07/17/24
11/1/1446
For some reason I wanted to "port" Jupyter Echo Kernel to Deno using deno-python. It shouldn't be too hard I already have relatively complex projects using it: Stimulator Share
Here is the python kernel
from ipykernel.kernelbase import Kernel
class EchoKernel(Kernel):
implementation = 'Echo'
implementation_version = '1.0'
language = 'no-op'
language_version = '0.1'
language_info = {
'name': 'Any text',
'mimetype': 'text/plain',
'file_extension': '.txt',
}
banner = "Echo kernel - as useful as a parrot"
def do_execute(self, code, silent, store_history=True, user_expressions=None,
allow_stdin=False):
if not silent:
stream_content = {'name': 'stdout', 'text': code}
self.send_response(self.iopub_socket, 'stream', stream_content)
return {'status': 'ok',
# The base class increments the execution count
'execution_count': self.execution_count,
'payload': [],
'user_expressions': {},
}
if __name__ == '__main__':
from ipykernel.kernelapp import IPKernelApp
IPKernelApp.launch_instance(kernel_class=EchoKernel)
Here is a start at porting (file is called a.ts)
#!/usr/bin/env -S deno run --allow-all --unstable-ffi
import { NamedArgument, PyObject, python } from "jsr:@denosaurs/python";
const m = python.runModule(`
from ipykernel.kernelbase import Kernel
class EchoKernel(Kernel):
implementation = 'Echo'
implementation_version = '1.0'
language = 'no-op'
language_version = '0.1'
language_info = {
'name': 'Any text',
'mimetype': 'text/plain',
'file_extension': '.txt',
}
banner = "Echo kernel - as useful as a parrot"
`);
// NOTE: this also modifies m.EchoKernel
const kernel = PyObject.from(m.EchoKernel);
kernel.setAttr(
"do_execute",
python.callback(() => {
//TODO: implement this
return {
status: "ok",
execution_count: 0,
payload: [],
user_expressions: {},
};
}),
);
if (import.meta.main) {
const IPKernelApp = python.import("ipykernel.kernelapp").IPKernelApp;
IPKernelApp.launch_instance(new NamedArgument("kernel_class", kernel));
}
Ok wasn't that hard, chmod +x ./a.ts && ./a.ts
NOTE: When using the `ipython kernel` entry point, Ctrl-C will not work.
To exit, you will have to explicitly quit this process, by either sending
"quit" from a client, or using Ctrl-\ in UNIX-like environments.
To read more about this, see https://github.com/ipython/ipython/issues/2049
To connect another client to this kernel, use:
--existing kernel-15074.json
fish: Job 1, 'deno run -A a.ts' terminated by signal SIGSEGV (Address boundary error)
Hmm, it worked but then segfaulted, so gdb to the rescue
gdb --args deno run -A --unstable-ffi a.ts
(gdb) r
Thread 1 "deno" received sig``nal SIGSEGV, Segmentation fault.
0x00007ffff7e1dfb0 in __strncmp_sse42 () from /lib64/libc.so.6
Ok we're comparing something, lets check what it is, arguments are passed in linux x86 in rdi then rsi
info registers
rsi 0x55555c25b900 93825106557184
rdi 0x5555 21845
rsi seems like a valid pointer, but rdi is definitely not, lets just check
rsi first and try to print it as a cstring
(gdb) x/s $rsi
0x55555c25b900: "JSCallback:anonymous"
Where are we doing this?
(gdb) bt
#0 0x00007ffff7e1dfb0 in __strncmp_sse42 () from /lib64/libc.so.6
#1 0x00007ffff4bf79f1 in find_signature
Ok so whats find_signature, lets check cpython
/*
* finds the beginning of the docstring's introspection signature.
* if present, returns a pointer pointing to the first '('.
* otherwise returns NULL.
*
* doesn't guarantee that the signature is valid, only that it
* has a valid prefix. (the signature must also pass skip_signature.)
*/
static const char *
find_signature(const char *name, const char *doc)
We're getting an invalid pointer for doc.
Lets look at deno-python to see how we're creating name, and doc. doc
is created here
const pyMethodDef = new Uint8Array(8 + 8 + 4 + 8);
const view = new DataView(pyMethodDef.buffer);
const LE =
new Uint8Array(new Uint32Array([0x12345678]).buffer)[0] !== 0x7;
const nameBuf = new TextEncoder().encode(
"JSCallback:" + (v.callback.name || "anonymous") + "\0",
);
view.setBigUint64(
0,
BigInt(Deno.UnsafePointer.value(Deno.UnsafePointer.of(nameBuf)!)),
LE,
);
view.setBigUint64(
8,
BigInt(Deno.UnsafePointer.value(v.unsafe.pointer)),
LE,
);
view.setInt32(16, 0x1 | 0x2, LE);
view.setBigUint64(
20,
BigInt(Deno.UnsafePointer.value(Deno.UnsafePointer.of(nameBuf)!)),
LE,
);
const fn = py.PyCFunction_NewEx(
pyMet hodDef,
PyObject.from(null).handle,
null,
);
We're suspecting that something is wrong with pyMethodDef buffer creation. Looking at the docs the fields seems correct to me
const char *ml_name -> 8 bytes
PyCFunction ml_meth -> 8 bytes
int ml_flags -> 4 bytes
const char *ml_doc -> 8bytes
The bug is there though, can you spot it .... After I asked around (deno discord have a couple of ffi magicians there) I have my answer:
from AapoAlas
Yeah, the last pointer is not correctly aligned. Pointers should be 8 byte aligned (regardless of architecture), but it's at byte index 20: 20/8 does not an integer make.
So 24 is the correct place for it
The 4th field is a pointer so it needs to be 8 byte aligned, but since the 3rd field is only 4 bytes, there are 4 bytes of padding that are automatically inserted
The fix turns out to be simple https://github.com/denosaurs/deno_python/pull/65/files
diff --git a/src/python.ts b/src/python.ts
index e09b821..9c41ea1 100644
--- a/src/python.ts
+++ b/src/python.ts
@@ -452,7 +452,9 @@ export class PyObject {
}
return new PyObject(list);
} else if (v instanceof Callback) {
- const pyMethodDef = new Uint8Array(8 + 8 + 4 + 8);
+ // https://docs.python.org/3/c-api/structures.html#c.PyMethodDef
+ // there are extra 4 bytes of padding after ml_flags field
+ const pyMethodDef = new Uint8Array(8 + 8 + 4 + 4 + 8);
const view = new DataView(pyMethodDef.buffer);
const LE =
new Uint8Array(new Uint32Array([0x12345678]).buffer)[0] !== 0x7;
@@ -471,7 +473,7 @@ export class PyObject {
);
view.setInt32(16, 0x1 | 0x2, LE);
view.setBigUint64(
- 20,
+ 24,
BigInt(Deno.UnsafePointer.value(Deno.UnsafePointer.of(nameBuf)!)),
LE,
);
Running the kernel, it doesn't segfault anymore, but unfortunately it just exits.
Debugging that is another part of the story, in the meantime you can jump to the pr where I fixed it https://github.com/denosaurs/deno_python/pull/67 https://github.com/denosaurs/deno_python/pull/68