I am having a dictionary,
my_dict = {'a':[1,2,3], 'b':[4,5] , 'c':[7,1,2])
I want to use this dictionary inside a Cython nogil function . So , I tried to declare it as
cdef dict cy_dict = my_dict
Up to this stage is fine.
Now I need to iterate over the keys of my_dict and if the values are in list, iterate over it. In Python , it is quite easy as follows:
for key in my_dict:
if isinstance(my_dict[key], (list, tuple)):
###### Iterate over the value of the list or tuple
for value in list:
## Do some over operation.
But, inside Cython, I want to implement the same that too inside nogil . As, python objects are not allowed inside nogil, I am all stuck up here.
with nogil:
#### same implementation of the same in Cython
Can anyone please help me out ?
You can't use Python dict without the GIL because everything you could do with it involves manipulating Python objects. You most sensible option is to accept that you need the GIL. There's a less sensible option too involving C++ maps, but it may be hard to apply for your specific case.
You can use with gil: to reacquire the GIL. There is obvious an overhead here (parts using the GIL can't be executed in parallel, and there may be a delay which it waits for the GIL). However, if the dictionary manipulation is a small chunk of a larger piece of Cython code this may not be too bad:
with nogil:
# some large chunk of computationally intensive code goes here
with gil:
# your dictionary code
# more computationally intensive stuff here
The other less sensible option is to use C++ maps (along side other C++ standard library data types). Cython can wrap these and automatically convert them. To give a trivial example based on your example data:
from libcpp.map cimport map
from libcpp.string cimport string
from libcpp.vector cimport vector
from cython.operator cimport dereference, preincrement
def f():
my_dict = {'a':[1,2,3], 'b':[4,5] , 'c':[7,1,2]}
# the following conversion has an computational cost to it
# and must be done with the GIL. Depending on your design
# you might be able to ensure it's only done once so that the
# cost doesn't matter much
cdef map[string,vector[int]] m = my_dict
# cdef statements can't go inside no gil, but much of the work can
cdef map[string,vector[int]].iterator end = m.end()
cdef map[string,vector[int]].iterator it = m.begin()
cdef int total_length = 0
with nogil: # all this stuff can now go inside nogil
while it != end:
total_length += dereference(it).second.size()
preincrement(it)
print total_length
(you need to compile this with language='c++').
The obvious disadvantage to this is that the data-types inside the dict must be known in advance (it can't be an arbitrary Python object). However, since you can't manipulate arbitrary Python objects inside a nogil block you're pretty restricted anyway.
6-year later addendum: I don't recommend the "use C++ objects everywhere" approach as a general approach. The Cython-C++ interface is a bit clunky and you can spend a lot of time working around it. The Python containers are actually better than you think. Everyone tends to forget about the cost of converting their C++ objects to/from Python objects. People rarely consider if they really need to release the GIL or if they just read an article on the internet somewhere saying that the GIL is bad..
It's good for some tasks, but think carefully before blindly replacing all your list with vector, dict with map etc.. As a rule, if your C++ types live entirely within your function it may be a good move (but think twice...). If they're being converted as input or output arguments then think a third time.
Related
I am trying to convert a list of objects (GeoJSON) to shapely objects using cython, but I am running into a error:
This piece of code seems to be the issue: cdef object result[N]. How do I declare a list/array from a given list?
Here is my current code:
def convert_geoms(list array):
cdef int i, N=len(array)
cdef double x, s=0.0
cdef object result[N] # ERROR HERE
for i in range(N):
g = build_geometry_objects2(array[i])
result[i] = g
return result
There's two issues with cdef object result[N]:
It creates a C array of Python objects - this doesn't really work because C arrays aren't easily integrated with the Python object reference counting (in this you'd need to copy the whole array to something else when you returned it anyway, since it's a local variable that's only scoped to the function).
For C arrays of the form sometype result[N], N must be known at compile-time. In this case N is different for each function call, so the variable definition is invalid anyway.
There's multiple solutions - most of them involve just accepting that you're using Python objects so not worrying about specifying the types and just writing valid Python code. I'd probably write it as a list comprehension. I suspect Cython will do surprisingly well at producing optimized code for that
return [ build_geometry_objects2(array[i]) for i in range(len(array)) ]
# or
return [ build_geometry_objects2(a) for a in array ]
The second version is probably better, but if it matters you can time it.
If the performance really matters you can use Python C API calls which you can cimport from cpython.list. See Cythonize list of all splits of a string for an example of something similar where list creation is optimized this way. The advantage of PyList_New is that it creates an appropriately sized list at the start filled with NULL pointers, which you can then fill in.
In Cython I would like to store an array of functions, but the functions don't all have the same signature. Specifically, some have two parameters and some three.
I defined the following:
ctypedef long (*func2param)(long param1, long param2)
ctypedef long (*funct3param)(long param1, long param2, long param3)
However, even if I had just one such signature, I'm still not sure how to go about making it work. Trying to assign a cdef function to an array of one of the above types gives me:
func_array2[i] = func_list[i][FUNCTION]
Cannot convert Python object to 'func2param'
Trying to cast gives:
func_array2[i] = <func2param>func_list[i][FUNCTION]
Python objects cannot be cast to pointers of primitive types
I can't think of anything useful you can do with an array of function pointers of unknown type - it isn't safe to call them (since you don't know the signature) and there really isn't anything else to do with function pointers. Therefore you at least need to find some way of storing what type of pointer it is.
One option would be to store a struct containing both pointers:
cdef struct FuncPtrStruct:
func2param f2p
func3param f3p
You then set one to NULL, store in the other one, and only call the non-NULL one The array specification would then be similar to cdef FuncPtrStruct array[10].
However, I'd probably use a C Union instead to store both pointers in the same memory location (+ an enum to identify the type). This is a little more effort to set up (you need an enum to define the type of the union, the union itself, and a struct containing the enum and the union); however the advantage is that you can add a lot more different types of function pointers without using more memory (for the "two-type" case the memory is probably equal):
# cpdef if you want to use the enum from Python too
cdef enum FuncType:
twoArg, threeArg
cdef union FuncPtrUnion:
func2param f2p
func3param f3p
cdef struct FuncPtrHolder:
FuncType type_
FuncPtrUnion value
Just to illustrate how you'd use it:
cdef long f(long x1, long x2):
print("f",x1,x2)
return 0
cdef long g(long x1, long x2, long x3):
print("g",x1,x2,x3)
return 1
def example():
cdef FuncPtrHolder fArray[10]
for i in range(10):
if i%2:
fArray[i].type_ = twoArg
fArray[i].value.f2p = &f
else:
fArray[i].type_ = threeArg
fArray[i].value.f3p = &g
# use
for i in range(10):
if fArray[i].type_ == twoArg:
fArray[i].value.f2p(i,i+1)
elif fArray[i].type_ == threeArg:
fArray[i].value.f3p(i,i+1,i+2)
It looks like in your code you have some list of Python objects and this is why you're getting compile errors. Without code it's impossible to know why, but I think Cython can automatically generate Python wrappers for cdef functions so I'd guess you've somehow made a list of those wrappers. If you want to handle Python lists of FuncPtrHolder (or otherwise use it from Python) you'd have to wrap it in a cdef class.
In this case my preferred, simpler solution would probably be to just use func3param and have the "two parameter" functions simply ignore the third argument. This means all the function pointers would have a consistent signature, which would make a lot more sense to me.
I would like to use something like a structarray in cython, and I would like this structarray as easily accessible in python as in cython.
Based on a whim I used a recarray using a dtype that looks like the struct that I would like to use. Curiously, it just works and allows me to use a c structarray that, over the hood ;), is a numpy recarray for the python user.
Here is my example
# This is a "structarray in cython with numpy recarrays" testfile
import numpy as np
cimport numpy as np
# My structarray has nodes with fields x and y
# This also works without packed, but I have seen packed used in other places where people asked similar questions
# I assume that for two doubles that is equivalent but is necessary for in8s in between
cdef packed struct node:
double x
double y
# I suppose that would be the equivalent numpy dtype?
# Note: During compilation it warns me about double to float downcasts, but I do not see where
nodetype = [('x' , np.float64),('y', np.float64)]
def fun():
# Make 10 element recarray
# (Just looked it up. A point where 1-based indexing would save a look in the docs)
mynode1 = np.recarray(10,dtype=nodetype)
# Recarray with cdef struct
mynode1 = np.recarray(10,dtype=nodetype)
# Fill it with non-garbage somewhere
mynode1[2].x=1.0
mynode1[2].y=2.0
# Brave: give recarray element to a c function assuming its equivalent to the struct
ny = cfuny(mynode1[2])
assert ny==2.0 # works!
# Test memoryview, assuming type node
cdef node [:] nview = mynode1
ny = cfunyv(nview,2)
assert ny==2.0 # works!
# This sets the numpy recarray value with a c function the gts a memoryview
cfunyv_set(nview,5,9.0)
assert mynode1[5].y==9.0 # alsow works!
return 0
# return node element y from c struct node
cdef double cfuny(node n):
return n.y
# give element i from memoryview of recarray to c function expecting a c struct
cdef double cfunyv(node [:] n, int i):
return cfuny(n[i])
# write into recarray with a function expecting a memoryview with type node
cdef int cfunyv_set(node [:] n,int i,double val):
n[i].y = val
return 0
Of course I am not the first to try this.
Here for example the same thing is done, and it even states that this usage would be part of the manual here, but I cannot find this on the page. I suspect it was there at some point. There are also several discussions involving the use of strings in such a custom type (e.g. here), and from the answers I gather that the possibility of casting a recarray on a cstruct is intended behaviour, as the discussion talks about incorporating a regression test about the given example and having fixed the string error at some point.
My question
I could not find any documentation that states that this should work besides forum answers. Can someone show me where that is documented?
And, for some additional curiosity
Will this likely break at any point during the development of numpy or cython?
From the other forum entries on the subject it seems that packed is necessary for this to work once more interesting datatypes are part of the struct. I am not a compiler expert and have never used structure packing myself, but I suspect that whether a structure gets packed or not depends on the compiler settings. Does that mean that someone who compiles numpy without packing structures needs to compile this cython code without the packed?
This doesn't seem to be directly documented. Best reference I can give you is the typed memoryview docs here.
Rather than specific cython support for numpy structured dtypes this instead seems a consequence of support for the PEP 3118 buffer protocol. numpy exposes a Py_buffer struct for its arrays, and cython knows how to cast those into structs.
The packing is necessary. My understanding is x86 is aligned on itemsize byte boundaries, whereas as a numpy structured dtype is packed into the minimum space possible. Probably clearest by example:
%%cython
import numpy as np
cdef struct Thing:
char a
# 7 bytes padding, double must be 8 byte aligned
double b
thing_dtype = np.dtype([('a', np.byte), ('b', np.double)])
print('dtype size: ', thing_dtype.itemsize)
print('unpacked struct size', sizeof(Thing))
dtype size: 9
unpacked struct size 16
Just answering the final sub-question:
From the other forum entries on the subject it seems that packed is necessary for this to work once more interesting datatypes are part of the struct. I am not a compiler expert and have never used structure packing myself, but I suspect that whether a structure gets packed or not depends on the compiler settings. Does that mean that someone who compiles numpy without packing structures needs to compile this cython code without the packed?
Numpy's behaviour is decided at runtime rather than compile-time. It will calculate the minimum amount of space a structure can need and allocate blocks of that. It won't be changed by any compiler settings so should be reliable.
cdef packed struct is therefore always needed to match numpy. However, it does not generate standards compliant C code. Instead, it uses extensions to GCC, MSVC (and others). Therefore it works fine on the major C compilers that currently exist, but in principle might fail on a future compiler. It looks like it should be possible to use the C11 standard alignas to achieve the same thing in a standards compliant way, so Cython could hopefully be modified to do that if needed.
I'm trying to speed up a piece of code that generates all possible splits of a string.
splits('foo') -> [('f', 'oo'), ('fo', 'o'), ('foo', '')]
The code for this in python is very simple:
def splits(text):
return [(text[:i + 1], text[i + 1:])
for i in range(len(text))]
Is there a way to speed this up via cython or some other means? For context, the greater purpose of this code is to find the split of a string with the highest probability.
This isn't the sort of problem that Cython tends to help with much. It's using slicing, which ends up largely the same speed as pure Python (i.e. actually pretty good).
Using a 100 character long byte string (b'0'*100) and 10000 iterations in timeit I get:
Your code as written - 0.37s
Your code as written but compiled in Cython - 0.21s
Your code with the line cdef int i and compiled in Cython - 0.20s (this is reproducably a small improvement. It's more significant with longer strings)
Your cdef int i and the parameter typed to bytes text - 0.28s (i.e. worse).
Best speed is got by using the Python C API directly (see code below) - 0.11s. I've chosen to do this mostly in Cython (but calling the API functions myself) for convenience, but you could write very similar code in C directly with a little more manual error checking. I've written this for the Python 3 API assuming you're using bytes objects (i.e. PyBytes instead of PyString) so if you're using Python 2, or Unicode and Python 3 you'll have to change it a little.
from cpython cimport *
cdef extern from "Python.h":
# This isn't included in the cpython definitions
# using PyObject* rather than object lets us control refcounting
PyObject* Py_BuildValue(const char*,...) except NULL
def split(text):
cdef Py_ssize_t l,i
cdef char* s
# Cython automatically checks the return value and raises an error if
# these fail. This provides a type-check on text
PyBytes_AsStringAndSize(text,&s,&l)
output = PyList_New(l)
for i in range(l):
# PyList_SET_ITEM steals a reference
# the casting is necessary to ensure that Cython doesn't
# decref the result of Py_BuildValue
PyList_SET_ITEM(output,i,
<object>Py_BuildValue('y#y#',s,i+1,s+i+1,l-(i+1)))
return output
If you don't want to go all the way with using the C API then a version that preallocates the list output = [None]*len(text) and does a for-loop rather than a list comprehension is marginally more efficient than your original version - 0.18s
In summary, just compiling it in Cython gives you a decent speed up (a bit less than 2x) and setting the type of i helps a little. This is all you can really achieve with Cython conventionally. To get full speed you basically need to resort to using the Python C API directly. That gets you a little under a 4x speed up which I think is pretty decent.
The Cython documentation explains very well what they allow for, how you can declare them, and how to use them.
However, it is still not clear to me what they really are. For example, a simple assignment from a numpy array like this:
my_arr = np.empty(10, np.int32)
cdef int [:] new_arr = my_arr
can make the accessing/assignment of my_arr faster.
What is it happening behind the scenes? Numpy should already allocate the elements in memory in a contiguous fashion, so what's the deal with memoryviews? Apparently not that much, in fact the memoryview assignment of the numpy array new_arr should be equivalent to
cdef np.ndarray[np.int32_t, ndim=1] new_arr = np.empty(10, np.int32)
in terms of speed. However, memoryviews are considered more general than numpy array buffer; could you make a simple example in which the added 'generalization' is important/interesting?
Furthermore, if I have already allocated a pointer in order to make things as fast as possible, what is the advantage of casting it to a typed memoryview? (the answer to this question might be the same of the one above)
cdef int *my_arr = <int *> malloc(N * sizeof(int))
cdef int[:] new_arr = <int[:N]>my_arr
What is a memoryview:
When you write in a function:
cdef double[:] a
you end up with a __Pyx_memviewslice object:
typedef struct {
struct __pyx_memoryview_obj *memview;
char *data;
Py_ssize_t shape[8];
Py_ssize_t strides[8];
Py_ssize_t suboffsets[8];
} __Pyx_memviewslice;
The memoryview contains a C pointer some some data which it (usually) doesn't directly own. It also contains a pointer to an underlying Python object (struct __pyx_memoryview_obj *memview;). If the data is owned by a Python object then memview holds a reference to that and ensures the Python object that holds the data is kept alive as long as the memoryview is around.
The combination of the pointer to the raw data, and information of how to index it (shape, strides and suboffsets) allows Cython to do indexing the using the raw data pointers and some simple C maths (which is very efficient). e.g.:
x=a[0]
gives something like:
(*((double *) ( /* dim=0 */ (__pyx_v_a.data + __pyx_t_2 * __pyx_v_a.strides[0]) )));
In contrast, if you work with untyped objects and write something like:
a = np.array([1,2,3]) # note no typedef
x = x[0]
the indexing is done as:
__Pyx_GetItemInt(__pyx_v_a, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1);
which itself expands to a whole bunch of Python C-api calls (so is slow). Ultimately it calls a's __getitem__ method.
Compared to typed numpy arrays: there really isn't a huge difference.
If you do something like:
cdef np.ndarray[np.int32_t, ndim=1] new_arr
it works practically very like a memoryview, with access to raw pointers and the speed should be very similar.
The advantage to using memoryviews is that you can use a wider range of array types with them (such as the standard library array), so you're more flexible about the types your functions can be called with. This fits in with the general Python idea of "duck-typing" - that your code should work with any parameter that behaves the right way (rather than checking the type).
A second (small) advantage is that you don't need the numpy headers to build your module.
A third (possibly larger) advantage is that memoryviews can be initialised without the GIL while cdef np.ndarrays can't (http://docs.cython.org/src/userguide/memoryviews.html#comparison-to-the-old-buffer-support)
A slight disadvantage to memoryviews is that they seem to be slightly slower to set up.
Compared to just using malloced int pointers:
You won't get any speed advantage (but neither will you get too much speed loss). The minor advantages of converting using a memoryview are:
You can write functions that can be used either from Python or internally within Cython:
cpdef do_something_useful(double[:] x):
# can be called from Python with any array type or from Cython
# with something that's already a memoryview
....
You can let Cython handle the freeing of memory for this type of array, which could simplify your life for things that have an unknown lifetime. See http://docs.cython.org/src/userguide/memoryviews.html#cython-arrays and especially .callback_free_data.
You can pass your data back to python python code (it'll get the underlying __pyx_memoryview_obj or something similar). Be very careful of memory management here (i.e. see point 2!).
The other thing you can do is handle things like 2D arrays defined as pointer to pointer (e.g. double**). See http://docs.cython.org/src/userguide/memoryviews.html#specifying-more-general-memory-layouts. I generally don't like this type of array, but if you have existing C code that already uses if then you can interface with that (and pass it back to Python so your Python code can also use it).