[sage-support] Re: lists in cython
On Sep 25, 2008, at 7:06 PM, Jason Grout wrote: cesarnda wrote: why the line: def primes(int kmax): is in yellow? It's yellow because it's handling a python function call (parsing the arguments, converting a python object to an int, ...) If you click on the line, you can see the actual C code that Cython generated for you. Doing that, you'll notice that there are quite a few more python calls stemming from yellow lines than the white lines. The more yellow a line is, the slower it will probably run because it is doing more python stuff than just straight C stuff. Some python stuff is unavoidable, though, like the def statement above. Note that the coloring of the lines is heuristic; it's not a guarantee that those lines are the ones that are running slowly. But it does help quite a bit if you want to speed up your code: make sure that the inner loops don't have very much yellow in them. Yep. The color of a line is proportional to (or at least an increasing function of) the number of times the Python C API is invoked. Pure white should be 100% C. As Jason mentioned, it is important to note that yellow does not necessarily mean slow, simply that there's lots of implicit stuff going on that's often not obvious by looking at the code (and is very helpful in caching stuff like unnecessary coercions due to forgetting to cdef a variable). Personally, I think the coloring of the lines and the ability to click on them is one of the neatest features about developing cython in the notebook. Thanks :). From the command line you can run cython -a. - Robert --~--~-~--~~~---~--~~ To post to this group, send email to sage-support@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-support URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-support] Re: lists in cython
On Sep 25, 6:45 pm, cesarnda [EMAIL PROTECTED] wrote: ... result = [] ... result.append(n) ... if I compile in the notebook I get a html file showing me the following lines in yellow: def primes(int kmax): result = [] result.append(n) return result how can I modify this example to avoid the yellow lines? As other people pointed out, there is not much hope for the def and the return line. But wouldn't it be possible to do cdef list result = [] ? And isn't there a quick, dirty and potentially unsafe way of appending to a list? Or at least for assigning a value to some list entry? I think I have seen it somewhere, but I don't remember the name. Cheers Simon --~--~-~--~~~---~--~~ To post to this group, send email to sage-support@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-support URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-support] Re: lists in cython
On Sep 26, 2008, at 12:09 AM, Simon King wrote: On Sep 25, 6:45 pm, cesarnda [EMAIL PROTECTED] wrote: ... result = [] ... result.append(n) ... if I compile in the notebook I get a html file showing me the following lines in yellow: def primes(int kmax): result = [] result.append(n) return result how can I modify this example to avoid the yellow lines? As other people pointed out, there is not much hope for the def and the return line. But wouldn't it be possible to do cdef list result = [] Yep, you could do this. The resulting C code calls PyList_New(0) which is the fastest way to make a list. And isn't there a quick, dirty and potentially unsafe way of appending to a list? Since it knows result is a list (due to the cdef above), it uses PyList_Append, the fastest way to append to a list. Or at least for assigning a value to some list entry? I think I have seen it somewhere, but I don't remember the name. Yep. Currently it calls __Pyx_SetItemInt which does an inline runtime boundscheck and check for a list, and if it's OK uses a macro to reset the specified entry right there. We could (should) optimize this in the case it already knows it's a list, but with good branch prediction it's probably within 5% of as fast as it could be period. - Robert --~--~-~--~~~---~--~~ To post to this group, send email to sage-support@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-support URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-support] Re: lists in cython
On Sep 25, 2008, at 3:45 PM, cesarnda wrote: in http://www.cosc.canterbury.ac.nz/greg.ewing/python/Pyrex/ there is the following example: def primes(int kmax): cdef int n, k, i cdef int p[1000] result = [] if kmax 1000: kmax = 1000 k = 0 n = 2 while k kmax: i = 0 while i k and n % p[i] 0: i = i + 1 if i == k: p[k] = n k = k + 1 result.append(n) n = n + 1 return result if I compile in the notebook I get a html file showing me the following lines in yellow: def primes(int kmax): result = [] result.append(n) return result how can I modify this example to avoid the yellow lines? You can't, but they're not very yellow (i.e. there's not really a faster way of doing those operations). - Robert --~--~-~--~~~---~--~~ To post to this group, send email to sage-support@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-support URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-support] Re: lists in cython
I already did that and I get this:
cdef list codeSet = []
__pyx_1 = PyList_New(0); if (unlikely(!__pyx_1)) {__pyx_filename =
__pyx_f[0]; __pyx_lineno = 210; __pyx_clineno = __LINE__; goto
__pyx_L1_error;}
__pyx_v_codeSet = __pyx_1;
__pyx_1 = 0;
and if I don't do it that way I get:
addVector = []
__pyx_2 = PyList_New(0); if (unlikely(!__pyx_2))
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 215; __pyx_clineno =
__LINE__; goto __pyx_L1_error;}
Py_DECREF(__pyx_v_addVector);
__pyx_v_addVector = ((PyObject *)__pyx_2);
__pyx_2 = 0;
On Sep 26, 2:55 am, Robert Bradshaw [EMAIL PROTECTED]
wrote:
On Sep 26, 2008, at 12:09 AM, Simon King wrote:
On Sep 25, 6:45 pm, cesarnda [EMAIL PROTECTED] wrote:
...
result = []
...
result.append(n)
...
if I compile in the notebook I get a html file showing me the
following lines in yellow:
def primes(int kmax):
result = []
result.append(n)
return result
how can I modify this example to avoid the yellow lines?
As other people pointed out, there is not much hope for the def and
the return line.
But wouldn't it be possible to do
cdef list result = []
Yep, you could do this. The resulting C code calls PyList_New(0)
which is the fastest way to make a list.
And isn't there a quick, dirty and potentially unsafe way of appending
to a list?
Since it knows result is a list (due to the cdef above), it uses
PyList_Append, the fastest way to append to a list.
Or at least for assigning a value to some list entry? I
think I have seen it somewhere, but I don't remember the name.
Yep. Currently it calls __Pyx_SetItemInt which does an inline runtime
boundscheck and check for a list, and if it's OK uses a macro to
reset the specified entry right there. We could (should) optimize
this in the case it already knows it's a list, but with good branch
prediction it's probably within 5% of as fast as it could be period.
- Robert
--~--~-~--~~~---~--~~
To post to this group, send email to sage-support@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
For more options, visit this group at
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URLs: http://www.sagemath.org
-~--~~~~--~~--~--~---
[sage-support] Re: lists in cython
On Sep 26, 2008, at 8:21 AM, cesarnda wrote:
I already did that and I get this:
cdef list codeSet = []
__pyx_1 = PyList_New(0); if (unlikely(!__pyx_1)) {__pyx_filename =
__pyx_f[0]; __pyx_lineno = 210; __pyx_clineno = __LINE__; goto
__pyx_L1_error;}
__pyx_v_codeSet = __pyx_1;
__pyx_1 = 0;
and if I don't do it that way I get:
addVector = []
__pyx_2 = PyList_New(0); if (unlikely(!__pyx_2))
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 215; __pyx_clineno =
__LINE__; goto __pyx_L1_error;}
Py_DECREF(__pyx_v_addVector);
__pyx_v_addVector = ((PyObject *)__pyx_2);
__pyx_2 = 0;
Yes, that is correct. Is this not what you want?
On Sep 26, 2:55 am, Robert Bradshaw [EMAIL PROTECTED]
wrote:
On Sep 26, 2008, at 12:09 AM, Simon King wrote:
On Sep 25, 6:45 pm, cesarnda [EMAIL PROTECTED] wrote:
...
result = []
...
result.append(n)
...
if I compile in the notebook I get a html file showing me the
following lines in yellow:
def primes(int kmax):
result = []
result.append(n)
return result
how can I modify this example to avoid the yellow lines?
As other people pointed out, there is not much hope for the def
and
the return line.
But wouldn't it be possible to do
cdef list result = []
Yep, you could do this. The resulting C code calls PyList_New(0)
which is the fastest way to make a list.
And isn't there a quick, dirty and potentially unsafe way of
appending
to a list?
Since it knows result is a list (due to the cdef above), it uses
PyList_Append, the fastest way to append to a list.
Or at least for assigning a value to some list entry? I
think I have seen it somewhere, but I don't remember the name.
Yep. Currently it calls __Pyx_SetItemInt which does an inline runtime
boundscheck and check for a list, and if it's OK uses a macro to
reset the specified entry right there. We could (should) optimize
this in the case it already knows it's a list, but with good branch
prediction it's probably within 5% of as fast as it could be period.
- Robert
--~--~-~--~~~---~--~~
To post to this group, send email to sage-support@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
For more options, visit this group at
http://groups.google.com/group/sage-support
URLs: http://www.sagemath.org
-~--~~~~--~~--~--~---
[sage-support] Re: lists in cython
Actually I wanted it less yellow, if I do that or only
codeSet = []
or
codeSet = ([])
the result is the same.
On Sep 26, 1:43 pm, Robert Bradshaw [EMAIL PROTECTED]
wrote:
On Sep 26, 2008, at 8:21 AM, cesarnda wrote:
I already did that and I get this:
cdef list codeSet = []
__pyx_1 = PyList_New(0); if (unlikely(!__pyx_1)) {__pyx_filename =
__pyx_f[0]; __pyx_lineno = 210; __pyx_clineno = __LINE__; goto
__pyx_L1_error;}
__pyx_v_codeSet = __pyx_1;
__pyx_1 = 0;
and if I don't do it that way I get:
addVector = []
__pyx_2 = PyList_New(0); if (unlikely(!__pyx_2))
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 215; __pyx_clineno =
__LINE__; goto __pyx_L1_error;}
Py_DECREF(__pyx_v_addVector);
__pyx_v_addVector = ((PyObject *)__pyx_2);
__pyx_2 = 0;
Yes, that is correct. Is this not what you want?
On Sep 26, 2:55 am, Robert Bradshaw [EMAIL PROTECTED]
wrote:
On Sep 26, 2008, at 12:09 AM, Simon King wrote:
On Sep 25, 6:45 pm, cesarnda [EMAIL PROTECTED] wrote:
...
result = []
...
result.append(n)
...
if I compile in the notebook I get a html file showing me the
following lines in yellow:
def primes(int kmax):
result = []
result.append(n)
return result
how can I modify this example to avoid the yellow lines?
As other people pointed out, there is not much hope for the def
and
the return line.
But wouldn't it be possible to do
cdef list result = []
Yep, you could do this. The resulting C code calls PyList_New(0)
which is the fastest way to make a list.
And isn't there a quick, dirty and potentially unsafe way of
appending
to a list?
Since it knows result is a list (due to the cdef above), it uses
PyList_Append, the fastest way to append to a list.
Or at least for assigning a value to some list entry? I
think I have seen it somewhere, but I don't remember the name.
Yep. Currently it calls __Pyx_SetItemInt which does an inline runtime
boundscheck and check for a list, and if it's OK uses a macro to
reset the specified entry right there. We could (should) optimize
this in the case it already knows it's a list, but with good branch
prediction it's probably within 5% of as fast as it could be period.
- Robert
--~--~-~--~~~---~--~~
To post to this group, send email to sage-support@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
For more options, visit this group at
http://groups.google.com/group/sage-support
URLs: http://www.sagemath.org
-~--~~~~--~~--~--~---
[sage-support] Re: lists in cython
On Sep 26, 2008, at 6:04 PM, cesarnda wrote:
Actually I wanted it less yellow, if I do that or only
codeSet = []
or
codeSet = ([])
the result is the same.
You can't create a list in a less yellow way than calling PyList_New
(0), and that's all its doing so you're optimal.
- Robert
On Sep 26, 1:43 pm, Robert Bradshaw [EMAIL PROTECTED]
wrote:
On Sep 26, 2008, at 8:21 AM, cesarnda wrote:
I already did that and I get this:
cdef list codeSet = []
__pyx_1 = PyList_New(0); if (unlikely(!__pyx_1)) {__pyx_filename =
__pyx_f[0]; __pyx_lineno = 210; __pyx_clineno = __LINE__; goto
__pyx_L1_error;}
__pyx_v_codeSet = __pyx_1;
__pyx_1 = 0;
and if I don't do it that way I get:
addVector = []
__pyx_2 = PyList_New(0); if (unlikely(!__pyx_2))
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 215; __pyx_clineno =
__LINE__; goto __pyx_L1_error;}
Py_DECREF(__pyx_v_addVector);
__pyx_v_addVector = ((PyObject *)__pyx_2);
__pyx_2 = 0;
Yes, that is correct. Is this not what you want?
On Sep 26, 2:55 am, Robert Bradshaw [EMAIL PROTECTED]
wrote:
On Sep 26, 2008, at 12:09 AM, Simon King wrote:
On Sep 25, 6:45 pm, cesarnda [EMAIL PROTECTED] wrote:
...
result = []
...
result.append(n)
...
if I compile in the notebook I get a html file showing me the
following lines in yellow:
def primes(int kmax):
result = []
result.append(n)
return result
how can I modify this example to avoid the yellow lines?
As other people pointed out, there is not much hope for the def
and
the return line.
But wouldn't it be possible to do
cdef list result = []
Yep, you could do this. The resulting C code calls PyList_New(0)
which is the fastest way to make a list.
And isn't there a quick, dirty and potentially unsafe way of
appending
to a list?
Since it knows result is a list (due to the cdef above), it uses
PyList_Append, the fastest way to append to a list.
Or at least for assigning a value to some list entry? I
think I have seen it somewhere, but I don't remember the name.
Yep. Currently it calls __Pyx_SetItemInt which does an inline
runtime
boundscheck and check for a list, and if it's OK uses a macro to
reset the specified entry right there. We could (should) optimize
this in the case it already knows it's a list, but with good branch
prediction it's probably within 5% of as fast as it could be
period.
- Robert
--~--~-~--~~~---~--~~
To post to this group, send email to sage-support@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
For more options, visit this group at
http://groups.google.com/group/sage-support
URLs: http://www.sagemath.org
-~--~~~~--~~--~--~---
[sage-support] Re: lists in cython
why the line: def primes(int kmax): is in yellow? On Sep 25, 8:03 pm, Robert Bradshaw [EMAIL PROTECTED] wrote: On Sep 25, 2008, at 3:45 PM, cesarnda wrote: inhttp://www.cosc.canterbury.ac.nz/greg.ewing/python/Pyrex/there is the following example: def primes(int kmax): cdef int n, k, i cdef int p[1000] result = [] if kmax 1000: kmax = 1000 k = 0 n = 2 while k kmax: i = 0 while i k and n % p[i] 0: i = i + 1 if i == k: p[k] = n k = k + 1 result.append(n) n = n + 1 return result if I compile in the notebook I get a html file showing me the following lines in yellow: def primes(int kmax): result = [] result.append(n) return result how can I modify this example to avoid the yellow lines? You can't, but they're not very yellow (i.e. there's not really a faster way of doing those operations). - Robert --~--~-~--~~~---~--~~ To post to this group, send email to sage-support@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-support URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-support] Re: lists in cython
cesarnda wrote: why the line: def primes(int kmax): is in yellow? If you click on the line, you can see the actual C code that Cython generated for you. Doing that, you'll notice that there are quite a few more python calls stemming from yellow lines than the white lines. The more yellow a line is, the slower it will probably run because it is doing more python stuff than just straight C stuff. Some python stuff is unavoidable, though, like the def statement above. Note that the coloring of the lines is heuristic; it's not a guarantee that those lines are the ones that are running slowly. But it does help quite a bit if you want to speed up your code: make sure that the inner loops don't have very much yellow in them. Personally, I think the coloring of the lines and the ability to click on them is one of the neatest features about developing cython in the notebook. Jason --~--~-~--~~~---~--~~ To post to this group, send email to sage-support@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-support URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-support] Re: #if in cython?
On 10/13/07, Simon King [EMAIL PROTECTED] wrote: Dear sage-supporters, a question on pyrex/cython: I have type definitions depending on an environment variable, such as #if ZZZ==zzz typedef unsigned char FEL; #elif ZZZ==bigzzz typedef unsigned short FEL; Is there a way to do a similar thing in pyrex/cython? Yours sincerely This question belongs in the cython or pyrex mailing lists, rather than sage-support, so I've forwarded it there. William --~--~-~--~~~---~--~~ To post to this group, send email to sage-support@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-support URLs: http://sage.math.washington.edu/sage/ and http://sage.scipy.org/sage/ -~--~~~~--~~--~--~---
[sage-support] Re: #if in cython?
On Oct 14, 2:37 am, Simon King [EMAIL PROTECTED] wrote: Dear William, you wrote: This question belongs in the cython or pyrex mailing lists, rather than sage-support, so I've forwarded it there. After posting my question, i found an answer to my question in the web: Pyrex 0.9.6 provides conditional compilation. Seehttp://www.cosc.canterbury.ac.nz/greg.ewing/python/Pyrex/version/Doc/... (However, i didn't succeed to make it work on some easy examples, so it seems i need more information) I do think that my question remains a question for sage, since sage - cython apparently does not provide that new pyrex functionality. The line DEF VARI = Value is accepted by pyrexc, but not by sage -cython. There has been a very recent release of pyrex and the changes/updates from that release haven't made it into Cython's latest release yet (at least not the one in the official tree) Can you tell me the web address of the pyrex or cython mailin lists, so that i can read answers? See http://developer.berlios.de/projects/cython/ Yours Simon Cheers, Michael --~--~-~--~~~---~--~~ To post to this group, send email to sage-support@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-support URLs: http://sage.math.washington.edu/sage/ and http://sage.scipy.org/sage/ -~--~~~~--~~--~--~---
