Hunting for bugs in Julia for Data Analysis

By: Blog by Bogumił Kamiński

Re-posted from: https://bkamins.github.io/julialang/2023/03/03/errata.html

Introduction

A few months ago my Julia for Data Analysis book was released.
I tried very hard to make it correct. Regrettably, I failed.

Fortunately my readers are more careful than me and they found several issues
in my book. I keep their log in the Errata section of the GitHub
repository of the book.

In this post I want to share you my experience about the kinds of bugs
slipped into the book and comment how I think they could be avoided.

My experience is that there are three important classes of issues:

  • various misprints and typographical errors;
  • consistency of code execution across Julia versions;
  • factual errors.

Let me go through these classes in sequence.

Misprints and typographical errors

Such errors sneak in for many reasons. Let me highlight some that have bitten
me and could be avoided.

First is printing of non-standard UTF-8 characters. These are nasty. In my
version of the book things look nice, but when it went through printing
preparation process, somehow on the way some characters got messed up.
For example in Chapter 6, section 6.4.1, page 132
codeunits("ε") is printed as codeunits("?").

Takeaway: before your book goes to press always carefully check these parts of
the text where you use non-standard UTF-8 characters (a common case in Julia).

Second is the side effect of using multi-selection or auto-replace in your
editor. For example in Chapter 3, section 3.2.3, page 59 I have
an issue that I write sort(v::AbstractVector; kwthe.) instead of
sort(v::AbstractVector; kws...). It is clear that I must have used some
pattern matching and replaced s.. with the. I do not even remember why.

Takeaway: multi-selection and auto-replace are nice, but never do them
globally; it is best to review every change before it is applied (do not make
them automatically in one shot; it is hart to resist, but this is what you
really should not do).

Consistency across versions of Julia

There are many flavors of this issue. It can mostly be resolved by strict use
of Project.toml and Manifest.toml files, but sometimes unexpected things happen.

For example in Chapter 1, section 1.2.1, page 7 I show the following snippet:

julia> function sum_n(n)
           s = 0
           for i in 1:n
               s += i
           end
           return s
       end
sum_n (generic function with 1 method)

julia> @time sum_n(1_000_000_000)
  0.000001 seconds
500000000500000000

This timing is surprisingly fast (and the reason is explained in the book).
The issue is that this is the situation under Julia 1.7 as this is the version
of the language I used in the book.

Under Julia 1.8 and Julia 1.9 running the same code takes longer
(tested under Julia 1.9-beta4):

julia> @time sum_n(1_000_000_000)
  2.265569 seconds
500000000500000000

The reason for this inconsistency is a bug in the @time macro introduced in
Julia 1.8 release. The sum_n(1_000_000_000) call (without @time) is executed
fast. Here is a simplified benchmark (run under Julia 1.9-beta4) showing this:

julia> let
           start = time_ns()
           v = sum_n(1_000_000_000)
           stop=time_ns()
           v, Int(stop - start)
       end
(500000000500000000, 1000)

Unfortunately there is an issue with the @time macro used in global scope
that causes the timing to be inaccurate. This bug needs to be resolved in
Base Julia. See this issue for details.

Takeaway: things can change as software evolves; always make sure to
explicitly tell your readers which version and configuration of software they
should use to run your code.

Factual errors

This one is most problematic, as I really feel bad, when I find that I have
written something that is not fully correct. Let me give you an example
from Chapter 2, section 2.3.1, page 30.

The Julia Manual in the Short Circuit Evaluation section states:

Instead of if <cond> <statement> end, one can write <cond> && <statement>
(which could be read as: <cond> and then <statement>).
Similarly, instead of if if ! <cond> <statement> end, one can write
<cond> || <statement> (which could be read as: <cond> or else <statement>).

Similarly, in my book I have considered the following expressions:

x > 0 && println(x)

and

if x > 0
    println(x)
end

where x = -7.

I write in the book that Julia interprets them both in the same way.

Indeed it is true that the same expressions get evaluated in both cases.
However, in general if statement and doing short-circuit evaluation are
not equivalent.

What is the difference? If the condition would be false then the value of if
statement (without else) is nothing and the value of the expression using
short-circuiting is false. Here is an example:

julia> x = -7
-7

julia> show(x > 0 && println(x))
false
julia> show(if x > 0
           println(x)
       end)
nothing

The difference is subtle, but in cases when you would use the produced
value later in your code it could become important.

Takeaway: always carefully consider all aspects of code that you present.

Conclusions

As a conclusion I would like to ask all readers of my book to share with me
your feedback. I will try to incorporate it in the next release of the book
in the best way I can.

Hunting for bugs in Julia for Data Analysis

By: Blog by Bogumił Kamiński

Re-posted from: https://bkamins.github.io/julialang/2023/03/03/errata.html

Introduction

A few months ago my Julia for Data Analysis book was released.
I tried very hard to make it correct. Regrettably, I failed.

Fortunately my readers are more careful than me and they found several issues
in my book. I keep their log in the Errata section of the GitHub
repository of the book.

In this post I want to share you my experience about the kinds of bugs
slipped into the book and comment how I think they could be avoided.

My experience is that there are three important classes of issues:

  • various misprints and typographical errors;
  • consistency of code execution across Julia versions;
  • factual errors.

Let me go through these classes in sequence.

Misprints and typographical errors

Such errors sneak in for many reasons. Let me highlight some that have bitten
me and could be avoided.

First is printing of non-standard UTF-8 characters. These are nasty. In my
version of the book things look nice, but when it went through printing
preparation process, somehow on the way some characters got messed up.
For example in Chapter 6, section 6.4.1, page 132
codeunits("ε") is printed as codeunits("?").

Takeaway: before your book goes to press always carefully check these parts of
the text where you use non-standard UTF-8 characters (a common case in Julia).

Second is the side effect of using multi-selection or auto-replace in your
editor. For example in Chapter 3, section 3.2.3, page 59 I have
an issue that I write sort(v::AbstractVector; kwthe.) instead of
sort(v::AbstractVector; kws...). It is clear that I must have used some
pattern matching and replaced s.. with the. I do not even remember why.

Takeaway: multi-selection and auto-replace are nice, but never do them
globally; it is best to review every change before it is applied (do not make
them automatically in one shot; it is hart to resist, but this is what you
really should not do).

Consistency across versions of Julia

There are many flavors of this issue. It can mostly be resolved by strict use
of Project.toml and Manifest.toml files, but sometimes unexpected things happen.

For example in Chapter 1, section 1.2.1, page 7 I show the following snippet:

julia> function sum_n(n)
           s = 0
           for i in 1:n
               s += i
           end
           return s
       end
sum_n (generic function with 1 method)

julia> @time sum_n(1_000_000_000)
  0.000001 seconds
500000000500000000

This timing is surprisingly fast (and the reason is explained in the book).
The issue is that this is the situation under Julia 1.7 as this is the version
of the language I used in the book.

Under Julia 1.8 and Julia 1.9 running the same code takes longer
(tested under Julia 1.9-beta4):

julia> @time sum_n(1_000_000_000)
  2.265569 seconds
500000000500000000

The reason for this inconsistency is a bug in the @time macro introduced in
Julia 1.8 release. The sum_n(1_000_000_000) call (without @time) is executed
fast. Here is a simplified benchmark (run under Julia 1.9-beta4) showing this:

julia> let
           start = time_ns()
           v = sum_n(1_000_000_000)
           stop=time_ns()
           v, Int(stop - start)
       end
(500000000500000000, 1000)

Unfortunately there is an issue with the @time macro used in global scope
that causes the timing to be inaccurate. This bug needs to be resolved in
Base Julia. See this issue for details.

Takeaway: things can change as software evolves; always make sure to
explicitly tell your readers which version and configuration of software they
should use to run your code.

Factual errors

This one is most problematic, as I really feel bad, when I find that I have
written something that is not fully correct. Let me give you an example
from Chapter 2, section 2.3.1, page 30.

The Julia Manual in the Short Circuit Evaluation section states:

Instead of if <cond> <statement> end, one can write <cond> && <statement>
(which could be read as: <cond> and then <statement>).
Similarly, instead of if if ! <cond> <statement> end, one can write
<cond> || <statement> (which could be read as: <cond> or else <statement>).

Similarly, in my book I have considered the following expressions:

x > 0 && println(x)

and

if x > 0
    println(x)
end

where x = -7.

I write in the book that Julia interprets them both in the same way.

Indeed it is true that the same expressions get evaluated in both cases.
However, in general if statement and doing short-circuit evaluation are
not equivalent.

What is the difference? If the condition would be false then the value of if
statement (without else) is nothing and the value of the expression using
short-circuiting is false. Here is an example:

julia> x = -7
-7

julia> show(x > 0 && println(x))
false
julia> show(if x > 0
           println(x)
       end)
nothing

The difference is subtle, but in cases when you would use the produced
value later in your code it could become important.

Takeaway: always carefully consider all aspects of code that you present.

Conclusions

As a conclusion I would like to ask all readers of my book to share with me
your feedback. I will try to incorporate it in the next release of the book
in the best way I can.

Metal.jl 0.2: Metal Performance Shaders

By: Tim Besard

Re-posted from: https://juliagpu.org/post/2023-03-03-metal_0.2/index.html

Metal.jl 0.2 marks a significant milestone in the development of the Metal.jl package. The release comes with initial support for the Metal Perform Shaders (MPS) framework for accelerating common operations like matrix multiplications, as well as various improvements for writing Metal kernels in Julia.

Metal Performance Shaders

Quoting the Apple documentation, The Metal Performance Shaders (MPS) framework contains a collection of highly optimized compute and graphics shaders for use in Metal applications. With Metal.jl 0.2, we have added initial support for this framework, and used it to accelerate the matrix multiplication operation:

julia> n = p = m = 2048
julia> flops = n*m*(2p-1)
17175674880julia> a = MtlArray(rand(Float32, n, p));
julia> b = MtlArray(rand(Float32, p, m));
julia> c = MtlArray(zeros(Float32, n, m));julia> bench = @benchmark Metal.@sync mul!(c, a, b)
BenchmarkTools.Trial: 518 samples with 1 evaluation.
 Range (min … max):  9.366 ms …  13.354 ms  ┊ GC (min … max): 0.00% … 0.00%
 Time  (median):     9.629 ms               ┊ GC (median):    0.00%
 Time  (mean ± σ):   9.646 ms ± 192.169 μs  ┊ GC (mean ± σ):  0.00% ± 0.00%               ▃▂▅▅▆▆▆▇█▇▇▆▅▄▄▁▁ ▁
  ▄▁▄▄▄▄▆▆▆▄▄▁▇█████████████████▄█▄▁▆▁▄▁▆▁▇▁▄▄▁▁▄▄▇▁▄▆▄▁▁▁▁▁▄ █
  9.37 ms      Histogram: log(frequency) by time      10.1 ms < Memory estimate: 352 bytes, allocs estimate: 12.julia> flops / (minimum(bench.times)/1e9)
1.83e12

The benchmark above shows that on an 8-core M1 Pro matrix multiplication now reaches 1.8 TFLOPS (out of the 2.6TFLOPS of theoretical performance). The accelerated matrix multiplication is available for a variety of input types, incuding mixed-mode operations, and as shown above is integrated with the LinearAlgebra.jl mul! interface.

Of course, the MPS framework offers more than just matrix multiplication, and we expect to support more of it in the future. If you have a specific operation you would like to use from Julia, please let us know by opening an issue on the Metal.jl repository.

GPU profiling support

To support the development of Metal kernels, Max Hawkins has added support for GPU profiling. Similar to how this works in CUDA.jl, you can run code under the Metal.@profile macro to record its execution. However, this does first require setting the METAL_CAPTURE_ENABLED environment flag before import Metal.jl:

julia> ENV["METAL_CAPTURE_ENABLED"] = 1julia> using Metaljulia> a = mtl(rand(1024, 1024))
julia> Metal.@profile sum(a)
[ Info: GPU frame capture saved to jl_metal.gputrace/

The resulting capture can be opened with Xcode, presenting a timeline that's similar to other profilers:

XCode viewing a Metal.jl capture trace

Other improvements

  • Julia 1.9 is supported, but requires an up-to-date macOS version (issues have been encountered on macOS 12.4);

  • An mtl function has been added for converting Julia arrays to Metal arrays, similar to the cu function in CUDA.jl;

  • Multiple GPUs are supported, and the device! function can be used to select one;

  • Coverage for SIMD Group functions has been improved, so it's is now possible to use simdgroup_load, simdgroup_store, simdgroup_multiply, and simdgroup_multiply_accumulate in kernels functions.

Future work

Although Metal.jl is now usable for a variety of applications, there is still work to be done before it can be considered production-ready. In particular:

  • there are known performance issues with mapreduce, and other operations that realy on CartesianIndices;

  • the libcmt wrapper library for interfacing with the Metal APIs is cumbersome to use and improve, and we are looking into native ObjectiveC FFI instead;

  • the MPS wrappers are incomplete, and similar to the Metal APIs requires a replacement to libcmt to be improved;

  • support for atomic operations is missing, which is required to implement a full-featured KernelAbstractions.jl back-end.

Once (most of) these issues are addressed, we should be able to release Metal.jl 1.0.