an `import Random`.

Author: vchuravy

base/compiler/typeinfer.jl

@@ -3,6 +3,7 @@
 # Tracking of newly-inferred CodeInstances during precompilation
 const track_newly_inferred = RefValue{Bool}(false)
 const newly_inferred = CodeInstance[]
+const newly_deleted = Method[]
 
 # build (and start inferring) the inference frame for the top-level MethodInstance
 function typeinf(interp::AbstractInterpreter, result::InferenceResult, cache_mode::Symbol)

base/loading.jl

@@ -2350,6 +2350,7 @@ function include_package_for_output(pkg::PkgId, input::String, depot_path::Vecto
     end
 
     ccall(:jl_set_newly_inferred, Cvoid, (Any,), Core.Compiler.newly_inferred)
+    ccall(:jl_set_newly_deleted, Cvoid, (Any,), Core.Compiler.newly_deleted)
     Core.Compiler.track_newly_inferred.x = true
     try
         Base.include(Base.__toplevel__, input)

base/stubs.jl

@@ -35,7 +35,8 @@ function delete_stubs(mod)
         if obj isa Function
             ms = Base.methods(obj, mod)
             for m in ms
-                Base.delete_method(m)
+                ccall(:jl_push_newly_deleted, Cvoid, (Any,), m)
+                ccall(:jl_method_table_disable_incremental, Cvoid, (Any, Any), Base.get_methodtable(m), m)
             end
         end
     end

doc/src/devdocs/locks.md

@@ -45,6 +45,7 @@ The following is a leaf lock (level 2), and only acquires level 1 locks (safepoi
 >   * Module->lock
 >   * JLDebuginfoPlugin::PluginMutex
 >   * newly_inferred_mutex
+>   * newly_deleted_mutex
 
 The following is a level 3 lock, which can only acquire level 1 or level 2 locks internally:
 

src/clangsa/GCChecker.cpp

@@ -1440,7 +1440,8 @@ bool GCChecker::evalCall(const CallEvent &Call, CheckerContext &C) const {
   } else if (name == "JL_GC_PUSH1" || name == "JL_GC_PUSH2" ||
              name == "JL_GC_PUSH3" || name == "JL_GC_PUSH4" ||
              name == "JL_GC_PUSH5" || name == "JL_GC_PUSH6" ||
-             name == "JL_GC_PUSH7" || name == "JL_GC_PUSH8") {
+             name == "JL_GC_PUSH7" || name == "JL_GC_PUSH8" ||
+             name == "JL_GC_PUSH9") {
     ProgramStateRef State = C.getState();
     // Transform slots to roots, transform values to rooted
     unsigned NumArgs = CE->getNumArgs();

src/gf.c

@@ -1857,9 +1857,9 @@ static jl_typemap_entry_t *do_typemap_search(jl_methtable_t *mt JL_PROPAGATES_RO
 }
 #endif
 
-static void jl_method_table_invalidate(jl_methtable_t *mt, jl_typemap_entry_t *methodentry, size_t max_world)
+static void jl_method_table_invalidate(jl_methtable_t *mt, jl_typemap_entry_t *methodentry, size_t max_world, int tracked)
 {
-    if (jl_options.incremental && jl_generating_output())
+    if (!tracked && jl_options.incremental && jl_generating_output())
         jl_error("Method deletion is not possible during Module precompile.");
     jl_method_t *method = methodentry->func.method;
     assert(!method->is_for_opaque_closure);
@@ -1916,10 +1916,22 @@ JL_DLLEXPORT void jl_method_table_disable(jl_methtable_t *mt, jl_method_t *metho
     JL_LOCK(&mt->writelock);
     // Narrow the world age on the method to make it uncallable
     size_t world = jl_atomic_fetch_add(&jl_world_counter, 1);
-    jl_method_table_invalidate(mt, methodentry, world);
+    jl_method_table_invalidate(mt, methodentry, world, 0);
     JL_UNLOCK(&mt->writelock);
 }
 
+JL_DLLEXPORT void jl_method_table_disable_incremental(jl_methtable_t *mt, jl_method_t *method)
+{
+    jl_typemap_entry_t *methodentry = do_typemap_search(mt, method);
+    JL_LOCK(&mt->writelock);
+    // Narrow the world age on the method to make it uncallable
+    // size_t world = jl_atomic_load_acquire(&jl_world_counter);
+    size_t world = jl_atomic_fetch_add(&jl_world_counter, 1);
+    jl_method_table_invalidate(mt, methodentry, world, 1);
+    JL_UNLOCK(&mt->writelock);
+}
+
+
 static int jl_type_intersection2(jl_value_t *t1, jl_value_t *t2, jl_value_t **isect JL_REQUIRE_ROOTED_SLOT, jl_value_t **isect2 JL_REQUIRE_ROOTED_SLOT)
 {
     *isect2 = NULL;
@@ -2010,7 +2022,7 @@ JL_DLLEXPORT void jl_method_table_insert(jl_methtable_t *mt, jl_method_t *method
         oldvalue = (jl_value_t*)replaced;
         invalidated = 1;
         method_overwrite(newentry, replaced->func.method);
-        jl_method_table_invalidate(mt, replaced, max_world);
+        jl_method_table_invalidate(mt, replaced, max_world, 0);
     }
     else {
         jl_method_t *const *d;

src/init.c

@@ -718,6 +718,7 @@ static void jl_set_io_wait(int v)
 extern jl_mutex_t jl_modules_mutex;
 extern jl_mutex_t precomp_statement_out_lock;
 extern jl_mutex_t newly_inferred_mutex;
+extern jl_mutex_t newly_deleted_mutex;
 extern jl_mutex_t global_roots_lock;
 extern jl_mutex_t profile_show_peek_cond_lock;
 
@@ -736,6 +737,7 @@ static void init_global_mutexes(void) {
     JL_MUTEX_INIT(&jl_modules_mutex, "jl_modules_mutex");
     JL_MUTEX_INIT(&precomp_statement_out_lock, "precomp_statement_out_lock");
     JL_MUTEX_INIT(&newly_inferred_mutex, "newly_inferred_mutex");
+    JL_MUTEX_INIT(&newly_deleted_mutex, "newly_deleted_mutex");
     JL_MUTEX_INIT(&global_roots_lock, "global_roots_lock");
     JL_MUTEX_INIT(&jl_codegen_lock, "jl_codegen_lock");
     JL_MUTEX_INIT(&typecache_lock, "typecache_lock");

src/jl_exported_funcs.inc

@@ -310,6 +310,7 @@
     XX(jl_method_instance_add_backedge) \
     XX(jl_method_table_add_backedge) \
     XX(jl_method_table_disable) \
+    XX(jl_method_table_disable_incremental) \
     XX(jl_method_table_for) \
     XX(jl_method_table_insert) \
     XX(jl_methtable_lookup) \

src/julia.h

@@ -948,6 +948,7 @@ extern void JL_GC_PUSH4(void *, void *, void *, void *)  JL_NOTSAFEPOINT;
 extern void JL_GC_PUSH5(void *, void *, void *, void *, void *)  JL_NOTSAFEPOINT;
 extern void JL_GC_PUSH7(void *, void *, void *, void *, void *, void *, void *)  JL_NOTSAFEPOINT;
 extern void JL_GC_PUSH8(void *, void *, void *, void *, void *, void *, void *, void *)  JL_NOTSAFEPOINT;
+extern void JL_GC_PUSH9(void *, void *, void *, void *, void *, void *, void *, void *, void *)  JL_NOTSAFEPOINT;
 extern void _JL_GC_PUSHARGS(jl_value_t **, size_t) JL_NOTSAFEPOINT;
 // This is necessary, because otherwise the analyzer considers this undefined
 // behavior and terminates the exploration
@@ -990,6 +991,9 @@ extern void JL_GC_POP() JL_NOTSAFEPOINT;
 #define JL_GC_PUSH8(arg1, arg2, arg3, arg4, arg5, arg6, arg7, arg8)                                     \
   void *__gc_stkf[] = {(void*)JL_GC_ENCODE_PUSH(8), jl_pgcstack, arg1, arg2, arg3, arg4, arg5, arg6, arg7, arg8}; \
   jl_pgcstack = (jl_gcframe_t*)__gc_stkf;
+#define JL_GC_PUSH9(arg1, arg2, arg3, arg4, arg5, arg6, arg7, arg8, arg9)                                     \
+  void *__gc_stkf[] = {(void*)JL_GC_ENCODE_PUSH(9), jl_pgcstack, arg1, arg2, arg3, arg4, arg5, arg6, arg7, arg8, arg9}; \
+  jl_pgcstack = (jl_gcframe_t*)__gc_stkf;
 
 
 #define JL_GC_PUSHARGS(rts_var,n)                                                                       \
@@ -2041,6 +2045,9 @@ JL_DLLEXPORT jl_value_t *jl_restore_incremental(const char *fname, jl_array_t *d
 
 JL_DLLEXPORT void jl_set_newly_inferred(jl_value_t *newly_inferred);
 JL_DLLEXPORT void jl_push_newly_inferred(jl_value_t *ci);
+JL_DLLEXPORT void jl_method_table_disable_incremental(jl_methtable_t *mt, jl_method_t *m);
+JL_DLLEXPORT void jl_set_newly_deleted(jl_value_t *newly_deleted);
+JL_DLLEXPORT void jl_push_newly_deleted(jl_value_t *m);
 JL_DLLEXPORT void jl_write_compiler_output(void);
 
 // parsing

src/staticdata.c

@@ -2523,7 +2523,7 @@ static void jl_prepare_serialization_data(jl_array_t *mod_array, jl_array_t *new
 static void jl_save_system_image_to_stream(ios_t *f, jl_array_t *mod_array,
                                            jl_array_t *worklist, jl_array_t *extext_methods,
                                            jl_array_t *new_specializations, jl_array_t *method_roots_list,
-                                           jl_array_t *ext_targets, jl_array_t *edges) JL_GC_DISABLED
+                                           jl_array_t *ext_targets, jl_array_t *edges, jl_array_t *newly_deleted) JL_GC_DISABLED
 {
     htable_new(&field_replace, 0);
     // strip metadata and IR when requested
@@ -2644,6 +2644,10 @@ static void jl_save_system_image_to_stream(ios_t *f, jl_array_t *mod_array,
             jl_queue_for_serialization(&s, ext_targets);
             jl_queue_for_serialization(&s, edges);
         }
+        if (newly_deleted) {
+            jl_queue_for_serialization(&s, newly_deleted);
+        }
+
         jl_serialize_reachable(&s);
         // step 1.2: ensure all gvars are part of the sysimage too
         record_gvars(&s, &gvars);
@@ -2793,6 +2797,7 @@ static void jl_save_system_image_to_stream(ios_t *f, jl_array_t *mod_array,
             jl_write_value(&s, method_roots_list);
             jl_write_value(&s, ext_targets);
             jl_write_value(&s, edges);
+            jl_write_value(&s, newly_deleted);
         }
         write_uint32(f, jl_array_len(s.link_ids_gctags));
         ios_write(f, (char*)jl_array_data(s.link_ids_gctags, uint32_t), jl_array_len(s.link_ids_gctags) * sizeof(uint32_t));
@@ -2874,11 +2879,11 @@ JL_DLLEXPORT void jl_create_system_image(void **_native_data, jl_array_t *workli
     }
 
     jl_array_t *mod_array = NULL, *extext_methods = NULL, *new_specializations = NULL;
-    jl_array_t *method_roots_list = NULL, *ext_targets = NULL, *edges = NULL;
+    jl_array_t *method_roots_list = NULL, *ext_targets = NULL, *edges = NULL, *_newly_deleted = NULL;
     int64_t checksumpos = 0;
     int64_t checksumpos_ff = 0;
     int64_t datastartpos = 0;
-    JL_GC_PUSH6(&mod_array, &extext_methods, &new_specializations, &method_roots_list, &ext_targets, &edges);
+    JL_GC_PUSH7(&mod_array, &extext_methods, &new_specializations, &method_roots_list, &ext_targets, &edges, &_newly_deleted);
 
     if (worklist) {
         mod_array = jl_get_loaded_modules();  // __toplevel__ modules loaded in this session (from Base.loaded_modules_array)
@@ -2925,7 +2930,10 @@ JL_DLLEXPORT void jl_create_system_image(void **_native_data, jl_array_t *workli
     }
     if (_native_data != NULL)
         native_functions = *_native_data;
-    jl_save_system_image_to_stream(ff, mod_array, worklist, extext_methods, new_specializations, method_roots_list, ext_targets, edges);
+    // Otherwise serialization will be confused.
+    if (newly_deleted)
+        _newly_deleted = jl_array_copy(newly_deleted);
+    jl_save_system_image_to_stream(ff, mod_array, worklist, extext_methods, new_specializations, method_roots_list, ext_targets, edges, _newly_deleted);
     if (_native_data != NULL)
         native_functions = NULL;
     // make sure we don't run any Julia code concurrently before this point
@@ -3009,6 +3017,7 @@ static void jl_restore_system_image_from_stream_(ios_t *f, jl_image_t *image, jl
                                                  jl_array_t **extext_methods,
                                                  jl_array_t **new_specializations, jl_array_t **method_roots_list,
                                                  jl_array_t **ext_targets, jl_array_t **edges,
+                                                 jl_array_t **newly_deleted,
                                                  char **base, arraylist_t *ccallable_list, pkgcachesizes *cachesizes) JL_GC_DISABLED
 {
     int en = jl_gc_enable(0);
@@ -3070,7 +3079,7 @@ static void jl_restore_system_image_from_stream_(ios_t *f, jl_image_t *image, jl
     assert(!ios_eof(f));
     s.s = f;
     uintptr_t offset_restored = 0, offset_init_order = 0, offset_extext_methods = 0, offset_new_specializations = 0, offset_method_roots_list = 0;
-    uintptr_t offset_ext_targets = 0, offset_edges = 0;
+    uintptr_t offset_ext_targets = 0, offset_edges = 0, offset_newly_deleted = 0;
     if (!s.incremental) {
         size_t i;
         for (i = 0; tags[i] != NULL; i++) {
@@ -3104,6 +3113,7 @@ static void jl_restore_system_image_from_stream_(ios_t *f, jl_image_t *image, jl
         offset_method_roots_list = jl_read_offset(&s);
         offset_ext_targets = jl_read_offset(&s);
         offset_edges = jl_read_offset(&s);
+        offset_newly_deleted = jl_read_offset(&s);
     }
     s.buildid_depmods_idxs = depmod_to_imageidx(depmods);
     size_t nlinks_gctags = read_uint32(f);
@@ -3137,6 +3147,7 @@ static void jl_restore_system_image_from_stream_(ios_t *f, jl_image_t *image, jl
         *method_roots_list = (jl_array_t*)jl_delayed_reloc(&s, offset_method_roots_list);
         *ext_targets = (jl_array_t*)jl_delayed_reloc(&s, offset_ext_targets);
         *edges = (jl_array_t*)jl_delayed_reloc(&s, offset_edges);
+        *newly_deleted = (jl_array_t*)jl_delayed_reloc(&s, offset_newly_deleted);
         if (!*new_specializations)
             *new_specializations = jl_alloc_vec_any(0);
     }
@@ -3326,6 +3337,11 @@ static void jl_restore_system_image_from_stream_(ios_t *f, jl_image_t *image, jl
         assert(jl_is_datatype(obj));
         jl_cache_type_((jl_datatype_t*)obj);
     }
+
+    // Delete methods before inserting new ones.
+    if (newly_deleted)
+        jl_delete_methods(*newly_deleted);
+
     // Perform fixups: things like updating world ages, inserting methods & specializations, etc.
     size_t world = jl_atomic_load_acquire(&jl_world_counter);
     for (size_t i = 0; i < s.uniquing_objs.len; i++) {
@@ -3549,11 +3565,11 @@ static jl_value_t *jl_restore_package_image_from_stream(void* pkgimage_handle, i
     assert(datastartpos > 0 && datastartpos < dataendpos);
     needs_permalloc = jl_options.permalloc_pkgimg || needs_permalloc;
     jl_value_t *restored = NULL;
-    jl_array_t *init_order = NULL, *extext_methods = NULL, *new_specializations = NULL, *method_roots_list = NULL, *ext_targets = NULL, *edges = NULL;
+    jl_array_t *init_order = NULL, *extext_methods = NULL, *new_specializations = NULL, *method_roots_list = NULL, *ext_targets = NULL, *edges = NULL, *newly_deleted = NULL;
     jl_svec_t *cachesizes_sv = NULL;
     char *base;
     arraylist_t ccallable_list;
-    JL_GC_PUSH8(&restored, &init_order, &extext_methods, &new_specializations, &method_roots_list, &ext_targets, &edges, &cachesizes_sv);
+    JL_GC_PUSH9(&restored, &init_order, &extext_methods, &new_specializations, &method_roots_list, &ext_targets, &edges, &newly_deleted, &cachesizes_sv);
 
     { // make a permanent in-memory copy of f (excluding the header)
         ios_bufmode(f, bm_none);
@@ -3577,11 +3593,12 @@ static jl_value_t *jl_restore_package_image_from_stream(void* pkgimage_handle, i
                 ios_close(f);
             ios_static_buffer(f, sysimg, len);
             pkgcachesizes cachesizes;
-            jl_restore_system_image_from_stream_(f, image, depmods, checksum, (jl_array_t**)&restored, &init_order, &extext_methods, &new_specializations, &method_roots_list, &ext_targets, &edges, &base, &ccallable_list, &cachesizes);
+            jl_restore_system_image_from_stream_(f, image, depmods, checksum, (jl_array_t**)&restored, &init_order, &extext_methods, &new_specializations, &method_roots_list, &ext_targets, &edges, &newly_deleted, &base, &ccallable_list, &cachesizes);
             JL_SIGATOMIC_END();
 
             // Insert method extensions
             jl_insert_methods(extext_methods);
+
             // No special processing of `new_specializations` is required because recaching handled it
             // Add roots to methods
             jl_copy_roots(method_roots_list, jl_worklist_key((jl_array_t*)restored));
@@ -3617,7 +3634,7 @@ static jl_value_t *jl_restore_package_image_from_stream(void* pkgimage_handle, i
 static void jl_restore_system_image_from_stream(ios_t *f, jl_image_t *image, uint32_t checksum)
 {
     JL_TIMING(LOAD_IMAGE, LOAD_Sysimg);
-    jl_restore_system_image_from_stream_(f, image, NULL, checksum | ((uint64_t)0xfdfcfbfa << 32), NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL);
+    jl_restore_system_image_from_stream_(f, image, NULL, checksum | ((uint64_t)0xfdfcfbfa << 32), NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL);
 }
 
 JL_DLLEXPORT jl_value_t *jl_restore_incremental_from_buf(void* pkgimage_handle, const char *buf, jl_image_t *image, size_t sz, jl_array_t *depmods, int completeinfo, const char *pkgname, int needs_permalloc)