pyodide/packages/numpy/patches/segfault-PyArray_PyIntAsIntp.patch

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 1/2] Fix segfault in PyArray_PyIntAsIntp in Chrome v89 #1384

Resolves https://github.com/pyodide/pyodide/issues/1384.

There seems to be a bug in the v8 wasm runtime. The failure occurs in the numpy
definition of PyArray_IntpFromIndexSequence in the following code:
```C
vals[i] = PyArray_PyIntAsIntp(op);    // line 958
Py_DECREF(op);                        // line 959
if(vals[i] == -1) {                   // line 960, fails here "RuntimeError: memory access out of bounds"

}
```
This is compiled to the following:
```wat
;; First calculate &vals[i]. vals is an array of i32, so this is vals + 4*i.
;; line 958: vals[i] = PyArray_PyIntAsIntp(op);
local.get $var1 ;; vals
local.get $var3 ;; i
i32.const 2 
i32.shl ;; i << 2
i32.add ;; &vals[i] == vals + 4*i
local.tee $var7 ;; v7 = &vals[i], leave &vals[i] on stack
(; Snipped out argument setup and inlined PyArray_PyIntAsIntp ;)
call $PyArray_PyIntAsIntp
i32.store ;; vals[i] = PyArray_PyIntAsIntp(op) ;; Store to vals[i]
;; line 959: Py_DECREF(op);
(; Snipped out Py_DECREF(op) ;)
block $label1
    ;; line 960: if(vals[i] == -1) {
    local.get $var7 ;; &vals[i]
    i32.load ;; Load vals[i] back <== Fails here "RuntimeError: memory access out of bounds"
    i32.const -1 
    i32.ne ;; vals[i] != -1
    br_if $label1
```

It doesn't make a whole lot of sense that it fails here, we just succesfully
stored to vals[i] so why does it fail when we load back? Unforunately the bug
disappears when devtools are open making it very difficult to assess what state
the wasm VM is in when the bug is triggered.

The goal here was to refactor the source to remove the offending load
instruction. There are several options for how to change it, I chose the
following:
```C
int x = PyArray_PyIntAsIntp(op);    // line 958
Py_DECREF(op);                      // line 959
if(x == -1) {                       // line 960

}
vals[i] = x;                        // line 971
```
Updated WAT looks like what you'd expect:
```wat
    ;; line 958: int x = PyArray_PyIntAsIntp(op);
    (; Snipped out argument setup and inlined PyArray_PyIntAsIntp ;)
    call $PyArray_PyIntAsIntp
    ;; Now instead of storing result into vals[i], we store it in a local variable
    local.set $var6 
    ;; line 959: Py_DECREF(op)
    (; Snipped out Py_DECREF(op) ;)
    ;; line 960: if(x == -1)
    block $label1
        local.get $var6 ;; now check value of local variable
        i32.const -1
        i32.ne
        br_if $label1
        (; Snipped out body of conditional ;)
    end $label1
    ;; line 971: vals[i] = x
    local.get $var1 ;; vals
    local.get $var3 ;; i
    i32.const 2   
    i32.shl         ;; 4*i
    i32.add         ;; vals + 4*i
    local.get $var6 ;; x
    i32.store
```
Indeed the offending `i32.load` is gone and so is the crash.

---
 numpy/core/src/multiarray/conversion_utils.c | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/numpy/core/src/multiarray/conversion_utils.c b/numpy/core/src/multiarray/conversion_utils.c
index 52cb58726..5467f4d78 100644
--- a/numpy/core/src/multiarray/conversion_utils.c
+++ b/numpy/core/src/multiarray/conversion_utils.c
@@ -955,9 +955,9 @@ PyArray_IntpFromIndexSequence(PyObject *seq, npy_intp *vals, npy_intp maxvals)
                 return -1;
             }
 
-            vals[i] = PyArray_PyIntAsIntp(op);
+            npy_intp x = PyArray_PyIntAsIntp(op);
             Py_DECREF(op);
-            if(vals[i] == -1) {
+            if(x == -1) {
                 err = PyErr_Occurred();
                 if (err &&
                         PyErr_GivenExceptionMatches(err, PyExc_OverflowError)) {
@@ -968,6 +968,7 @@ PyArray_IntpFromIndexSequence(PyObject *seq, npy_intp *vals, npy_intp maxvals)
                     return -1;
                 }
             }
+            vals[i] = x;
         }
     }
     return nd;
-- 
2.17.1