PUT SOME Numba in YOUR SQLite

https://slides.com/phillipcloud/slumba

SLUMBA

About me

WARNING:
Hacks AHEAD

PLEASE:
ASK QUESTIONs

TAKEAWAY:

NUMBA iS POWEFUL

TAKEAWAY:

not Hard to extend

Extending SQlite

  • UDF: User-Defined Function
  • UDAF: User-Defined Aggregate Function

USING PYTHON

UDFS

In [6]: import sqlite3

In [7]: con = sqlite3.connect(':memory:')

In [8]: def incr(x):
   ...:     return x + 1
   ...: 

In [9]: con.create_function('incr', 1, incr)

In [10]: list(con.execute('select incr(1)'))
Out[10]: [(2,)]

UDAFS

In [12]: class Average:
    ...:     def __init__(self):
    ...:         self.total = 0.0
    ...:         self.count = 0
    ...:
    ...:     def step(self, value):
    ...:         if value is not None:
    ...:             self.total += value
    ...:             self.count += 1
    ...:
    ...:     def finalize(self):
    ...:         if self.count:
    ...:             return self.total / self.count
    ...:         return None
    ...:

In [13]: con = sqlite3.connect(":memory:")

In [14]: con.create_aggregate("my_avg", 1, Average)

In [15]: query = "SELECT my_avg(column1) FROM (VALUES (1), (2), (3))"

In [15]: con.execute(query).fetchall()
Out[15]: [(2.0,)]
v
1
2
NULL
4
5 
total = 0.0
count = 0

UDAF EXECUTION

Scratch space, step and finalize

SELECT AVG(v)
FROM t
total = 1.0
count = 1
total = 3.0
count = 2
total = 3.0
count = 2
total = 7.0
count = 3
total = 12.0
count = 4
total / count

step(1)

finalize

step(2)

step(N)

step(4)

step(5)

3.0

USING The C LANGUage

Don't copy any of this code

Public service ANNouncment

SQLITE C API - STEP

(Called once for each row)

void step(sqlite3_context* ctx, int argc, sqlite3_value** argv) {
  static const size_t nbytes = sizeof(Average);
  void* raw_ctx = sqlite3_aggregate_context(ctx, nbytes);
  Average* agg_ctx = (Average*) raw_ctx;
  if (agg_ctx != NULL) {
    sqlite3_value* argument = argv[0];
    int argument_type = sqlite3_value_type(argument);

    if (argument_type != SQLITE_NULL) {
      double value = sqlite3_value_double(argument);
      agg_ctx->total += value;
      agg_ctx->count += 1;
    }
  }
}
typedef struct {
  double value;
  int64_t count;
} Average;

SQLITE C API - FINALIZE

(Called exactly once, after all rows have been traversed)

void finalize(sqlite3_context* ctx) {
    static const size_t nbytes = sizeof(Average);
    void* raw_ctx = sqlite3_aggregate_context(ctx, 0);
    Average* agg_ctx = (Average*) raw_ctx;
    if (agg_ctx != NULL) {
	if (agg_ctx->count > 0) {
	    double average = agg_ctx->total / agg_ctx->count;
	    sqlite3_result_double(ctx, average);
	} else {
	    sqlite3_result_null(ctx);
	}
    }
}

GOAL:
PYTHON API + C SPEED

(Keep the stdlib API)

C refresher

  • Function pointers are pointers
  • Pointers are integers
  • => Function pointers are integers
  • Not all integers are function pointers

But some are

😈

EVIL C refresher

never call UNTRUSTED functioN pointers

SERiOUSLY, DON'T

NUMBA

NUmba

Core:

  • JIT compiler for Python

Add'l Features:

  • jitclass
  • Extensible
  • cfunc
  • powerful static analysis
  • Community

NUmba

Core:

  • JIT compiler for Python

Add'l Features:

  • jitclass
  • Extensible
  • cfunc
  • powerful static analysis
  • Community
from numba import jit


@jit
def fast_sum(array):
    total = 0.0
    for el in array:
        total += el
    return total

jitclass

In [12]: class Average:
    ...:     value: float
    ...:     count: int
    ...:
    ...:     def __init__(self):
    ...:         self.value = 0.0
    ...:         self.count = 0
    ...:
    ...:     def step(self, value):
    ...:         if value is not None:
    ...:             self.value += value
    ...:             self.count += 1
    ...:
    ...:     def finalize(self):
    ...:         if self.count:
    ...:             return self.value / self.count
    ...:         return None
In [12]: @jitclass
    ...: class Average:
    ...:     value: float
    ...:     count: int
    ...:
    ...:     def __init__(self):
    ...:         self.value = 0.0
    ...:         self.count = 0
    ...:
    ...:     def step(self, value):
    ...:         if value is not None:
    ...:             self.value += value
    ...:             self.count += 1
    ...:
    ...:     def finalize(self):
    ...:         if self.count:
    ...:             return self.value / self.count
    ...:         return None

JITCLASS

// tons of runtime overhead, comparatively
typedef PyObject* Average;
typedef struct {
  double value;
  int64_t count;
} Average;

From this

To this*

more specific GOAL:

call A JITted METHOD From A C FUNCTION defined in PYTHON

... that matches the SQLite C API

@CFUNC

Kind of evil

😈

In [33]: from numba import cfunc, float64

In [34]: @cfunc(float64(float64))
    ...: def my_incr(x):
    ...:     return x + 1
    ...:
In [33]: from numba import cfunc, float64

In [34]: @cfunc(float64(float64))
    ...: def my_incr(x):
    ...:     return x + 1
    ...:

In [35]: my_incr.address
Out[35]: 139623106748448

wat

SLUMBA

  • Numba: LLVM codegen/cfunc
  • User: step/finalize methods
  • Slumba: ???

slumba
NUMBSQL

Important Renaming information

Tying it all together

1. USER DEFINES A JITClass

from typing import Optional
from numba import jitclass




@jitclass
class Avg:
    total: float
    count: int

    def __init__(self) -> None:
        self.total = 0.0
        self.count = 0

    def step(self, value: Optional[float]) -> None:
        if value is not None:
	    self.total += value
	    self.count += 1

    def finalize(self) -> Optional[float]:
	if not self.count:
	    return None
        return self.total / self.count

1. USER DEFINES A JITClass

from typing import Optional
from numba import jitclass
from numbsql import sqlite_udaf


@sqlite_udaf
@jitclass
class Avg:
    total: float
    count: int

    def __init__(self) -> None:
        self.total = 0.0
        self.count = 0

    def step(self, value: Optional[float]) -> None:
        if value is not None:
	    self.total += value
	    self.count += 1

    def finalize(self) -> Optional[float]:
	if not self.count:
	    return None
        return self.total / self.count

2. numbsqL DEFINES WRAPPERS

@cfunc(void(voidptr, intc, CPointer(voidptr)))
def step(ctx, argc, argv):
    raw_pointer = sqlite3_aggregate_context(ctx, sizeof(cls))
    agg_ctx = unsafe_cast(raw_pointer, cls)
    if not_null(agg_ctx):
        agg_ctx.step(*make_arg_tuple(step_func, argv))
@cfunc(void(voidptr))
def finalize(ctx):
    raw_pointer = sqlite3_aggregate_context(ctx, 0)
    agg_ctx = unsafe_cast(raw_pointer, cls)
    if not_null(agg_ctx):
        result = agg_ctx.finalize()
        if result is None:
            sqlite3_result_null(ctx)
        else:
            result_setter = get_result_setter(result)
            result_setter(ctx, result)
@cfunc(void(voidptr, intc, CPointer(voidptr)))
def step(ctx, argc, argv):
    raw_pointer = sqlite3_aggregate_context(ctx, sizeof(cls))
    agg_ctx = unsafe_cast(raw_pointer, cls)
    if not_null(agg_ctx):
        agg_ctx.step(*make_arg_tuple(step_func, argv))

STEp

  1. Allocate space for the class
  2. Cast pointer to our type
  3. If allocation didn't return a null pointer
    1. construct an argument tuple given a function signature and arguments
  4. Call the step method
@cfunc(void(voidptr, intc, CPointer(voidptr)))
def step(ctx, argc, argv):
    raw_pointer = sqlite3_aggregate_context(ctx, sizeof(cls))
    agg_ctx = unsafe_cast(raw_pointer, cls)
    if not_null(agg_ctx):
        agg_ctx.step(*make_arg_tuple(step_func, argv))

STEp

@cfunc(void(voidptr, intc, CPointer(voidptr)))
def step(ctx, argc, argv):
    raw_pointer = sqlite3_aggregate_context(ctx, sizeof(cls))
    agg_ctx = unsafe_cast(raw_pointer, cls)
    if not_null(agg_ctx):
        agg_ctx.step(*make_arg_tuple(step_func, argv))

To clarify what's happening here:

  1. make_arg_tuple is producing a tuple
  2. numba recognizes that the tuple has the same number of arguments as the step call
  3. unrolls the tuple into a sequence of loads
  4. passes that to the method

TYPE INFERENCE IS HARD ...

# double my_func(sqlite3_context* ctx,
#                int64_t narg,
#                sqlite3_value**);

@cfunc(float64(voidptr, int64, CPointer(voidptr)))
def step(ctx, argc, argv):
    args = ()  # tuple of *shrug*

    for i in range(argc):
        # sqlite3_value* argument
        arg = argv[i]

        # note: *runtime* type
        value_type = sqlite3_value_type(arg)

        # check the runtime type
        if value_type == SQLITE_FLOAT:
            args += (sqlite3_value_double(arg),)

        elif value_type == SQLITE_INTEGER:
            args += (sqlite3_value_int64(arg),)

    # this is our jitclass method, and we must
    # know the number of arguments and their
    # types at *compile* time
    return agg_ctx.my_jitclass_method(*args)

... BUT we require

argument types

WhaT are we solving??

TypE inference is hard not necessary

def codegen(context, builder, signature, args):
    _, argv = args
    converted_args = []
    for i, argtype in enumerate(argtypes):


        instr =


        converted_args.append(instr)

    res = context.make_tuple(
        builder, tuple_type, converted_args)
    return imputils.impl_ret_untracked(
        context, builder, tuple_type, res)

make_arg_tuple

Face-melting calls into llvmlite

make_arg_tuple

converted_args = []

for i, argtype in enumerate(argtypes):
    # get the appropriate ctypes extraction routine
    ctypes_function = VALUE_EXTRACTORS[argtype]

    # create a numba function type for the converter
    converter = ctypes_utils.make_function_type(ctypes_function)

    # get the function pointer instruction out
    fn = context.get_constant_generic(
        builder, converter, ctypes_function)

    # get a pointer to the ith argument
    element_pointer = cgutils.gep(builder, argv, i)

    # deref that pointer
    element = builder.load(element_pointer)

    # call the value extraction routine
    value = builder.call(fn, [element])

    # add value to the argument list
    converted_args.append(value)
sqlite3_value_double🐍
double my_udf(double value);
void step(sqlite3_context* ctx, int argc, sqlite3_value** argv);
element_pointer = argv + i;
element = *element_pointer;
double value = sqlite3_value_double(ctx, element);
double (*fn)(sqlite3_context*, double);
my_udf(*converted_args)

taken from the user-defined signature

3. NUMBA JITS all the things

numba

Python

numbsql

LLVM

4. USER REGISTERS THE AGG WITH THE DB

>>> con = sqlite3.connect(...)
>>> create_aggregate(con, 'myavg', 1, Avg)

What does numbsql PROVIDE?

numbsql adds the following Numba intrinsics

  • sizeof
  • unsafe_cast
  • safe_decref
  • get_sqlite3_result_function
  • is_not_null_pointer
  • init
  • make_arg_tuple

QUESTIONS?

benchmarks

WHole-TABLE AGG

SQLite Builtin

Legend

Numba

Python

LOW CARD. GROUP BY

HIGH CARD. GROUP BY

Scalar ADD ONE

Scalar string length

what numbsql CAN't do

STATEFUL HEAP STUFF

  • String support is limited to scalar functions
  • No support for BLOB (yet)
  • No support for complex data types

GENERAL ISSUES WITH NUMBA

  • Memory management inflexible
  • jitclass performance in some scenarios
  • custom intrinsics can be unapproachable

Thank you!

slumba

By Phillip Cloud

Made with Slides.com

slumba

Melt your mind by learning how to run jit-compiled numba functions inside of SQLite. Not for the faint of heart.

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