From ralf.gommers at gmail.com  Thu Nov  1 01:46:26 2012
From: ralf.gommers at gmail.com (Ralf Gommers)
Date: Thu, 1 Nov 2012 06:46:26 +0100
Subject: [SciPy-Dev] scipy.test() segfault
In-Reply-To: <CAE7vhgPm1L9MiPQLJ5x1E3znQ8Si0e4ru6N0pcdw4r7mYErtpw@mail.gmail.com>
References: <CAE7vhgPm1L9MiPQLJ5x1E3znQ8Si0e4ru6N0pcdw4r7mYErtpw@mail.gmail.com>
Message-ID: <CABL7CQgD9amaJ1axmnBS9sO4dsNQk9XxYXHdTRg3pveiAunDbg@mail.gmail.com>

Some context would be nice. How did you build (compilers, platform) and how
do you make it crash? sigtoolsmodule.c hasn't been touched recently, so
does it crash with 0.11.0 too?


On Wed, Oct 31, 2012 at 8:03 PM, Nils Wagner <nils106 at googlemail.com> wrote:

> Program received signal SIGSEGV, Segmentation fault.
> 0x00007ffff7ab2b26 in PyObject_RichCompare () from
> /usr/lib64/libpython2.7.so.1.0
> (gdb) bt
> #0  0x00007ffff7ab2b26 in PyObject_RichCompare () from
> /usr/lib64/libpython2.7.so.1.0
> #1  0x00007ffff7ab2def in PyObject_RichCompareBool () from
> /usr/lib64/libpython2.7.so.1.0
> #2  0x00007fffe3ba8584 in OBJECT_compare (ip1=<optimized out>,
> ip2=<optimized out>) at scipy/signal/sigtoolsmodule.c:827
> #3  0x00007ffff74b8b64 in msort_with_tmp.part.0 () from /lib64/libc.so.6
> #4  0x00007ffff74b8e9b in qsort_r () from /lib64/libc.so.6
> #5  0x00007fffe3ba90d6 in PyArray_OrderFilterND (op1=<optimized out>,
> op2=<optimized out>, order=54989472)
>     at scipy/signal/sigtoolsmodule.c:969
> #6  0x00007fffe3ba92a7 in sigtools_order_filterND
> (__NPY_UNUSED_TAGGEDdummy=<optimized out>, args=<optimized out>)
>     at scipy/signal/sigtoolsmodule.c:1135
> #7  0x00007ffff7affcaa in PyEval_EvalFrameEx () from
> /usr/lib64/libpython2.7.so.1.0
> #8  0x00007ffff7b059c3 in PyEval_EvalCodeEx () from
> /usr/lib64/libpython2.7.so.1.0
> #9  0x00007ffff7aff7ce in PyEval_EvalFrameEx () from
> /usr/lib64/libpython2.7.so.1.0
> #10 0x00007ffff7b0204f in PyEval_EvalFrameEx () from
> /usr/lib64/libpython2.7.so.1.0
> #11 0x00007ffff7b05727 in PyEval_EvalCodeEx () from
> /usr/lib64/libpython2.7.so.1.0
> #12 0x00007ffff7a9ddc8 in ?? () from /usr/lib64/libpython2.7.so.1.0
> #13 0x00007ffff7a7d464 in PyObject_Call () from
> /usr/lib64/libpython2.7.so.1.0
> #14 0x00007ffff7b00cae in PyEval_EvalFrameEx () from
> /usr/lib64/libpython2.7.so.1.0
> #15 0x00007ffff7b05727 in PyEval_EvalCodeEx () from
> /usr/lib64/libpython2.7.so.1.0
> #16 0x00007ffff7a9dba1 in ?? () from /usr/lib64/libpython2.7.so.1.0
> #17 0x00007ffff7a7d464 in PyObject_Call () from
> /usr/lib64/libpython2.7.so.1.0
> #18 0x00007ffff7a87c8e in ?? () from /usr/lib64/libpython2.7.so.1.0
> #19 0x00007ffff7a7d464 in PyObject_Call () from
> /usr/lib64/libpython2.7.so.1.0
> #20 0x00007ffff7acb84a in ?? () from /usr/lib64/libpython2.7.so.1.0
> #21 0x00007ffff7a7d464 in PyObject_Call () from
> /usr/lib64/libpython2.7.so.1.0
> #22 0x00007ffff7affe75 in PyEval_EvalFrameEx () from
> /usr/lib64/libpython2.7.so.1.0
> #23 0x00007ffff7b0204f in PyEval_EvalFrameEx () from
> /usr/lib64/libpython2.7.so.1.0
> #24 0x00007ffff7b05727 in PyEval_EvalCodeEx () from
> /usr/lib64/libpython2.7.so.1.0
> #25 0x00007ffff7a9ddc8 in ?? () from /usr/lib64/libpython2.7.so.1.0
> #26 0x00007ffff7a7d464 in PyObject_Call () from
> /usr/lib64/libpython2.7.so.1.0
> #27 0x00007ffff7b00cae in PyEval_EvalFrameEx () from
> /usr/lib64/libpython2.7.so.1.0
> #28 0x00007ffff7b05727 in PyEval_EvalCodeEx () from
> /usr/lib64/libpython2.7.so.1.0
> #29 0x00007ffff7a9dba1 in ?? () from /usr/lib64/libpython2.7.so.1.0
> #30 0x00007ffff7a7d464 in PyObject_Call () from
> /usr/lib64/libpython2.7.so.1.0
> #31 0x00007ffff7a87c8e in ?? () from /usr/lib64/libpython2.7.so.1.0
> #32 0x00007ffff7a7d464 in PyObject_Call () from
> /usr/lib64/libpython2.7.so.1.0
> #33 0x00007ffff7acb84a in ?? () from /usr/lib64/libpython2.7.so.1.0
> #34 0x00007ffff7a7d464 in PyObject_Call () from
> /usr/lib64/libpython2.7.so.1.0
> #35 0x00007ffff7affe75 in PyEval_EvalFrameEx () from
> /usr/lib64/libpython2.7.so.1.0
> #36 0x00007ffff7b05727 in PyEval_EvalCodeEx () from
> /usr/lib64/libpython2.7.so.1.0
>
> >> scipy.__version__
> '0.12.0.dev-bb436fa'
> x86_64 GNU/Linux
>
>
> _______________________________________________
> SciPy-Dev mailing list
> SciPy-Dev at scipy.org
> http://mail.scipy.org/mailman/listinfo/scipy-dev
>
>
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From nils106 at googlemail.com  Fri Nov  2 14:14:36 2012
From: nils106 at googlemail.com (Nils Wagner)
Date: Fri, 2 Nov 2012 18:14:36 +0000
Subject: [SciPy-Dev] scipy.test() segfault
In-Reply-To: <CABL7CQgD9amaJ1axmnBS9sO4dsNQk9XxYXHdTRg3pveiAunDbg@mail.gmail.com>
References: <CAE7vhgPm1L9MiPQLJ5x1E3znQ8Si0e4ru6N0pcdw4r7mYErtpw@mail.gmail.com>
	<CABL7CQgD9amaJ1axmnBS9sO4dsNQk9XxYXHdTRg3pveiAunDbg@mail.gmail.com>
Message-ID: <CAE7vhgOR_A+3tEd-Dn9tsydbhBH_2HcXw6RsSuG__9XSZwE5_g@mail.gmail.com>

AFAIK the segfault was introduced recently.
gcc (SUSE Linux) 4.6.2
GNU Fortran (SUSE Linux) 4.6.2
x86_64 GNU/Linux
Python 2.7.2 (default, Aug 19 2011, 20:41:43) [GCC] on linux2


>>>import scipy
>>> scipy.__version__
'0.12.0.dev-bb436fa'
>>>scipy.test(verbose=10)
...
test_rank3 (test_signaltools.TestLinearFilterObject) ... ok
test_basic (test_signaltools.TestMedFilt) ... ok
Ticket #1124. Ensure this does not segfault. ... Segmentation fault

Nils
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From ralf.gommers at gmail.com  Sat Nov  3 12:53:41 2012
From: ralf.gommers at gmail.com (Ralf Gommers)
Date: Sat, 3 Nov 2012 17:53:41 +0100
Subject: [SciPy-Dev] scipy.test() segfault
In-Reply-To: <CAE7vhgOR_A+3tEd-Dn9tsydbhBH_2HcXw6RsSuG__9XSZwE5_g@mail.gmail.com>
References: <CAE7vhgPm1L9MiPQLJ5x1E3znQ8Si0e4ru6N0pcdw4r7mYErtpw@mail.gmail.com>
	<CABL7CQgD9amaJ1axmnBS9sO4dsNQk9XxYXHdTRg3pveiAunDbg@mail.gmail.com>
	<CAE7vhgOR_A+3tEd-Dn9tsydbhBH_2HcXw6RsSuG__9XSZwE5_g@mail.gmail.com>
Message-ID: <CABL7CQjU5uBdTshmVkAGpnQvTbejrPBWvCppfvO5JNhFgaanyg@mail.gmail.com>

On Fri, Nov 2, 2012 at 7:14 PM, Nils Wagner <nils106 at googlemail.com> wrote:

> AFAIK the segfault was introduced recently.
> gcc (SUSE Linux) 4.6.2
> GNU Fortran (SUSE Linux) 4.6.2
> x86_64 GNU/Linux
> Python 2.7.2 (default, Aug 19 2011, 20:41:43) [GCC] on linux2
>
>
> >>>import scipy
> >>> scipy.__version__
> '0.12.0.dev-bb436fa'
> >>>scipy.test(verbose=10)
> ...
> test_rank3 (test_signaltools.TestLinearFilterObject) ... ok
> test_basic (test_signaltools.TestMedFilt) ... ok
> Ticket #1124. Ensure this does not segfault. ... Segmentation fault


Are you running numpy master? If so, does this segfault with an older
released version of numpy too? The relevant code in sigtoolsmodule.c hasn't
been touched in a long time.

Ralf
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From nils106 at googlemail.com  Sat Nov  3 13:51:04 2012
From: nils106 at googlemail.com (Nils Wagner)
Date: Sat, 3 Nov 2012 17:51:04 +0000
Subject: [SciPy-Dev] scipy.test() segfault
In-Reply-To: <CABL7CQjU5uBdTshmVkAGpnQvTbejrPBWvCppfvO5JNhFgaanyg@mail.gmail.com>
References: <CAE7vhgPm1L9MiPQLJ5x1E3znQ8Si0e4ru6N0pcdw4r7mYErtpw@mail.gmail.com>
	<CABL7CQgD9amaJ1axmnBS9sO4dsNQk9XxYXHdTRg3pveiAunDbg@mail.gmail.com>
	<CAE7vhgOR_A+3tEd-Dn9tsydbhBH_2HcXw6RsSuG__9XSZwE5_g@mail.gmail.com>
	<CABL7CQjU5uBdTshmVkAGpnQvTbejrPBWvCppfvO5JNhFgaanyg@mail.gmail.com>
Message-ID: <CAE7vhgMMqNdskKUOMjby+fUMKJGGG-Q4B4_RY4x6RZwuFdqCuA@mail.gmail.com>

I am using NumPy version 1.8.0.dev-526b764

Nils


On Sat, Nov 3, 2012 at 4:53 PM, Ralf Gommers <ralf.gommers at gmail.com> wrote:

>
>
>
> On Fri, Nov 2, 2012 at 7:14 PM, Nils Wagner <nils106 at googlemail.com>wrote:
>
>> AFAIK the segfault was introduced recently.
>> gcc (SUSE Linux) 4.6.2
>> GNU Fortran (SUSE Linux) 4.6.2
>> x86_64 GNU/Linux
>> Python 2.7.2 (default, Aug 19 2011, 20:41:43) [GCC] on linux2
>>
>>
>> >>>import scipy
>> >>> scipy.__version__
>> '0.12.0.dev-bb436fa'
>> >>>scipy.test(verbose=10)
>> ...
>> test_rank3 (test_signaltools.TestLinearFilterObject) ... ok
>> test_basic (test_signaltools.TestMedFilt) ... ok
>> Ticket #1124. Ensure this does not segfault. ... Segmentation fault
>
>
> Are you running numpy master? If so, does this segfault with an older
> released version of numpy too? The relevant code in sigtoolsmodule.c hasn't
> been touched in a long time.
>
> Ralf
>
>
> _______________________________________________
> SciPy-Dev mailing list
> SciPy-Dev at scipy.org
> http://mail.scipy.org/mailman/listinfo/scipy-dev
>
>
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From ralf.gommers at gmail.com  Sat Nov  3 16:11:05 2012
From: ralf.gommers at gmail.com (Ralf Gommers)
Date: Sat, 3 Nov 2012 21:11:05 +0100
Subject: [SciPy-Dev] scipy.test() segfault
In-Reply-To: <CAE7vhgMMqNdskKUOMjby+fUMKJGGG-Q4B4_RY4x6RZwuFdqCuA@mail.gmail.com>
References: <CAE7vhgPm1L9MiPQLJ5x1E3znQ8Si0e4ru6N0pcdw4r7mYErtpw@mail.gmail.com>
	<CABL7CQgD9amaJ1axmnBS9sO4dsNQk9XxYXHdTRg3pveiAunDbg@mail.gmail.com>
	<CAE7vhgOR_A+3tEd-Dn9tsydbhBH_2HcXw6RsSuG__9XSZwE5_g@mail.gmail.com>
	<CABL7CQjU5uBdTshmVkAGpnQvTbejrPBWvCppfvO5JNhFgaanyg@mail.gmail.com>
	<CAE7vhgMMqNdskKUOMjby+fUMKJGGG-Q4B4_RY4x6RZwuFdqCuA@mail.gmail.com>
Message-ID: <CABL7CQj-Q0xhr=tPyJ5f57VcF8AqN_hpN=YS63yQZFZQiw2xsQ@mail.gmail.com>

On Sat, Nov 3, 2012 at 6:51 PM, Nils Wagner <nils106 at googlemail.com> wrote:

> I am using NumPy version 1.8.0.dev-526b764
>

So can you try with 1.6.2?

Ralf



> Nils
>
>
> On Sat, Nov 3, 2012 at 4:53 PM, Ralf Gommers <ralf.gommers at gmail.com>wrote:
>
>>
>>
>>
>> On Fri, Nov 2, 2012 at 7:14 PM, Nils Wagner <nils106 at googlemail.com>wrote:
>>
>>> AFAIK the segfault was introduced recently.
>>> gcc (SUSE Linux) 4.6.2
>>> GNU Fortran (SUSE Linux) 4.6.2
>>> x86_64 GNU/Linux
>>> Python 2.7.2 (default, Aug 19 2011, 20:41:43) [GCC] on linux2
>>>
>>>
>>> >>>import scipy
>>> >>> scipy.__version__
>>> '0.12.0.dev-bb436fa'
>>> >>>scipy.test(verbose=10)
>>> ...
>>> test_rank3 (test_signaltools.TestLinearFilterObject) ... ok
>>> test_basic (test_signaltools.TestMedFilt) ... ok
>>> Ticket #1124. Ensure this does not segfault. ... Segmentation fault
>>
>>
>> Are you running numpy master? If so, does this segfault with an older
>> released version of numpy too? The relevant code in sigtoolsmodule.c hasn't
>> been touched in a long time.
>>
>> Ralf
>>
>>
>> _______________________________________________
>> SciPy-Dev mailing list
>> SciPy-Dev at scipy.org
>> http://mail.scipy.org/mailman/listinfo/scipy-dev
>>
>>
>
> _______________________________________________
> SciPy-Dev mailing list
> SciPy-Dev at scipy.org
> http://mail.scipy.org/mailman/listinfo/scipy-dev
>
>
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From pav at iki.fi  Sat Nov  3 16:35:44 2012
From: pav at iki.fi (Pauli Virtanen)
Date: Sat, 03 Nov 2012 22:35:44 +0200
Subject: [SciPy-Dev] scipy.test() segfault
In-Reply-To: <CAE7vhgOR_A+3tEd-Dn9tsydbhBH_2HcXw6RsSuG__9XSZwE5_g@mail.gmail.com>
References: <CAE7vhgPm1L9MiPQLJ5x1E3znQ8Si0e4ru6N0pcdw4r7mYErtpw@mail.gmail.com>
	<CABL7CQgD9amaJ1axmnBS9sO4dsNQk9XxYXHdTRg3pveiAunDbg@mail.gmail.com>
	<CAE7vhgOR_A+3tEd-Dn9tsydbhBH_2HcXw6RsSuG__9XSZwE5_g@mail.gmail.com>
Message-ID: <k73v6u$tro$1@ger.gmane.org>

02.11.2012 20:14, Nils Wagner kirjoitti:
> AFAIK the segfault was introduced recently.
> gcc (SUSE Linux) 4.6.2
> GNU Fortran (SUSE Linux) 4.6.2
> x86_64 GNU/Linux
> Python 2.7.2 (default, Aug 19 2011, 20:41:43) [GCC] on linux2
> '0.12.0.dev-bb436fa'
> NumPy version 1.8.0.dev-526b764

Doesn't crash for me for this Numpy/Scipy version combination (Ubuntu
12.10).

gcc-4.7 (Ubuntu/Linaro 4.7.2-2ubuntu1) 4.7.2
GNU Fortran (Ubuntu/Linaro 4.7.2-2ubuntu1) 4.7.2
x86_64 GNU/Linux
Python 2.7.3 (default, Sep 26 2012, 21:51:14) [GCC 4.7.2] on linux2

However, Valgrind shows:

==31561== Invalid read of size 8
==31561==    at 0x4C2CD88: memcpy@@GLIBC_2.14 (in
/usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==31561==    by 0xE25A608: fill_buffer (sigtoolsmodule.c:796)
==31561==    by 0xE25B344: PyArray_OrderFilterND (sigtoolsmodule.c:968)
==31561==    by 0xE25C075: sigtools_order_filterND (sigtoolsmodule.c:1135)
==31561==    by 0x45F911: PyEval_EvalFrameEx (in /usr/bin/python2.7)
==31561==    by 0x467208: PyEval_EvalCodeEx (in /usr/bin/python2.7)
==31561==    by 0x45FF76: PyEval_EvalFrameEx (in /usr/bin/python2.7)
==31561==    by 0x467208: PyEval_EvalCodeEx (in /usr/bin/python2.7)
==31561==    by 0x4D0241: PyEval_EvalCode (in /usr/bin/python2.7)
==31561==    by 0x5102BA: ??? (in /usr/bin/python2.7)
==31561==    by 0x4D01E3: PyRun_StringFlags (in /usr/bin/python2.7)
==31561==    by 0x419F54: PyRun_SimpleStringFlags (in /usr/bin/python2.7)
==31561==  Address 0x7f0e510 is 16 bytes before a block of size 8 alloc'd
==31561==    at 0x4C2B3F8: malloc (in
/usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==31561==    by 0x68572A5: PyDataMem_NEW (multiarraymodule.c:3491)
==31561==    by 0x67A81EE: PyArray_NewFromDescr (ctors.c:970)
==31561==    by 0x67A9CA7: PyArray_FromAny (ctors.c:1649)
==31561==    by 0x67AA069: PyArray_CheckFromAny (ctors.c:1757)
==31561==    by 0x6851D58: _array_fromobject (multiarraymodule.c:1655)
==31561==    by 0x464E18: PyEval_EvalFrameEx (in /usr/bin/python2.7)
==31561==    by 0x467208: PyEval_EvalCodeEx (in /usr/bin/python2.7)
==31561==    by 0x45FF76: PyEval_EvalFrameEx (in /usr/bin/python2.7)
==31561==    by 0x467208: PyEval_EvalCodeEx (in /usr/bin/python2.7)
==31561==    by 0x45FF76: PyEval_EvalFrameEx (in /usr/bin/python2.7)
==31561==    by 0x467208: PyEval_EvalCodeEx (in /usr/bin/python2.7)


-- 
Pauli Virtanen



From nils106 at googlemail.com  Mon Nov  5 14:37:27 2012
From: nils106 at googlemail.com (Nils Wagner)
Date: Mon, 5 Nov 2012 19:37:27 +0000
Subject: [SciPy-Dev] scipy.test() segfault
In-Reply-To: <CABL7CQj-Q0xhr=tPyJ5f57VcF8AqN_hpN=YS63yQZFZQiw2xsQ@mail.gmail.com>
References: <CAE7vhgPm1L9MiPQLJ5x1E3znQ8Si0e4ru6N0pcdw4r7mYErtpw@mail.gmail.com>
	<CABL7CQgD9amaJ1axmnBS9sO4dsNQk9XxYXHdTRg3pveiAunDbg@mail.gmail.com>
	<CAE7vhgOR_A+3tEd-Dn9tsydbhBH_2HcXw6RsSuG__9XSZwE5_g@mail.gmail.com>
	<CABL7CQjU5uBdTshmVkAGpnQvTbejrPBWvCppfvO5JNhFgaanyg@mail.gmail.com>
	<CAE7vhgMMqNdskKUOMjby+fUMKJGGG-Q4B4_RY4x6RZwuFdqCuA@mail.gmail.com>
	<CABL7CQj-Q0xhr=tPyJ5f57VcF8AqN_hpN=YS63yQZFZQiw2xsQ@mail.gmail.com>
Message-ID: <CAE7vhgO_Qc9Jsj5NanhB6sViaah1ghxSttzP=+=hb0k7+TfYaw@mail.gmail.com>

Sure. It works fine with numpy 1.6.2

>>> scipy.__version__
'0.12.0.dev-2f17ff2'
>>> scipy.test()
Running unit tests for scipy
NumPy version 1.6.2
NumPy is installed in
/home/nwagner/local/lib64/python2.7/site-packages/numpy
SciPy version 0.12.0.dev-2f17ff2
SciPy is installed in
/home/nwagner/local/lib64/python2.7/site-packages/scipy
Python version 2.7.2 (default, Aug 19 2011, 20:41:43) [GCC]
nose version 1.1.2
...............
----------------------------------------------------------------------
Ran 5592 tests in 179.134s

OK (KNOWNFAIL=14, SKIP=28)
<nose.result.TextTestResult run=5592 errors=0 failures=0>


Nils


On Sat, Nov 3, 2012 at 8:11 PM, Ralf Gommers <ralf.gommers at gmail.com> wrote:

>
>
>
> On Sat, Nov 3, 2012 at 6:51 PM, Nils Wagner <nils106 at googlemail.com>wrote:
>
>> I am using NumPy version 1.8.0.dev-526b764
>>
>
> So can you try with 1.6.2?
>
> Ralf
>
>
>
>> Nils
>>
>>
>> On Sat, Nov 3, 2012 at 4:53 PM, Ralf Gommers <ralf.gommers at gmail.com>wrote:
>>
>>>
>>>
>>>
>>> On Fri, Nov 2, 2012 at 7:14 PM, Nils Wagner <nils106 at googlemail.com>wrote:
>>>
>>>> AFAIK the segfault was introduced recently.
>>>> gcc (SUSE Linux) 4.6.2
>>>> GNU Fortran (SUSE Linux) 4.6.2
>>>> x86_64 GNU/Linux
>>>> Python 2.7.2 (default, Aug 19 2011, 20:41:43) [GCC] on linux2
>>>>
>>>>
>>>> >>>import scipy
>>>> >>> scipy.__version__
>>>> '0.12.0.dev-bb436fa'
>>>> >>>scipy.test(verbose=10)
>>>> ...
>>>> test_rank3 (test_signaltools.TestLinearFilterObject) ... ok
>>>> test_basic (test_signaltools.TestMedFilt) ... ok
>>>> Ticket #1124. Ensure this does not segfault. ... Segmentation fault
>>>
>>>
>>> Are you running numpy master? If so, does this segfault with an older
>>> released version of numpy too? The relevant code in sigtoolsmodule.c hasn't
>>> been touched in a long time.
>>>
>>> Ralf
>>>
>>>
>>> _______________________________________________
>>> SciPy-Dev mailing list
>>> SciPy-Dev at scipy.org
>>> http://mail.scipy.org/mailman/listinfo/scipy-dev
>>>
>>>
>>
>> _______________________________________________
>> SciPy-Dev mailing list
>> SciPy-Dev at scipy.org
>> http://mail.scipy.org/mailman/listinfo/scipy-dev
>>
>>
>
> _______________________________________________
> SciPy-Dev mailing list
> SciPy-Dev at scipy.org
> http://mail.scipy.org/mailman/listinfo/scipy-dev
>
>
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From ralf.gommers at gmail.com  Mon Nov  5 15:19:39 2012
From: ralf.gommers at gmail.com (Ralf Gommers)
Date: Mon, 5 Nov 2012 21:19:39 +0100
Subject: [SciPy-Dev] scipy.test() segfault
In-Reply-To: <CAE7vhgO_Qc9Jsj5NanhB6sViaah1ghxSttzP=+=hb0k7+TfYaw@mail.gmail.com>
References: <CAE7vhgPm1L9MiPQLJ5x1E3znQ8Si0e4ru6N0pcdw4r7mYErtpw@mail.gmail.com>
	<CABL7CQgD9amaJ1axmnBS9sO4dsNQk9XxYXHdTRg3pveiAunDbg@mail.gmail.com>
	<CAE7vhgOR_A+3tEd-Dn9tsydbhBH_2HcXw6RsSuG__9XSZwE5_g@mail.gmail.com>
	<CABL7CQjU5uBdTshmVkAGpnQvTbejrPBWvCppfvO5JNhFgaanyg@mail.gmail.com>
	<CAE7vhgMMqNdskKUOMjby+fUMKJGGG-Q4B4_RY4x6RZwuFdqCuA@mail.gmail.com>
	<CABL7CQj-Q0xhr=tPyJ5f57VcF8AqN_hpN=YS63yQZFZQiw2xsQ@mail.gmail.com>
	<CAE7vhgO_Qc9Jsj5NanhB6sViaah1ghxSttzP=+=hb0k7+TfYaw@mail.gmail.com>
Message-ID: <CABL7CQgAOFBpfNbix4BaXdZNb50vF4fH6v83eU305NBP5mneqg@mail.gmail.com>

On Mon, Nov 5, 2012 at 8:37 PM, Nils Wagner <nils106 at googlemail.com> wrote:

> Sure. It works fine with numpy 1.6.2
>

Thanks Nils. I've been able to reproduce this now. It's caused by
https://github.com/numpy/numpy/pull/2694. Will follow up on the numpy list.

Ralf


>
> >>> scipy.__version__
> '0.12.0.dev-2f17ff2'
> >>> scipy.test()
> Running unit tests for scipy
> NumPy version 1.6.2
> NumPy is installed in
> /home/nwagner/local/lib64/python2.7/site-packages/numpy
> SciPy version 0.12.0.dev-2f17ff2
> SciPy is installed in
> /home/nwagner/local/lib64/python2.7/site-packages/scipy
> Python version 2.7.2 (default, Aug 19 2011, 20:41:43) [GCC]
> nose version 1.1.2
> ...............
> ----------------------------------------------------------------------
> Ran 5592 tests in 179.134s
>
> OK (KNOWNFAIL=14, SKIP=28)
> <nose.result.TextTestResult run=5592 errors=0 failures=0>
>
>
> Nils
>
>
>
> On Sat, Nov 3, 2012 at 8:11 PM, Ralf Gommers <ralf.gommers at gmail.com>wrote:
>
>>
>>
>>
>> On Sat, Nov 3, 2012 at 6:51 PM, Nils Wagner <nils106 at googlemail.com>wrote:
>>
>>> I am using NumPy version 1.8.0.dev-526b764
>>>
>>
>> So can you try with 1.6.2?
>>
>> Ralf
>>
>>
>>
>>> Nils
>>>
>>>
>>> On Sat, Nov 3, 2012 at 4:53 PM, Ralf Gommers <ralf.gommers at gmail.com>wrote:
>>>
>>>>
>>>>
>>>>
>>>> On Fri, Nov 2, 2012 at 7:14 PM, Nils Wagner <nils106 at googlemail.com>wrote:
>>>>
>>>>> AFAIK the segfault was introduced recently.
>>>>> gcc (SUSE Linux) 4.6.2
>>>>> GNU Fortran (SUSE Linux) 4.6.2
>>>>> x86_64 GNU/Linux
>>>>> Python 2.7.2 (default, Aug 19 2011, 20:41:43) [GCC] on linux2
>>>>>
>>>>>
>>>>> >>>import scipy
>>>>> >>> scipy.__version__
>>>>> '0.12.0.dev-bb436fa'
>>>>> >>>scipy.test(verbose=10)
>>>>> ...
>>>>> test_rank3 (test_signaltools.TestLinearFilterObject) ... ok
>>>>> test_basic (test_signaltools.TestMedFilt) ... ok
>>>>> Ticket #1124. Ensure this does not segfault. ... Segmentation fault
>>>>
>>>>
>>>> Are you running numpy master? If so, does this segfault with an older
>>>> released version of numpy too? The relevant code in sigtoolsmodule.c hasn't
>>>> been touched in a long time.
>>>>
>>>> Ralf
>>>>
>>>>
>>>> _______________________________________________
>>>> SciPy-Dev mailing list
>>>> SciPy-Dev at scipy.org
>>>> http://mail.scipy.org/mailman/listinfo/scipy-dev
>>>>
>>>>
>>>
>>> _______________________________________________
>>> SciPy-Dev mailing list
>>> SciPy-Dev at scipy.org
>>> http://mail.scipy.org/mailman/listinfo/scipy-dev
>>>
>>>
>>
>> _______________________________________________
>> SciPy-Dev mailing list
>> SciPy-Dev at scipy.org
>> http://mail.scipy.org/mailman/listinfo/scipy-dev
>>
>>
>
> _______________________________________________
> SciPy-Dev mailing list
> SciPy-Dev at scipy.org
> http://mail.scipy.org/mailman/listinfo/scipy-dev
>
>
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From jtravs at gmail.com  Sun Nov 11 18:54:23 2012
From: jtravs at gmail.com (John Travers)
Date: Mon, 12 Nov 2012 00:54:23 +0100
Subject: [SciPy-Dev] Review request: interp2d with partial redgrid backend
Message-ID: <CAKKCUahT32mjn3f7CyB1nQs_QaPp6utDtZ0pXFikuAugOqnr7g@mail.gmail.com>

Hi All,

It has been a long time since I submitted any scipy hacks, but I got
hit by an old issue of mine so decided to do something about it.

The current interp2d backend uses the surfit routine from dierkx's
fitpack, which is not meant for interpolation (which we choose when we
set s=0.0). From the surfit.f code:

c   to choose s very small is strongly discouraged. this considerably
c   increases computation time and memory requirements. it may also
c   cause rank-deficiency (ier<-2) and endager numerical stability.

I originally raised this a long time ago with ticket #286 which
proposed replacing surfit with regrid which does not suffer from this
problem. However as is rightly stated in the comments to that ticket,
it changed interp2d to only work on rectangular grids rather than
scattered data which is not acceptable (and an API breakage).

So I propose to find a step by step solution to this. First the
following code uses regrid whenever possible:

https://github.com/jtravs/scipy/compare/master...interp2d_rectangular_fixes

This fixes #286, #776, #898 and parts of #1364, #1072, and #703.

Following this I hope to improve the docs a little and find a better
solution to the scattered data problem rather than using surfit (which
is great for smoothing BTW).

Please note that this is my first attempt at the whole git workflow
thing for scipy, so I hope this code review request is the right way
to go. I hope to submit quite a few more changes, so please correct me
where I go wrong!

Cheers,
John


From pav at iki.fi  Mon Nov 12 14:15:48 2012
From: pav at iki.fi (Pauli Virtanen)
Date: Mon, 12 Nov 2012 21:15:48 +0200
Subject: [SciPy-Dev] Review request: interp2d with partial redgrid
	backend
In-Reply-To: <CAKKCUahT32mjn3f7CyB1nQs_QaPp6utDtZ0pXFikuAugOqnr7g@mail.gmail.com>
References: <CAKKCUahT32mjn3f7CyB1nQs_QaPp6utDtZ0pXFikuAugOqnr7g@mail.gmail.com>
Message-ID: <k7rht3$3v6$1@ger.gmane.org>

Hi,

12.11.2012 01:54, John Travers kirjoitti:
[clip]
> So I propose to find a step by step solution to this. First the
> following code uses regrid whenever possible:
> 
> https://github.com/jtravs/scipy/compare/master...interp2d_rectangular_fixes
> 
> This fixes #286, #776, #898 and parts of #1364, #1072, and #703.

Looks like an useful improvement to me. I think you can already make it
a pull request by clicking the button on Github, so that we can more
easily discuss minor code details there.

Cheers,
Pauli




From pav at iki.fi  Mon Nov 12 14:27:19 2012
From: pav at iki.fi (Pauli Virtanen)
Date: Mon, 12 Nov 2012 21:27:19 +0200
Subject: [SciPy-Dev] Review request: interp2d with partial redgrid
	backend
In-Reply-To: <CAKKCUahT32mjn3f7CyB1nQs_QaPp6utDtZ0pXFikuAugOqnr7g@mail.gmail.com>
References: <CAKKCUahT32mjn3f7CyB1nQs_QaPp6utDtZ0pXFikuAugOqnr7g@mail.gmail.com>
Message-ID: <k7riil$ai9$1@ger.gmane.org>

12.11.2012 01:54, John Travers kirjoitti:
[clip]
> Following this I hope to improve the docs a little and find a better
> solution to the scattered data problem rather than using surfit (which
> is great for smoothing BTW).

Currently, we have the Delaunay tesselation based interpolation routines
(LinearNDInterpolation et al.) and RBF, in addition to Fitpack's splines.

However, the tesselation doesn't scale very well to large datasets in
high dimensions as the number of simplices explodes, and our RBF
implementation would need some fine tuning (i.e. the automatic parameter
choices it makes are not optimal). Fitpack's problem are well known. So
there certainly would be some room for improvement here.

We'd also need an easy-to-use gridded data intepolation routine. Tensor
product interpolation is sort of easy [1], but I didn't immediately see
an efficient and easy way to evaluate z(i) = interpolator(x(i), y(i))
[as opposed to z(i,j) = interpolator(x(i), y(j))] in that way. To do
this, one probably would have to really construct the spline
representation rather than just reusing existing interpolators one after
another.

Best,
Pauli

[1]
http://stackoverflow.com/questions/13333265/vector-array-output-from-scipy-ndimage-map-coordinates/13336119#13336119



From charlesr.harris at gmail.com  Tue Nov 13 01:14:43 2012
From: charlesr.harris at gmail.com (Charles R Harris)
Date: Mon, 12 Nov 2012 23:14:43 -0700
Subject: [SciPy-Dev] Review request: interp2d with partial redgrid
	backend
In-Reply-To: <k7riil$ai9$1@ger.gmane.org>
References: <CAKKCUahT32mjn3f7CyB1nQs_QaPp6utDtZ0pXFikuAugOqnr7g@mail.gmail.com>
	<k7riil$ai9$1@ger.gmane.org>
Message-ID: <CAB6mnxK-k-2_Dy_vRQpuEF=sVMD_NOpez-O8bqfTbk+fU1jFtA@mail.gmail.com>

On Mon, Nov 12, 2012 at 12:27 PM, Pauli Virtanen <pav at iki.fi> wrote:

> 12.11.2012 01:54, John Travers kirjoitti:
> [clip]
> > Following this I hope to improve the docs a little and find a better
> > solution to the scattered data problem rather than using surfit (which
> > is great for smoothing BTW).
>
> Currently, we have the Delaunay tesselation based interpolation routines
> (LinearNDInterpolation et al.) and RBF, in addition to Fitpack's splines.
>
> However, the tesselation doesn't scale very well to large datasets in
> high dimensions as the number of simplices explodes, and our RBF
> implementation would need some fine tuning (i.e. the automatic parameter
> choices it makes are not optimal). Fitpack's problem are well known. So
> there certainly would be some room for improvement here.
>
> We'd also need an easy-to-use gridded data intepolation routine. Tensor
> product interpolation is sort of easy [1], but I didn't immediately see
> an efficient and easy way to evaluate z(i) = interpolator(x(i), y(i))
> [as opposed to z(i,j) = interpolator(x(i), y(j))] in that way. To do
> this, one probably would have to really construct the spline
> representation rather than just reusing existing interpolators one after
> another.
>
>
I haven't looked at the spline case, but for the multidimensional numpy
polynomials there is a 'tensor' keyword in the evaluation that lets it be
used for both cases.

Chuck
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From jtravs at gmail.com  Tue Nov 13 03:45:05 2012
From: jtravs at gmail.com (John Travers)
Date: Tue, 13 Nov 2012 09:45:05 +0100
Subject: [SciPy-Dev] Review request: interp2d with partial redgrid
	backend
In-Reply-To: <k7rht3$3v6$1@ger.gmane.org>
References: <CAKKCUahT32mjn3f7CyB1nQs_QaPp6utDtZ0pXFikuAugOqnr7g@mail.gmail.com>
	<k7rht3$3v6$1@ger.gmane.org>
Message-ID: <50A20891.1000307@gmail.com>

On 12/11/12 20:15, Pauli Virtanen wrote:
> Hi,
>
> 12.11.2012 01:54, John Travers kirjoitti:
> [clip]
>> So I propose to find a step by step solution to this. First the
>> following code uses regrid whenever possible:
>>
>> https://github.com/jtravs/scipy/compare/master...interp2d_rectangular_fixes
>>
>> This fixes #286, #776, #898 and parts of #1364, #1072, and #703.
>
> Looks like an useful improvement to me. I think you can already make it
> a pull request by clicking the button on Github, so that we can more
> easily discuss minor code details there.
>

OK, I did this:

https://github.com/scipy/scipy/pull/353

Cheers,
J



From jtravs at gmail.com  Tue Nov 13 03:49:06 2012
From: jtravs at gmail.com (John Travers)
Date: Tue, 13 Nov 2012 09:49:06 +0100
Subject: [SciPy-Dev] Review request: interp2d with partial redgrid
	backend
In-Reply-To: <k7riil$ai9$1@ger.gmane.org>
References: <CAKKCUahT32mjn3f7CyB1nQs_QaPp6utDtZ0pXFikuAugOqnr7g@mail.gmail.com>
	<k7riil$ai9$1@ger.gmane.org>
Message-ID: <50A20982.1080700@gmail.com>

On 12/11/12 20:27, Pauli Virtanen wrote:
> 12.11.2012 01:54, John Travers kirjoitti:
> [clip]
>> Following this I hope to improve the docs a little and find a better
>> solution to the scattered data problem rather than using surfit (which
>> is great for smoothing BTW).
>
> Currently, we have the Delaunay tesselation based interpolation routines
> (LinearNDInterpolation et al.) and RBF, in addition to Fitpack's splines.
>
> However, the tesselation doesn't scale very well to large datasets in
> high dimensions as the number of simplices explodes, and our RBF
> implementation would need some fine tuning (i.e. the automatic parameter
> choices it makes are not optimal). Fitpack's problem are well known. So
> there certainly would be some room for improvement here.
>

OK, that is interesting, I was looking at using the NDInterpolation 
routines for this.

I think the rectangular grid is the most common use case of interp2d, so 
if we can get that working much better it is a good start. Irregular 
data is the sort of problem where it should be expected to try a few of 
the different routines available to get something which works well.

Cheers,
J



From lists at hilboll.de  Tue Nov 13 04:38:48 2012
From: lists at hilboll.de (Andreas Hilboll)
Date: Tue, 13 Nov 2012 10:38:48 +0100
Subject: [SciPy-Dev] Building docs from current master
Message-ID: <50A21528.1030008@hilboll.de>

Hi,

trying to build the docs from current master, I run into this problem::

   IOError: [Errno 2] No such file or directory:
u'/home2/hilboll/src/scipy/doc/source/examples/normdiscr_plot1.py'

Indeed, there's no folder ``doc/source/examples`` in master. Is this
intended? What am I doing wrong?

Cheers,
Andreas.


From denis at laxalde.org  Tue Nov 13 04:59:18 2012
From: denis at laxalde.org (Denis Laxalde)
Date: Tue, 13 Nov 2012 10:59:18 +0100
Subject: [SciPy-Dev] Building docs from current master
In-Reply-To: <50A21528.1030008@hilboll.de>
References: <50A21528.1030008@hilboll.de>
Message-ID: <50A219F6.1000106@laxalde.org>

Andreas Hilboll wrote:
> trying to build the docs from current master, I run into this problem::
>
>     IOError: [Errno 2] No such file or directory:
> u'/home2/hilboll/src/scipy/doc/source/examples/normdiscr_plot1.py'
>
> Indeed, there's no folder ``doc/source/examples`` in master. Is this
> intended? What am I doing wrong?

See http://projects.scipy.org/scipy/ticket/1671

-- 
Denis Laxalde


From ralf.gommers at gmail.com  Tue Nov 13 14:53:28 2012
From: ralf.gommers at gmail.com (Ralf Gommers)
Date: Tue, 13 Nov 2012 20:53:28 +0100
Subject: [SciPy-Dev] Building docs from current master
In-Reply-To: <50A219F6.1000106@laxalde.org>
References: <50A21528.1030008@hilboll.de>
	<50A219F6.1000106@laxalde.org>
Message-ID: <CABL7CQiy2R2Fzc3wArzVUzuYqpYmGgmJubjao6F+4zdfDK426w@mail.gmail.com>

On Tue, Nov 13, 2012 at 10:59 AM, Denis Laxalde <denis at laxalde.org> wrote:

> Andreas Hilboll wrote:
> > trying to build the docs from current master, I run into this problem::
> >
> >     IOError: [Errno 2] No such file or directory:
> > u'/home2/hilboll/src/scipy/doc/source/examples/normdiscr_plot1.py'
> >
> > Indeed, there's no folder ``doc/source/examples`` in master. Is this
> > intended? What am I doing wrong?
>
> See http://projects.scipy.org/scipy/ticket/1671


I had a look at this again, and I can finally reproduce this issue on
Linux. On OS X - where I built the releases till now - the code works as
is. I'll investigate in more detail why it works now on OS X and how I can
keep it working after changing the code as in the patch attached to #1671.

Ralf
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From beamesleach at gmail.com  Thu Nov 15 07:46:08 2012
From: beamesleach at gmail.com (Alex Leach)
Date: Thu, 15 Nov 2012 12:46:08 +0000
Subject: [SciPy-Dev] Faster expm
Message-ID: <1551017.DFfHvI0K1W@metabuntu>

Dear List,

I did some work a while back, which needed to calculate matrix exponentials, 
for which I used the EXPOKIT toolkit: 
http://www.maths.uq.edu.au/expokit/download.html

EXPOKIT is written in Fortran, and I found that f2py did a pretty good job of 
creating a Python interface. More recently, I separated out the code and did 
some speed comparisons against scipy.linalg.expm. If I could direct your 
attention to the scipy-user mailing list, you'll find the build method and 
benchmark comparisons up there:
http://mail.scipy.org/pipermail/scipy-user/2012-November/033588.html

Wrapping EXPOKIT for Python has been done before, by a colleague of the 
original author, so I can't take all the credit. A presentation he gave, with 
some usage and build instructions can be found here (Pg 16-22): 
http://sf.anu.edu.au/~mhk900/Python_Workshop/short.pdf

After some feedback from others on the SciPy-user mailing list, I obtained 
permission from the original author, Roger B. Sidje, to distribute EXPOKIT 
with SciPy under the BSD license.

So, I've done a little more work over the last couple of days, in an attempt 
to merge EXPOKIT into SciPy, but of course there's still more work to be done. 
Unfortunately, I've run out of time to do this myself, (I've got to write my 
PhD thesis, which has nothing to do with this) so I'd like to pass over what 
I've done and forget about it, at least for the next 6 months or so.

If you'd be interested in taking this off my hands, please let me know. I've 
had the small dense routines for Pad? approximation working for ages, but the 
routines for Krylov projection of general sparse matrices are still giving 
some problems.

Specifically, there's some STOP statements in the Fortran code that quit the 
program without raising exceptions. I haven't been able to get past these, so 
either the signature file I've edited is incorrect,the sparse matrix I've been 
testing with is wrong or too small, or something else is wrong.

I've just made a fork of scipy on github, to which I've just pushed the files 
I've been working on:

NEW:
scipy/linalg/src/expokit.f
scipy/linalg/expokit.pyf.src
scipy/linalg/time_expm.py
scipy/linalg/expowrap.py
MODIFIED:
scipy/linalg/setup.py

expokit.f       - EXPOKIT source code, with some very minor changes (Cf2py 
comments and changed matvec function call, as per above presentation)
expokit.pyf.src - f2py signature file I've been editing from auto-generated 
version.
time_expm.py    - script I was testing everything with, before adding to 
expowrap.py.. Should not be included in distribution.
expowrap.py     - where I was going to put the python wrapper function. Was 
attempting to write a drop-in replacement for scipy.linalg.expm, but the 
sparse routines were giving problems...

If you have any questions, please don't hesitate to ask.

Kind regards,
Alex
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From pav at iki.fi  Thu Nov 15 12:08:18 2012
From: pav at iki.fi (Pauli Virtanen)
Date: Thu, 15 Nov 2012 17:08:18 +0000 (UTC)
Subject: [SciPy-Dev] Faster expm
References: <1551017.DFfHvI0K1W@metabuntu>
Message-ID: <loom.20121115T180243-410@post.gmane.org>

Hi,

Alex Leach <beamesleach <at> gmail.com> writes:
> I did some work a while back, which needed to calculate matrix exponentials, 
for which I used the EXPOKIT toolkit: 
http://www.maths.uq.edu.au/expokit/download.html
[clip]
> I've just made a fork of scipy on github, to which I've just
> pushed the files I've been working on:

Could you give a link to your fork?

Or, you can just file a pull request --- just say there that it's 
work-in-progress, and someone else can then take it over from there.

Best,
Pauli Virtanen




From beamesleach at gmail.com  Thu Nov 15 12:31:26 2012
From: beamesleach at gmail.com (Alex Leach)
Date: Thu, 15 Nov 2012 17:31:26 +0000
Subject: [SciPy-Dev] Faster expm
In-Reply-To: <loom.20121115T180243-410@post.gmane.org>
References: <1551017.DFfHvI0K1W@metabuntu>
	<loom.20121115T180243-410@post.gmane.org>
Message-ID: <1378727.vRGAN9kaHN@metabuntu>

Hi Pauli,

On Thursday 15 Nov 2012 17:08:18 Pauli Virtanen wrote:
> Could you give a link to your fork?

Of course. Sorry, completely forgot to put it in before:-
https://github.com/alexleach/scipy

> 
> Or, you can just file a pull request --- just say there that it's
> work-in-progress, and someone else can then take it over from there.

Could do. Is that easier for you guys?

Cheers,
Alex
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From njs at pobox.com  Thu Nov 15 12:36:51 2012
From: njs at pobox.com (Nathaniel Smith)
Date: Thu, 15 Nov 2012 17:36:51 +0000
Subject: [SciPy-Dev] Faster expm
In-Reply-To: <1551017.DFfHvI0K1W@metabuntu>
References: <1551017.DFfHvI0K1W@metabuntu>
Message-ID: <CAPJVwBmadUxdishCYvrTeZ+2D_E0C_iGdbC45QqwPXPEVLbJug@mail.gmail.com>

On Thu, Nov 15, 2012 at 12:46 PM, Alex Leach <beamesleach at gmail.com> wrote:
> Wrapping EXPOKIT for Python has been done before, by a colleague of the
> original author, so I can't take all the credit. A presentation he gave,
> with some usage and build instructions can be found here (Pg 16-22):
> http://sf.anu.edu.au/~mhk900/Python_Workshop/short.pdf

Did you copy his code, and if so, do we need to worry about its
license? (I guess to the extent that it's just a literal listing of
the functions inside the .f file, there's nothing copyrightable,
but...)

-n


From beamesleach at gmail.com  Thu Nov 15 12:51:32 2012
From: beamesleach at gmail.com (Alex Leach)
Date: Thu, 15 Nov 2012 17:51:32 +0000
Subject: [SciPy-Dev] Faster expm
In-Reply-To: <CAPJVwBmadUxdishCYvrTeZ+2D_E0C_iGdbC45QqwPXPEVLbJug@mail.gmail.com>
References: <1551017.DFfHvI0K1W@metabuntu>
	<CAPJVwBmadUxdishCYvrTeZ+2D_E0C_iGdbC45QqwPXPEVLbJug@mail.gmail.com>
Message-ID: <5484256.uLZiC4Qk2P@metabuntu>

On Thursday 15 Nov 2012 17:36:51 Nathaniel Smith wrote:
 > On Thu, Nov 15, 2012 at 12:46 PM, Alex Leach <beamesleach at gmail.com> wrote:
> > Wrapping EXPOKIT for Python has been done before, by a colleague of the
> > original author, so I can't take all the credit. A presentation he gave,
> > with some usage and build instructions can be found here (Pg 16-22):
> > http://sf.anu.edu.au/~mhk900/Python_Workshop/short.pdf
> 
> Did you copy his code, and if so, do we need to worry about its
> license? (I guess to the extent that it's just a literal listing of
> the functions inside the .f file, there's nothing copyrightable,
> but...)

No, not really. He's put some code up from the auto-generated signature file, 
which we'd both edited. I was double-checking his matvec signature against 
what I had generated and edited, and I did copy the argument names he used.

The usage example from Python seems incomplete, and did not inspire my Python 
code at all. The Python code there demonstrates how to call dmexpv, which I 
don't think would be used by SciPy, either.. dmexpv computes Krylov projection 
for Sparse Markov matrices, if that makes sense. I thought we'd just want 
dgexpv, which is for general sparse matrices.

The only bit which I copied was the modification to the matvec calls in 
expokit.f (bottom of Page 20). As it's a modification to Expokit, which we've 
been granted permission to use, modify and distribute, I think we're safe.

Cheers,
Alex
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From pav at iki.fi  Thu Nov 15 13:05:21 2012
From: pav at iki.fi (Pauli Virtanen)
Date: Thu, 15 Nov 2012 18:05:21 +0000 (UTC)
Subject: [SciPy-Dev] Faster expm
References: <1551017.DFfHvI0K1W@metabuntu>
	<loom.20121115T180243-410@post.gmane.org>
	<1378727.vRGAN9kaHN@metabuntu>
Message-ID: <loom.20121115T190409-296@post.gmane.org>

Alex Leach <beamesleach <at> gmail.com> writes:
[clip] 
> > Or, you can just file a pull request --- just say there that it's
> > work-in-progress, and someone else can then take it over from there.
> ?
> Could do. Is that easier for you guys?

Yes, it's a bit easier to keep a tab on it that way.
Thanks a lot!

Best,
Pauli Virtanen



From beamesleach at gmail.com  Thu Nov 15 19:18:44 2012
From: beamesleach at gmail.com (Alex Leach)
Date: Fri, 16 Nov 2012 00:18:44 +0000
Subject: [SciPy-Dev] Faster expm
In-Reply-To: <loom.20121115T180243-410@post.gmane.org>
References: <1551017.DFfHvI0K1W@metabuntu>
	<loom.20121115T180243-410@post.gmane.org>
Message-ID: <2712566.9DEd64Xb37@metabuntu>

Hi,

On Thursday 15 Nov 2012 17:08:18 Pauli Virtanen wrote:
> Or, you can just file a pull request --- just say there that it's
> work-in-progress, and someone else can then take it over from there.

Done :)
At https://github.com/scipy/scipy/pull/354

Cheers,
Alex
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From sturla at molden.no  Mon Nov 19 12:12:23 2012
From: sturla at molden.no (Sturla Molden)
Date: Mon, 19 Nov 2012 18:12:23 +0100
Subject: [SciPy-Dev] Use OpenBLAS for the binary releases?
Message-ID: <50AA6877.7010806@molden.no>

I think NumPy and SciPy should consider to use OpenBLAS (a fork of 
GotoBLAS2) instead of ATLAS or f2c'd Netlib BLAS for the binary releases.

Here are its virtues:

* Very easy to build: Just a makefile, no configuration script or 
special build tools.

* Building ATLAS can be a PITA. So why bother?

* Faster than ATLAS, sometimes faster than MKL.

* Multithreaded BLAS kernels: OpenMP on Unix, Windows threads on Windows.

* The quality of its ancestor GotoBLAS is undisputed. I was the BLAS 
implementation of choice for major HPC projects around the World.

* Free as in BSD licensed.

* Funded and developed for use in major Chinese HPC projects. Actively 
maintained. (GotoBLAS2 is abandonware.)

* Open source. The C sources are a pleasure to read, and very easy to 
verify.

* No OpenMP on Windows means no dependency on pthreads-win32 (an LGPL 
library) when building with MinGW.

* Builds on Windows with MinGW and MSYS, and perhaps even without MSYS.

* Cygwin is not needed on Windows (this is just BS from the GotoBLAS 
documentation). Thus, 64-buit builds are possible (I've built it using 
TDM-GCC for Win64 and 32-bit MSYS).


Sturla


From dreid at dwightreid.com  Tue Nov 20 13:01:43 2012
From: dreid at dwightreid.com (dwight reid)
Date: Tue, 20 Nov 2012 10:01:43 -0800 (PST)
Subject: [SciPy-Dev] Python Scipy Block Diagram Editor with ACG
In-Reply-To: <1353433995.49181.YahooMailNeo@web5717.biz.mail.ne1.yahoo.com>
References: <1353433995.49181.YahooMailNeo@web5717.biz.mail.ne1.yahoo.com>
Message-ID: <1353434503.64271.YahooMailNeo@web5717.biz.mail.ne1.yahoo.com>



Hey Guys,

I am Dwight Reid an electrical engineer and lecturer at the University of Technology (also IEEE member and branch counselor)? in Jamaica. Some months ago I had started working on a block diagram editor for python that I dream one day will become a reasonable alternative to Matlab Simulink. I want to put a special emphasis on automatic code generation (ACG) and so far I have done ACG for python Scipy and also for the arduino, these are however just an implementation of some basic functions.

As is, the block diagram editing is done in libre office draw and you have to manually type in the functions and commands, I have 
attached an example exported to pdf.

Would anyone be willing to help with this, I have no experience developing with the open source community.

I think it would definitely get more people using python since it is much easier to program graphically and it would be very useful to scientific computing. I imagine a better, moretailored graphic editor with predefined blocks that you can pull out like simulink or scilab xcos (maybe a stripped down libre office draw), implementing this is beyond my current skill level so it goes slowly.

I hope I'm clear enough, let me know what you think.

?? ? ?? Dwight 
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From eraldo.pomponi at gmail.com  Tue Nov 20 13:13:32 2012
From: eraldo.pomponi at gmail.com (Eraldo Pomponi)
Date: Tue, 20 Nov 2012 19:13:32 +0100
Subject: [SciPy-Dev] Python Scipy Block Diagram Editor with ACG
In-Reply-To: <1353434503.64271.YahooMailNeo@web5717.biz.mail.ne1.yahoo.com>
References: <1353433995.49181.YahooMailNeo@web5717.biz.mail.ne1.yahoo.com>
	<1353434503.64271.YahooMailNeo@web5717.biz.mail.ne1.yahoo.com>
Message-ID: <CAEaCG7defGi85QjN=WTYPCYLApw+cspC51E2O37KAKqsx4oO5g@mail.gmail.com>

Dear Dwight,

Have a look at Enthought BlockCanvas (
http://code.enthought.com/projects/block_canvas/  and
https://github.com/enthought/blockcanvas)

Cheers,
Eraldo



On Tue, Nov 20, 2012 at 7:01 PM, dwight reid <dreid at dwightreid.com> wrote:

>
>
> Hey Guys,
>
> I am Dwight Reid an electrical engineer and lecturer at the University of
> Technology (also IEEE member and branch counselor)  in Jamaica. Some months
> ago I had started working on a block diagram editor for python that I dream
> one day will become a reasonable alternative to Matlab Simulink. I want to
> put a special emphasis on automatic code generation (ACG) and so far I have
> done ACG for python Scipy and also for the arduino, these are however just
> an implementation of some basic functions.
>
> As is, the block diagram editing is done in libre office draw and you have
> to manually type in the functions and commands, I have
> attached an example exported to pdf.
>
> Would anyone be willing to help with this, I have no experience developing
> with the open source community.
>
> I think it would definitely get more people using python since it is much
> easier to program graphically and it would be very useful to scientific
> computing. I imagine a better, moretailored graphic editor with predefined
> blocks that you can pull out like simulink or scilab xcos (maybe a stripped
> down libre office draw), implementing this is beyond my current skill level
> so it goes slowly.
>
> I hope I'm clear enough, let me know what you think.
>
>         Dwight
> _______________________________________________
> SciPy-Dev mailing list
> SciPy-Dev at scipy.org
> http://mail.scipy.org/mailman/listinfo/scipy-dev
>
>
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From tim at cerazone.net  Tue Nov 20 13:41:37 2012
From: tim at cerazone.net (Cera, Tim)
Date: Tue, 20 Nov 2012 13:41:37 -0500
Subject: [SciPy-Dev] Python Scipy Block Diagram Editor with ACG
In-Reply-To: <1353434503.64271.YahooMailNeo@web5717.biz.mail.ne1.yahoo.com>
References: <1353433995.49181.YahooMailNeo@web5717.biz.mail.ne1.yahoo.com>
	<1353434503.64271.YahooMailNeo@web5717.biz.mail.ne1.yahoo.com>
Message-ID: <CAO5s+D-8+Bg69rhbP9QbqwS-ZDUhkLrQo59i3HAXp-rP4Axj3w@mail.gmail.com>

> As is, the block diagram editing is done in libre office draw and you have
> to manually type in the functions and commands, I have
> attached an example exported to pdf.



Would anyone be willing to help with this, I have no experience developing
> with the open source community.
>

I won't be able to help, except to give some information.  Found this
http://wiki.python.org/moin/FlowBasedProgramming a long time ago which
might be useful.  Some of the links are broken now, and some of the others
are really old, but something there might be helpful.

In general, flow based programming hasn't caught on.   I think partially
because of reasons described in the old saying, "To hell with tradition, we
are going to do it like we always did!"

Kindest regards,
Tim
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From charlesr.harris at gmail.com  Tue Nov 20 16:22:03 2012
From: charlesr.harris at gmail.com (Charles R Harris)
Date: Tue, 20 Nov 2012 14:22:03 -0700
Subject: [SciPy-Dev] Python Scipy Block Diagram Editor with ACG
In-Reply-To: <CAO5s+D-8+Bg69rhbP9QbqwS-ZDUhkLrQo59i3HAXp-rP4Axj3w@mail.gmail.com>
References: <1353433995.49181.YahooMailNeo@web5717.biz.mail.ne1.yahoo.com>
	<1353434503.64271.YahooMailNeo@web5717.biz.mail.ne1.yahoo.com>
	<CAO5s+D-8+Bg69rhbP9QbqwS-ZDUhkLrQo59i3HAXp-rP4Axj3w@mail.gmail.com>
Message-ID: <CAB6mnx+R1D1W0868ccZxpUprW4qcA=GSsH2XuAUAjUwhqhruPg@mail.gmail.com>

On Tue, Nov 20, 2012 at 11:41 AM, Cera, Tim <tim at cerazone.net> wrote:

>
> As is, the block diagram editing is done in libre office draw and you have
>> to manually type in the functions and commands, I have
>> attached an example exported to pdf.
>
>
>
> Would anyone be willing to help with this, I have no experience developing
>> with the open source community.
>>
>
> I won't be able to help, except to give some information.  Found this
> http://wiki.python.org/moin/FlowBasedProgramming a long time ago which
> might be useful.  Some of the links are broken now, and some of the others
> are really old, but something there might be helpful.
>
> In general, flow based programming hasn't caught on.   I think partially
> because of reasons described in the old saying, "To hell with tradition, we
> are going to do it like we always did!"
>
>
Simulink is pretty widely used, especially for modelling and rapid
development of control software.  Equipment vendors provide blocks for
their devices, gyroscopes and such, that can be used for the models and
then Matlab will generate control code to run on the targeted system.
Simulink itself is basically a way of setting up a big system of DEs, but
what really makes it go are the vendor blocks and code generation.

Chuck
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From ndbecker2 at gmail.com  Wed Nov 21 10:01:38 2012
From: ndbecker2 at gmail.com (Neal Becker)
Date: Wed, 21 Nov 2012 10:01:38 -0500
Subject: [SciPy-Dev] Python Scipy Block Diagram Editor with ACG
References: <1353433995.49181.YahooMailNeo@web5717.biz.mail.ne1.yahoo.com>
	<1353434503.64271.YahooMailNeo@web5717.biz.mail.ne1.yahoo.com>
	<CAO5s+D-8+Bg69rhbP9QbqwS-ZDUhkLrQo59i3HAXp-rP4Axj3w@mail.gmail.com>
	<CAB6mnx+R1D1W0868ccZxpUprW4qcA=GSsH2XuAUAjUwhqhruPg@mail.gmail.com>
Message-ID: <k8iqcg$jje$1@ger.gmane.org>

Charles R Harris wrote:

> On Tue, Nov 20, 2012 at 11:41 AM, Cera, Tim <tim at cerazone.net> wrote:
> 
>>
>> As is, the block diagram editing is done in libre office draw and you have
>>> to manually type in the functions and commands, I have
>>> attached an example exported to pdf.
>>
>>
>>
>> Would anyone be willing to help with this, I have no experience developing
>>> with the open source community.
>>>
>>
>> I won't be able to help, except to give some information.  Found this
>> http://wiki.python.org/moin/FlowBasedProgramming a long time ago which
>> might be useful.  Some of the links are broken now, and some of the others
>> are really old, but something there might be helpful.
>>
>> In general, flow based programming hasn't caught on.   I think partially
>> because of reasons described in the old saying, "To hell with tradition, we
>> are going to do it like we always did!"
>>
>>
> Simulink is pretty widely used, especially for modelling and rapid
> development of control software.  Equipment vendors provide blocks for
> their devices, gyroscopes and such, that can be used for the models and
> then Matlab will generate control code to run on the targeted system.
> Simulink itself is basically a way of setting up a big system of DEs, but
> what really makes it go are the vendor blocks and code generation.
> 
> Chuck

So why would vlsi guys use text (e.g., verilog) to design a cpu, instead of 
schematics?

1. IMO, graphical representations work nicely for low-complexity, but not 
productive for highly complex systems

2. It is less productive to manipulate a graphical  representation

3. text can be manipulated by all your favorite tools, more open ecosystem, no 
lockin, proprietary formats



From charlesr.harris at gmail.com  Wed Nov 21 10:48:44 2012
From: charlesr.harris at gmail.com (Charles R Harris)
Date: Wed, 21 Nov 2012 08:48:44 -0700
Subject: [SciPy-Dev] Python Scipy Block Diagram Editor with ACG
In-Reply-To: <k8iqcg$jje$1@ger.gmane.org>
References: <1353433995.49181.YahooMailNeo@web5717.biz.mail.ne1.yahoo.com>
	<1353434503.64271.YahooMailNeo@web5717.biz.mail.ne1.yahoo.com>
	<CAO5s+D-8+Bg69rhbP9QbqwS-ZDUhkLrQo59i3HAXp-rP4Axj3w@mail.gmail.com>
	<CAB6mnx+R1D1W0868ccZxpUprW4qcA=GSsH2XuAUAjUwhqhruPg@mail.gmail.com>
	<k8iqcg$jje$1@ger.gmane.org>
Message-ID: <CAB6mnx+T-oq81HUKOrb98ykcA0WhtoSHTgE226YQU8==U76ekg@mail.gmail.com>

On Wed, Nov 21, 2012 at 8:01 AM, Neal Becker <ndbecker2 at gmail.com> wrote:

> Charles R Harris wrote:
>
> > On Tue, Nov 20, 2012 at 11:41 AM, Cera, Tim <tim at cerazone.net> wrote:
> >
> >>
> >> As is, the block diagram editing is done in libre office draw and you
> have
> >>> to manually type in the functions and commands, I have
> >>> attached an example exported to pdf.
> >>
> >>
> >>
> >> Would anyone be willing to help with this, I have no experience
> developing
> >>> with the open source community.
> >>>
> >>
> >> I won't be able to help, except to give some information.  Found this
> >> http://wiki.python.org/moin/FlowBasedProgramming a long time ago which
> >> might be useful.  Some of the links are broken now, and some of the
> others
> >> are really old, but something there might be helpful.
> >>
> >> In general, flow based programming hasn't caught on.   I think partially
> >> because of reasons described in the old saying, "To hell with
> tradition, we
> >> are going to do it like we always did!"
> >>
> >>
> > Simulink is pretty widely used, especially for modelling and rapid
> > development of control software.  Equipment vendors provide blocks for
> > their devices, gyroscopes and such, that can be used for the models and
> > then Matlab will generate control code to run on the targeted system.
> > Simulink itself is basically a way of setting up a big system of DEs, but
> > what really makes it go are the vendor blocks and code generation.
> >
> > Chuck
>
> So why would vlsi guys use text (e.g., verilog) to design a cpu, instead of
> schematics?
>
> 1. IMO, graphical representations work nicely for low-complexity, but not
> productive for highly complex systems
>
> 2. It is less productive to manipulate a graphical  representation
>
> 3. text can be manipulated by all your favorite tools, more open
> ecosystem, no
> lockin, proprietary formats
>
>
I'm not saying it's the best way, just that Simulink is widely used and is
part of a mature ecosystem. FPGA design software, say Xilinx ISE, does have
a visual front end, generally in tabular form. In that regard it is rather
like gui design tools where objects can be opened and their attributes set.
I think the thing that makes all of those tools go is code generation, the
ability run simulations, and to insert probes that display values in
graphical form as the simulation progresses. IIRC, Simulink can also be
used to drive hardware for breadboarding designs.

Chuck
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From eraldo.pomponi at gmail.com  Wed Nov 21 11:21:15 2012
From: eraldo.pomponi at gmail.com (Eraldo Pomponi)
Date: Wed, 21 Nov 2012 17:21:15 +0100
Subject: [SciPy-Dev] Python Scipy Block Diagram Editor with ACG
In-Reply-To: <CAB6mnx+T-oq81HUKOrb98ykcA0WhtoSHTgE226YQU8==U76ekg@mail.gmail.com>
References: <1353433995.49181.YahooMailNeo@web5717.biz.mail.ne1.yahoo.com>
	<1353434503.64271.YahooMailNeo@web5717.biz.mail.ne1.yahoo.com>
	<CAO5s+D-8+Bg69rhbP9QbqwS-ZDUhkLrQo59i3HAXp-rP4Axj3w@mail.gmail.com>
	<CAB6mnx+R1D1W0868ccZxpUprW4qcA=GSsH2XuAUAjUwhqhruPg@mail.gmail.com>
	<k8iqcg$jje$1@ger.gmane.org>
	<CAB6mnx+T-oq81HUKOrb98ykcA0WhtoSHTgE226YQU8==U76ekg@mail.gmail.com>
Message-ID: <CAEaCG7dkeAnHbb4kh9EG3cOKNToRQjtmre1F_cCCJf0hGuQUJg@mail.gmail.com>

AFAIK the best example of visual programming/interaction is LabView (
http://www.ni.com/labview/).
I agree that many scientist don't like it but it is really widely adopted
not just for control theory and application.
It was also the subject of a "Patent Litigation" between MatWorks
(Simulink) and NI (
http://www.ni.com/pdf/products/us/patent_litigation_faq.pdf)......
Ni won!
I think that it shows pretty much cleanly that complex projects can be
managed completely graphically if  the environment is enough mature for
that.
LabView seems to meet that requirement. Of course it is NOT open. This is
why I do not use it.

Cheers,
Eraldo




On Wed, Nov 21, 2012 at 4:48 PM, Charles R Harris <charlesr.harris at gmail.com
> wrote:

>
>
> On Wed, Nov 21, 2012 at 8:01 AM, Neal Becker <ndbecker2 at gmail.com> wrote:
>
>> Charles R Harris wrote:
>>
>> > On Tue, Nov 20, 2012 at 11:41 AM, Cera, Tim <tim at cerazone.net> wrote:
>> >
>> >>
>> >> As is, the block diagram editing is done in libre office draw and you
>> have
>> >>> to manually type in the functions and commands, I have
>> >>> attached an example exported to pdf.
>> >>
>> >>
>> >>
>> >> Would anyone be willing to help with this, I have no experience
>> developing
>> >>> with the open source community.
>> >>>
>> >>
>> >> I won't be able to help, except to give some information.  Found this
>> >> http://wiki.python.org/moin/FlowBasedProgramming a long time ago which
>> >> might be useful.  Some of the links are broken now, and some of the
>> others
>> >> are really old, but something there might be helpful.
>> >>
>> >> In general, flow based programming hasn't caught on.   I think
>> partially
>> >> because of reasons described in the old saying, "To hell with
>> tradition, we
>> >> are going to do it like we always did!"
>> >>
>> >>
>> > Simulink is pretty widely used, especially for modelling and rapid
>> > development of control software.  Equipment vendors provide blocks for
>> > their devices, gyroscopes and such, that can be used for the models and
>> > then Matlab will generate control code to run on the targeted system.
>> > Simulink itself is basically a way of setting up a big system of DEs,
>> but
>> > what really makes it go are the vendor blocks and code generation.
>> >
>> > Chuck
>>
>> So why would vlsi guys use text (e.g., verilog) to design a cpu, instead
>> of
>> schematics?
>>
>> 1. IMO, graphical representations work nicely for low-complexity, but not
>> productive for highly complex systems
>>
>> 2. It is less productive to manipulate a graphical  representation
>>
>> 3. text can be manipulated by all your favorite tools, more open
>> ecosystem, no
>> lockin, proprietary formats
>>
>>
> I'm not saying it's the best way, just that Simulink is widely used and is
> part of a mature ecosystem. FPGA design software, say Xilinx ISE, does have
> a visual front end, generally in tabular form. In that regard it is rather
> like gui design tools where objects can be opened and their attributes set.
> I think the thing that makes all of those tools go is code generation, the
> ability run simulations, and to insert probes that display values in
> graphical form as the simulation progresses. IIRC, Simulink can also be
> used to drive hardware for breadboarding designs.
>
> Chuck
>
>
> _______________________________________________
> SciPy-Dev mailing list
> SciPy-Dev at scipy.org
> http://mail.scipy.org/mailman/listinfo/scipy-dev
>
>
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From cimrman3 at ntc.zcu.cz  Wed Nov 21 13:08:51 2012
From: cimrman3 at ntc.zcu.cz (Robert Cimrman)
Date: Wed, 21 Nov 2012 19:08:51 +0100
Subject: [SciPy-Dev] ANN: SfePy 2012.4
Message-ID: <50AD18B3.1010705@ntc.zcu.cz>

I am pleased to announce release 2012.4 of SfePy.

Description
-----------
SfePy (simple finite elements in Python) is a software for solving
systems of coupled partial differential equations by the finite element
method. The code is based on NumPy and SciPy packages. It is distributed
under the new BSD license.

Home page: http://sfepy.org
Downloads, mailing list, wiki: http://code.google.com/p/sfepy/
Git (source) repository, issue tracker: http://github.com/sfepy

Highlights of this release
--------------------------
- initial support for hierarchical basis on quadrilateral and brick elements
- unified C/Cython structures for reference mappings
- new linear combination boundary condition: edge direction
- new examples showing some advanced features

For full release notes see http://docs.sfepy.org/doc/release_notes.html#id1
(rather long and technical).

Best regards,
Robert Cimrman and Contributors (*)

(*) Contributors to this release (alphabetical order):

Bjarke Dalslet, Vladim?r Luke?, Maty?? Nov?k


From bussonniermatthias at gmail.com  Wed Nov 21 13:43:58 2012
From: bussonniermatthias at gmail.com (Matthias BUSSONNIER)
Date: Wed, 21 Nov 2012 19:43:58 +0100
Subject: [SciPy-Dev] Python Scipy Block Diagram Editor with ACG
In-Reply-To: <CAEaCG7dkeAnHbb4kh9EG3cOKNToRQjtmre1F_cCCJf0hGuQUJg@mail.gmail.com>
References: <1353433995.49181.YahooMailNeo@web5717.biz.mail.ne1.yahoo.com>
	<1353434503.64271.YahooMailNeo@web5717.biz.mail.ne1.yahoo.com>
	<CAO5s+D-8+Bg69rhbP9QbqwS-ZDUhkLrQo59i3HAXp-rP4Axj3w@mail.gmail.com>
	<CAB6mnx+R1D1W0868ccZxpUprW4qcA=GSsH2XuAUAjUwhqhruPg@mail.gmail.com>
	<k8iqcg$jje$1@ger.gmane.org>
	<CAB6mnx+T-oq81HUKOrb98ykcA0WhtoSHTgE226YQU8==U76ekg@mail.gmail.com>
	<CAEaCG7dkeAnHbb4kh9EG3cOKNToRQjtmre1F_cCCJf0hGuQUJg@mail.gmail.com>
Message-ID: <6D43A24A-E58B-4C98-8A5E-736A3B7D3E62@gmail.com>

Hi list, 

Le 21 nov. 2012 ? 17:21, Eraldo Pomponi a ?crit :

> AFAIK the best example of visual programming/interaction is LabView (http://www.ni.com/labview/). 
> I agree that many scientist don't like it but it is really widely adopted not just for control theory and application. 
> It was also the subject of a "Patent Litigation" between MatWorks (Simulink) and NI (http://www.ni.com/pdf/products/us/patent_litigation_faq.pdf)......
> Ni won! 
> I think that it shows pretty much cleanly that complex projects can be managed completely graphically if  the environment is enough mature for that. 
> LabView seems to meet that requirement. Of course it is NOT open. This is why I do not use it. 


It is not because something is widely adopted that it is well used, and does its job.
In this case it does not prove that Labview allow to managed correctly things,
at best that people achieve to (sort of) work with that.

To be working in a lab that does use labview and to be forced to use it, 
one of the main reason lab view is used it because it comes with drivers for instrument, 
and support that goes with it.

The others being:
  *  it is already use by others nearby scientist.
  *  scientist think do not know how to program,
  *  they need a visual interface fast
  * The lab have already paid for the license you better have to use it.


We use labview for are optical tweezer and microscope control, which is a pretty big piece of software in labview.
The code exist for years, when I arrived each files had a v0.1, v0.1.1?.v0.9-bis, first file was 4 year old.
The working copy was the v0.8-smth. The way labview is made we have to copy and past things all around,
have global variable, it is not unit tested.
We all know theses are good programming practice BTW.

For versioning system .vi files are binary blob (800 kb diff to just move a wire so that it avoid a text label ??? )
So no way to know what modification have been made except trusting the commit message. 

I had to throw away 2 month of data / 2 month of lab view coding because one commit was introducing a bug, 
and there was no way to remove just the effect of this commit.

I suppose most of these problem could be fixed in some non trivial way, but they are not in labview.

As a Scientist and a Programmer IMHO the project is not managed in any way. 
And I don't see how one can really manage a project in labview.

A good managed project should be easily 
  * shared, 
  * explained 
  * reusable by other (other can be me in 3 years),

And right now, no labview project I know of have survived their creator / been modified by others. 
Which is really scary in an era of reproducible science.

The others things that concern me is the inability to search for help.

Question/anwser are made of **screenshot**. 
You don't even know what the boxes are and what they do, they don't have name. 
You don't know in which submenu to get them. 
Boxes can have several representation.
Sometime boxes change appearance when you change an option in it !

Inability to search for help is also due to that fact that as things don't have name, 
you can't search for it, and everyone is reinventing its naming.

All that and other make me think that labview is not good for complex project.

I hope those are issues that can be solved by people that are trying to do the same,
but some of those are IMHO inherent to the graphical paradigm used.
Rapidly, crossing wires are unavoidable in 2d space for example.

As a bonus, that also highlight another problem.
Try to guess what this simplified snippet does
http://imgur.com/PEgeq,n47uH#1  
http://imgur.com/PEgeq,n47uH#0 (condition of the if statement set to true)

It also allow people that does not know labview to understand what it looks like.

Solution in  rot13 : 
Vg gel gb perngr svyr jvgu tvira anzr, vs fhpu n svyr rkvfg vg vaperzragf gur anzr ...
Qvq fbzrobql frr gur raq bs gur sbe ybbc ng gur obggbz bs gur fperrafubg ?

TL;DR: 
  I think Labview Sucks, I hope other FlowPrograming will find a way to correct It, I wish them Luck.

-- 
Matthias



> 
> Cheers,
> Eraldo 
> 
> 
> 
> 
> On Wed, Nov 21, 2012 at 4:48 PM, Charles R Harris <charlesr.harris at gmail.com> wrote:
> 
> 
> On Wed, Nov 21, 2012 at 8:01 AM, Neal Becker <ndbecker2 at gmail.com> wrote:
> Charles R Harris wrote:
> 
> > On Tue, Nov 20, 2012 at 11:41 AM, Cera, Tim <tim at cerazone.net> wrote:
> >
> >>
> >> As is, the block diagram editing is done in libre office draw and you have
> >>> to manually type in the functions and commands, I have
> >>> attached an example exported to pdf.
> >>
> >>
> >>
> >> Would anyone be willing to help with this, I have no experience developing
> >>> with the open source community.
> >>>
> >>
> >> I won't be able to help, except to give some information.  Found this
> >> http://wiki.python.org/moin/FlowBasedProgramming a long time ago which
> >> might be useful.  Some of the links are broken now, and some of the others
> >> are really old, but something there might be helpful.
> >>
> >> In general, flow based programming hasn't caught on.   I think partially
> >> because of reasons described in the old saying, "To hell with tradition, we
> >> are going to do it like we always did!"
> >>
> >>
> > Simulink is pretty widely used, especially for modelling and rapid
> > development of control software.  Equipment vendors provide blocks for
> > their devices, gyroscopes and such, that can be used for the models and
> > then Matlab will generate control code to run on the targeted system.
> > Simulink itself is basically a way of setting up a big system of DEs, but
> > what really makes it go are the vendor blocks and code generation.
> >
> > Chuck
> 
> So why would vlsi guys use text (e.g., verilog) to design a cpu, instead of
> schematics?
> 
> 1. IMO, graphical representations work nicely for low-complexity, but not
> productive for highly complex systems
> 
> 2. It is less productive to manipulate a graphical  representation
> 
> 3. text can be manipulated by all your favorite tools, more open ecosystem, no
> lockin, proprietary formats
> 
> 
> I'm not saying it's the best way, just that Simulink is widely used and is part of a mature ecosystem. FPGA design software, say Xilinx ISE, does have a visual front end, generally in tabular form. In that regard it is rather like gui design tools where objects can be opened and their attributes set. I think the thing that makes all of those tools go is code generation, the ability run simulations, and to insert probes that display values in graphical form as the simulation progresses. IIRC, Simulink can also be used to drive hardware for breadboarding designs.
> 
> Chuck  
> 
> 
> _______________________________________________
> SciPy-Dev mailing list
> SciPy-Dev at scipy.org
> http://mail.scipy.org/mailman/listinfo/scipy-dev
> 
> 
> _______________________________________________
> SciPy-Dev mailing list
> SciPy-Dev at scipy.org
> http://mail.scipy.org/mailman/listinfo/scipy-dev

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From dreid at dwightreid.com  Wed Nov 21 17:56:51 2012
From: dreid at dwightreid.com (dwight reid)
Date: Wed, 21 Nov 2012 14:56:51 -0800 (PST)
Subject: [SciPy-Dev] Python Scipy Block Diagram Editor with ACG
In-Reply-To: <6D43A24A-E58B-4C98-8A5E-736A3B7D3E62@gmail.com>
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Message-ID: <1353538611.12061.YahooMailNeo@web5720.biz.mail.ne1.yahoo.com>

Guys,
I think graphical programming is more appreciated by people who are not traditional programmers but who have to use programming as a tool to get a bigger job done. A common example is control system development, like for an aircraft. Simulink got popular because it allows the designer to model the dynamics of the system with generic blocks, simulate that system and then design and tweak a controller to work with the system. So it allows simulating the system the way you would do a circuit in a good spice simulator and with code generation you can then implement your final controller with the click of a button (somewhat). 

Its a powerful tool and obviously engineers love it. The block diagram seems to make it easier to understand what the program is doing and we must note that most new designs start as block diagrams anyway.

As we know there are good ways and bad ways of doing things, a text based code can be just as impossible to debug if it is not documented properly as a complicated block diagram.

DR




________________________________
 From: Matthias BUSSONNIER <bussonniermatthias at gmail.com>
To: SciPy Developers List <scipy-dev at scipy.org> 
Sent: Wednesday, November 21, 2012 1:43 PM
Subject: Re: [SciPy-Dev] Python Scipy Block Diagram Editor with ACG
 

Hi list,?

Le 21 nov. 2012 ? 17:21, Eraldo Pomponi a ?crit :

AFAIK the best example of visual programming/interaction is LabView (http://www.ni.com/labview/).?
>
>I agree that many scientist don't like it but it is really widely adopted not just for control theory and application.?
>It was also the subject of a "Patent Litigation" between MatWorks (Simulink) and NI (http://www.ni.com/pdf/products/us/patent_litigation_faq.pdf)......
>Ni won!?
>I think that it shows?pretty?much cleanly that complex projects can be managed completely graphically if ?the environment is enough mature for that.?
>
>LabView seems to meet that requirement. Of course it is NOT open. This is why I do not use it.?


It is not because something is widely adopted that it is well used, and does its job.
In this case it does not prove that Labview allow to managed correctly things,
at best?that people achieve to (sort of) work with that.

To be working in a lab that does use labview and to be forced to use it,?
one of the main reason lab view is used it because it comes with drivers for instrument,?
and support that goes with it.

The others being:
? * ?it is already use by others nearby scientist.
? * ?scientist think do not know how to program,
? * ?they need a visual interface fast
? * The lab have already paid for the license you better have to use it.


We use labview for are optical tweezer and microscope control, which is a pretty big piece of software in labview.
The code exist for years, when I arrived each files had a v0.1, v0.1.1?.v0.9-bis, first file was 4 year old.
The working copy was the v0.8-smth.?The way labview is made we have to copy and past things all around,
have global variable, it is not unit tested.
We all know theses are good programming practice BTW.

For versioning system .vi files are binary blob (800 kb diff to just move a wire so that it avoid a text label ??? )
So no way to know what modification have been made except trusting the commit message.?

I had to throw away 2 month of data / 2 month of lab view coding because one commit was introducing a bug,?
and there was no way to remove just the effect of this commit.

I suppose most of these problem could be fixed in some non trivial way, but they are not in labview.

As a Scientist and a Programmer IMHO the project is not managed in any way.?
And I don't see how one can really manage a project in labview.

A good managed project should be easily?
? * shared,?
? * explained?
? * reusable by other (other can be me in 3 years),

And right now, no labview project I know of have survived their creator / been modified by others.?
Which is really scary in an era?of reproducible science.

The others things that concern me is the inability to search for help.

Question/anwser are made of **screenshot**.?
You don't even know what the boxes are and what they do, they don't have name.?
You don't know in which submenu to get them.?
Boxes can have several representation.
Sometime boxes change appearance when you change an option in it !

Inability to search for help is also due to that fact that as things don't have name,?
you can't search for it, and everyone is reinventing its naming.

All that and other make me think that labview is not good for complex project.

I hope those are issues that can be solved by people that are trying to do the same,
but some of those are IMHO inherent to the graphical paradigm used.
Rapidly, crossing wires are unavoidable in 2d space for example.

As a bonus, that also highlight another problem.
Try to guess what this simplified snippet does
http://imgur.com/PEgeq,n47uH#1??
http://imgur.com/PEgeq,n47uH#0?(condition of the if statement set to true)

It also allow people that does not know labview to understand what it looks like.

Solution in ?rot13 :?
Vg gel gb perngr svyr jvgu tvira anzr, vs fhpu n svyr rkvfg vg vaperzragf gur anzr ...
Qvq fbzrobql frr gur raq bs gur sbe ybbc ng gur obggbz bs gur fperrafubg ?

TL;DR:?
? I think Labview Sucks, I hope other FlowPrograming will find a way to correct It, I wish them Luck.

--?
Matthias




>
>Cheers,
>Eraldo?
>
>
>
>
>
>
>
>On Wed, Nov 21, 2012 at 4:48 PM, Charles R Harris <charlesr.harris at gmail.com> wrote:
>
>
>>
>>
>>On Wed, Nov 21, 2012 at 8:01 AM, Neal Becker <ndbecker2 at gmail.com> wrote:
>>
>>Charles R Harris wrote:
>>>
>>>> On Tue, Nov 20, 2012 at 11:41 AM, Cera, Tim <tim at cerazone.net> wrote:
>>>>
>>>>>
>>>>> As is, the block diagram editing is done in libre office draw and you have
>>>>>> to manually type in the functions and commands, I have
>>>>>> attached an example exported to pdf.
>>>>>
>>>>>
>>>>>
>>>>> Would anyone be willing to help with this, I have no experience developing
>>>>>> with the open source community.
>>>>>>
>>>>>
>>>>> I won't be able to help, except to give some information. ?Found this
>>>>> http://wiki.python.org/moin/FlowBasedProgramming a long time ago which
>>>>> might be useful. ?Some of the links are broken now, and some of the others
>>>>> are really old, but something there might be helpful.
>>>>>
>>>>> In general, flow based programming hasn't caught on. ? I think partially
>>>>> because of reasons described in the old saying, "To hell with tradition, we
>>>>> are going to do it like we always did!"
>>>>>
>>>>>
>>>> Simulink is pretty widely used, especially for modelling and rapid
>>>> development of control software. ?Equipment vendors provide blocks for
>>>> their devices, gyroscopes and such, that can be used for the models and
>>>> then Matlab will generate control code to run on the targeted system.
>>>> Simulink itself is basically a way of setting up a big system of DEs, but
>>>> what really makes it go are the vendor blocks and code generation.
>>>>
>>>> Chuck
>>>
>>>So why would vlsi guys use text (e.g., verilog) to design a cpu, instead of
>>>schematics?
>>>
>>>1. IMO, graphical representations work nicely for low-complexity, but not
>>>productive for highly complex systems
>>>
>>>2. It is less productive to manipulate a graphical ?representation
>>>
>>>3. text can be manipulated by all your favorite tools, more open ecosystem, no
>>>lockin, proprietary formats
>>>
>>>
>>>
>>
>>I'm not saying it's the best way, just that Simulink is widely used and is part of a mature ecosystem. FPGA design software, say Xilinx ISE, does have a visual front end, generally in tabular form. In that regard it is rather like gui design tools where objects can be opened and their attributes set. I think the thing that makes all of those tools go is code generation, the ability run simulations, and to insert probes that display values in graphical form as the simulation progresses. IIRC, Simulink can also be used to drive hardware for breadboarding designs.
>>
>>Chuck? 
>>
>>
>>_______________________________________________
>>SciPy-Dev mailing list
>>SciPy-Dev at scipy.org
>>http://mail.scipy.org/mailman/listinfo/scipy-dev
>>
>>
>
_______________________________________________
>SciPy-Dev mailing list
>SciPy-Dev at scipy.org
>http://mail.scipy.org/mailman/listinfo/scipy-dev
>

_______________________________________________
SciPy-Dev mailing list
SciPy-Dev at scipy.org
http://mail.scipy.org/mailman/listinfo/scipy-dev
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From benny.malengier at gmail.com  Thu Nov 22 03:59:27 2012
From: benny.malengier at gmail.com (Benny Malengier)
Date: Thu, 22 Nov 2012 09:59:27 +0100
Subject: [SciPy-Dev] Python Scipy Block Diagram Editor with ACG
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2012/11/21 dwight reid <dreid at dwightreid.com>

> Guys,
> I think graphical programming is more appreciated by people who are not
> traditional programmers but who have to use programming as a tool to get a
> bigger job done. A common example is control system development, like for
> an aircraft. Simulink got popular because it allows the designer to model
> the dynamics of the system with generic blocks, simulate that system and
> then design and tweak a controller to work with the system. So it allows
> simulating the system the way you would do a circuit in a good spice
> simulator and with code generation you can then implement your final
> controller with the click of a button (somewhat).
>
> Its a powerful tool and obviously engineers love it. The block diagram
> seems to make it easier to understand what the program is doing and we must
> note that most new designs start as block diagrams anyway.
>
> As we know there are good ways and bad ways of doing things, a text based
> code can be just as impossible to debug if it is not documented properly as
> a complicated block diagram.
>

About all this, I'm no expert, but is Modelica not the way to go here?
http://en.wikipedia.org/wiki/Modelica

That does code generation, and uses ode/dae solvers to solve the resulting
equations. There have been open source attempts at a visual part:
http://www.euclides.dia.uned.es/Interactive/
https://www.modelica.org/Different-views-of-Modelica

I am sure they would welcome contribution of extra parts

There are two competing open source implementatins (JModelica,
openmodelica), and they use sundials ode solver or others to solve it.
They have python bridges that allow use of scipy:
https://openmodelica.org/index.php/home/tools/212 and
http://www.jmodelica.org/page/69

It has been mentioned many times on this list already that the current ode
solvers in scipy are _not_ state of the art. Several python wrappers of the
vastly improved sundials solvers are available on the internet (one partly
by me, scikit odes, no release, use trunk).

So, although better ode/dae solvers should be part of scipy in my view, the
block diagram approach is better aligned with the modelica approach I
believe.

Benny


>
> DR
>
>
>   ------------------------------
> *From:* Matthias BUSSONNIER <bussonniermatthias at gmail.com>
> *To:* SciPy Developers List <scipy-dev at scipy.org>
> *Sent:* Wednesday, November 21, 2012 1:43 PM
> *Subject:* Re: [SciPy-Dev] Python Scipy Block Diagram Editor with ACG
>
> Hi list,
>
> Le 21 nov. 2012 ? 17:21, Eraldo Pomponi a ?crit :
>
> AFAIK the best example of visual programming/interaction is LabView (
> http://www.ni.com/labview/).
> I agree that many scientist don't like it but it is really widely adopted
> not just for control theory and application.
> It was also the subject of a "Patent Litigation" between MatWorks
> (Simulink) and NI (
> http://www.ni.com/pdf/products/us/patent_litigation_faq.pdf)......
> Ni won!
> I think that it shows pretty much cleanly that complex projects can be
> managed completely graphically if  the environment is enough mature for
> that.
> LabView seems to meet that requirement. Of course it is NOT open. This is
> why I do not use it.
>
>
>
> It is not because something is widely adopted that it is well used, and
> does its job.
> In this case it does not prove that Labview allow to managed correctly
> things,
> at best that people achieve to (sort of) work with that.
>
> To be working in a lab that does use labview and to be forced to use it,
> one of the main reason lab view is used it because it comes with drivers
> for instrument,
> and support that goes with it.
>
> The others being:
>   *  it is already use by others nearby scientist.
>   *  scientist think do not know how to program,
>   *  they need a visual interface fast
>   * The lab have already paid for the license you better have to use it.
>
>
> We use labview for are optical tweezer and microscope control, which is a
> pretty big piece of software in labview.
> The code exist for years, when I arrived each files had a v0.1,
> v0.1.1?.v0.9-bis, first file was 4 year old.
> The working copy was the v0.8-smth. The way labview is made we have to
> copy and past things all around,
> have global variable, it is not unit tested.
> We all know theses are good programming practice BTW.
>
> For versioning system .vi files are binary blob (800 kb diff to just move
> a wire so that it avoid a text label ??? )
> So no way to know what modification have been made except trusting the
> commit message.
>
> I had to throw away 2 month of data / 2 month of lab view coding because
> one commit was introducing a bug,
> and there was no way to remove just the effect of this commit.
>
> I suppose most of these problem could be fixed in some non trivial way,
> but they are not in labview.
>
> As a Scientist and a Programmer IMHO the project is not managed in any
> way.
> And I don't see how one can really manage a project in labview.
>
> A good managed project should be easily
>   * shared,
>   * explained
>   * reusable by other (other can be me in 3 years),
>
> And right now, no labview project I know of have survived their creator /
> been modified by others.
> Which is really scary in an era of reproducible science.
>
> The others things that concern me is the inability to search for help.
>
> Question/anwser are made of **screenshot**.
> You don't even know what the boxes are and what they do, they don't have
> name.
> You don't know in which submenu to get them.
> Boxes can have several representation.
> Sometime boxes change appearance when you change an option in it !
>
> Inability to search for help is also due to that fact that as things don't
> have name,
> you can't search for it, and everyone is reinventing its naming.
>
> All that and other make me think that labview is not good for complex
> project.
>
> I hope those are issues that can be solved by people that are trying to do
> the same,
> but some of those are IMHO inherent to the graphical paradigm used.
> Rapidly, crossing wires are unavoidable in 2d space for example.
>
> As a bonus, that also highlight another problem.
> Try to guess what this simplified snippet does
> http://imgur.com/PEgeq,n47uH#1
> http://imgur.com/PEgeq,n47uH#0 (condition of the if statement set to true)
>
> It also allow people that does not know labview to understand what it
> looks like.
>
> Solution in  rot13 :
> Vg gel gb perngr svyr jvgu tvira anzr, vs fhpu n svyr rkvfg vg vaperzragf
> gur anzr ...
> Qvq fbzrobql frr gur raq bs gur sbe ybbc ng gur obggbz bs gur fperrafubg ?
>
> TL;DR:
>   I think Labview Sucks, I hope other FlowPrograming will find a way to
> correct It, I wish them Luck.
>
> --
> Matthias
>
>
>
>
> Cheers,
> Eraldo
>
>
>
>
> On Wed, Nov 21, 2012 at 4:48 PM, Charles R Harris <
> charlesr.harris at gmail.com> wrote:
>
>
>
> On Wed, Nov 21, 2012 at 8:01 AM, Neal Becker <ndbecker2 at gmail.com> wrote:
>
> Charles R Harris wrote:
>
> > On Tue, Nov 20, 2012 at 11:41 AM, Cera, Tim <tim at cerazone.net> wrote:
> >
> >>
> >> As is, the block diagram editing is done in libre office draw and you
> have
> >>> to manually type in the functions and commands, I have
> >>> attached an example exported to pdf.
> >>
> >>
> >>
> >> Would anyone be willing to help with this, I have no experience
> developing
> >>> with the open source community.
> >>>
> >>
> >> I won't be able to help, except to give some information.  Found this
> >> http://wiki.python.org/moin/FlowBasedProgramming a long time ago which
> >> might be useful.  Some of the links are broken now, and some of the
> others
> >> are really old, but something there might be helpful.
> >>
> >> In general, flow based programming hasn't caught on.   I think partially
> >> because of reasons described in the old saying, "To hell with
> tradition, we
> >> are going to do it like we always did!"
> >>
> >>
> > Simulink is pretty widely used, especially for modelling and rapid
> > development of control software.  Equipment vendors provide blocks for
> > their devices, gyroscopes and such, that can be used for the models and
> > then Matlab will generate control code to run on the targeted system.
> > Simulink itself is basically a way of setting up a big system of DEs, but
> > what really makes it go are the vendor blocks and code generation.
> >
> > Chuck
>
> So why would vlsi guys use text (e.g., verilog) to design a cpu, instead of
> schematics?
>
> 1. IMO, graphical representations work nicely for low-complexity, but not
> productive for highly complex systems
>
> 2. It is less productive to manipulate a graphical  representation
>
> 3. text can be manipulated by all your favorite tools, more open
> ecosystem, no
> lockin, proprietary formats
>
>
> I'm not saying it's the best way, just that Simulink is widely used and is
> part of a mature ecosystem. FPGA design software, say Xilinx ISE, does have
> a visual front end, generally in tabular form. In that regard it is rather
> like gui design tools where objects can be opened and their attributes set.
> I think the thing that makes all of those tools go is code generation, the
> ability run simulations, and to insert probes that display values in
> graphical form as the simulation progresses. IIRC, Simulink can also be
> used to drive hardware for breadboarding designs.
>
> Chuck
>
>
> _______________________________________________
> SciPy-Dev mailing list
> SciPy-Dev at scipy.org
> http://mail.scipy.org/mailman/listinfo/scipy-dev
>
>
> _______________________________________________
> SciPy-Dev mailing list
> SciPy-Dev at scipy.org
> http://mail.scipy.org/mailman/listinfo/scipy-dev
>
>
>
> _______________________________________________
> SciPy-Dev mailing list
> SciPy-Dev at scipy.org
> http://mail.scipy.org/mailman/listinfo/scipy-dev
>
>
>
> _______________________________________________
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> http://mail.scipy.org/mailman/listinfo/scipy-dev
>
>
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From pierre.haessig at crans.org  Thu Nov 22 04:17:20 2012
From: pierre.haessig at crans.org (Pierre Haessig)
Date: Thu, 22 Nov 2012 10:17:20 +0100
Subject: [SciPy-Dev] Python Scipy Block Diagram Editor with ACG
In-Reply-To: <1353538611.12061.YahooMailNeo@web5720.biz.mail.ne1.yahoo.com>
References: <1353433995.49181.YahooMailNeo@web5717.biz.mail.ne1.yahoo.com>
	<1353434503.64271.YahooMailNeo@web5717.biz.mail.ne1.yahoo.com>
	<CAO5s+D-8+Bg69rhbP9QbqwS-ZDUhkLrQo59i3HAXp-rP4Axj3w@mail.gmail.com>
	<CAB6mnx+R1D1W0868ccZxpUprW4qcA=GSsH2XuAUAjUwhqhruPg@mail.gmail.com>
	<k8iqcg$jje$1@ger.gmane.org>
	<CAB6mnx+T-oq81HUKOrb98ykcA0WhtoSHTgE226YQU8==U76ekg@mail.gmail.com>
	<CAEaCG7dkeAnHbb4kh9EG3cOKNToRQjtmre1F_cCCJf0hGuQUJg@mail.gmail.com>
	<6D43A24A-E58B-4C98-8A5E-736A3B7D3E62@gmail.com>
	<1353538611.12061.YahooMailNeo@web5720.biz.mail.ne1.yahoo.com>
Message-ID: <50ADEDA0.4070101@crans.org>

Hi,

I think a block diagram editor would be a great addition to the Python
scientific ecosystem. I've had this in mind for some years now, but
never put it seriously on my programming agenda.

Now, I would really make the difference between :
1) a block diagram editor ("Simulink/xcos/Modelica-like") which, as
Chuck said, is really a tool to describe a dynamical system (either a
physical system or a control system).
2) a visual programming environment, like Labview, which has many flaws
that Matthias forcefully described ;-)

Now, to come back closer to what Dwight presented, I think that using
the GUI from an existing Office suite won't lead far enough.
I've experienced a bit GUI programming on the closely related matter of
a schematic editor (schematics of electrical circuits : see
http://www.youtube.com/watch?v=HYv-6w8FCf4&feature=player_detailpage#t=39s).
This GUI is done in Python+Qt (PyQt or PySide as a matter of licensing
taste) with the key element being a QGraphicsView
(http://qt-project.org/doc/qt-4.8/graphicsview.html)  which handles the
display of the schematic.
I've really had a positive feeling with this graphical framework from
Qt. (However, I didn't practice with many others to allow for a fair
comparison).
Also, these years have seen the growing popularity of browser-based
editors (like https://www.circuitlab.com/) so that it may be worth
studying javascript/HTML5 frameworks (which I unfortunately never did).

Best,
Pierre

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From dreid at dwightreid.com  Thu Nov 22 12:09:57 2012
From: dreid at dwightreid.com (dwight reid)
Date: Thu, 22 Nov 2012 09:09:57 -0800 (PST)
Subject: [SciPy-Dev] Python Scipy Block Diagram Editor with ACG
In-Reply-To: <50ADEDA0.4070101@crans.org>
References: <1353433995.49181.YahooMailNeo@web5717.biz.mail.ne1.yahoo.com>
	<1353434503.64271.YahooMailNeo@web5717.biz.mail.ne1.yahoo.com>
	<CAO5s+D-8+Bg69rhbP9QbqwS-ZDUhkLrQo59i3HAXp-rP4Axj3w@mail.gmail.com>
	<CAB6mnx+R1D1W0868ccZxpUprW4qcA=GSsH2XuAUAjUwhqhruPg@mail.gmail.com>
	<k8iqcg$jje$1@ger.gmane.org>
	<CAB6mnx+T-oq81HUKOrb98ykcA0WhtoSHTgE226YQU8==U76ekg@mail.gmail.com>
	<CAEaCG7dkeAnHbb4kh9EG3cOKNToRQjtmre1F_cCCJf0hGuQUJg@mail.gmail.com>
	<6D43A24A-E58B-4C98-8A5E-736A3B7D3E62@gmail.com>
	<1353538611.12061.YahooMailNeo@web5720.biz.mail.ne1.yahoo.com>
	<50ADEDA0.4070101@crans.org>
Message-ID: <1353604197.39644.YahooMailNeo@web5708.biz.mail.ne1.yahoo.com>

Guys,

I agree with Pierre that the GUI from an existing Office suite won't lead far enough, which is where I need the help actually (with the GUI programming). I was hoping to maybe strip down Libre office draw and then tailor it to suit this application but from what I've seen so far it may be easier to build from scratch. 

Currently I am just parsing the .odf file, which is essentially XML. This proves relatively easy and I was hoping to continue with this file format for the GUI. If anyone knows of a minimal drawing program (open sourced of course) that can produce the .odf file or a similar format I would try to use it, also if there are any suggestions regarding a file format or general approach that would be welcomed.

Scilab Xcos looked like they were trying code generation for some micro-controllers but they seem to have stopped, does anyone have any experience using it for code generation?


For openModelica I would need to be pointed in the direction of using it for code generation, I haven't looked extensively but so far I can't see how to generate code with it. 



________________________________
 From: Pierre Haessig <pierre.haessig at crans.org>
To: SciPy Developers List <scipy-dev at scipy.org> 
Sent: Thursday, November 22, 2012 4:17 AM
Subject: Re: [SciPy-Dev] Python Scipy Block Diagram Editor with ACG
 
Hi,

I think a block diagram editor would be a great addition to the Python
scientific ecosystem. I've had this in mind for some years now, but
never put it seriously on my programming agenda.

Now, I would really make the difference between :
1) a block diagram editor ("Simulink/xcos/Modelica-like") which, as
Chuck said, is really a tool to describe a dynamical system (either a
physical system or a control system).
2) a visual programming environment, like Labview, which has many flaws
that Matthias forcefully described ;-)

Now, to come back closer to what Dwight presented, I think that using
the GUI from an existing Office suite won't lead far enough.
I've experienced a bit GUI programming on the closely related matter of
a schematic editor (schematics of electrical circuits : see
http://www.youtube.com/watch?v=HYv-6w8FCf4&feature=player_detailpage#t=39s).
This GUI is done in Python+Qt (PyQt or PySide as a matter of licensing
taste) with the key element being a QGraphicsView
(http://qt-project.org/doc/qt-4.8/graphicsview.html)? which handles the
display of the schematic.
I've really had a positive feeling with this graphical framework from
Qt. (However, I didn't practice with many others to allow for a fair
comparison).
Also, these years have seen the growing popularity of browser-based
editors (like https://www.circuitlab.com/) so that it may be worth
studying javascript/HTML5 frameworks (which I unfortunately never did).

Best,
Pierre


_______________________________________________
SciPy-Dev mailing list
SciPy-Dev at scipy.org
http://mail.scipy.org/mailman/listinfo/scipy-dev
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From mcp.stras at gmail.com  Sat Nov 24 00:50:51 2012
From: mcp.stras at gmail.com (Martin Campos Pinto)
Date: Sat, 24 Nov 2012 06:50:51 +0100
Subject: [SciPy-Dev] Gmres with Sparse Complex Matrices gives Segmentation
 fault (or NULL result)
Message-ID: <50B0603B.3070801@gmail.com>

Hi all, I am having some troubles using iterative solvers with sparse complex matrices. (I first posted that issue on the SciPy-User mailing list but I guess this one is more appropriate.)

So, here is an example with gmres: the script

from scipy import sparse
from numpy.linalg import norm
from numpy.random import rand
import scipy.sparse.linalg as spla

C = sparse.lil_matrix((10, 10), dtype=complex)
C.setdiag(rand(10))
C[0,3] = 1j
C = C.tocsr()
c = rand(10)+rand(10)*1j

x = spla.spsolve(C, c)
print "spsolve: norm(C*x - c) = ", norm(C*x - c)

(x,info) = spla.gmres(C, c)
print "gmres: norm(C*x - c) = ", norm(C*x - c)

gives as output:

spsolve: norm(C*x - c) =  1.57621370006e-16
Segmentation fault


Actually, sometimes I get this error message instead of a Segmentation fault:

Traceback (most recent call last):
  File "test_gmres_cplx.py", line 45, in <module>
    (x,info) = spla.gmres(C, c)
  File "/Library/Frameworks/EPD64.framework/Versions/7.2/lib/python2.7/site-packages/scipy/sparse/linalg/isolve/iterative.py", line 437, in gmres
    revcom(b, x, restrt, work, work2, iter_, resid, info, ndx1, ndx2, ijob)
SystemError: NULL result without error in PyObject_Call



Note that I have tested gmres with real sparse matrices, and it runs fine: Indeed

C = sparse.lil_matrix((10, 10))
C.setdiag(rand(10))
C = C.tocsr()
c = rand(10)

x = spla.spsolve(C, c)
print "spsolve: norm(C*x - c) = ", norm(C*x - c)

(x,info) = spla.gmres(C, c)
print "gmres: norm(C*x - c) = ", norm(C*x - c)

gives

spsolve: norm(C*x - c) =  6.93889390391e-18
gmres: norm(C*x - c) =  5.28860261481e-16


I have looked on the web for solutions but haven't found any. Some very old posts indicate similar errors but they don't come with an answer,
and I imagine that if those were due to bugs, they should have been fixed by now...

Am I doing something stupid here, or is that a real problem ? Is somebody aware of a solution ?
(I am using scipy version 0.10.1)

Thanks,
Martin

-- 
Martin Campos Pinto
LJLL, UPMC & CNRS



From pav at iki.fi  Sat Nov 24 04:40:06 2012
From: pav at iki.fi (Pauli Virtanen)
Date: Sat, 24 Nov 2012 11:40:06 +0200
Subject: [SciPy-Dev] Gmres with Sparse Complex Matrices gives
 Segmentation fault (or NULL result)
In-Reply-To: <50B0603B.3070801@gmail.com>
References: <50B0603B.3070801@gmail.com>
Message-ID: <k8q4lk$oa6$1@ger.gmane.org>

24.11.2012 07:50, Martin Campos Pinto kirjoitti:
[clip]
> I have looked on the web for solutions but haven't found any. Some very old posts
> indicate similar errors but they don't come with an answer,
> and I imagine that if those were due to bugs, they should have been fixed by now...
> 
> Am I doing something stupid here, or is that a real problem ? Is somebody aware of a solution ?
> (I am using scipy version 0.10.1)

I don't get a crash with this code example. Valgrind also does not show
anything, so I suppose this is something occurring only on OSX.

There are some known issues on OSX with Accelerate, but I'm not sure if
they are in play here.

Can you run `scipy.test("full", verbose=2)` without seeing problems?

-- 
Pauli Virtanen



From mcp.stras at gmail.com  Sat Nov 24 14:45:52 2012
From: mcp.stras at gmail.com (Martin Campos Pinto)
Date: Sat, 24 Nov 2012 20:45:52 +0100
Subject: [SciPy-Dev] Gmres with Sparse Complex Matrices gives
 Segmentation fault (or NULL result)
In-Reply-To: <k8q4lk$oa6$1@ger.gmane.org>
References: <50B0603B.3070801@gmail.com> <k8q4lk$oa6$1@ger.gmane.org>
Message-ID: <50B123F0.5060500@gmail.com>

Hi, thank you for the quick answer.

The run `scipy.test("full", verbose=2)' fails with the following error 
message (I'm only pasting the last few lines, but I can send the whole 
output if necessary...)


======================================================================
ERROR: Failure: ImportError 
(dlopen(/Library/Frameworks/EPD64.framework/Versions/7.2/lib/python2.7/site-packages/scipy/linalg/atlas_version.so, 
2): Symbol not found: _ATL_buildinfo
   Referenced from: 
/Library/Frameworks/EPD64.framework/Versions/7.2/lib/python2.7/site-packages/scipy/linalg/atlas_version.so
   Expected in: dynamic lookup
)
----------------------------------------------------------------------
Traceback (most recent call last):
   File 
"/Library/Frameworks/EPD64.framework/Versions/7.2/lib/python2.7/site-packages/nose/loader.py", 
line 390, in loadTestsFromName
     addr.filename, addr.module)
   File 
"/Library/Frameworks/EPD64.framework/Versions/7.2/lib/python2.7/site-packages/nose/importer.py", 
line 39, in importFromPath
     return self.importFromDir(dir_path, fqname)
   File 
"/Library/Frameworks/EPD64.framework/Versions/7.2/lib/python2.7/site-packages/nose/importer.py", 
line 86, in importFromDir
     mod = load_module(part_fqname, fh, filename, desc)
   File 
"/Library/Frameworks/EPD64.framework/Versions/7.2/lib/python2.7/site-packages/scipy/linalg/tests/test_atlas_version.py", 
line 6, in <module>
     import scipy.linalg.atlas_version
ImportError: 
dlopen(/Library/Frameworks/EPD64.framework/Versions/7.2/lib/python2.7/site-packages/scipy/linalg/atlas_version.so, 
2): Symbol not found: _ATL_buildinfo
   Referenced from: 
/Library/Frameworks/EPD64.framework/Versions/7.2/lib/python2.7/site-packages/scipy/linalg/atlas_version.so
   Expected in: dynamic lookup


======================================================================
FAIL: test_dot (test_blas.TestFBLAS1Simple)
----------------------------------------------------------------------
Traceback (most recent call last):
   File 
"/Library/Frameworks/EPD64.framework/Versions/7.2/lib/python2.7/site-packages/scipy/lib/blas/tests/test_blas.py", 
line 71, in test_dot
     assert_almost_equal(f([3j,-4,3-4j],[2,3,1]),-9+2j)
   File 
"/Library/Frameworks/EPD64.framework/Versions/7.2/lib/python2.7/site-packages/numpy/testing/utils.py", 
line 448, in assert_almost_equal
     raise AssertionError(msg)
AssertionError:
Arrays are not almost equal to 7 decimals
  ACTUAL: 0j
  DESIRED: (-9+2j)

======================================================================
FAIL: test_complex_dotc (test_blas.TestFBLAS1Simple)
----------------------------------------------------------------------
Traceback (most recent call last):
   File 
"/Library/Frameworks/EPD64.framework/Versions/7.2/lib/python2.7/site-packages/scipy/linalg/tests/test_blas.py", 
line 121, in test_complex_dotc
     assert_almost_equal(f([3j,-4,3-4j],[2,3j,1]),3-14j)
   File 
"/Library/Frameworks/EPD64.framework/Versions/7.2/lib/python2.7/site-packages/numpy/testing/utils.py", 
line 448, in assert_almost_equal
     raise AssertionError(msg)
AssertionError:
Arrays are not almost equal to 7 decimals
  ACTUAL: 0j
  DESIRED: (3-14j)

======================================================================
FAIL: test_complex_dotu (test_blas.TestFBLAS1Simple)
----------------------------------------------------------------------
Traceback (most recent call last):
   File 
"/Library/Frameworks/EPD64.framework/Versions/7.2/lib/python2.7/site-packages/scipy/linalg/tests/test_blas.py", 
line 115, in test_complex_dotu
     assert_almost_equal(f([3j,-4,3-4j],[2,3,1]),-9+2j)
   File 
"/Library/Frameworks/EPD64.framework/Versions/7.2/lib/python2.7/site-packages/numpy/testing/utils.py", 
line 448, in assert_almost_equal
     raise AssertionError(msg)
AssertionError:
Arrays are not almost equal to 7 decimals
  ACTUAL: 0j
  DESIRED: (-9+2j)

----------------------------------------------------------------------
Ran 5045 tests in 899.955s

FAILED (KNOWNFAIL=14, SKIP=29, errors=1, failures=3)





Le 11/24/12 10:40 AM, Pauli Virtanen a ?crit :
> 24.11.2012 07:50, Martin Campos Pinto kirjoitti:
> [clip]
>> I have looked on the web for solutions but haven't found any. Some very old posts
>> indicate similar errors but they don't come with an answer,
>> and I imagine that if those were due to bugs, they should have been fixed by now...
>>
>> Am I doing something stupid here, or is that a real problem ? Is somebody aware of a solution ?
>> (I am using scipy version 0.10.1)
> I don't get a crash with this code example. Valgrind also does not show
> anything, so I suppose this is something occurring only on OSX.
>
> There are some known issues on OSX with Accelerate, but I'm not sure if
> they are in play here.
>
> Can you run `scipy.test("full", verbose=2)` without seeing problems?
>

-- 
Martin Campos Pinto
http://www-irma.u-strasbg.fr/~campos



From hardbyte at gmail.com  Sat Nov 24 22:29:55 2012
From: hardbyte at gmail.com (Brian Thorne)
Date: Sun, 25 Nov 2012 16:29:55 +1300
Subject: [SciPy-Dev] Python Scipy Block Diagram Editor with ACG
In-Reply-To: <1353604197.39644.YahooMailNeo@web5708.biz.mail.ne1.yahoo.com>
References: <1353433995.49181.YahooMailNeo@web5717.biz.mail.ne1.yahoo.com>
	<1353434503.64271.YahooMailNeo@web5717.biz.mail.ne1.yahoo.com>
	<CAO5s+D-8+Bg69rhbP9QbqwS-ZDUhkLrQo59i3HAXp-rP4Axj3w@mail.gmail.com>
	<CAB6mnx+R1D1W0868ccZxpUprW4qcA=GSsH2XuAUAjUwhqhruPg@mail.gmail.com>
	<k8iqcg$jje$1@ger.gmane.org>
	<CAB6mnx+T-oq81HUKOrb98ykcA0WhtoSHTgE226YQU8==U76ekg@mail.gmail.com>
	<CAEaCG7dkeAnHbb4kh9EG3cOKNToRQjtmre1F_cCCJf0hGuQUJg@mail.gmail.com>
	<6D43A24A-E58B-4C98-8A5E-736A3B7D3E62@gmail.com>
	<1353538611.12061.YahooMailNeo@web5720.biz.mail.ne1.yahoo.com>
	<50ADEDA0.4070101@crans.org>
	<1353604197.39644.YahooMailNeo@web5708.biz.mail.ne1.yahoo.com>
Message-ID: <CAENe87rbqMcr5xgndy315pTvYzEME+4L3tZ4zdUw7tR6cEOoBQ@mail.gmail.com>

The PySimulator paper might be relevant - they tied into Modelica and have
a plugin based GUI [1].

[1] http://elib.dlr.de/77223/1/ecp12076523_PfeifferHellererHartwegOtter.pdf


On 23 November 2012 06:09, dwight reid <dreid at dwightreid.com> wrote:

> Guys,
>
> I agree with Pierre that the GUI from an existing Office suite won't lead
> far enough, which is where I need the help actually (with the GUI
> programming). I was hoping to maybe strip down Libre office draw and then
> tailor it to suit this application but from what I've seen so far it may be
> easier to build from scratch.
> Currently I am just parsing the .odf file, which is essentially XML. This
> proves relatively easy and I was hoping to continue with this file format
> for the GUI. If anyone knows of a minimal drawing program (open sourced of
> course) that can produce the .odf file or a similar format I would try to
> use it, also if there are any suggestions regarding a file format or
> general approach that would be welcomed.
>
> Scilab Xcos looked like they were trying code generation for some
> micro-controllers but they seem to have stopped, does anyone have any
> experience using it for code generation?
>
> For openModelica I would need to be pointed in the direction of using it
> for code generation, I haven't looked extensively but so far I can't see
> how to generate code with it.
>
>   ------------------------------
> *From:* Pierre Haessig <pierre.haessig at crans.org>
>
> *To:* SciPy Developers List <scipy-dev at scipy.org>
> *Sent:* Thursday, November 22, 2012 4:17 AM
>
> *Subject:* Re: [SciPy-Dev] Python Scipy Block Diagram Editor with ACG
>
> Hi,
>
> I think a block diagram editor would be a great addition to the Python
> scientific ecosystem. I've had this in mind for some years now, but
> never put it seriously on my programming agenda.
>
> Now, I would really make the difference between :
> 1) a block diagram editor ("Simulink/xcos/Modelica-like") which, as
> Chuck said, is really a tool to describe a dynamical system (either a
> physical system or a control system).
> 2) a visual programming environment, like Labview, which has many flaws
> that Matthias forcefully described ;-)
>
> Now, to come back closer to what Dwight presented, I think that using
> the GUI from an existing Office suite won't lead far enough.
> I've experienced a bit GUI programming on the closely related matter of
> a schematic editor (schematics of electrical circuits : see
> http://www.youtube.com/watch?v=HYv-6w8FCf4&feature=player_detailpage#t=39s
> ).
> This GUI is done in Python+Qt (PyQt or PySide as a matter of licensing
> taste) with the key element being a QGraphicsView
> (http://qt-project.org/doc/qt-4.8/graphicsview.html)  which handles the
> display of the schematic.
> I've really had a positive feeling with this graphical framework from
> Qt. (However, I didn't practice with many others to allow for a fair
> comparison).
> Also, these years have seen the growing popularity of browser-based
> editors (like https://www.circuitlab.com/) so that it may be worth
> studying javascript/HTML5 frameworks (which I unfortunately never did).
>
> Best,
> Pierre
>
>
> _______________________________________________
> SciPy-Dev mailing list
> SciPy-Dev at scipy.org
> http://mail.scipy.org/mailman/listinfo/scipy-dev
>
>
>
> _______________________________________________
> SciPy-Dev mailing list
> SciPy-Dev at scipy.org
> http://mail.scipy.org/mailman/listinfo/scipy-dev
>
>
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From pierre.haessig at crans.org  Sun Nov 25 15:11:23 2012
From: pierre.haessig at crans.org (Pierre Haessig)
Date: Sun, 25 Nov 2012 21:11:23 +0100
Subject: [SciPy-Dev] Python Scipy Block Diagram Editor with ACG
In-Reply-To: <CAENe87rbqMcr5xgndy315pTvYzEME+4L3tZ4zdUw7tR6cEOoBQ@mail.gmail.com>
References: <1353433995.49181.YahooMailNeo@web5717.biz.mail.ne1.yahoo.com>
	<1353434503.64271.YahooMailNeo@web5717.biz.mail.ne1.yahoo.com>
	<CAO5s+D-8+Bg69rhbP9QbqwS-ZDUhkLrQo59i3HAXp-rP4Axj3w@mail.gmail.com>
	<CAB6mnx+R1D1W0868ccZxpUprW4qcA=GSsH2XuAUAjUwhqhruPg@mail.gmail.com>
	<k8iqcg$jje$1@ger.gmane.org>
	<CAB6mnx+T-oq81HUKOrb98ykcA0WhtoSHTgE226YQU8==U76ekg@mail.gmail.com>
	<CAEaCG7dkeAnHbb4kh9EG3cOKNToRQjtmre1F_cCCJf0hGuQUJg@mail.gmail.com>
	<6D43A24A-E58B-4C98-8A5E-736A3B7D3E62@gmail.com>
	<1353538611.12061.YahooMailNeo@web5720.biz.mail.ne1.yahoo.com>
	<50ADEDA0.4070101@crans.org>
	<1353604197.39644.YahooMailNeo@web5708.biz.mail.ne1.yahoo.com>
	<CAENe87rbqMcr5xgndy315pTvYzEME+4L3tZ4zdUw7tR6cEOoBQ@mail.gmail.com>
Message-ID: <50B27B6B.6000206@crans.org>

Le 25/11/2012 04:29, Brian Thorne a ?crit :
> The PySimulator paper might be relevant - they tied into Modelica and
> have a plugin based GUI [1].
>
> [1] http://elib.dlr.de/77223/1/ecp12076523_PfeifferHellererHartwegOtter.pdf
This new project is pretty exciting ! Thanks for sharing.

However, though it is said to be open source, I didn't find any code on
https://code.google.com/p/pysimulator/ which seems to be the project
homepage.
I only trace fresh development news on 
http://www.vworker.com/RentACoder/misc/BidRequests/ShowBidRequest.asp?lngBidRequestId=1995703
which is a development method I'm not familiar with.

Best,
Pierre
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From hardbyte at gmail.com  Sun Nov 25 16:07:11 2012
From: hardbyte at gmail.com (Brian Thorne)
Date: Mon, 26 Nov 2012 10:07:11 +1300
Subject: [SciPy-Dev] Python Scipy Block Diagram Editor with ACG
In-Reply-To: <50B27B6B.6000206@crans.org>
References: <1353433995.49181.YahooMailNeo@web5717.biz.mail.ne1.yahoo.com>
	<1353434503.64271.YahooMailNeo@web5717.biz.mail.ne1.yahoo.com>
	<CAO5s+D-8+Bg69rhbP9QbqwS-ZDUhkLrQo59i3HAXp-rP4Axj3w@mail.gmail.com>
	<CAB6mnx+R1D1W0868ccZxpUprW4qcA=GSsH2XuAUAjUwhqhruPg@mail.gmail.com>
	<k8iqcg$jje$1@ger.gmane.org>
	<CAB6mnx+T-oq81HUKOrb98ykcA0WhtoSHTgE226YQU8==U76ekg@mail.gmail.com>
	<CAEaCG7dkeAnHbb4kh9EG3cOKNToRQjtmre1F_cCCJf0hGuQUJg@mail.gmail.com>
	<6D43A24A-E58B-4C98-8A5E-736A3B7D3E62@gmail.com>
	<1353538611.12061.YahooMailNeo@web5720.biz.mail.ne1.yahoo.com>
	<50ADEDA0.4070101@crans.org>
	<1353604197.39644.YahooMailNeo@web5708.biz.mail.ne1.yahoo.com>
	<CAENe87rbqMcr5xgndy315pTvYzEME+4L3tZ4zdUw7tR6cEOoBQ@mail.gmail.com>
	<50B27B6B.6000206@crans.org>
Message-ID: <CAENe87rN_LdZ8n-EPSEzgtDt21=YKrKSFbx_cbm2gY0rRdBGMw@mail.gmail.com>

It seems they have put their code on
https://code.google.com/p/pysimulator/as a download but haven't put it
under source control.

Cheers,
Brian


On 26 November 2012 09:11, Pierre Haessig <pierre.haessig at crans.org> wrote:

>  Le 25/11/2012 04:29, Brian Thorne a ?crit :
>
> The PySimulator paper might be relevant - they tied into Modelica and have
> a plugin based GUI [1].
>
>  [1]
> http://elib.dlr.de/77223/1/ecp12076523_PfeifferHellererHartwegOtter.pdf
>
> This new project is pretty exciting ! Thanks for sharing.
>
> However, though it is said to be open source, I didn't find any code on
> https://code.google.com/p/pysimulator/ which seems to be the project
> homepage.
> I only trace fresh development news on
> http://www.vworker.com/RentACoder/misc/BidRequests/ShowBidRequest.asp?lngBidRequestId=1995703which is a development method I'm not familiar with.
>
> Best,
> Pierre
>
> _______________________________________________
> SciPy-Dev mailing list
> SciPy-Dev at scipy.org
> http://mail.scipy.org/mailman/listinfo/scipy-dev
>
>
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From mcp.stras at gmail.com  Tue Nov 27 23:56:02 2012
From: mcp.stras at gmail.com (Martin Campos Pinto)
Date: Wed, 28 Nov 2012 05:56:02 +0100
Subject: [SciPy-Dev] Gmres with Sparse Complex Matrices gives
 Segmentation fault (or NULL result)
In-Reply-To: <k8q4lk$oa6$1@ger.gmane.org>
References: <50B0603B.3070801@gmail.com> <k8q4lk$oa6$1@ger.gmane.org>
Message-ID: <50B59962.1020205@gmail.com>

Hi,

I have just tried with scipy version 0.11.0, installed with mac ports 
and gmres runs without crashing.
Since scipy 0.10.1 was the package provided with EPD I first thought it 
should run fine...

Thank you,
Martin

-- ps. Also, just to check I have run your test `scipy.test("full", 
verbose=2)' with scipy 0.11.0 and there still is a problem.


Python 2.7.3 (default, Oct 22 2012, 06:12:28)
[GCC 4.2.1 (Apple Inc. build 5666) (dot 3)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
 >>> import scipy
 >>> scipy.test("full", verbose=2)
Running unit tests for scipy
NumPy version 1.6.2
NumPy is installed in 
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy
SciPy version 0.11.0
SciPy is installed in 
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy
Python version 2.7.3 (default, Oct 22 2012, 06:12:28) [GCC 4.2.1 (Apple 
Inc. build 5666) (dot 3)]
nose version 1.2.1
Tests cophenet(Z) on tdist data set. ... ok
Tests cophenet(Z, Y) on tdist data set. ... ok
Tests correspond(Z, y) on linkage and CDMs over observation sets of 
different sizes. ... ok
Tests correspond(Z, y) on linkage and CDMs over observation sets of 
different sizes. Correspondance should be false. ... ok
Tests correspond(Z, y) on linkage and CDMs over observation sets of 
different sizes. Correspondance should be false. ... ok
Tests correspond(Z, y) with empty linkage and condensed distance matrix. 
... ok
Tests num_obs_linkage with observation matrices of multiple sizes. ... ok
Tests dendrogram calculation on single linkage of the tdist data set. ... ok
Tests fcluster(Z, criterion='maxclust', t=2) on a random 3-cluster data 
set. ... ok

(...)

test_exclusive_end (test_slice_handler.TestBuildSliceAtom) ... ok
match slice from a[1:] ... ok
match slice from a[1::] ... ok
match slice from a[1:2] ... ok
match slice from a[1:2:] ... ok
match slice from a[1:2:3] ... ok
match slice from a[1::3] ... ok
match slice from a[:] ... ok
match slice from a[::] ... ok
match slice from a[:2] ... ok
match slice from a[:2:] ... ok
match slice from a[:2:3] ... ok
match slice from a[:1+i+2:] ... ok
match slice from a[0] ... ok
match slice from a[::3] ... ok
transform a[:] to slice notation ... ok
transform a[:,:] = b[:,1:1+2:3] *(c[1-2+i:,:] - c[:,:]) ... ok
test_type_match_array (test_standard_array_spec.TestArrayConverter) ... ok
test_type_match_int (test_standard_array_spec.TestArrayConverter) ... ok
test_type_match_string (test_standard_array_spec.TestArrayConverter) ... ok

======================================================================
FAIL: test_iv_cephes_vs_amos_mass_test (test_basic.TestBessel)
----------------------------------------------------------------------
Traceback (most recent call last):
   File 
"/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/special/tests/test_basic.py", 
line 1659, in test_iv_cephes_vs_amos_mass_test
     assert_(dc[k] < 2e-7, (v[k], x[k], special.iv(v[k], x[k]), 
special.iv(v[k], x[k]+0j)))
   File 
"/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/testing/utils.py", 
line 34, in assert_
     raise AssertionError(msg)
AssertionError: (189.2947429454936, 3.0238805556481037, 
4.089165443940765e-317, 0j)

----------------------------------------------------------------------
Ran 6217 tests in 1046.384s

FAILED (KNOWNFAIL=15, SKIP=32, failures=1)
<nose.result.TextTestResult run=6217 errors=0 failures=1>





Le 11/24/12 10:40 AM, Pauli Virtanen a ?crit :
> 24.11.2012 07:50, Martin Campos Pinto kirjoitti:
> [clip]
>> I have looked on the web for solutions but haven't found any. Some very old posts
>> indicate similar errors but they don't come with an answer,
>> and I imagine that if those were due to bugs, they should have been fixed by now...
>>
>> Am I doing something stupid here, or is that a real problem ? Is somebody aware of a solution ?
>> (I am using scipy version 0.10.1)
> I don't get a crash with this code example. Valgrind also does not show
> anything, so I suppose this is something occurring only on OSX.
>
> There are some known issues on OSX with Accelerate, but I'm not sure if
> they are in play here.
>
> Can you run `scipy.test("full", verbose=2)` without seeing problems?
>

-- 
Martin Campos Pinto
http://www-irma.u-strasbg.fr/~campos



From jrocher at enthought.com  Wed Nov 28 13:21:21 2012
From: jrocher at enthought.com (Jonathan Rocher)
Date: Wed, 28 Nov 2012 12:21:21 -0600
Subject: [SciPy-Dev] Request for Feedback/Authorization: a new public
	repository for the conference
Message-ID: <CAOzk5QeFo++4xOZagAZV-eeAW-QzQxqHMUTUUpGCg8FUDoGLyg@mail.gmail.com>

Dear all,

Andy Terrel and I are the co-chairs of the Scipy2013 conference in Austin
next June in Austin. We are very excited about this coming edition and will
post regularly to these lists for feedback and announcements.

But for now, we would like to consolidate its organization under a public
open source project inside the Scipy organization on github. We propose
that the project be called scipy-conference. The repo would host documents
useful to run the conference as well as code to set up the website and the
backend.

I write here to ask if the community is ok with that and to ask for the
rights to create/manage that new repository.

Thanks in advance,
Jonathan

-- 
Jonathan Rocher, PhD
Scientific software developer
Enthought, Inc.
jrocher at enthought.com
1-512-536-1057
http://www.enthought.com
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From pav at iki.fi  Wed Nov 28 13:26:19 2012
From: pav at iki.fi (Pauli Virtanen)
Date: Wed, 28 Nov 2012 20:26:19 +0200
Subject: [SciPy-Dev] Gmres with Sparse Complex Matrices gives
 Segmentation fault (or NULL result)
In-Reply-To: <50B59962.1020205@gmail.com>
References: <50B0603B.3070801@gmail.com> <k8q4lk$oa6$1@ger.gmane.org>
	<50B59962.1020205@gmail.com>
Message-ID: <k95l0a$rj5$1@ger.gmane.org>

Hi,

28.11.2012 06:56, Martin Campos Pinto kirjoitti:
> I have just tried with scipy version 0.11.0, installed with mac ports 
> and gmres runs without crashing.
> Since scipy 0.10.1 was the package provided with EPD I first thought it 
> should run fine...

That is sort of strange in itself, given that there are essentially no
changes between 0.10.1 and 0.11.0 in that part of code. The test suite
also includes complex-valued test problems for gmres, so it not crashing
is also not immediately understood.

If the crashing version was 0.9.0 or earlier, then I'd understand what
is going on... If you still can, double-checking what
'print scipy.__version__' said could be useful.

But nice to hear it works now. (And for future reference, PyAMG contains
pure-python Krylov solvers, including gmres.)

Best,
Pauli




From robert.kern at gmail.com  Wed Nov 28 13:28:09 2012
From: robert.kern at gmail.com (Robert Kern)
Date: Wed, 28 Nov 2012 19:28:09 +0100
Subject: [SciPy-Dev] Request for Feedback/Authorization: a new public
 repository for the conference
In-Reply-To: <CAOzk5QeFo++4xOZagAZV-eeAW-QzQxqHMUTUUpGCg8FUDoGLyg@mail.gmail.com>
References: <CAOzk5QeFo++4xOZagAZV-eeAW-QzQxqHMUTUUpGCg8FUDoGLyg@mail.gmail.com>
Message-ID: <CAF6FJis+C7u--VKQ0==Mu-qUCExyW3PQr+n+7XTejMQv8=bjTg@mail.gmail.com>

On Wed, Nov 28, 2012 at 7:21 PM, Jonathan Rocher <jrocher at enthought.com> wrote:
> Dear all,
>
> Andy Terrel and I are the co-chairs of the Scipy2013 conference in Austin
> next June in Austin. We are very excited about this coming edition and will
> post regularly to these lists for feedback and announcements.
>
> But for now, we would like to consolidate its organization under a public
> open source project inside the Scipy organization on github. We propose that
> the project be called scipy-conference. The repo would host documents useful
> to run the conference as well as code to set up the website and the backend.
>
> I write here to ask if the community is ok with that and to ask for the
> rights to create/manage that new repository.

+1. If there is no strenuous objection in short order, I will make a
"SciPy Conference" team under the scipy organization and add you two
to it.

--
Robert Kern


From scopatz at gmail.com  Wed Nov 28 13:33:41 2012
From: scopatz at gmail.com (Anthony Scopatz)
Date: Wed, 28 Nov 2012 12:33:41 -0600
Subject: [SciPy-Dev] Request for Feedback/Authorization: a new public
 repository for the conference
In-Reply-To: <CAF6FJis+C7u--VKQ0==Mu-qUCExyW3PQr+n+7XTejMQv8=bjTg@mail.gmail.com>
References: <CAOzk5QeFo++4xOZagAZV-eeAW-QzQxqHMUTUUpGCg8FUDoGLyg@mail.gmail.com>
	<CAF6FJis+C7u--VKQ0==Mu-qUCExyW3PQr+n+7XTejMQv8=bjTg@mail.gmail.com>
Message-ID: <CAPk-6T4d3XiUmLZpfWg8T1e8CZ-0aR757y5f3f+osh+2-gArVQ@mail.gmail.com>

On Wed, Nov 28, 2012 at 12:28 PM, Robert Kern <robert.kern at gmail.com> wrote:

> On Wed, Nov 28, 2012 at 7:21 PM, Jonathan Rocher <jrocher at enthought.com>
> wrote:
> > Dear all,
> >
> > Andy Terrel and I are the co-chairs of the Scipy2013 conference in Austin
> > next June in Austin. We are very excited about this coming edition and
> will
> > post regularly to these lists for feedback and announcements.
> >
> > But for now, we would like to consolidate its organization under a public
> > open source project inside the Scipy organization on github. We propose
> that
> > the project be called scipy-conference. The repo would host documents
> useful
> > to run the conference as well as code to set up the website and the
> backend.
> >
> > I write here to ask if the community is ok with that and to ask for the
> > rights to create/manage that new repository.
>
> +1. If there is no strenuous objection in short order, I will make a
> "SciPy Conference" team under the scipy organization and add you two
> to it.
>

+1 as well.


>
> --
> Robert Kern
> _______________________________________________
> SciPy-Dev mailing list
> SciPy-Dev at scipy.org
> http://mail.scipy.org/mailman/listinfo/scipy-dev
>
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From pav at iki.fi  Wed Nov 28 13:30:53 2012
From: pav at iki.fi (Pauli Virtanen)
Date: Wed, 28 Nov 2012 20:30:53 +0200
Subject: [SciPy-Dev] Request for Feedback/Authorization: a new public
 repository for the conference
In-Reply-To: <CAF6FJis+C7u--VKQ0==Mu-qUCExyW3PQr+n+7XTejMQv8=bjTg@mail.gmail.com>
References: <CAOzk5QeFo++4xOZagAZV-eeAW-QzQxqHMUTUUpGCg8FUDoGLyg@mail.gmail.com>
	<CAF6FJis+C7u--VKQ0==Mu-qUCExyW3PQr+n+7XTejMQv8=bjTg@mail.gmail.com>
Message-ID: <k95l8q$tdd$1@ger.gmane.org>

28.11.2012 20:28, Robert Kern kirjoitti:
[clip]
> +1. If there is no strenuous objection in short order, I will make a
> "SciPy Conference" team under the scipy organization and add you two
> to it.

+1 also from me.

-- 
Pauli Virtanen




From robert.kern at gmail.com  Wed Nov 28 13:37:32 2012
From: robert.kern at gmail.com (Robert Kern)
Date: Wed, 28 Nov 2012 19:37:32 +0100
Subject: [SciPy-Dev] Request for Feedback/Authorization: a new public
 repository for the conference
In-Reply-To: <k95l8q$tdd$1@ger.gmane.org>
References: <CAOzk5QeFo++4xOZagAZV-eeAW-QzQxqHMUTUUpGCg8FUDoGLyg@mail.gmail.com>
	<CAF6FJis+C7u--VKQ0==Mu-qUCExyW3PQr+n+7XTejMQv8=bjTg@mail.gmail.com>
	<k95l8q$tdd$1@ger.gmane.org>
Message-ID: <CAF6FJisfOMWsx8LSvyC6K6Pu_vb4rYYHKXqiQf97mCwGKC9GZw@mail.gmail.com>

On Wed, Nov 28, 2012 at 7:30 PM, Pauli Virtanen <pav at iki.fi> wrote:
> 28.11.2012 20:28, Robert Kern kirjoitti:
> [clip]
>> +1. If there is no strenuous objection in short order, I will make a
>> "SciPy Conference" team under the scipy organization and add you two
>> to it.
>
> +1 also from me.

On the basis of exit polls, I'm calling this election early. Done.

--
Robert Kern


From jrocher at enthought.com  Wed Nov 28 13:44:44 2012
From: jrocher at enthought.com (Jonathan Rocher)
Date: Wed, 28 Nov 2012 12:44:44 -0600
Subject: [SciPy-Dev] Request for Feedback/Authorization: a new public
 repository for the conference
In-Reply-To: <CAF6FJisfOMWsx8LSvyC6K6Pu_vb4rYYHKXqiQf97mCwGKC9GZw@mail.gmail.com>
References: <CAOzk5QeFo++4xOZagAZV-eeAW-QzQxqHMUTUUpGCg8FUDoGLyg@mail.gmail.com>
	<CAF6FJis+C7u--VKQ0==Mu-qUCExyW3PQr+n+7XTejMQv8=bjTg@mail.gmail.com>
	<k95l8q$tdd$1@ger.gmane.org>
	<CAF6FJisfOMWsx8LSvyC6K6Pu_vb4rYYHKXqiQf97mCwGKC9GZw@mail.gmail.com>
Message-ID: <CAOzk5QdrwSM1+sD8HwpmDJ-VsYcYsHL_gnvdVVXFHdR_CRTxPw@mail.gmail.com>

:)


On Wed, Nov 28, 2012 at 12:37 PM, Robert Kern <robert.kern at gmail.com> wrote:

> On Wed, Nov 28, 2012 at 7:30 PM, Pauli Virtanen <pav at iki.fi> wrote:
> > 28.11.2012 20:28, Robert Kern kirjoitti:
> > [clip]
> >> +1. If there is no strenuous objection in short order, I will make a
> >> "SciPy Conference" team under the scipy organization and add you two
> >> to it.
> >
> > +1 also from me.
>
> On the basis of exit polls, I'm calling this election early. Done.
>
> --
> Robert Kern
> _______________________________________________
> SciPy-Dev mailing list
> SciPy-Dev at scipy.org
> http://mail.scipy.org/mailman/listinfo/scipy-dev
>



-- 
Jonathan Rocher, PhD
Scientific software developer
Enthought, Inc.
jrocher at enthought.com
1-512-536-1057
http://www.enthought.com
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From jrocher at enthought.com  Wed Nov 28 14:33:40 2012
From: jrocher at enthought.com (Jonathan Rocher)
Date: Wed, 28 Nov 2012 13:33:40 -0600
Subject: [SciPy-Dev] [SciPy-User] Request for Feedback/Authorization: a
 new public repository for the conference
In-Reply-To: <k95nvs$m7a$1@ger.gmane.org>
References: <CAOzk5QeFo++4xOZagAZV-eeAW-QzQxqHMUTUUpGCg8FUDoGLyg@mail.gmail.com>
	<CAF6FJis+C7u--VKQ0==Mu-qUCExyW3PQr+n+7XTejMQv8=bjTg@mail.gmail.com>
	<k95l8q$tdd$1@ger.gmane.org>
	<CAF6FJisfOMWsx8LSvyC6K6Pu_vb4rYYHKXqiQf97mCwGKC9GZw@mail.gmail.com>
	<k95nvs$m7a$1@ger.gmane.org>
Message-ID: <CAOzk5QdGJK7rvNrj7qOT6d++KTiQkwqQ2ooLThx96w4c5KVwBA@mail.gmail.com>

Thanks to all.

Jonathan


On Wed, Nov 28, 2012 at 1:17 PM, Pauli Virtanen <pav at iki.fi> wrote:

> 28.11.2012 20:37, Robert Kern kirjoitti:
> > On Wed, Nov 28, 2012 at 7:30 PM, Pauli Virtanen <pav at iki.fi> wrote:
> >> 28.11.2012 20:28, Robert Kern kirjoitti:
> >> [clip]
> >>> +1. If there is no strenuous objection in short order, I will make a
> >>> "SciPy Conference" team under the scipy organization and add you two
> >>> to it.
> >>
> >> +1 also from me.
> >
> > On the basis of exit polls, I'm calling this election early. Done.
>
> The repo is now also there, so things should be ready to roll.
>
> --
> Pauli Virtanen
>
>
> _______________________________________________
> SciPy-User mailing list
> SciPy-User at scipy.org
> http://mail.scipy.org/mailman/listinfo/scipy-user
>



-- 
Jonathan Rocher, PhD
Scientific software developer
Enthought, Inc.
jrocher at enthought.com
1-512-536-1057
http://www.enthought.com
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From jtravs at gmail.com  Thu Nov 29 10:35:00 2012
From: jtravs at gmail.com (John Travers)
Date: Thu, 29 Nov 2012 16:35:00 +0100
Subject: [SciPy-Dev] PR: Add solout support to dopri5 and dop853
Message-ID: <FC8BF45E-A4E9-4ECF-B3DE-53E19CE53568@gmail.com>

Hi all,

I realise that the ode code has its problems/detractors, but I needed a long requested feature, so I tried to add it:

https://github.com/scipy/scipy/pull/366

This enables the use of a callback function which is called at each internal integration step of dopri5 or dop853. This is useful to monitor the ode evolution at its natural time-scale without increasing the output density. It also enables stopping the integration mid-way.

This feature was requested quite a while ago, just before my absence from scipy development:

http://mail.scipy.org/pipermail/scipy-dev/2010-September/015540.html

Comments/improvements welcome.

Cheers,
John