On Mon, Jan 14, 2013 at 2:57 PM, Benjamin Root ben.r...@ou.edu wrote:
I am also +1 on the idea of having a filled() and filled_like() function (I
learned a long time ago to just do a = np.empty() and a.fill() rather than
the multiplication trick I learned from Matlab). However, the collision
On Sat, Jan 5, 2013 at 1:03 PM, Robin robi...@gmail.com wrote:
If not, is there a reasonable way to build numpy.linalg such that
it interfaces with MKL correctly ?
I managed to get this to work in the end. Since Matlab uses MKL with
ILP64 interface it is not possible to get Numpy to use
EPD which is built against MKL -
but I think the problem is that Intel provide two different interfaces
- ILP64 with 64 bit integer indices and LP64 with 32 bit integers.
Matlab link against the ILP64 version, whereas Enthought use the LP64
version - so there are still incompatible.
Cheers
Robin
]
and verify that there's a whole lot of 0s in the matrix, specifically,
c[574519:].sum()
356.0
c[574520:].sum()
0.0
is the case on Linux 64-bit; is it the case on Windows 64?
Yes - I get exactly the same numbers in 64 bit windows with 1.6.1.
Cheers
Robin
, ..., 0, 0, 0],
[0, 0, 0, ..., 0, 0, 0]], dtype=uint8)
In [41]: a[581350:,0].sum()
Out[41]: 0
Cheers
Robin
Thanks,
David
On Mon, Jan 23, 2012 at 05:23:28AM -0500, David Warde-Farley wrote:
A colleague has run into this weird behaviour with NumPy 1.6.1, EPD 7.1-2,
on Linux (Fedora
='uint8'))
1 loops, best of 3: 27.8 s per loop
In this case repeat() peaked at about 1gb of ram usage while np.kron hit about
1.7gb.
Thanks again Warren. I'd tried way too many variations on reshape and rollaxis,
and should have come to the Numpy list a lot sooner!
-Robin
On Dec 3, 2011, at 12
there, but it seems
doable.
Anyone know what combination of manipulations would work with the result of
np.tile?
-Robin
On Dec 3, 2011, at 11:05 AM, Olivier Delalleau wrote:
You can also use numpy.tile
-=- Olivier
2011/12/3 Robin Kraft
Thanks Warren, this is great, and even handles
],
[1, 1, 2, 2],
[3, 3, 4, 4],
[3, 3, 4, 4]]])
On Dec. 3, 2011, at 12:50PM, Derek Homeier wrote:
On 03.12.2011, at 6:22PM, Robin Kraft wrote:
That does repeat the elements, but doesn't get them into the desired order.
In [4]: print a
[[1 2]
[3 4]]
In [7
some combination of np.resize or np.repeat and reshape + rollaxis
would do the trick, but I'm at a loss.
Many thanks!
-Robin
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-threaded) embedded CPython situations, see for
example pymex [1] which embeds Python + Numpy in a Matlab mex file and
works really well.
This seems to a be a problem specific to Jepp.
Just wanted to mention it in case it puts someone off trying something
unnecessarily in the future.
Cheers
Robin
[1
it by following the symlink that is the
gfortran command and looking for an appropriate lib/ directory near
the target of that.
Cheers
Robin
On Wed, Jul 20, 2011 at 9:02 PM, Brandt Belson bbel...@princeton.edu wrote:
Hello,
I'm struggling to create openmp subroutines. I've simplified the problem
If I add a 1s sleep in the inner product function shows a much more
significant improvement (ie if it were a longer computation):
Not threaded: 50.6744170189
Using 8 processes: 8.152393
Still not quite linear but certainly an improvement.
Cheers
Robin
On Thu, Jun 16, 2011 at 9:19 PM, Robin
myutil.data = listofdata
p = multiprocessing.Pool(8)
def mymapfunc(i):
return mydatafunc(myutil.data[i])
p.map(mymapfunc, range(len(myutil.data)))
Actually that won't work because mymapfunc needs to be in a module so
it can be pickled but hopefully you get the idea.
Cheers
Robin
IPs
.
Cheers
Robin
On Thu, Jun 16, 2011 at 9:05 PM, Brandt Belson bbel...@princeton.edu wrote:
Hi all,
Thanks for the replies. As mentioned, I'm parallelizing so that I can take
many inner products simultaneously (which I agree is embarrassingly
parallel). The library I'm writing asks the user
I think numpy doesn't use umfpack. scipy.sparse used to, but now the
umfpack stuff has been moved out to a scikit.
So you probably won't see anything about those libraries, but if you
install scikits.umfpack and it works then you must be linked
correctly.
Cheers
Robin
On Fri, Feb 18, 2011 at 11
Git is having some kind of major outage:
http://status.github.com/
The site and git access is unavailable due to a database failure. We're
researching the issue.
On Nov 14, 2010, at 3:29 PM, numpy-discussion-requ...@scipy.org wrote:
Message: 5
Date: Sun, 14 Nov 2010 13:29:03 -0700
From:
installed components, check that the
Microsoft SDK contains the amd64 version of the C/C++ compiler
cl.exe. This is usually installed into
C:\Program Files (x86)\Microsoft Visual Studio 9.0\VC\bin\amd64\cl.exe
Cheers
Robin
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On Wed, Aug 18, 2010 at 8:20 AM, Sturla Molden stu...@molden.no wrote:
Den 18. aug. 2010 kl. 08.19 skrev Martin Raspaud
martin.rasp...@smhi.se:
Once upon a time, when my boss wanted me to use matlab, I found myself
implementing a python interpreter in matlab...
There are just two sane
Robin
In the following simple example I am building a tridiagonal array with
plain python for loops and by calling a simple fortran subroutine that does
the same thing.
Here goes the python script:
import numpy as np
import time
import learnf90_05
import sys
run = sys.argv[1]
try
.)
multi-dimensional arrays? Stefan's slides are beautiful but my brain starts to
hurt if I try to follow them line by line.
-Robin
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it isn't
square and can't be reshaped appropriately (np.tile(np.arange(2**2).reshape(2,
2), 4)):
array([[0, 1, 0, 1, 0, 1, 0, 1],
[2, 3, 2, 3, 2, 3, 2, 3]])
Inefficient sample code below. Advice greatly appreciated!
-Robin
import numpy as np
from math import sqrt
from time import time
def rs
about 2008.
http://www.microsoft.com/downloads/details.aspx?familyid=7B0B0339-613A-46E6-AB4D-080D4D4A8C4Edisplaylang=en
Cheers
Robin
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scipy tests)
Cheers
Robin
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Hi,
I am having some problems with win64 with all my tests failing.
I installed amd64 Python from Python.org and numpy and scipy from
http://www.lfd.uci.edu/~gohlke/pythonlibs/
I noticed that on windows sys.maxint is the 32bit value (2147483647
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that and the problems with scipy.sparse (spsolve doesn't
work) cover all of the errors I'm seeing... (I detailed those in a
seperate mail to the scipy list).
Cheers
Robin
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with
visual studio that were causing the segfaults. Makes me think of the
old phrase - problem is between keyboard and chair.
Cheers
Robin
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-into-matlab-mex-win64
Anyway I'm completely in the dark but wondered if some of the experts
on here would be able to spot something (perhaps to do with
incompatible C runtimes - I am not sure what runtime Python is built
with but I thought it was VS 2008).
Cheers
Robin
/release2009a/win64.html
So I thought on the matlab/mex side 2008 should be fine, and I thought
since Python is built with 2008 that should also be OK. But obviously
something isn't!
Cheers
Robin
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http
To build against the python.org 2.5 you need to use the older gcc:
export CC=/usr/bin/gcc-4.0
export CXX=/usr/bin/g++-4.0
should do it. By default snow leopard uses 4.2 now, which doesn't
support the -Wno-long-double option used when building python.
Cheers
Robin
On Mon, Apr 19, 2010 at 3:55
You can build numpy against Accelerate through macports by specifying
the +no_atlas variant.
Last time I tried I ran into this issue:
http://trac.macports.org/ticket/22201
but it looks like it should be fixed now.
Cheers
Robin
On Mon, Jan 18, 2010 at 8:15 PM, Mark Lescroart lescr...@usc.edu
Robin
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Hi,
Could we have a ma aware numpy.ma.log2 please, similar to np.ma.log
and np.ma.log10?
I think it should be as simple as the patch below but perhaps I've
missed something:
Thanks,
Robin
--- core.py.orig2009-12-13 15:14:14.0 +
+++ core.py 2009-12-13 15:14:53.0
-
see this paper by Travis Oliphant for details:
http://hdl.handle.net/1877/438
Cheers
Robin
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problem - I will just avoid unloading the
mex function (with clear function). But I thought it might be
indicative of a memory leak or some other problem since I think in
theory it should work (It does if numpy isn't imported).
Cheers
Robin
I forgot to add it doesn't happen if Py_Finalize isn't called - if I
take that out and just let the OS/matlab unload the mex function then
I can run it many times without the error, but it does leak a bit of
memory each time.
Cheers
Robin
On Fri, Nov 13, 2009 at 5:23 PM, Robin robi...@gmail.com
I'm trying to embed Python in a MATLAB mex file. I've been coming
under some pressure to make my Python code available to my MATLAB
colleagues so I am trying to come up with a relatively general way of
calling numerical python code from Matlab.
I get a similar but different error trying to do
function is... but I'm
getting a bit out of my depth with linker options, and I guess numpy
is always loaded dynamically anyway and will stick around.
Easy enough to work around it anyway - but just wanted to check what
was going on.
Cheers
Robin
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On Fri, Nov 13, 2009 at 6:50 PM, Pauli Virtanen pav...@iki.fi wrote:
Fri, 13 Nov 2009 17:23:19 +, Robin wrote:
I'm trying to embed Python in a MATLAB mex file. I've been coming under
some pressure to make my Python code available to my MATLAB colleagues
so I am trying to come up
On Fri, Nov 13, 2009 at 7:48 PM, Sturla Molden stu...@molden.no wrote:
Robin skrev:
I had assumed when matlab unloads the mex function it would also
unload python - but it looks like other dynamic libs pulled in from
the mex function (in this case python and in turn numpy) aren't
unloaded
to use some other suffix than .f,
but I've not tried that.
Then f2py file.f
That's great thanks very much! It's more or less exactly what I was hoping for.
I wonder if it's possible to get distutils to do the preprocess step
from a setup.py script?
Cheers
Robin
. But the
performance was more or less the same (always several times slower the
32 bit att gfortran).
Any advice appreciated.
Cheers
Robin
subroutine bincount (x,c,n,m)
implicit none
integer, intent(in) :: n,m
integer, dimension(0:n-1), intent(in) :: x
integer, dimension(0:m-1
fortran with f2py from python in a way that
doesn't require the code to be changed depending on platform?
Or should I just pack it all in and use weave?
Robin
On Tue, Nov 3, 2009 at 4:29 PM, Robin robi...@gmail.com wrote:
Hi,
I'm not sure if this is of much interest but it's been really puzzling
On Tue, Nov 3, 2009 at 6:14 PM, Robin robi...@gmail.com wrote:
After some more pootling about I figured out a lot of the performance
loss comes from using 32 bit integers by default when compiles 64 bit.
I asked this question on stackoverflow:
http://stackoverflow.com/questions/1668899/fortran
the place for f2py tickets? Or is there an obvious fix.
Inspecting gfint.so shows the same symbols for both architectures, and
_on_exit is listed there with a U which I guess means undefined.
Cheers
Robin
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Just noticed this is only supported on linux - sorry for the noise
(not having a very good day today!)
Robin
On Tue, Nov 3, 2009 at 6:47 PM, Robin robi...@gmail.com wrote:
Hi,
When I try to build a fortran module with f2py from '1.4.0.dev7618'
with gfortran 4.2.3 from att.com and apple gcc
I just tried to send the message below to f2py-users -
f2py-us...@cens.ioc.ee, but delivery failed.
Not sure where else to report this so hopefully here is ok.
Cheers
Robin
-- Forwarded message --
From: Mail Delivery Subsystem mailer-dae...@googlemail.com
Date: Tue, Nov 3
supposed to be working. Certainly more traffic more recently
than the google group.
Cheers
Robin
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in the
ticket - but it won't be fixed in a release until 2.7.
Cheers
Robin
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the wx installer to install into the
virtualenv).
I was wondering what others do?
Cheers
Robin
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On Wed, Oct 21, 2009 at 10:28 AM, David Cournapeau
da...@ar.media.kyoto-u.ac.jp wrote:
Robin wrote:
Hi,
I was wondering what the recommended way to run numpy/scipy on mac os
x 10.6 is. I understood previously it was recommended to use
python.org python and keep everything seperate from
Thanks...
On Wed, Oct 21, 2009 at 11:41 AM, David Cournapeau
da...@ar.media.kyoto-u.ac.jp wrote:
Robin wrote:
Thanks - that looks ideal. I take it $HOME/.local is searched first so
numpy will be used fromt here in preference to the system numpy.
Yes, unless framework-enabled python does
).
Cheers
Robin
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Forgot to include the fortran code used:
jm-g26b101:fortran robince$ cat test.f95
subroutine bincount (x,c,n,m)
implicit none
integer, intent(in) :: n,m
integer, dimension(0:n-1), intent(in) :: x
integer, dimension(0:m-1), intent(out) :: c
integer :: i
c = 0
do i = 0,
than np.bincount, but still
significantly slower than the fortran. Is this to be expected or am I
missing something in the cython?
In [14]: timeit ctest.bincount(x,1024)
100 loops, best of 3: 3.31 ms per loop
Cheers
Robin
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, 2.6 64bit). Is this right, or would different binaries be
required for XP, Vista, 7 etc. ?
Can anyone point me to a smallish Python package that includes fortran
code in this way that I could look to for inspiration?
Cheers
Robin
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to the fortran subroutine - so I
wondered how f2py creates it (I think I traced it to
array_from_pyobj() but I couldn't really understand what it was doing
or whether it would always be zeros). I guess as you say though it is
always safer to initialize explicitly
Cheers
Robin
or Virtualbox or some other virtualisation software. With
recent CPU's there is very little performance penalty (running 32bit
on a 64bit host) and it can be very convenient (it is easy to map
network drives between guest and host which perform very well since
the 'network' is virtual)
Cheers
Robin
Robin
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wrong with my build or
the current svn state? I am using macports python 2.5.4 on os x 10.5.7
Cheers
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for the noise...
Robin
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know there isn't really a good answer. There is xcorr in
pylab, but it isn't vectorised like xcorr from matlab...
Cheers
Robin
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8.177351741233e-01 ;
7.092517323839e-01 9.458774967489e-01 8.595104463863e-01 ] ],[ 4 3 2
])
Hope someone else finds it useful.
Cheers
Robin
On Tue, May 12, 2009 at 2:12 PM, Robin robi...@gmail.com wrote:
[crossposted to numpy-discussion and mlabwrap-user]
Hi,
I wrote a little utility class
it pretty painful, so I hope it can be useful to
someone else!
I will try and do one for Python for copying and pasting to Matlab,
but I'm expecting that to be a lot easier!
Cheers
Robin
array.m
Description: Binary data
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session?
Thanks
Robin
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2009/4/29 Stéfan van der Walt ste...@sun.ac.za:
2009/4/29 Robin robi...@gmail.com:
I have been using seterr to try to catch where Nans are appearing in
my analysis.
I used all: 'warn' which worked the first time I ran the function, but
as specified in the documentation it only warns 'once
).
There is some information about this on the wiki:
http://scipy.org/ParallelProgramming
Cheers
Robin
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I'm not
sure if I can do it without loops.
Thanks for any help
Cheers
Robin
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On Thu, Mar 5, 2009 at 10:40 AM, Robin robi...@gmail.com wrote:
Hi,
I have an indexing problem, and I know it's a bit lazy to ask the
list, sometime when people do interesting tricks come up so I hope no
one minds!
I have a 2D array X.shape = (a,b)
and I want to change it into new array
On Thu, Mar 5, 2009 at 10:40 AM, Robin robi...@gmail.com wrote:
Hi,
I have an indexing problem, and I know it's a bit lazy to ask the
list, sometime when people do interesting tricks come up so I hope no
one minds!
I have a 2D array X.shape = (a,b)
and I want to change it into new array
On Thu, Mar 5, 2009 at 10:57 AM, Robin robi...@gmail.com wrote:
On Thu, Mar 5, 2009 at 10:40 AM, Robin robi...@gmail.com wrote:
Hi,
I have an indexing problem, and I know it's a bit lazy to ask the
list, sometime when people do interesting tricks come up so I hope no
one minds!
I have a 2D
On Thu, Mar 5, 2009 at 9:15 PM, Stéfan van der Walt ste...@sun.ac.za wrote:
Hi Robin
2009/3/5 Robin robi...@gmail.com:
On Thu, Mar 5, 2009 at 10:57 AM, Robin robi...@gmail.com wrote:
On Thu, Mar 5, 2009 at 10:40 AM, Robin robi...@gmail.com wrote:
Hi,
I have an indexing problem, and I know
any problem (except for the machine running out of memory :)
Cheers
Robin
Cheers,
Todd
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Hi,
I made some changes to the ParallelProgramming wiki page to outline
use of the (multi)processing module as well as the threading module.
I'm very much not an expert on this - just researched it for myself,
so please feel free to correct/ extend/ delete as appropriate.
Robin
if numpy builds with
that, so maybe we should take that reference out.
Robin
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Success in business appears to be elusive for many people. So what is it
that makes people successful?
http://www.bestentrepreneur.net/2008/02/want-to-know-billionaires-formula.html
--~--~-~--~~~---~--~~
You received this message because you are subscribed to the
an afternoon of refactoring
everything into tiny functions to get anything useful out of the
normal profiler and see where the bottleneck in my code was.
Robin
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ndmin, numpy still complains.)
I think r_[x[0],x] will do you what you want...
Robin
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but installation is
probably simpler following the instructions on the wiki to use the
apple one...
Robin
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alone - and installing the
python.org for everyday use. The only problem with this is that the
system python works with dtrace while the normal one doesn't...
Cheers
Robin
I guess I always feel a sense of uncertainty with having two separate
Python installations as to which actually gets used
On Wed, Jun 4, 2008 at 10:59 AM, David Cournapeau
[EMAIL PROTECTED] wrote:
Robin wrote:
I think theres much less chance of problems using the system python
for system things and leaving it well alone - and installing the
python.org for everyday use. The only problem
] and element [0,1].
Hope this helps,
Robin
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On Fri, May 30, 2008 at 12:57 AM, Robin [EMAIL PROTECTED] wrote:
You are indexing here with a 1d list [0,1]. Since you don't provide a
column index you get rows 0 and 1.
If you do a[ [0,1] , [0,1] ] then you get element [0,0] and element [0,1].
Whoops - you get [0,0] and [1,1].
Robin
occurrence of i at a position p contributes
weights[p] instead of 1.
See also: histogram, digitize, unique.
Robin
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take the (1-)'s outside of the loop although
again I'm not sure how much difference it would make.
So sorry I can't give any concrete advise but I hope I've given some ideas...
Cheers
Robin
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Also you could use xrange instead of range...
Again, not sure of the size of the effect but it seems to be
recommended by the docstring.
Robin
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of methods to
speed up python code (incuding weave.blitz), which has Hoyt says would
be ideal in this case:
http://scipy.org/PerformancePython
Robin
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/Cookbook/Python/Recipe/511474
which does wonders for my code. I was wondering if this function
should be included in Numpy as it seems to provide an important
feature, or perhaps an entry on the wiki (in Cookbook section?)
Thanks,
Robin
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On Fri, Mar 7, 2008 at 9:06 AM, Fernando Perez [EMAIL PROTECTED] wrote:
Hi Robin,
As Ondrej pointed out, the expectation is a full-time commitment to
the project. Other than that it sounds like you might be able to
participate, and it's worth noting that this being open source, if you
a as an array with more than one element.
I think the array constructor expects lists of numbers, not of arrays
etc. To do what you want try
b = r_[1,2,a]
c = r_[a,1,2]
which works for a an array (and of more than one element).
Cheers
Robin
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that
interested students like myself can apply.
Thanks,
Robin
PS
My nick on IRC is 'thrope' and I try to hang out in there most of the
time I am online. I am also on Google Talk at this email address.
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128 makes unsigned again in
[0,256].
I'm not sure why they would be doing this - to me it looks they might
be using Image as a convenient way to store some other kind of data...
HTH,
Robin
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interactively in Ipython, you can do
%who ndarray
or
%whos ndarray
to get a list of arrays.
It might be possible to get this functionality within a script/program
through the ipython api, but I'm afraid I don't know much about that.
Cheers,
Robin
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I do get the problem with a recent(ish) svn, on OS X 10.5.1, python
2.5.1 (from python.org):
In [76]: A = array(['a','aa','b'])
In [77]: B = array(['d','e'])
In [78]: A.searchsorted(B)
Out[78]: array([3, 0])
In [79]: numpy.__version__
Out[79]: '1.0.5.dev4722'
2.5.1 (not apple one)
Numpy 1.0.5.dev4722
Robin
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ValueError: array must not contain infs or NaNs
--
Ran 713 tests in 0.697s
FAILED (errors=1)
Out[3]: unittest._TextTestResult run=713 errors=1 failures=0
Robin
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must not contain infs or NaNs
ValueError: array must not contain infs or NaNs
--
Ran 692 tests in 0.456s
FAILED (errors=1)
Out[2]: unittest._TextTestResult run=692 errors=1 failures=0
Thanks,
Robin
I can confirm the same behaviour with numpy '1.0.4.dev4271' on OS X
10.4with python
2.5.1 (installer from python.org).
For me the memory used by the python process grows at about 1MB/sec. The
memory isn't released when the loop is canceled.
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fine, but otherwise it
doesn't seem to work (even with --fcompiler=gnu95 etc)
Cheers
Robin
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(find([1;dtemp]));
indx = temp(dtemp0);
Pr(indx)= count ./ numel(data);% probability
Thanks
Robin
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.],
[ 160.],
[ 20.]])
In [157]: numpy.dot(x,y)
Out[157]: array([[ 64.]])
In [158]: sum(x*y.T)
Out[158]: 55924.0
Am I missing something?
Thanks,
Robin
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