"buffer not aligned on 8 byte boundary" errors when running numarray.testall.test()
Hi there all :) I am having trouble with my installation of numarray. :( I am a python newbie and a numarray extreme-newbie, so it could be that I don't yet have the first clue what I am doing. ;) Python 2.3.3 (#51, Feb 16 2004, 04:07:52) [MSC v.1200 32 bit (Intel)] on win32 numarray 1.0 The Python I am using is the one that comes with the "Enthought" version (www.enthought.com), a distro specifically designed to be useful for scientists, so it comes with numerical stuff and scipy and chaco and things like that preinstalled. I used the windows binary installer. However it came with Numeric and not numarray, so I installed numarray "by hand". This seemed to go ok, and it seems that there is no problem having both Numeric and numarray in the same installation, since they have (obviously) different names (still getting used to this whole modules and namespaces &c &c) At the bottom of this email I have pasted an example of what it was I was trying to do, and the error messages that the interpreter gave me - but before anyone bothers reading them in any detail, the essential error seems to be as follows: error: multiply_Float64_scalar_vector: buffer not aligned on 8 byte boundary. I have no idea what this means, but I do recall that when I ran the numarray.testall.test() procedure after first completing my installation a couple of days ago, it reported a *lot* of problems, many of which sounded quite similar to this. I hoped for the best and thought that perhaps I had "run the test wrong"(!) since numarray seemed to be working ok, and I had investigated many of the examples in chapters 3 and 4 of the user manual withour any obvious problems (chapter 3 = "high level overview" and chapter 4 = "array basics") I decided at the time to leave well enough alone until I actually came across odd or mysterious behaviour ...however that time has come all-too-soon... The procedure I am using to run the test is as described on page 11 of the excellent user's manual (release 0.8 at http://www.pfdubois.com/numpy/numarray.pdf): --------------------------------------------- Testing your Installation Once you have installed numarray, test it with: C:\numarray> python Python 2.2.2 (#18, Dec 30 2002, 02:26:03) [MSC 32 bit (Intel)] on win32 Type "copyright", "credits" or "license" for more information.
import numarray.testall as testall testall.test() numeric: (0, 1115) records: (0, 48) strings: (0, 166) objects: (0, 72) memmap: (0, 75) Each line in the above output indicates that 0 of X tests failed. X grows steadily with each release, so the numbers shown above may not be current.
Anyway, when I ran this, instead of the nice, comforting output above, I got about a million(!) errors and then a final count of 320 failures. This number is not always constant - I recall the first time I ran it it was 209. [I just ran it again and this time it was 324...it all has a rather disturbing air of semi-randomness...] So below is the (heavily snipped) output from the testall.test() run, and below that is the code where I first noticed a possibly similar error, and below *that* is the output of that code, with the highly suspicous error.... Any suggestions greatly appreciated! I can give you more info about the setup on my computer and so on if you need :) wendy langer ====================================================================== <output when I ran numarray.testall.test() > ==================================== IDLE 1.0.2 ==== No Subprocess ====
import numarray.testall as testall testall.test()
Failure in example: x+y from line #50 of first pass Exception raised: Traceback (most recent call last): File "C:\PYTHON23\lib\doctest.py", line 442, in _run_examples_inner compileflags, 1) in globs File "<string>", line 1, in ? File "C:\PYTHON23\Lib\site-packages\numarray\numarraycore.py", line 733, in __add__ return ufunc.add(self, operand) error: Int32asFloat64: buffer not aligned on 8 byte boundary. ***************************************************************** Failure in example: x[:] = 0.1 from line #72 of first pass Exception raised: Traceback (most recent call last): File "C:\PYTHON23\lib\doctest.py", line 442, in _run_examples_inner compileflags, 1) in globs File "<string>", line 1, in ? error: Float64asBool: buffer not aligned on 8 byte boundary. ***************************************************************** Failure in example: y from line #74 of first pass Expected: array([ 1., 1., 1., 1., 1., 1., 1., 1., 1., 1.]) Got: array([ 0., 0., 0., 0., 0., 0., 0., 0., 0., 0.]) ***************************************************************** Failure in example: x + z from line #141 of first pass Exception raised: Traceback (most recent call last): File "C:\PYTHON23\lib\doctest.py", line 442, in _run_examples_inner compileflags, 1) in globs File "<string>", line 1, in ? File "C:\PYTHON23\Lib\site-packages\numarray\numarraycore.py", line 733, in __add__ return ufunc.add(self, operand) error: Int32asFloat64: buffer not aligned on 8 byte boundary. ***************************************************************** <BIG SNIP!!!!!!!!!!!!> <snip a lot more errors> ***************************************************************** Failure in example: a2dma = average(a2dm, axis=1) from line #812 of numarray.ma.dtest Exception raised: Traceback (most recent call last): File "C:\PYTHON23\lib\doctest.py", line 442, in _run_examples_inner compileflags, 1) in globs File "<string>", line 1, in ? File "C:\PYTHON23\Lib\site-packages\numarray\ma\MA.py", line 1686, in average w = Numeric.choose(mask, (1.0, 0.0)) File "C:\PYTHON23\Lib\site-packages\numarray\ufunc.py", line 1666, in choose return _choose(selector, population, outarr, clipmode) File "C:\PYTHON23\Lib\site-packages\numarray\ufunc.py", line 1573, in __call__ result = self._doit(computation_mode, woutarr, cfunc, ufargs, 0) File "C:\PYTHON23\Lib\site-packages\numarray\ufunc.py", line 1558, in _doit blockingparameters) error: choose8bytes: buffer not aligned on 8 byte boundary. ***************************************************************** Failure in example: alltest(a2dma, [1.5, 4.0]) from line #813 of numarray.ma.dtest Exception raised: Traceback (most recent call last): File "C:\PYTHON23\lib\doctest.py", line 442, in _run_examples_inner compileflags, 1) in globs File "<string>", line 1, in ? NameError: name 'a2dma' is not defined ***************************************************************** 1 items had failures: 320 of 671 in numarray.ma.dtest ***Test Failed*** 320 failures. numarray.ma: (320, 671) </output when I ran numarray.testall.test() > ========================================================================= <my code> ======================== import numarray class anXmatrix: def __init__(self, stepsize = 3): self.stepsize = stepsize self.populate_matrix() def describe(self): print "I am a ", self.__class__ print "my stepsize is", self.stepsize print "my matrix is: \n" print self.matrix def populate_matrix(self): def xvalues(i,j): return self.stepsize*j mx = numarray.fromfunction(xvalues, (4,4)) self.matrix = mx if __name__ == '__main__': print " " print "Making anXmatrix..." r = anXmatrix(stepsize = 5) r.describe() r = anXmatrix(stepsize = 0.02) r.describe() </my code> ============================================================================ ======== <output from interpreter when I run my code> Making anXmatrix... I am a __main__.anXmatrix my stepsize is 5 my matrix is: [[ 0 5 10 15] [ 0 5 10 15] [ 0 5 10 15] [ 0 5 10 15]] Traceback (most recent call last): File "C:\Python23\Lib\site-packages\WendyStuff\wendycode\propagatorstuff\core_obj ects\domain_objects.py", line 97, in ? r = anXmatrix(stepsize = 0.02) File "C:\Python23\Lib\site-packages\WendyStuff\wendycode\propagatorstuff\core_obj ects\domain_objects.py", line 72, in __init__ self.populate_matrix() File "C:\Python23\Lib\site-packages\WendyStuff\wendycode\propagatorstuff\core_obj ects\domain_objects.py", line 86, in populate_matrix mx = numarray.fromfunction(xvalues, (4,4)) File "C:\PYTHON23\Lib\site-packages\numarray\generic.py", line 1094, in fromfunction return apply(function, tuple(indices(dimensions))) File "C:\Python23\Lib\site-packages\WendyStuff\wendycode\propagatorstuff\core_obj ects\domain_objects.py", line 84, in xvalues return self.stepsize*j File "C:\PYTHON23\Lib\site-packages\numarray\numarraycore.py", line 772, in __rmul__ r = ufunc.multiply(operand, self) error: multiply_Float64_scalar_vector: buffer not aligned on 8 byte boundary. ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ </output from interpreter when I run my code> ============================================================================ ======== "You see, wire telegraph is a kind of a very, very long cat. You pull his tail in New York and his head is meowing in Los Angeles. Do you understand this? And radio operates exactly the same way: you send signals here, they receive them there. The only difference is that there is no cat." Albert Einstein
On Thu, 2004-07-08 at 13:28, Wendy Langer wrote:
Hi there all :)
I am having trouble with my installation of numarray. :(
I am a python newbie and a numarray extreme-newbie, so it could be that I don't yet have the first clue what I am doing. ;)
Python 2.3.3 (#51, Feb 16 2004, 04:07:52) [MSC v.1200 32 bit (Intel)] on win32 numarray 1.0
The Python I am using is the one that comes with the "Enthought" version (www.enthought.com), a distro specifically designed to be useful for scientists, so it comes with numerical stuff and scipy and chaco and things like that preinstalled.
I used the windows binary installer. However it came with Numeric and not numarray, so I installed numarray "by hand". This seemed to go ok, and it seems that there is no problem having both Numeric and numarray in the same installation, since they have (obviously) different names (still getting used to this whole modules and namespaces &c &c)
I don't normally use SciPy, but I normally have both numarray and Numeric installed so there's no inherent conflict there.
At the bottom of this email I have pasted an example of what it was I was trying to do, and the error messages that the interpreter gave me - but before anyone bothers reading them in any detail, the essential error seems to be as follows:
error: multiply_Float64_scalar_vector: buffer not aligned on 8 byte boundary.
This is a low level exception triggered by a misaligned data buffer. It's low level so it's impossible to tell what the real problem is without more information.
I have no idea what this means, but I do recall that when I ran the numarray.testall.test() procedure after first completing my installation a couple of days ago, it reported a *lot* of problems, many of which sounded quite similar to this.
That sounds pretty bad. Here's roughly how it should look these days: % python
import numarray.testall as testall testall.test() numarray: ((0, 1165), (0, 1165)) numarray.records: (0, 48) numarray.strings: (0, 176) numarray.memmap: (0, 82) numarray.objects: (0, 105) numarray.memorytest: (0, 16) numarray.examples.convolve: ((0, 20), (0, 20), (0, 20), (0, 20)) numarray.convolve: (0, 52) numarray.fft: (0, 75) numarray.linear_algebra: ((0, 46), (0, 51)) numarray.image: (0, 27) numarray.nd_image: (0, 390) numarray.random_array: (0, 53) numarray.ma: (0, 671)
The tuple results for your test should all have leading zeros as above. The number of tests varies from release to release.
I hoped for the best and thought that perhaps I had "run the test wrong"(!) since numarray seemed to be working ok, and I had investigated many of the examples in chapters 3 and 4 of the user manual withour any obvious problems (chapter 3 = "high level overview" and chapter 4 = "array basics")
I decided at the time to leave well enough alone until I actually came across odd or mysterious behaviour ...however that time has come all-too-soon...
The procedure I am using to run the test is as described on page 11 of the excellent user's manual (release 0.8 at http://www.pfdubois.com/numpy/numarray.pdf):
There's an updated manual here: http://prdownloads.sourceforge.net/numpy/numarray-1.0.pdf?download
-- Testing your Installation Once you have installed numarray, test it with: C:\numarray> python Python 2.2.2 (#18, Dec 30 2002, 02:26:03) [MSC 32 bit (Intel)] on win32 Type "copyright", "credits" or "license" for more information.
import numarray.testall as testall testall.test() numeric: (0, 1115) records: (0, 48) strings: (0, 166) objects: (0, 72) memmap: (0, 75) Each line in the above output indicates that 0 of X tests failed. X grows steadily with each release, so the numbers shown above may not be current. --
Anyway, when I ran this, instead of the nice, comforting output above, I got about a million(!) errors and then a final count of 320 failures. This number is not always constant - I recall the first time I ran it it was 209. [I just ran it again and this time it was 324...it all has a rather disturbing air of semi-randomness...]
So below is the (heavily snipped) output from the testall.test() run, and below that is the code where I first noticed a possibly similar error, and below *that* is the output of that code, with the highly suspicous error....
Any suggestions greatly appreciated!
If you've ever had numarray installed before, go to your site-packages directory and delete numarray as well as any numarray.pth. Then reinstall numarray-1.0. Also, just do:
import numarray numarray
and see what kind of path is involved getting to the numarray module.
I can give you more info about the setup on my computer and so on if you need :)
I think you already included everything important; the exact variant of Windows you're using might be helpful; I'm not aware of any problems there though. It looks like you're on a well supported platform. I just tested pretty much the same configuration on Windows 2000 Pro, with Python-2.3.4, and it worked fine even with SciPy-0.3.
wendy langer
====================================================================== <output when I ran numarray.testall.test() >
<SNIP> There's something hugely wrong with your test output. I've never seen anything like it other than during development.
</output when I ran numarray.testall.test() >
========================================================================= <my code> ========================
import numarray
class anXmatrix: def __init__(self, stepsize = 3): self.stepsize = stepsize self.populate_matrix()
def describe(self): print "I am a ", self.__class__ print "my stepsize is", self.stepsize print "my matrix is: \n" print self.matrix
def populate_matrix(self):
def xvalues(i,j): return self.stepsize*j
mx = numarray.fromfunction(xvalues, (4,4)) self.matrix = mx
if __name__ == '__main__':
print " " print "Making anXmatrix..." r = anXmatrix(stepsize = 5) r.describe() r = anXmatrix(stepsize = 0.02) r.describe()
</my code>
============================================================================ Here's what I get when I run your code, windows or linux:
Making anXmatrix... I am a __main__.anXmatrix my stepsize is 5 my matrix is: [[ 0 5 10 15] [ 0 5 10 15] [ 0 5 10 15] [ 0 5 10 15]] I am a __main__.anXmatrix my stepsize is 0.02 my matrix is: [[ 0. 0.02 0.04 0.06] [ 0. 0.02 0.04 0.06] [ 0. 0.02 0.04 0.06] [ 0. 0.02 0.04 0.06]] Regards, Todd
participants (2)
-
Todd Miller -
Wendy Langer