ANN: NumPy 1.6.1 release candidate 2
Hi, I am pleased to announce the availability (only a little later than planned) of the second release candidate of NumPy 1.6.1. This is a bugfix release, list of fixed bugs: #1834 einsum fails for specific shapes #1837 einsum throws nan or freezes python for specific array shapes #1838 object <-> structured type arrays regression #1851 regression for SWIG based code in 1.6.0 #1863 Buggy results when operating on array copied with astype() #1870 Fix corner case of object array assignment #1843 Py3k: fix error with recarray #1885 nditer: Error in detecting double reduction loop #1874 f2py: fix --include_paths bug #1749 Fix ctypes.load_library() If no new problems are reported, the final release will be in one week. Sources and binaries can be found at https://sourceforge.net/projects/numpy/files/NumPy/1.6.1rc2/ Enjoy, Ralf
In article <BANLkTi=LXiTcrv1LgMtP=p9nF8eMr8=+hw@mail.gmail.com>, Ralf Gommers <ralf.gommers@googlemail.com> wrote:
https://sourceforge.net/projects/numpy/files/NumPy/1.6.1rc2/
Will there be a Mac binary for 32-bit pythons (one that is compatible with older versions of MacOS X)? At present I only see a 64-bit 10.6-only version. -- Russell
On Tue, Jul 5, 2011 at 11:41 PM, Russell E. Owen <rowen@uw.edu> wrote:
In article <BANLkTi=LXiTcrv1LgMtP=p9nF8eMr8=+hw@mail.gmail.com>, Ralf Gommers <ralf.gommers@googlemail.com> wrote:
https://sourceforge.net/projects/numpy/files/NumPy/1.6.1rc2/
Will there be a Mac binary for 32-bit pythons (one that is compatible with older versions of MacOS X)? At present I only see a 64-bit 10.6-only version.
Yes there will be for the final release (10.4-10.6 compatible). I can't create those on my own computer, so sometimes I don't make them for RCs.
Cheers, Ralf
In article <CABL7CQhNnjkzK9XNrLVDArSdKNwRM4eV0mXdUrJSaXq73EbwcQ@mail.gmail.com>, Ralf Gommers <ralf.gommers@googlemail.com> wrote:
On Tue, Jul 5, 2011 at 11:41 PM, Russell E. Owen <rowen@uw.edu> wrote:
In article <BANLkTi=LXiTcrv1LgMtP=p9nF8eMr8=+hw@mail.gmail.com>, Ralf Gommers <ralf.gommers@googlemail.com> wrote:
https://sourceforge.net/projects/numpy/files/NumPy/1.6.1rc2/
Will there be a Mac binary for 32-bit pythons (one that is compatible with older versions of MacOS X)? At present I only see a 64-bit 10.6-only version.
Yes there will be for the final release (10.4-10.6 compatible). I can't create those on my own computer, so sometimes I don't make them for RCs.
I'm glad they will be present for the final release. FYI: I built my own 1.6.1rc2 against Python 2.7.2 (the 32-bit Mac version from python.org). I reproduced a memory error that I've been trying to narrow down. This is ticket 1896: <http://projects.scipy.org/numpy/ticket/1896> and the problem is also in 1.6.0. -- Russell
On 7/6/2011 10:57 AM, Russell E. Owen wrote:
In article <CABL7CQhNnjkzK9XNrLVDArSdKNwRM4eV0mXdUrJSaXq73EbwcQ@mail.gmail.com>, Ralf Gommers<ralf.gommers@googlemail.com> wrote:
On Tue, Jul 5, 2011 at 11:41 PM, Russell E. Owen<rowen@uw.edu> wrote:
In article<BANLkTi=LXiTcrv1LgMtP=p9nF8eMr8=+hw@mail.gmail.com>, Ralf Gommers<ralf.gommers@googlemail.com> wrote:
https://sourceforge.net/projects/numpy/files/NumPy/1.6.1rc2/
Will there be a Mac binary for 32-bit pythons (one that is compatible with older versions of MacOS X)? At present I only see a 64-bit 10.6-only version.
Yes there will be for the final release (10.4-10.6 compatible). I can't create those on my own computer, so sometimes I don't make them for RCs.
I'm glad they will be present for the final release.
FYI: I built my own 1.6.1rc2 against Python 2.7.2 (the 32-bit Mac version from python.org). I reproduced a memory error that I've been trying to narrow down. This is ticket 1896: <http://projects.scipy.org/numpy/ticket/1896> and the problem is also in 1.6.0.
-- Russell
I can reproduce this error on Windows. It looks like a serious regression. Christoph
On Wed, Jul 6, 2011 at 1:56 PM, Christoph Gohlke <cgohlke@uci.edu> wrote:
On 7/6/2011 10:57 AM, Russell E. Owen wrote:
In article <CABL7CQhNnjkzK9XNrLVDArSdKNwRM4eV0mXdUrJSaXq73EbwcQ@mail.gmail.com>, Ralf Gommers<ralf.gommers@googlemail.com> wrote:
On Tue, Jul 5, 2011 at 11:41 PM, Russell E. Owen<rowen@uw.edu> wrote:
In article<BANLkTi=LXiTcrv1LgMtP=p9nF8eMr8=+hw@mail.gmail.com>, Ralf Gommers<ralf.gommers@googlemail.com> wrote:
https://sourceforge.net/projects/numpy/files/NumPy/1.6.1rc2/
Will there be a Mac binary for 32-bit pythons (one that is compatible with older versions of MacOS X)? At present I only see a 64-bit 10.6-only version.
Yes there will be for the final release (10.4-10.6 compatible). I can't create those on my own computer, so sometimes I don't make them for RCs.
I'm glad they will be present for the final release.
FYI: I built my own 1.6.1rc2 against Python 2.7.2 (the 32-bit Mac version from python.org). I reproduced a memory error that I've been trying to narrow down. This is ticket 1896: <http://projects.scipy.org/numpy/ticket/1896> and the problem is also in 1.6.0.
-- Russell
I can reproduce this error on Windows. It looks like a serious regression.
Christoph _______________________________________________ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
I do get this error in the code without tinker on the first loop. I did notice that the original array (dataArr) is float64 but the second array (scaledArr) is only float32. The problem is removed by changing the dtype of scaledArr to float64. Thus, it would appear some memory allocation related error to squeeze a float64 result into a memory allocated for a float32 array. Bruce
On Thu, Jul 7, 2011 at 9:56 AM, Bruce Southey <bsouthey@gmail.com> wrote:
On Wed, Jul 6, 2011 at 1:56 PM, Christoph Gohlke <cgohlke@uci.edu> wrote:
On 7/6/2011 10:57 AM, Russell E. Owen wrote:
In article <CABL7CQhNnjkzK9XNrLVDArSdKNwRM4eV0mXdUrJSaXq73EbwcQ@mail.gmail.com>, Ralf Gommers<ralf.gommers@googlemail.com> wrote:
On Tue, Jul 5, 2011 at 11:41 PM, Russell E. Owen<rowen@uw.edu> wrote:
In article<BANLkTi=LXiTcrv1LgMtP=p9nF8eMr8=+hw@mail.gmail.com>, Ralf Gommers<ralf.gommers@googlemail.com> wrote:
https://sourceforge.net/projects/numpy/files/NumPy/1.6.1rc2/
Will there be a Mac binary for 32-bit pythons (one that is compatible with older versions of MacOS X)? At present I only see a 64-bit 10.6-only version.
Yes there will be for the final release (10.4-10.6 compatible). I
can't
create those on my own computer, so sometimes I don't make them for RCs.
I'm glad they will be present for the final release.
FYI: I built my own 1.6.1rc2 against Python 2.7.2 (the 32-bit Mac version from python.org). I reproduced a memory error that I've been trying to narrow down. This is ticket 1896: <http://projects.scipy.org/numpy/ticket/1896> and the problem is also in 1.6.0.
-- Russell
I can reproduce this error on Windows. It looks like a serious regression.
Christoph _______________________________________________ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
I do get this error in the code without tinker on the first loop.
I did notice that the original array (dataArr) is float64 but the second array (scaledArr) is only float32. The problem is removed by changing the dtype of scaledArr to float64. Thus, it would appear some memory allocation related error to squeeze a float64 result into a memory allocated for a float32 array.
Can you try it on your platform with the pull request I've made which hopefully fixes it? Here's the link: https://github.com/numpy/numpy/pull/103 Thanks, Mark
Bruce _______________________________________________ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
On 07/07/2011 10:06 AM, Mark Wiebe wrote:
On Thu, Jul 7, 2011 at 9:56 AM, Bruce Southey <bsouthey@gmail.com <mailto:bsouthey@gmail.com>> wrote:
On Wed, Jul 6, 2011 at 1:56 PM, Christoph Gohlke <cgohlke@uci.edu <mailto:cgohlke@uci.edu>> wrote: > > > On 7/6/2011 10:57 AM, Russell E. Owen wrote: >> In article >> <CABL7CQhNnjkzK9XNrLVDArSdKNwRM4eV0mXdUrJSaXq73EbwcQ@mail.gmail.com <mailto:CABL7CQhNnjkzK9XNrLVDArSdKNwRM4eV0mXdUrJSaXq73EbwcQ@mail.gmail.com>>, >> Ralf Gommers<ralf.gommers@googlemail.com <mailto:ralf.gommers@googlemail.com>> wrote: >> >>> On Tue, Jul 5, 2011 at 11:41 PM, Russell E. Owen<rowen@uw.edu <mailto:rowen@uw.edu>> wrote: >>> >>>> In article<BANLkTi=LXiTcrv1LgMtP=p9nF8eMr8=+hw@mail.gmail.com <mailto:hw@mail.gmail.com>>, >>>> Ralf Gommers<ralf.gommers@googlemail.com <mailto:ralf.gommers@googlemail.com>> wrote: >>>> >>>>> https://sourceforge.net/projects/numpy/files/NumPy/1.6.1rc2/ >>>> >>>> Will there be a Mac binary for 32-bit pythons (one that is compatible >>>> with older versions of MacOS X)? At present I only see a 64-bit >>>> 10.6-only version. >>>> >>>> >>>> Yes there will be for the final release (10.4-10.6 compatible). I can't >>> create those on my own computer, so sometimes I don't make them for RCs. >> >> I'm glad they will be present for the final release. >> >> FYI: I built my own 1.6.1rc2 against Python 2.7.2 (the 32-bit Mac >> version from python.org <http://python.org>). I reproduced a memory error that I've been >> trying to narrow down. This is ticket 1896: >> <http://projects.scipy.org/numpy/ticket/1896> >> and the problem is also in 1.6.0. >> >> -- Russell >> > > > I can reproduce this error on Windows. It looks like a serious regression. > > Christoph > _______________________________________________ > NumPy-Discussion mailing list > NumPy-Discussion@scipy.org <mailto:NumPy-Discussion@scipy.org> > http://mail.scipy.org/mailman/listinfo/numpy-discussion > I do get this error in the code without tinker on the first loop.
I did notice that the original array (dataArr) is float64 but the second array (scaledArr) is only float32. The problem is removed by changing the dtype of scaledArr to float64. Thus, it would appear some memory allocation related error to squeeze a float64 result into a memory allocated for a float32 array.
Can you try it on your platform with the pull request I've made which hopefully fixes it? Here's the link:
https://github.com/numpy/numpy/pull/103
Thanks, Mark
I do not get the crash with Python2.7 on the users code. But I can not compile this branch under Python3.1 or Python3.2. The last error is below - I can look into this more if needed. Bruce creating build/temp.linux-x86_64-3.1/numpy/core/src/multiarray compile options: '-Inumpy/core/include -Ibuild/src.linux-x86_64-3.1/numpy/core/include/numpy -Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/src/npysort -Inumpy/core/include -I/usr/include/python3.1 -Ibuild/src.linux-x86_64-3.1/numpy/core/src/multiarray -Ibuild/src.linux-x86_64-3.1/numpy/core/src/umath -c' gcc: numpy/core/src/multiarray/multiarraymodule_onefile.c In file included from numpy/core/src/multiarray/multiarraymodule_onefile.c:17:0: numpy/core/src/multiarray/arraytypes.c.src: In function ‘VOID_getitem’: numpy/core/src/multiarray/arraytypes.c.src:631:94: error: ‘NPY_WRITEABLE’ undeclared (first use in this function) numpy/core/src/multiarray/arraytypes.c.src:631:94: note: each undeclared identifier is reported only once for each function it appears in numpy/core/src/multiarray/arraytypes.c.src:633:35: warning: assignment from incompatible pointer type In file included from numpy/core/src/multiarray/multiarraymodule_onefile.c:28:0: numpy/core/src/multiarray/getset.c: In function ‘array_data_get’: numpy/core/src/multiarray/getset.c:284:5: warning: passing argument 1 of ‘PyMemoryView_FromObject’ from incompatible pointer type /usr/include/python3.1/memoryobject.h:54:12: note: expected ‘struct PyObject *’ but argument is of type ‘struct PyArrayObject *’ numpy/core/src/multiarray/multiarraymodule_onefile.c: At top level: numpy/core/src/multiarray/scalartypes.c.src:2231:1: warning: ‘gentype_getsegcount’ defined but not used numpy/core/src/multiarray/scalartypes.c.src:2249:1: warning: ‘gentype_getcharbuf’ defined but not used numpy/core/src/multiarray/mapping.c:75:1: warning: ‘_array_ass_item’ defined but not used numpy/core/src/multiarray/number.c:266:1: warning: ‘array_divide’ defined but not used numpy/core/src/multiarray/number.c:464:1: warning: ‘array_inplace_divide’ defined but not used numpy/core/src/multiarray/buffer.c:25:1: warning: ‘array_getsegcount’ defined but not used numpy/core/src/multiarray/buffer.c:58:1: warning: ‘array_getwritebuf’ defined but not used numpy/core/src/multiarray/buffer.c:71:1: warning: ‘array_getcharbuf’ defined but not used In file included from numpy/core/src/multiarray/multiarraymodule_onefile.c:17:0: numpy/core/src/multiarray/arraytypes.c.src: In function âVOID_getitemâ: numpy/core/src/multiarray/arraytypes.c.src:631:94: error: âNPY_WRITEABLEâ undeclared (first use in this function) numpy/core/src/multiarray/arraytypes.c.src:631:94: note: each undeclared identifier is reported only once for each function it appears in numpy/core/src/multiarray/arraytypes.c.src:633:35: warning: assignment from incompatible pointer type In file included from numpy/core/src/multiarray/multiarraymodule_onefile.c:28:0: numpy/core/src/multiarray/getset.c: In function âarray_data_getâ: numpy/core/src/multiarray/getset.c:284:5: warning: passing argument 1 of âPyMemoryView_FromObjectâ from incompatible pointer type /usr/include/python3.1/memoryobject.h:54:12: note: expected âstruct PyObject *â but argument is of type âstruct PyArrayObject *â numpy/core/src/multiarray/multiarraymodule_onefile.c: At top level: numpy/core/src/multiarray/scalartypes.c.src:2231:1: warning: âgentype_getsegcountâ defined but not used numpy/core/src/multiarray/scalartypes.c.src:2249:1: warning: âgentype_getcharbufâ defined but not used numpy/core/src/multiarray/mapping.c:75:1: warning: â_array_ass_itemâ defined but not used numpy/core/src/multiarray/number.c:266:1: warning: âarray_divideâ defined but not used numpy/core/src/multiarray/number.c:464:1: warning: âarray_inplace_divideâ defined but not used numpy/core/src/multiarray/buffer.c:25:1: warning: âarray_getsegcountâ defined but not used numpy/core/src/multiarray/buffer.c:58:1: warning: âarray_getwritebufâ defined but not used numpy/core/src/multiarray/buffer.c:71:1: warning: âarray_getcharbufâ defined but not used error: Command "gcc -pthread -fno-strict-aliasing -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -Inumpy/core/include -Ibuild/src.linux-x86_64-3.1/numpy/core/include/numpy -Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/src/npysort -Inumpy/core/include -I/usr/include/python3.1 -Ibuild/src.linux-x86_64-3.1/numpy/core/src/multiarray -Ibuild/src.linux-x86_64-3.1/numpy/core/src/umath -c numpy/core/src/multiarray/multiarraymodule_onefile.c -o build/temp.linux-x86_64-3.1/numpy/core/src/multiarray/multiarraymodule_onefile.o" failed with exit status 1
On Thu, Jul 7, 2011 at 11:11 AM, Bruce Southey <bsouthey@gmail.com> wrote:
** On 07/07/2011 10:06 AM, Mark Wiebe wrote:
On Thu, Jul 7, 2011 at 9:56 AM, Bruce Southey <bsouthey@gmail.com> wrote:
On Wed, Jul 6, 2011 at 1:56 PM, Christoph Gohlke <cgohlke@uci.edu> wrote:
On 7/6/2011 10:57 AM, Russell E. Owen wrote:
In article <CABL7CQhNnjkzK9XNrLVDArSdKNwRM4eV0mXdUrJSaXq73EbwcQ@mail.gmail.com>, Ralf Gommers<ralf.gommers@googlemail.com> wrote:
On Tue, Jul 5, 2011 at 11:41 PM, Russell E. Owen<rowen@uw.edu>
wrote:
In article<BANLkTi=LXiTcrv1LgMtP=p9nF8eMr8=+hw@mail.gmail.com>, Ralf Gommers<ralf.gommers@googlemail.com> wrote:
> https://sourceforge.net/projects/numpy/files/NumPy/1.6.1rc2/
Will there be a Mac binary for 32-bit pythons (one that is compatible with older versions of MacOS X)? At present I only see a 64-bit 10.6-only version.
Yes there will be for the final release (10.4-10.6 compatible). I
can't
create those on my own computer, so sometimes I don't make them for RCs.
I'm glad they will be present for the final release.
FYI: I built my own 1.6.1rc2 against Python 2.7.2 (the 32-bit Mac version from python.org). I reproduced a memory error that I've been trying to narrow down. This is ticket 1896: <http://projects.scipy.org/numpy/ticket/1896> and the problem is also in 1.6.0.
-- Russell
I can reproduce this error on Windows. It looks like a serious regression.
Christoph _______________________________________________ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
I do get this error in the code without tinker on the first loop.
I did notice that the original array (dataArr) is float64 but the second array (scaledArr) is only float32. The problem is removed by changing the dtype of scaledArr to float64. Thus, it would appear some memory allocation related error to squeeze a float64 result into a memory allocated for a float32 array.
Can you try it on your platform with the pull request I've made which hopefully fixes it? Here's the link:
https://github.com/numpy/numpy/pull/103
Thanks, Mark
I do not get the crash with Python2.7 on the users code. But I can not compile this branch under Python3.1 or Python3.2. The last error is below - I can look into this more if needed.
I suspect you have gotten the missingdata branch by accident instead of the pull request's one. This is one thing I've found confusing/bad about github, is that the URL they provide always gives you the default branch. You need to switch to the crash1896 branch for the test. It does look like I missed something when cleaning up some NumPy API stuff, however. That build failure log is useful, thanks! -Mark
Bruce
creating build/temp.linux-x86_64-3.1/numpy/core/src/multiarray compile options: '-Inumpy/core/include -Ibuild/src.linux-x86_64-3.1/numpy/core/include/numpy -Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/src/npysort -Inumpy/core/include -I/usr/include/python3.1 -Ibuild/src.linux-x86_64-3.1/numpy/core/src/multiarray -Ibuild/src.linux-x86_64-3.1/numpy/core/src/umath -c' gcc: numpy/core/src/multiarray/multiarraymodule_onefile.c In file included from numpy/core/src/multiarray/multiarraymodule_onefile.c:17:0: numpy/core/src/multiarray/arraytypes.c.src: In function ‘VOID_getitem’: numpy/core/src/multiarray/arraytypes.c.src:631:94: error: ‘NPY_WRITEABLE’ undeclared (first use in this function) numpy/core/src/multiarray/arraytypes.c.src:631:94: note: each undeclared identifier is reported only once for each function it appears in numpy/core/src/multiarray/arraytypes.c.src:633:35: warning: assignment from incompatible pointer type In file included from numpy/core/src/multiarray/multiarraymodule_onefile.c:28:0: numpy/core/src/multiarray/getset.c: In function ‘array_data_get’: numpy/core/src/multiarray/getset.c:284:5: warning: passing argument 1 of ‘PyMemoryView_FromObject’ from incompatible pointer type /usr/include/python3.1/memoryobject.h:54:12: note: expected ‘struct PyObject *’ but argument is of type ‘struct PyArrayObject *’ numpy/core/src/multiarray/multiarraymodule_onefile.c: At top level: numpy/core/src/multiarray/scalartypes.c.src:2231:1: warning: ‘gentype_getsegcount’ defined but not used numpy/core/src/multiarray/scalartypes.c.src:2249:1: warning: ‘gentype_getcharbuf’ defined but not used numpy/core/src/multiarray/mapping.c:75:1: warning: ‘_array_ass_item’ defined but not used numpy/core/src/multiarray/number.c:266:1: warning: ‘array_divide’ defined but not used numpy/core/src/multiarray/number.c:464:1: warning: ‘array_inplace_divide’ defined but not used numpy/core/src/multiarray/buffer.c:25:1: warning: ‘array_getsegcount’ defined but not used numpy/core/src/multiarray/buffer.c:58:1: warning: ‘array_getwritebuf’ defined but not used numpy/core/src/multiarray/buffer.c:71:1: warning: ‘array_getcharbuf’ defined but not used In file included from numpy/core/src/multiarray/multiarraymodule_onefile.c:17:0: numpy/core/src/multiarray/arraytypes.c.src: In function âVOID_getitemâ: numpy/core/src/multiarray/arraytypes.c.src:631:94: error: âNPY_WRITEABLEâ undeclared (first use in this function) numpy/core/src/multiarray/arraytypes.c.src:631:94: note: each undeclared identifier is reported only once for each function it appears in numpy/core/src/multiarray/arraytypes.c.src:633:35: warning: assignment from incompatible pointer type In file included from numpy/core/src/multiarray/multiarraymodule_onefile.c:28:0: numpy/core/src/multiarray/getset.c: In function âarray_data_getâ: numpy/core/src/multiarray/getset.c:284:5: warning: passing argument 1 of âPyMemoryView_FromObjectâ from incompatible pointer type /usr/include/python3.1/memoryobject.h:54:12: note: expected âstruct PyObject *â but argument is of type âstruct PyArrayObject *â numpy/core/src/multiarray/multiarraymodule_onefile.c: At top level: numpy/core/src/multiarray/scalartypes.c.src:2231:1: warning: âgentype_getsegcountâ defined but not used numpy/core/src/multiarray/scalartypes.c.src:2249:1: warning: âgentype_getcharbufâ defined but not used numpy/core/src/multiarray/mapping.c:75:1: warning: â_array_ass_itemâ defined but not used numpy/core/src/multiarray/number.c:266:1: warning: âarray_divideâ defined but not used numpy/core/src/multiarray/number.c:464:1: warning: âarray_inplace_divideâ defined but not used numpy/core/src/multiarray/buffer.c:25:1: warning: âarray_getsegcountâ defined but not used numpy/core/src/multiarray/buffer.c:58:1: warning: âarray_getwritebufâ defined but not used numpy/core/src/multiarray/buffer.c:71:1: warning: âarray_getcharbufâ defined but not used error: Command "gcc -pthread -fno-strict-aliasing -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -Inumpy/core/include -Ibuild/src.linux-x86_64-3.1/numpy/core/include/numpy -Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/src/npysort -Inumpy/core/include -I/usr/include/python3.1 -Ibuild/src.linux-x86_64-3.1/numpy/core/src/multiarray -Ibuild/src.linux-x86_64-3.1/numpy/core/src/umath -c numpy/core/src/multiarray/multiarraymodule_onefile.c -o build/temp.linux-x86_64-3.1/numpy/core/src/multiarray/multiarraymodule_onefile.o" failed with exit status 1
_______________________________________________ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
On 07/07/2011 11:18 AM, Mark Wiebe wrote:
On Thu, Jul 7, 2011 at 11:11 AM, Bruce Southey <bsouthey@gmail.com <mailto:bsouthey@gmail.com>> wrote:
On 07/07/2011 10:06 AM, Mark Wiebe wrote:
On Thu, Jul 7, 2011 at 9:56 AM, Bruce Southey <bsouthey@gmail.com <mailto:bsouthey@gmail.com>> wrote:
On Wed, Jul 6, 2011 at 1:56 PM, Christoph Gohlke <cgohlke@uci.edu <mailto:cgohlke@uci.edu>> wrote: > > > On 7/6/2011 10:57 AM, Russell E. Owen wrote: >> In article >> <CABL7CQhNnjkzK9XNrLVDArSdKNwRM4eV0mXdUrJSaXq73EbwcQ@mail.gmail.com <mailto:CABL7CQhNnjkzK9XNrLVDArSdKNwRM4eV0mXdUrJSaXq73EbwcQ@mail.gmail.com>>, >> Ralf Gommers<ralf.gommers@googlemail.com <mailto:ralf.gommers@googlemail.com>> wrote: >> >>> On Tue, Jul 5, 2011 at 11:41 PM, Russell E. Owen<rowen@uw.edu <mailto:rowen@uw.edu>> wrote: >>> >>>> In article<BANLkTi=LXiTcrv1LgMtP=p9nF8eMr8=+hw@mail.gmail.com <mailto:hw@mail.gmail.com>>, >>>> Ralf Gommers<ralf.gommers@googlemail.com <mailto:ralf.gommers@googlemail.com>> wrote: >>>> >>>>> https://sourceforge.net/projects/numpy/files/NumPy/1.6.1rc2/ >>>> >>>> Will there be a Mac binary for 32-bit pythons (one that is compatible >>>> with older versions of MacOS X)? At present I only see a 64-bit >>>> 10.6-only version. >>>> >>>> >>>> Yes there will be for the final release (10.4-10.6 compatible). I can't >>> create those on my own computer, so sometimes I don't make them for RCs. >> >> I'm glad they will be present for the final release. >> >> FYI: I built my own 1.6.1rc2 against Python 2.7.2 (the 32-bit Mac >> version from python.org <http://python.org>). I reproduced a memory error that I've been >> trying to narrow down. This is ticket 1896: >> <http://projects.scipy.org/numpy/ticket/1896> >> and the problem is also in 1.6.0. >> >> -- Russell >> > > > I can reproduce this error on Windows. It looks like a serious regression. > > Christoph > _______________________________________________ > NumPy-Discussion mailing list > NumPy-Discussion@scipy.org <mailto:NumPy-Discussion@scipy.org> > http://mail.scipy.org/mailman/listinfo/numpy-discussion > I do get this error in the code without tinker on the first loop.
I did notice that the original array (dataArr) is float64 but the second array (scaledArr) is only float32. The problem is removed by changing the dtype of scaledArr to float64. Thus, it would appear some memory allocation related error to squeeze a float64 result into a memory allocated for a float32 array.
Can you try it on your platform with the pull request I've made which hopefully fixes it? Here's the link:
https://github.com/numpy/numpy/pull/103
Thanks, Mark
I do not get the crash with Python2.7 on the users code. But I can not compile this branch under Python3.1 or Python3.2. The last error is below - I can look into this more if needed.
I suspect you have gotten the missingdata branch by accident instead of the pull request's one. This is one thing I've found confusing/bad about github, is that the URL they provide always gives you the default branch. You need to switch to the crash1896 branch for the test.
It does look like I missed something when cleaning up some NumPy API stuff, however. That build failure log is useful, thanks!
-Mark
Yes, your are correct as I just check if the fix was present rather than ensuring I got the correct branch. So the correct branch fixes the Python3.x build issue. Bruce
On 07/01/2011 04:46 PM, Ralf Gommers wrote:
Hi,
I am pleased to announce the availability (only a little later than planned) of the second release candidate of NumPy 1.6.1. This is a bugfix release, list of fixed bugs: #1834 einsum fails for specific shapes #1837 einsum throws nan or freezes python for specific array shapes #1838 object <-> structured type arrays regression #1851 regression for SWIG based code in 1.6.0 #1863 Buggy results when operating on array copied with astype() #1870 Fix corner case of object array assignment #1843 Py3k: fix error with recarray #1885 nditer: Error in detecting double reduction loop #1874 f2py: fix --include_paths bug #1749 Fix ctypes.load_library()
If no new problems are reported, the final release will be in one week. Sources and binaries can be found at https://sourceforge.net/projects/numpy/files/NumPy/1.6.1rc2/
Enjoy, Ralf
_______________________________________________ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion I finally got around to testing these: I have no errors for my Windows 7 32-bit installs of Python 2.6, 2.7, 3.1 and 3.2 I have no errors for my Linux Fedora 14 64-bit system with Python2.4, Python2.5, Python2.6, Python2.7 and Python3.1
With Linux Fedora 14 64-bit system with Python3.2 provides two warnings that are due to the test but not numpy (ticket 1385 http://projects.scipy.org/scipy/ticket/1385): test_mmap (test_io.TestSaveLoad) ... /usr/local/lib/python3.2/site-packages/numpy/lib/format.py:575: ResourceWarning: unclosed file <_io.BufferedReader name='/tmp/tmpk9cum0'> mode=mode, offset=offset) ok test_lapack (test_build.TestF77Mismatch) ... /usr/local/lib/python3.2/subprocess.py:460: ResourceWarning: unclosed file <_io.BufferedReader name=3> return Popen(*popenargs, **kwargs).wait() /usr/local/lib/python3.2/subprocess.py:460: ResourceWarning: unclosed file <_io.BufferedReader name=8> return Popen(*popenargs, **kwargs).wait() ok With the special debug version of Python2.7, I still get the unicode related error of ticket 1578 http://projects.scipy.org/numpy/ticket/1578 Bruce
My system is Mac OSX 10.6.8, python.org 2.7.1. When I run numpy.test(), I see the following warning:
import numpy as np np.test() Running unit tests for numpy NumPy version 1.6.1rc2 NumPy is installed in /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy Python version 2.7.1 (r271:86882M, Nov 30 2010, 09:39:13) [GCC 4.0.1 (Apple Inc. build 5494)] nose version 0.11.3 .............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................../Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/numeric.py:1922: RuntimeWarning: invalid value encountered in absolute return all(less_equal(absolute(x-y), atol + rtol * absolute(y)))
Everything else completes with 3 KNOWNFAILs and 1 SKIP. This warning is not new to this release; I've seen it before but haven't tried tracking it down until today. It arises in allclose(). The comments state "If either array contains NaN, then False is returned." but no test for NaN is done, and NaNs are indeed what cause the warning. Inserting if any(isnan(x)) or any(isnan(y)): return False before current line number 1916 in numeric.py seems to fix it. Thanks to all for the great work. Numpy has saved me a lot of grief. Bob Pyle Cambridge, MA
On 07.07.2011, at 7:16PM, Robert Pyle wrote:
.............../Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/numeric.py:1922: RuntimeWarning: invalid value encountered in absolute return all(less_equal(absolute(x-y), atol + rtol * absolute(y)))
Everything else completes with 3 KNOWNFAILs and 1 SKIP. This warning is not new to this release; I've seen it before but haven't tried tracking it down until today.
It arises in allclose(). The comments state "If either array contains NaN, then False is returned." but no test for NaN is done, and NaNs are indeed what cause the warning.
Inserting
if any(isnan(x)) or any(isnan(y)): return False
before current line number 1916 in numeric.py seems to fix it.
The same warning is still present in the current master, I just never paid attention to it because the tests still pass (it does correctly identify NaNs because they are not less_equal the tolerance), but of course this should be properly fixed as you suggest. Cheers, Derek
On Fri, Jul 8, 2011 at 4:17 PM, Derek Homeier < derek@astro.physik.uni-goettingen.de> wrote:
On 07.07.2011, at 7:16PM, Robert Pyle wrote:
.............../Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/numeric.py:1922: RuntimeWarning: invalid value encountered in absolute
return all(less_equal(absolute(x-y), atol + rtol * absolute(y)))
Everything else completes with 3 KNOWNFAILs and 1 SKIP. This warning is not new to this release; I've seen it before but haven't tried tracking it down until today.
It arises in allclose(). The comments state "If either array contains NaN, then False is returned." but no test for NaN is done, and NaNs are indeed what cause the warning.
Inserting
if any(isnan(x)) or any(isnan(y)): return False
before current line number 1916 in numeric.py seems to fix it.
The same warning is still present in the current master, I just never paid attention to it because the tests still pass (it does correctly identify NaNs because they are not less_equal the tolerance), but of course this should be properly fixed as you suggest.
Under Python 2.6 I used to see this but it has disappeared. What's going on here?
$ python2.7
from numpy import * absolute(nan) __main__:1: RuntimeWarning: invalid value encountered in absolute nan
$ python2.6
from numpy import * absolute(nan) nan
Ralf
On 07/15/2011 03:13 AM, Ralf Gommers wrote:
On Fri, Jul 8, 2011 at 4:17 PM, Derek Homeier <derek@astro.physik.uni-goettingen.de <mailto:derek@astro.physik.uni-goettingen.de>> wrote:
On 07.07.2011, at 7:16PM, Robert Pyle wrote:
> .............../Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/numeric.py:1922: RuntimeWarning: invalid value encountered in absolute > return all(less_equal(absolute(x-y), atol + rtol * absolute(y))) > > > Everything else completes with 3 KNOWNFAILs and 1 SKIP. This warning is not new to this release; I've seen it before but haven't tried tracking it down until today. > > It arises in allclose(). The comments state "If either array contains NaN, then False is returned." but no test for NaN is done, and NaNs are indeed what cause the warning. > > Inserting > > if any(isnan(x)) or any(isnan(y)): > return False > > before current line number 1916 in numeric.py seems to fix it.
The same warning is still present in the current master, I just never paid attention to it because the tests still pass (it does correctly identify NaNs because they are not less_equal the tolerance), but of course this should be properly fixed as you suggest.
Under Python 2.6 I used to see this but it has disappeared. What's going on here?
$ python2.7
from numpy import * absolute(nan) __main__:1: RuntimeWarning: invalid value encountered in absolute nan
$ python2.6
from numpy import * absolute(nan) nan
Ralf
I do not see this with 64-bit Python2.7 on my Linux system. So perhaps Mac specific? By the way, all tests pass with Python 2.7 and 3.2 for rc3. Bruce $ python Python 2.7 (r27:82500, Sep 16 2010, 18:02:00) [GCC 4.5.1 20100907 (Red Hat 4.5.1-3)] on linux2 Type "help", "copyright", "credits" or "license" for more information.
import numpy as np np.__version__ '1.6.1rc3' np.absolute(np.nan) nan
$ python Python 2.7 (r27:82500, Sep 16 2010, 18:02:00) [GCC 4.5.1 20100907 (Red Hat 4.5.1-3)] on linux2 Type "help", "copyright", "credits" or "license" for more information.
from numpy import * absolute(nan) nan
participants (7)
-
Bruce Southey -
Christoph Gohlke -
Derek Homeier -
Mark Wiebe -
Ralf Gommers -
Robert Pyle -
Russell E. Owen