Programming

https://github.com/matthewfl/redmagic

This is a newly published repository from an experiment that I started during the summer to attempt to optimize Python’s runtime without impacting compatibility with C models and existing libraries.

There currently exists frameworks such as PyPy and Truffle/Graal which will generate a JIT when you design your programming language inside of their framework and use their compiler to generate a custom binary which implements a JIT for a given language.  One problem with these frameworks is that they require that an existing language is reimplemented essentially from scratch using a subset of Python or Java respectively.  Additionally, once a programming language is reimplemented, any existing modules which interface with internal aspects of the interpreter (any python C module) will not be compatible and will have to be rewritten.

Redmagic is similar to PyPy and Truffle/Graal in that it tries to be a framework for creating a JIT however it is different in that it tries to work with an existing C or C++ interpreter requiring only a few annotations inside the code to identify loops at the user level of the program. (cPython example)  It then generates traces of a user’s program by switching between letting the language’s interpreter run normally and on top of a virtual machine which records all instructions and branching directions.  Unlike other JITs it does not reorganize how memory is laid out and even goes as far as simulating pushing and popping of C level stack frames.  This means that at any point while running inside the virtual machine or inside the generated code, the system can resume the “normal” code simply by jumping to the corresponding instruction in the original interpreter.  This does come with the downside that it inherits all memory layout and pointer dereferencing performance issues that were present in the original interpreter.

Results: After much work on Redmagic, I have observed very slight (<2%) performance improvements in limited cases when working with cPython.  The issues of memory layouts (explored further in this post) seem to contribute significantly to Python’s performance issues and those are not addressed at all by the Redmagic implementation.  Additionally, it is not clear that these would be easy to address from Redmagic itself given that it is looking at a program from the level of x86 assembly instructions vs higher level representations where data-structures can be easily recovered.  I believe that there might be cases, possibly in math routines, where memory layouts have already been optimized and possibly allowing for more clever uses of branching could prove beneficial to performance.

This post is from a recent conversation that I had about the cost of abstractions in various languages. In choosing a programming language for a project, it is important to choose a language that gives a good mix of “time to develop” and “performance.” The first tends to be obvious from experience. However, for many, the performance of a programming language (and its implementations) is somewhat opaque. I am going to demonstrate the differences between Python, Java, and C++, as this gives a good sample of the differences between programming implementations. We can think of Python as representative of the general class of interpreter-based programming languages such as Ruby and Perl, and Javascript before 2005. Java represents the current state of the art in JIT technology and should generalize to general JVM targeted languages and even languages such as Javascript, which have seen countless hours invested in developing new implementations of the language. Finally, C++ is a “low level” language, however, it features a number of unique features, such as templates and stack allocation, which allows for zero cost abstractions which is sparsely seen in other languages.

What is abstraction

Abstraction in this post means the ability of the programmer to wrap a series of methods and data into some object which we are going to use throughout our program. An example of abstraction might be a class LogNumber which abstracts away the fact that we are representing some numbers inside of a log space instead of a linear space. This is fairly standard practice in machine learning applications and might even be necessary in some cases where the magnitude of the number is smaller than the range of a floating point number. If we have this abstraction then we can write an expression such as: LogNumber + LinearNumber and have the LinearNumber automatically converted into log space and thus we will get the correct behavior from our program. If we are programming without this abstraction and simply using primitive types, and we accidentally write float_in_log + float_in_linear we are going to get a number that is neither in log space or linear space and this is a bug. One of the most famous examples of this bug is with the Mars Climate Orbiter crashed due to a units mismatch between standard and metric system.

For the remainder of this post, we consider a simplified “LogNumber” class, A which is using a single 32 bit signed integer and getter and setter methods. One could easily imagine there being multiple getter and setter methods for when one wants to set a linear number to a log space number etc.

# Python
class A:
  def __init__(self, a):
    self._value = a
  def get(self):
    return self._value
  def set(self, a):
    self._value = a

// Java
class A {
  private int value;
  public A(int a) { value = a; }
  public int get() { return value; }
  public void set(int a) { value = a; }
}

// C++
class A {
private:
  int32_t value;
public:
  A(int32_t a) : value(a) {}
  int32_t get() { return value; }
  void set(int32_t a) { value = a; }
}

Memory overhead

First, let us consider the impact on memory that this abstraction has in each of these languages. Memory makes since as a place to start it is generally understood that the less memory that we use the more that we can fit into ram. Additionally, on modern hardware, accessing main memory tends to be a major bottle neck for performance with a read from main memory taking ~100 cycles while a local processor caches takes 10-20 cycles. As such, having an object which is twice as large means that we can fit half as many objects inside our processor cache and thus will end up performing costly accesses to main memory more often. Remember, while reading this next section, we are just wrapping a single 4 byte integer.

# Python
a_python = A(5)

// Java
A a_java = new A(5);

// C++
A *a_ptr_cpp = new A(5);

A a_stack_cpp(5);

Python: First for Python, in constructing the A class, we are going first to create a PyInstanceObject which contains 3 pointers plus the PyObject_HEAD which is 3 pointers plus a size_t bringing the size of this struct up to 56 bytes plus malloc overhead. (Note: the malloc overhead depends on the implementation of malloc used and could even be changed at runtime using something like LD_PRELOAD). Next, to actually save _value we have to construct the hash map that is going to back all the elements for this class instance. This means creating a PyDictObject which is a PyObject_HEAD, 3 size_t, 2 pointers, and 8 preallocated hash map slots for which each slot contains a size_t and 2 pointers bringing up the size of this object to 264 + malloc overhead. The number 5 in this case is a small integer and thus is already interned inside the python interpreter and the hash map key _value would be shared between all instances of this object and so we are not going to count it. Finally, we are going to have to maintain a pointer on Python’s stack to the object a_python that we just constructed. All together then this brings our total size to 328 + 2 * malloc overhead. Note: We could reduce the object size somewhat by using Python’s __slots__ feature which should avoid allocating an oversized hash map to back this object, however our object size is still going to be in the 100s of byte range.

Java: Next with Java, there is an 8 byte header that is added to all objects which contains information about the type of object and object state w.r.t. locking etc.  (more info) Additionally, Java will round the size of objects up to the next 8 byte increment which means that there will be 4 wasted bytes inside this particular object. Finally, we need to store a pointer to this object on our stack. One of the nice tricks in Java for saving memory is pointer compression where a pointer will be 4 bytes instead of 8 which is a significant savings given that Java programs tend to use a lot of pointers.  (pointer compression info). Together, this means that there will be 20 bytes in memory corresponding to this object.

C++: In the first case with a_ptr_cpp we can see that the object size will be 4 bytes as one would expect given the C++ standard. There will also be the additional malloc overhead associated with this object. This brings the total size for the a_ptr example to 12 + malloc overhead when including the stack pointer.
In the second case with a_stack_cpp we have this being directly allocated on the stack which means that we have no pointer or malloc overhead or pointer to the object, thus the total size is only 4 bytes. The fact that we are able to take a primitive type (int32_t) and wrap it inside some class and still consume the exact same amount of memory is what it means to have a zero cost abstraction.

Registers

Once C++ is compiled with some optimizations or a Java program has been running for long enough, it is feasible that both a_ptr_cpp and a_java are entirely stored inside a register saving 8 and 4 bytes respectively. Moreover, in the a_stack_cpp case we might have the integer value stored in a register, which means that the memory used in this case is 0 bytes.

Escape Analysis

For the C++ and Java case if a compiler can prove during optimizations that a dynamically allocated structure is not going to leave a method, then it is possible for that compiler to transform that object into a stack allocated object. This means that even for a_java and a_ptr_cpp could end up having zero memory consumption in the right circumstances.

// Java
{
  A a_java = new A(5);
  a_java.set(6);
  System.out.print(a_java.get());
  // we never let anything outside this block get the reference to a_java
}

// C++
{
  A *a_ptr_cpp = new A(5);
  a_ptr_cpp->set(6);
  cout << a_ptr_cpp->get();
  delete a_ptr_cpp;
  // the compiler is able to see where this object is constructed and destroyed
  // if we didn't delete it, then the fact the leak could still be considered an escape in C++
}

Array overhead

Arrays are basic primitive in nearly all languages when it comes to efficiently storing a number of similar objects. In the case of numerical processing applications, our main performance overheads are going to come down to how efficiently we store numbers and are able to access these values.

# Python
arr_python = [A(i) for i in range(10)]

// Java
A[] arr_java = new A[10];
for(int i = 0; i < arr_java.length; i++)
  arr_java[i] = new A(i);

// C++
A *arr_ptr_cpp[] = new A*[10];
for(int i = 0; i < 10; i++)
  arr_ptr_cpp[i] = new A(i);

A arr_obj_cpp[] = new A[10];
for(int i = 0; i < 10; i++)
  arr_obj_cpp[i] = A(i);

std::vector<A>; vec_obj_cpp(10);
for(int i = 0; i < vec_obj_cpp.size(); i++)
  vec_obj_cpp[i] = A(i);

A arr_stack_cpp[10];
for(int i = 0; < 10; i++)
  arr_stack_cpp[10] = A(i);

Python: First for python, when constructing a list we create a PyListObject which contains the PyObject_HEAD, a pointer to the head of the list and a size_t for the size of the list for 48 bytes. The list itself is simply a list of pointers to objects. Therefore the list object on its own will be 128 + 2 * malloc overhead. For every object, we are then going to have the same as we had above with 348 per object. This brings the total of this to 3608 bytes + 22 * malloc overhead.

Java: With Java, there are essentially two types of arrays. The first is an array of a primitive type (such as int[]) where the value of the integers will actually be stored inside the array itself. These arrays can be considered very efficient since there is a small overhead when storing a large number of primitive values. However, in this case, our array does not contain primitive types and instead must has to be an array of pointers. This means that the array itself will have the 12 byte overhead for each object created and then 10 pointers for which each is 4 bytes, making the list itself 48 bytes which is divisible by 8 so we do not have any additional wasted space here. Each object in the list will then be 16 bytes as before and we have a reference on the stack bringing the total for this up to 212 bytes.

C++: Finally with C++, we can see that there exist a number of possible implementations for an array of objects for which each of these have slightly different memory implications. In the arr_ptr_cpp case we are creating an array of pointers which is conceptually equivalent to the Python and Java implementations. Including the stack reference to this, it takes 120 + 11 * malloc overheads bytes in memory. Note: we are are going to have to explicitly deallocate all objects inside the array when freeing arr_obj_cpp which requires additional cognitive overhead when writing this program. In the second C++ example arr_obj_cpp we are allocating space inside the array for our object instead of using a pointer to reference the array. This means that the size of the array will only be 40 bytes bringing this implementations memory consumption to 48 + 1 * malloc overhead when including the stack pointer. The third case with vec_obj_cpp uses the C++ standard library and would be a more acceptable way of writing the arr_obj_cpp example and will use 2 additional size_t (16 bytes) to track the array’s size and amount allocated (64 + 1 * malloc overhead bytes). The final case is constructing an array directly on C++’s stack which means that we are avoiding the stack pointer reference as well as the malloc overhead and this will only require 40 bytes.
Again, we can see that C++ is capable of a zero overhead abstraction as in the last 3 examples the only overhead from directly using int32_t was O(1) bookkeeping.

Performance overhead

While the way in which data is stored is important, we also care about how these languages are going to perform when we go to execute our program.

# Python
a_python = A(5)
a_python.set(6)
print(a_python.get())

// Java
A a_java = new A(5);
a_java.set(5);
System.out.print(a_java.get());

// C++
A *a_ptr_cpp = new A(5);
a_ptr_cpp->set(6);
cout << a_ptr_cpp->get();

A a_stack_cpp(5);
a_stack_cpp.set(6);
cout << a_stack_cpp.get();

Python: First, Python is the simplest language in the comparison, given that it is a simple bytecode interpreter. This means that it will not be performing any static compile time optimizations or attempting to compile away this abstraction.
Looking at just the a.set(6) line, we can easily look at the Python’s bytecode using the dis library:

# Calling a.set
3 12 LOAD_FAST 0 (a)
15 LOAD_ATTR 1 (set)
18 LOAD_CONST 2 (6)
21 CALL_FUNCTION 1
24 POP_TOP

# Method a.set implementation
7 0 LOAD_FAST 1 (a)
3 LOAD_FAST 0 (self)
6 STORE_ATTR 0 (_value)
9 LOAD_CONST 0 (None)
12 RETURN_VALUE

We can easily see that there are 10 python bytecode instructions. Some of these instructions such as STORE_ATTR and LOAD_ATTR represent hash table lookups to identify the _value and set slots. Additionally, nearly all of these instructions represent writes into memory given that Python uses reference counting, and by loading objects onto Python’s stack requires incrementing the reference count. To see full implementations of these byte codes you can look at ceval.c. From prior experience with python’s internals, I would guess that this line represents about 2000-7000 CPU instructions with over 30 writes to memory and 100 reads.

Java: With Java, it is a bit more difficult to exactly measure how much overhead there is when evaluating this instruction. This is because the JIT will be constantly generating new versions of this code which are more efficient. If we were to evaluate this instruction exactly once, then our bytecode will be running on an interpreter which is conceptually similar to python, but by not having reference counting and not backing every object with a hash map means that this is going to be significantly more efficient and about 100-500 instructions. After we have executed this statement a few times, the JIT will generate more optimized code. The exact code that is generated depends on a number of factors including if at the call site for a.set(6) if there exist multiple implementations of set that we must dispatch to (multiple classes implementing the same interface). Assuming that there will only be a single implementation of set, then the JVM will end up inlining and optimizing this down to 1 instruction which writes to memory.

C++: When using a pointer in C++, we can see statically that there is only a single implementation of A::set and so the compiler will likely inline this method call. This means that similar to the Java case it will have 1 instruction to perform the write into memory. In the second case with a_stack_cpp we might represent this instruction as a single write into a register. While both of these cases are going to be a single instruction, the later of writing into a register instead of memory will be much more “efficient.” Additionally, in a larger context, we could imagine that the compiler completely removes the representation of a_stack_cpp and just inlines the value 6 or 5 whatever is appropriate.

Again, a_stack_cpp is giving a zero cost abstraction while a_ptr_cpp and a_java are giving us a low cost abstraction w.r.t. the number of instructions evaluated.

Meta template programming

The advantages of zero cost overheads really shine when combined with templates and meta programming techniques. By having templated classes, we are able to construct a single class which implements many basic features that we are able to reuse.  For example, suppose that we had a LogNumber class such that we could have LogNumber<LinearNumber<float> > and LogNumber<LinearNumber<double> > which use the same same which class implementation with two different sizes of numbers. We could even extend this to have LogNumber<LogNumber<LinearNumber<float> > > which would allow for us to easily represent a number in a log log space without having to reimplemented our LogNumber class.

If we implemented this templated class in Java, then we would have that every template parameter would require a pointer and another class instance. This means that in the LogNumber<LogNumber<LinearNumber<Float> > > we would require that there are 4 class instances and thus would require 4 pointer indirection to actually reach the floating point value and consume 64 bytes of memory.

In C++, this templated class does not use a pointer indirection when using a template. This means that the size of LogNumber<LogNumber<LinearNumber<float> > > and LinearNumber<float> will be exactly the same size. Additionally, accessing the stored number will only take a single memory access instruction and can be placed on the stack or used inside an array as shown above.

Conclusion

Abstraction is a very important concept when writing larger programs. Having zero cost abstraction available means that we can have both performant programs while reducing the mental burden on the programmer. When programming in a language such as Java or Python, we have to make a choice between developing the most performant program in that language and having a clean and reusable abstraction.

We see the power of zero cost abstractions aggressively used inside libraries such as Eigen, Dlib and Tensorflow as these libraries care immensely about the computational and storage efficiency. Using C++’s template system, these libraries contain a single implementation for a generic routine which can be customized by switching out a few minor methods without losing any performance.

I have been using Dropbox for a good amount of time now, and something that I have recently started using Dropbox for is as a back-end system for private git repositories.  While Github is great for public repos, if you just want to have a private project synced between a few computers or with another friend on Dropbox then the steps are more or less straight forward.

1) Open up a terminal and cd into your dropbox folder,

2) You have to make a bare git repository that is used to hold all of the git objects, this can be done by issuing the “git init –bare repo.git” command.  This will make a new directory called repo.git with all the supporting files.

3) At this point all that is left to do is link up your working git directory with the Dropbox one, the easiest way to do this is cd into the repo.git directory.  Then Issue the ‘pwd’ command, this will give you the absolute path (git will not use relative paths for some reason).  Then copy the output from pwd and then cd into your working directory, and issue the command “git remote add origin file://[Paste in what ever came from pwd]”

4) Now that your working directory is linked with the directory on Dropbox issue the command “git push origin master” to load all your files into the dropbox.  One thing that you will notice is that this will run a lot faster than when working with a remote repo over the internet.  The reason is that you are not pushing files onto the intern but into another folder on your computer.  If you look at you dropbox icon at this point you will see that it is syncing a number of files.  If you have worked up a larger number of changed between syncing with dropbox you might see that it is syncing in excess of 200 files with the server.

5) To load the project onto another computer you can use the “git clone file://[path to the dropbox repo.git folder]”  One thing to note before pulling any changes is to make sure that dropbox has finished syncing all of the files.  If you trying and pull or clone out of the Dropbox directory before it is done syncing then you can run into problem as git will look for files that are not there yet as dropbox has not finished syncing, so as a not of caution, wait for dropbox to finish syncing before cloning or pulling.

When you want to share a project with someone else, then all you have to do is share the repo.git folder with that person, they can then run a clone command of that file to make their own working directory.  While this does give an easy way to have free private 2 GB of git syncing space, there is no cool Github like web interface for looking at code.  And as another note, anyone that can modify the repo.git folder will be an ‘admin’ to the project as all the server is really is just syncing file between computers.