pyodide · rth · Apr 17, 2021 · Apr 15, 2021 · Apr 15, 2021 · Apr 15, 2021
diff --git a/Makefile b/Makefile
@@ -28,6 +28,7 @@ all: check \
 build/pyodide.asm.js: \
 	src/core/docstring.o \
 	src/core/error_handling.o \
+	src/core/numpy_patch.o \
 	src/core/hiwire.o \
 	src/core/js2python.o \
 	src/core/jsproxy.o \

diff --git a/packages/numpy/meta.yaml b/packages/numpy/meta.yaml
@@ -7,7 +7,8 @@ source:
   sha256: 16507ba6617f62ae3c6ab1725ae6f550331025d4d9a369b83f6d5a470446c342
 
   patches:
-    - patches/fix-i32-load-memory-access-oob.patch
+    - patches/segfault-PyArray_Broadcast.patch
+    - patches/segfault-PyArray_PyIntAsIntp.patch
     - patches/add-emscripten-cpu.patch
     - patches/disable-maybe-uninitialized.patch
     - patches/dont-include-execinfo.patch

diff --git a/packages/numpy/patches/segfault-PyArray_Broadcast.patch b/packages/numpy/patches/segfault-PyArray_Broadcast.patch
@@ -0,0 +1,71 @@
+From 6f91dceca26bb06bada90e0e0bbe770538928d5f Mon Sep 17 00:00:00 2001
+From: Hood <hood@mit.edu>
+Date: Fri, 16 Apr 2021 08:41:03 -0700
+Subject: [PATCH 2/2] Fix segfault in PyArray_Broadcast in chrome 89 #1474
+
+Resolves #1473.
+
+This is a similar situation as with #1384 (see the other patch) however in this
+case when I made modifications to `PyArray_Broadcast` to remove the offending
+load, the crash moved around to other locations corresponding to different spots
+in the source. After a significant amount of messing around with this, I just
+reimplemented the first part of the function in Javascript. See
+src/core/numpy_patch.c where we define PyArray_Broadcast_part1.
+
+---
+ numpy/core/src/multiarray/iterators.c | 32 +++++++++++++++++++++------
+ 1 file changed, 25 insertions(+), 7 deletions(-)
+
+diff --git a/numpy/core/src/multiarray/iterators.c b/numpy/core/src/multiarray/iterators.c
+index 9da811f69..b59d32da1 100644
+--- a/numpy/core/src/multiarray/iterators.c
++++ b/numpy/core/src/multiarray/iterators.c
+@@ -1153,13 +1153,13 @@ NPY_NO_EXPORT PyTypeObject PyArrayIter_Type = {
+
+ /** END of Array Iterator **/
+
+-/* Adjust dimensionality and strides for index object iterators
+-   --- i.e. broadcast
+-*/
+-/*NUMPY_API*/
+-NPY_NO_EXPORT int
+-PyArray_Broadcast(PyArrayMultiIterObject *mit)
+-{
++int
++PyArray_Broadcast_part1(void *mit);
++
++#ifndef __EMSCRIPTEN__
++int
++PyArray_Broadcast_part1(void *mit_void){
++    PyArrayMultiIterObject *mit = (PyArrayMultiIterObject *)mit_void;
+     int i, nd, k, j;
+     npy_intp tmp;
+     PyArrayIterObject *it;
+@@ -1195,6 +1195,24 @@ PyArray_Broadcast(PyArrayMultiIterObject *mit)
+             }
+         }
+     }
++    return 0;
++}
++#endif
++
++/* Adjust dimensionality and strides for index object iterators
++   --- i.e. broadcast
++*/
++/*NUMPY_API*/
++NPY_NO_EXPORT int
++PyArray_Broadcast(PyArrayMultiIterObject *mit)
++{
++    int i, nd, k, j;
++    npy_intp tmp;
++    PyArrayIterObject *it;
++
++    if(PyArray_Broadcast_part1((void*)mit) == -1){
++        return -1;
++    }
+
+     /*
+      * Reset the iterator dimensions and strides of each iterator
+-- 
+2.17.1
+
diff --git a/...ches/fix-i32-load-memory-access-oob.patch → ...atches/segfault-PyArray_PyIntAsIntp.patch b/...ches/fix-i32-load-memory-access-oob.patch → ...atches/segfault-PyArray_PyIntAsIntp.patch
@@ -1,7 +1,7 @@
-From 6cf164b6a1a7cc151aa52ab5bb9e20a95a6a5e67 Mon Sep 17 00:00:00 2001
+From c5a48b544d465673d900459d7e9226379f79e84a Mon Sep 17 00:00:00 2001
 From: Hood <hood@mit.edu>
 Date: Fri, 2 Apr 2021 14:24:24 -0700
-Subject: [PATCH] Fix "load" memory access out of bounds on Chrome v89 #1384
+Subject: [PATCH 1/2] Fix segfault in PyArray_PyIntAsIntp in Chrome v89 #1384
 
 Resolves https://github.com/pyodide/pyodide/issues/1384.
 
@@ -111,5 +111,5 @@ index 52cb58726..5467f4d78 100644
      }
      return nd;
 -- 
-
+2.17.1
 
diff --git a/src/core/main.c b/src/core/main.c
@@ -90,6 +90,10 @@ run_python_simple_inner(char* code)
   return result ? 0 : -1;
 }
 
+// from numpy_patch.c (no need for a header just for this)
+int
+numpy_patch_init();
+
 int
 main(int argc, char** argv)
 {
@@ -121,6 +125,7 @@ main(int argc, char** argv)
   TRY_INIT_WITH_CORE_MODULE(error_handling);
   TRY_INIT(hiwire);
   TRY_INIT(docstring);
+  TRY_INIT(numpy_patch);
   TRY_INIT(js2python);
   TRY_INIT_WITH_CORE_MODULE(python2js);
   TRY_INIT(python2js_buffer);

diff --git a/src/core/numpy_patch.c b/src/core/numpy_patch.c
@@ -0,0 +1,266 @@
+#define PY_SSIZE_T_CLEAN
+#include "Python.h"
+
+#include "error_handling.h"
+
+// Stuff copied from ndarraytypes.h to check offsets
+// First we need a couple of things.
+typedef int npy_intp;
+typedef void PyArray_Descr; // makes it opaque
+typedef bool npy_bool;
+
+#if true /* begin copied from numpy */
+
+#define NPY_MAXDIMS 32
+#define NPY_MAXARGS 32
+
+/*
+ * The main array object structure.
+ *
+ * It has been recommended to use the inline functions defined below
+ * (PyArray_DATA and friends) to access fields here for a number of
+ * releases. Direct access to the members themselves is deprecated.
+ * To ensure that your code does not use deprecated access,
+ * #define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION
+ * (or NPY_1_8_API_VERSION or higher as required).
+ */
+/* This struct will be moved to a private header in a future release */
+typedef struct tagPyArrayObject_fields
+{
+  PyObject_HEAD
+    /* Pointer to the raw data buffer */
+    char* data;
+  /* The number of dimensions, also called 'ndim' */
+  int nd;
+  /* The size in each dimension, also called 'shape' */
+  npy_intp* dimensions;
+  /*
+   * Number of bytes to jump to get to the
+   * next element in each dimension
+   */
+  npy_intp* strides;
+  /*
+   * This object is decref'd upon
+   * deletion of array. Except in the
+   * case of WRITEBACKIFCOPY which has
+   * special handling.
+   *
+   * For views it points to the original
+   * array, collapsed so no chains of
+   * views occur.
+   *
+   * For creation from buffer object it
+   * points to an object that should be
+   * decref'd on deletion
+   *
+   * For WRITEBACKIFCOPY flag this is an
+   * array to-be-updated upon calling
+   * PyArray_ResolveWritebackIfCopy
+   */
+  PyObject* base;
+  /* Pointer to type structure */
+  PyArray_Descr* descr;
+  /* Flags describing array -- see below */
+  int flags;
+  /* For weak references */
+  PyObject* weakreflist;
+} PyArrayObject_fields;
+
+/*
+ * Can't put this in npy_deprecated_api.h like the others.
+ * PyArrayObject field access is deprecated as of NumPy 1.7.
+ */
+typedef PyArrayObject_fields PyArrayObject;
+
+/* FWD declaration */
+typedef struct PyArrayIterObject_tag PyArrayIterObject;
+
+/*
+ * type of the function which translates a set of coordinates to a
+ * pointer to the data
+ */
+typedef char* (*npy_iter_get_dataptr_t)(PyArrayIterObject* iter, npy_intp*);
+
+struct PyArrayIterObject_tag
+{
+  PyObject_HEAD int nd_m1; /* number of dimensions - 1 */
+  npy_intp index, size;
+  npy_intp coordinates[NPY_MAXDIMS]; /* N-dimensional loop */
+  npy_intp dims_m1[NPY_MAXDIMS];     /* ao->dimensions - 1 */
+  npy_intp strides[NPY_MAXDIMS];     /* ao->strides or fake */
+  npy_intp backstrides[NPY_MAXDIMS]; /* how far to jump back */
+  npy_intp factors[NPY_MAXDIMS];     /* shape factors */
+  PyArrayObject* ao;
+  char* dataptr; /* pointer to current item*/
+  npy_bool contiguous;
+
+  npy_intp bounds[NPY_MAXDIMS][2];
+  npy_intp limits[NPY_MAXDIMS][2];
+  npy_intp limits_sizes[NPY_MAXDIMS];
+  npy_iter_get_dataptr_t translate;
+};
+
+typedef struct
+{
+  PyObject_HEAD int numiter;             /* number of iters */
+  npy_intp size;                         /* broadcasted size */
+  npy_intp index;                        /* current index */
+  int nd;                                /* number of dims */
+  npy_intp dimensions[NPY_MAXDIMS];      /* dimensions */
+  PyArrayIterObject* iters[NPY_MAXARGS]; /* iterators */
+} PyArrayMultiIterObject;
+
+#endif /* end copied from numpy */
+
+// To minimize change of confusion, make sure variables in here don't match any
+// variables used in PyArray_Broadcast_part1
+#define offset_Array_nd 12
+#define offset_Array_dimensions 16
+
+#define offset_Iter_ao 660
+
+#define offset_MultIter_numiter 8
+#define offset_MultIter_nd 20
+#define offset_MultIter_dimensions 24
+#define offset_MultIter_iters 152
+
+/**
+ * Check that our offsets match the numpy declarations.
+ */
+// clang-format off
+int numpy_patch_init(){
+  assert(offset_Array_nd         == offsetof(PyArrayObject, nd));
+  assert(offset_Array_dimensions == offsetof(PyArrayObject, dimensions));
+
+  assert(offset_Iter_ao == offsetof(PyArrayIterObject, ao));
+
+  assert(offset_MultIter_numiter    == offsetof(PyArrayMultiIterObject, numiter));
+  assert(offset_MultIter_nd         == offsetof(PyArrayMultiIterObject, nd));
+  assert(offset_MultIter_dimensions == offsetof(PyArrayMultiIterObject, dimensions));
+  assert(offset_MultIter_iters      == offsetof(PyArrayMultiIterObject, iters));
+  return 0;
+}
+// clang-format on
+
+// clang-format off
+#define LOAD(ptr)            HEAP32[(ptr)/4]
+#define LOAD_ARRAY(ptr, idx) LOAD(ptr + 4*idx)
+
+#define Array_nd(ptr)                 LOAD(ptr + offset_Array_nd)
+#define Array_dimensions(ptr)         LOAD(ptr + offset_Array_dimensions)
+
+#define Iter_array(ptr)               LOAD(ptr + offset_Iter_ao)
+
+#define MultiIter_numiter(ptr)          LOAD(ptr + offset_MultIter_numiter)
+#define MultiIter_nd(ptr)               LOAD(ptr + offset_MultIter_nd)
+#define MultiIter_iter(ptr, index)      LOAD_ARRAY(ptr + offset_MultIter_iters, index)
+#define MultiIter_dimension(ptr, index) LOAD_ARRAY(ptr + offset_MultIter_dimensions, index)
+// clang-format on
+
+/**
+ * It's annoying to set errors from Javascript.
+ */
+void
+set_shape_mismatch_err()
+{
+  PyErr_SetString(
+    PyExc_ValueError,
+    "shape mismatch: objects cannot be broadcast to a single shape");
+}
+
+/**
+ * This is basically a 1-1 port of the first segment of PyArray_Broadcast.
+ * I rearranged the code a small amount to save effort.
+ * Pretty much all that happened is that we destroyed type information, replaced
+ * declarations with "let", and had to make special macros to do most memory
+ * access which is much more annoying than in Javascript.
+ *
+ * See below for the C equivalent.
+ */
+EM_JS_NUM(int, PyArray_Broadcast_part1, (void* mit), {
+  let numiter = MultiIter_numiter(mit);
+  /* Discover the broadcast number of dimensions */
+  let nd = 0;
+  for (let i = 0; i < numiter; i++) {
+    let cur_nd = Array_nd(Iter_array(MultiIter_iter(mit, i)));
+    nd = (cur_nd > nd) ? cur_nd : nd;
+  }
+  MultiIter_nd(mit) = nd;
+
+  /* Discover the broadcast shape in each dimension */
+  let start_offset = (mit + offset_MultIter_dimensions) / 4;
+  HEAP32.subarray(start_offset, start_offset + nd).fill(1);
+
+  for (let j = 0; j < numiter; j++) {
+    let it = MultiIter_iter(mit, j);
+    for (i = 0; i < nd; i++) {
+      /* This prepends 1 to shapes not already equal to nd */
+      let cur_array = Iter_array(it);
+      let cur_nd = Array_nd(cur_array);
+      let k = i + cur_nd - nd;
+      if (k >= 0) {
+        let tmp = LOAD_ARRAY(Array_dimensions(cur_array), k);
+        if (tmp == 1) {
+          continue;
+        }
+        let mit_dim_i = MultiIter_dimension(mit, i);
+        if (mit_dim_i == 1) {
+          MultiIter_dimension(mit, i) = tmp;
+        } else if (mit_dim_i != tmp) {
+          _set_shape_mismatch_err();
+          return -1;
+        }
+      }
+    }
+  }
+})
+
+// Here is the C code I based the above function on.
+// This is lightly reorganized from the original definition.
+/*
+NPY_NO_EXPORT int
+PyArray_Broadcast(PyArrayMultiIterObject *mit)
+{
+    int i, nd, k, j;
+    npy_intp tmp, tmp2;
+    PyArrayIterObject *it;
+    PyArrayIterObject **it_ptr;
+
+    / * Discover the broadcast number of dimensions * /
+    for (i = 0, nd = 0; i < mit->numiter; i++) {
+        nd = PyArray_MAX(nd, PyArray_NDIM(mit->iters[i]->ao));
+    }
+    mit->nd = nd;
+
+    / * Discover the broadcast shape in each dimension * /
+    for (i = 0; i < nd; i++) {
+        mit->dimensions[i] = 1;
+    }
+
+    for (j = 0; j < mit->numiter; j++) {
+        it = mit->iters[j];
+        for (i = 0; i < nd; i++) {
+            / * This prepends 1 to shapes not already equal to nd * /
+            k = i + PyArray_NDIM(it->ao) - nd;
+            if (k >= 0) {
+                tmp = PyArray_DIMS(it->ao)[k];
+                if (tmp == 1) {
+                    continue;
+                }
+                if (mit->dimensions[i] == 1) {
+                    mit->dimensions[i] = tmp;
+                }
+                else if (mit->dimensions[i] != tmp) {
+                    PyErr_SetString(PyExc_ValueError,
+                                    "shape mismatch: objects" \
+                                    " cannot be broadcast" \
+                                    " to a single shape");
+                    return -1;
+                }
+            }
+        }
+    }
+
+  // Rest of function skipped
+}
+*/