From jorgen.stenarson at bostream.nu  Thu Apr  6 14:26:22 2006
From: jorgen.stenarson at bostream.nu (=?ISO-8859-1?Q?J=F6rgen_Stenarson?=)
Date: Thu, 06 Apr 2006 20:26:22 +0200
Subject: [IPython-dev] memory leak?
Message-ID: <44355D4E.10905@bostream.nu>

hi,

lately I have been using ipython to %run scripts that create large 
numeric arrays (in my case say 1000x1000 complex numbers). The problem I 
see is that when I rerun the script its like all variables created in 
that file are not freed even though if they have not been accessed in a 
way that would put them in the In or Out cache. For instance %running a 
file containing

import Numeric
a=Numeric.zeros((1000,1000),"D")

repeatedly without any intervening commands will have memory usage go up 
with every invocation of %run. But using execfile from an ordinary 
python prompt on the same file this is not the case. Is this a known 
problem (I'm on windows)? If it is, is there some way to manually free 
this memory?

/J?rgen



From Fernando.Perez at colorado.edu  Fri Apr  7 04:46:27 2006
From: Fernando.Perez at colorado.edu (Fernando Perez)
Date: Fri, 07 Apr 2006 10:46:27 +0200
Subject: [IPython-dev] memory leak?
In-Reply-To: <44355D4E.10905@bostream.nu>
References: <44355D4E.10905@bostream.nu>
Message-ID: <443626E3.3050702@colorado.edu>

J?rgen Stenarson wrote:
> hi,
> 
> lately I have been using ipython to %run scripts that create large 
> numeric arrays (in my case say 1000x1000 complex numbers). The problem I 
> see is that when I rerun the script its like all variables created in 
> that file are not freed even though if they have not been accessed in a 
> way that would put them in the In or Out cache. For instance %running a 
> file containing
> 
> import Numeric
> a=Numeric.zeros((1000,1000),"D")
> 
> repeatedly without any intervening commands will have memory usage go up 
> with every invocation of %run. But using execfile from an ordinary 
> python prompt on the same file this is not the case. Is this a known 
> problem (I'm on windows)? If it is, is there some way to manually free 
> this memory?

I suspect the difference comes from the fact that ipython  updates the 
interactive namespace with the namespace where execfile() ran, so you do end 
up holding a reference to 'a' in your user namespace.  However, on each run 
this reference gets updated, so at least all previous instances should be freed.

IPython can't strictly speaking _leak_ memory in the C sense, given that we 
have no extension code of our own.  What can happen is that we hold references 
to stuff which prevent garbage collection from doing its job.  Just a 
technicality (since the end effect is the same, lost memory), but I wanted to 
clarify the language.

Try running a garbage collection manually,  that may help:

import gc
gc.collect()

and let us know what you see.

Cheers,

f



From jorgen.stenarson at bostream.nu  Fri Apr  7 13:45:28 2006
From: jorgen.stenarson at bostream.nu (=?ISO-8859-1?Q?J=F6rgen_Stenarson?=)
Date: Fri, 07 Apr 2006 19:45:28 +0200
Subject: [IPython-dev] memory leak?
In-Reply-To: <443626E3.3050702@colorado.edu>
References: <44355D4E.10905@bostream.nu> <443626E3.3050702@colorado.edu>
Message-ID: <4436A538.2050102@bostream.nu>

Fernando Perez skrev:
> J?rgen Stenarson wrote:
>> hi,
>>
>> lately I have been using ipython to %run scripts that create large 
>> numeric arrays (in my case say 1000x1000 complex numbers). The problem 
>> I see is that when I rerun the script its like all variables created 
>> in that file are not freed even though if they have not been accessed 
>> in a way that would put them in the In or Out cache. For instance 
>> %running a file containing
>>
>> import Numeric
>> a=Numeric.zeros((1000,1000),"D")
>>
>> repeatedly without any intervening commands will have memory usage go 
>> up with every invocation of %run. But using execfile from an ordinary 
>> python prompt on the same file this is not the case. Is this a known 
>> problem (I'm on windows)? If it is, is there some way to manually free 
>> this memory?
> 
> I suspect the difference comes from the fact that ipython  updates the 
> interactive namespace with the namespace where execfile() ran, so you do 
> end up holding a reference to 'a' in your user namespace.  However, on 
> each run this reference gets updated, so at least all previous instances 
> should be freed.
> 
> IPython can't strictly speaking _leak_ memory in the C sense, given that 
> we have no extension code of our own.  What can happen is that we hold 
> references to stuff which prevent garbage collection from doing its 
> job.  Just a technicality (since the end effect is the same, lost 
> memory), but I wanted to clarify the language.
> 
> Try running a garbage collection manually,  that may help:
> 
> import gc
> gc.collect()
> 
> and let us know what you see.
> 
> Cheers,
> 
> f
> 

Hi,

The gc.collect() works as long as I have not done something that will 
put results in Out. I have tried Out.clear() and deleting all _x where x 
is a number. But that doesn't do the trick, is there some other way of 
clearing the output cache?

/J?rgen



From hans_meine at gmx.net  Sat Apr  8 07:59:50 2006
From: hans_meine at gmx.net (Hans Meine)
Date: Sat, 8 Apr 2006 13:59:50 +0200
Subject: [IPython-dev] memory leak?
In-Reply-To: <4436A538.2050102@bostream.nu>
References: <44355D4E.10905@bostream.nu> <443626E3.3050702@colorado.edu>
	<4436A538.2050102@bostream.nu>
Message-ID: <200604081359.51145.hans_meine@gmx.net>

On Friday 07 April 2006 19:45, J?rgen Stenarson wrote:
> The gc.collect() works as long as I have not done something that will
> put results in Out. I have tried Out.clear() and deleting all _x where x
> is a number. But that doesn't do the trick, is there some other way of
> clearing the output cache?

Ah, yes!  That would be a feature I have been looking for many times 
already! :-)

Sth. like the following would be great:

%clearout - clear whole cache
%clearout 112 - clear one line
%clearout :100 140:150 113 - clear multiple (sub)ranges

/me looking forward to Fernandos' "That has been there for ages" comment.
(Or to his time machine?) ;-)

-- 
Ciao, /  /                                                    .o.
     /--/                                                     ..o
    /  / ANS                                                  ooo
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From vivainio at gmail.com  Sat Apr  8 19:45:53 2006
From: vivainio at gmail.com (Ville Vainio)
Date: Sat, 8 Apr 2006 16:45:53 -0700
Subject: [IPython-dev] memory leak?
In-Reply-To: <200604081359.51145.hans_meine@gmx.net>
References: <44355D4E.10905@bostream.nu> <443626E3.3050702@colorado.edu>
	<200604081359.51145.hans_meine@gmx.net>
Message-ID: <46cb515a0604081645y5b492116kcfe03c2b84a079b0@mail.gmail.com>

On 4/8/06, Hans Meine <hans_meine at gmx.net> wrote:

> Sth. like the following would be great:
>
> %clearout - clear whole cache
> %clearout 112 - clear one line
> %clearout :100 140:150 113 - clear multiple (sub)ranges

I'll take a look at this over the next week, I have winter holiday so
I should have plenty of time & energy to play with stuff like this.

--
Ville Vainio - vivainio.googlepages.com
vainio.blogspot.com - g[mail | talk]='vivainio'



From vivainio at gmail.com  Sun Apr  9 14:54:55 2006
From: vivainio at gmail.com (Ville Vainio)
Date: Sun, 9 Apr 2006 11:54:55 -0700
Subject: [IPython-dev] [IPython-user] running ipython from command line
	with pysh	profile does not work
In-Reply-To: <70ec82800604090929i6a4b9f78s60d86eeee5ff1551@mail.gmail.com>
References: <70ec82800604090048h528e214u8a9051fcbfedf31c@mail.gmail.com>
	<46cb515a0604090232t1db4f6ddvc1ce05d2d6a9d781@mail.gmail.com>
	<70ec82800604090241p7bdb1f87ubd7d2bed441fec87@mail.gmail.com>
	<46cb515a0604090414w4544878eu6ea24efc8e8939f7@mail.gmail.com>
	<70ec82800604090929i6a4b9f78s60d86eeee5ff1551@mail.gmail.com>
Message-ID: <46cb515a0604091154w50e5844eu5d7d19b48dcfdc55@mail.gmail.com>

On 4/9/06, Krishna Mohan Gundu <gkmohan at gmail.com> wrote:

> I have a question for the developers. Is there any good reason, why
> magic commands and system commands cannot span multiple lines using
> escaping newline. I needed this, as my job has some pretty long sed
> commands. I modified iplib.py to get the functionality I needed. I can
> post the diff if you are interested. I will play with this feature a
> bit more as I need it.

The backslash character is "magical" for both python and the
underlying mechanism (os.system/magic handling). In the name of
simplicity, the magical behaviour on python side was sacrificed (and
indeed, it was broken for a long time anyway) and \ is passed to
underlying mechanism as-is.

Do post the diff against the current svn, though, so we can take a
look and discuss it.

--
Ville Vainio - vivainio.googlepages.com
vainio.blogspot.com - g[mail | talk]='vivainio'



From Fernando.Perez at colorado.edu  Mon Apr 10 03:40:37 2006
From: Fernando.Perez at colorado.edu (Fernando Perez)
Date: Mon, 10 Apr 2006 09:40:37 +0200
Subject: [IPython-dev] memory leak?
In-Reply-To: <46cb515a0604081645y5b492116kcfe03c2b84a079b0@mail.gmail.com>
References: <44355D4E.10905@bostream.nu> <443626E3.3050702@colorado.edu>
	<200604081359.51145.hans_meine@gmx.net>
	<46cb515a0604081645y5b492116kcfe03c2b84a079b0@mail.gmail.com>
Message-ID: <443A0BF5.20407@colorado.edu>

Ville Vainio wrote:
> On 4/8/06, Hans Meine <hans_meine at gmx.net> wrote:
> 
> 
>>Sth. like the following would be great:
>>
>>%clearout - clear whole cache
>>%clearout 112 - clear one line
>>%clearout :100 140:150 113 - clear multiple (sub)ranges
> 
> 
> I'll take a look at this over the next week, I have winter holiday so
> I should have plenty of time & energy to play with stuff like this.

Yes, something like this would be nice to have.  Note that the cache object 
already has some basic flushing capabilities:

__IP.outputcache.flush??

which would be good to reuse/extend/cleanup.

In the meantime, the OP can use at least

__IP.outputcache.flush()

for a full flush of the output cache (if not a line-targetted one).

Cheers,

f



From Fernando.Perez at colorado.edu  Mon Apr 10 03:43:40 2006
From: Fernando.Perez at colorado.edu (Fernando Perez)
Date: Mon, 10 Apr 2006 09:43:40 +0200
Subject: [IPython-dev] memory leak?
In-Reply-To: <443A0BF5.20407@colorado.edu>
References: <44355D4E.10905@bostream.nu> <443626E3.3050702@colorado.edu>
	<200604081359.51145.hans_meine@gmx.net>
	<46cb515a0604081645y5b492116kcfe03c2b84a079b0@mail.gmail.com>
	<443A0BF5.20407@colorado.edu>
Message-ID: <443A0CAC.5050405@colorado.edu>

Fernando Perez wrote:
> Ville Vainio wrote:
> 
>>On 4/8/06, Hans Meine <hans_meine at gmx.net> wrote:
>>
>>
>>
>>>Sth. like the following would be great:
>>>
>>>%clearout - clear whole cache
>>>%clearout 112 - clear one line
>>>%clearout :100 140:150 113 - clear multiple (sub)ranges
>>
>>
>>I'll take a look at this over the next week, I have winter holiday so
>>I should have plenty of time & energy to play with stuff like this.
> 
> 
> Yes, something like this would be nice to have.  Note that the cache object 
> already has some basic flushing capabilities:
> 
> __IP.outputcache.flush??
> 
> which would be good to reuse/extend/cleanup.
> 
> In the meantime, the OP can use at least
> 
> __IP.outputcache.flush()
> 
> for a full flush of the output cache (if not a line-targetted one).

I should have added that a

gc.collect()

would probably be a good idea to have at the end of that flush() method.  I 
also noticed that the Out[] object isn't really correctly flushed, only the 
_NN variables are deleted (that code was probably written before Out[] existed 
as a proper cache).  Just some pointers...

Cheers,

f



From vivainio at gmail.com  Tue Apr 11 10:40:22 2006
From: vivainio at gmail.com (Ville Vainio)
Date: Tue, 11 Apr 2006 07:40:22 -0700
Subject: [IPython-dev] memory leak?
In-Reply-To: <200604081359.51145.hans_meine@gmx.net>
References: <44355D4E.10905@bostream.nu> <443626E3.3050702@colorado.edu>
	<200604081359.51145.hans_meine@gmx.net>
Message-ID: <46cb515a0604110740r773d018cgefaa6057a95487dd@mail.gmail.com>

On 4/8/06, Hans Meine <hans_meine at gmx.net> wrote:

> Sth. like the following would be great:
>
> %clearout - clear whole cache
> %clearout 112 - clear one line
> %clearout :100 140:150 113 - clear multiple (sub)ranges

Now

%clear in
%clear out

works in SVN. At this point I didn't see it necessary to support
specifically targeted clears, typically users will probably store
valueable (non-throwaway) output cache data in variables anyway.

--
Ville Vainio - vivainio.googlepages.com
vainio.blogspot.com - g[mail | talk]='vivainio'



From ravi at ati.com  Tue Apr 11 12:50:39 2006
From: ravi at ati.com (Ravikiran Rajagopal)
Date: Tue, 11 Apr 2006 12:50:39 -0400
Subject: [IPython-dev] Embedding threaded IPython without IPShellEmbed
Message-ID: <200604111250.39047.ravi@ati.com>

Hi,

Background:
  I am trying to use python as a scripting language for a C++ application. The 
application has a lot of arrays that are exposed to python (via 
Boost.Python). For debugging and extension code development, I would like to 
be able to open up a python interpreter, and interactively manipulate the 
data structures (using new scipy) and visualize them (using matplotlib).

Problem:
  After Py_Initialize, I load up scipy via PyRun_SimpleString. Then, from C++ 
code, I would like to call the interpreter. Without ipython, I could use 
PyRun_InteractiveLoop, which would return control to my application on EOF. I 
would like to be able to do the same with ipython. The trick is also very 
straightforward: create an IPShellEmbed instance via PyRun_SimpleString, and 
then call its __call__ method using PyRun_SimpleString whenever I needed an 
interpreter.
  However, IPShellEmbed does not support threading options, and that makes it 
a pain to use Matplotlib. As far as I can see, the only option with 
IPShellEmbed is to use a single threaded back end (such as Tk) for MPL. I 
would much prefer to use the GTKAgg back end for MPL, since I would be able 
to keep the plot windows responsive (in a separate thread) while my 
application goes about its number crunching.
  I realize that I only need one instance of the embedded shell. In this case, 
I would like to make ipython do the necessary thread setup options (see code 
later) which works perfectly fine when calling the mainloop directly. 
However, I need ipython to return control back to the application without 
exiting the GTK/Qt main loop. How do I do this? In other words, how do I get 
in and out of the ipython mainloop interactively?

Code for simply using embedded ipython with pylab GTK backend support:

const char *ipython_ini = "import sys\n"
                          "sys.argv = ['','-pylab']\n"
                          "import IPython.Shell\n"
                          "IPython.Shell.start().mainloop()\n";
PyRun_SimpleString( ipythonini );

Code for embedding IPShellEmbed (no pylab support):

const char *ipython_ini = "import sys\n"
                          "sys.argv = ['','-pylab']\n"
                          "import IPython.Shell\n"
                          "ish = IPython.Shell.IPShellEmbed(sys.argv)\n";
const char *ipython_run = "ish()\n"
PyRun_SimpleString( ipython_ini );
// Much later in the code
PyRun_SimpleString( ipython_run );

Code example of what I would like to have but does NOT work:

const char *ipython_ini = "import sys\n"
                          "sys.argv = ['','-pylab']\n"
                          "import IPython.Shell\n"
                          "ish = IPython.Shell.start()\n";
const char *ipython_run = "ish.embed_mainloop()\n"
PyRun_SimpleString( ipython_ini );
// Much later in the code
PyRun_SimpleString( ipython_run );


Any help is greatly appreciated.

Thanks,
Ravi



From jorgen.stenarson at bostream.nu  Tue Apr 11 14:11:28 2006
From: jorgen.stenarson at bostream.nu (=?ISO-8859-1?Q?J=F6rgen_Stenarson?=)
Date: Tue, 11 Apr 2006 20:11:28 +0200
Subject: [IPython-dev] memory leak?
In-Reply-To: <46cb515a0604110740r773d018cgefaa6057a95487dd@mail.gmail.com>
References: <44355D4E.10905@bostream.nu> <443626E3.3050702@colorado.edu>
	<200604081359.51145.hans_meine@gmx.net>
	<46cb515a0604110740r773d018cgefaa6057a95487dd@mail.gmail.com>
Message-ID: <443BF150.8060403@bostream.nu>

Ville Vainio skrev:
> On 4/8/06, Hans Meine <hans_meine at gmx.net> wrote:
> 
>> Sth. like the following would be great:
>>
>> %clearout - clear whole cache
>> %clearout 112 - clear one line
>> %clearout :100 140:150 113 - clear multiple (sub)ranges
> 
> Now
> 
> %clear in
> %clear out
> 
> works in SVN. At this point I didn't see it necessary to support
> specifically targeted clears, typically users will probably store
> valueable (non-throwaway) output cache data in variables anyway.
> 
> --
> Ville Vainio - vivainio.googlepages.com
> vainio.blogspot.com - g[mail | talk]='vivainio'
> 
> _______________________________________________
> IPython-dev mailing list
> IPython-dev at scipy.net
> http://scipy.net/mailman/listinfo/ipython-dev
> 

Ville,

I think there is one more thing that needs clearing and that is the 
entries list in the outputcache object. In my attached patch I have 
removed it completely because I could not see that it was used for 
anything use for it. I have also attached a patch for another option to 
the clear command:
%clear array   which will delete all arrays from the user_ns namespace 
if ipython was started in -pylab mode. Arrays are determined by 
pylab.arraytype.

There is still some strangeness in the garbage collection process 
though. If I run
In[1] %run some_script.py
In[2] a   #array variable in script
Out[2] array(...)
In[3] %run some_script.py
In[4] a   #array variable in script
Out[4] array(...)
In[5] %run some_script.py
In[5] a   #array variable in script
Out[5] array(...)
In[6] %run some_script.py
In[7]%clear out

I get back some memory. If I then run gc.collect() a few times at the 
prompt I will get back some more for each call to gc.collect() this will 
stabilize after a few calls. I'm not sure what the reason is but I 
thought I should mention it.

/J?rgen
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From hans_meine at gmx.net  Sat Apr 15 10:18:45 2006
From: hans_meine at gmx.net (Hans Meine)
Date: Sat, 15 Apr 2006 16:18:45 +0200
Subject: [IPython-dev] Missing Import in pspersistence.py
Message-ID: <200604151618.51918.hans_meine@gmx.net>

Hi!

I could not start IPython because I got crash log; The reason is a missing 
import of sys in pspersistence.py:

--- IPython/Extensions/pspersistence.py (Revision 1265)
+++ IPython/Extensions/pspersistence.py (Arbeitskopie)
@@ -12,7 +12,7 @@

 import pickleshare

-import inspect,pickle,os,textwrap
+import inspect,pickle,os,sys,textwrap
 from IPython.FakeModule import FakeModule

 def restore_aliases(self):

BTW: Isn't the %store per-profile, analoguous to the history?
(I use to store objects of classes defined in extension modules loaded by the 
profile, but the error conceiled by the above crash was that it was trying to 
load these when starting w/o profile.)

Greetings and a happy easter!
  Hans
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From vivainio at gmail.com  Sun Apr 16 11:06:26 2006
From: vivainio at gmail.com (Ville Vainio)
Date: Sun, 16 Apr 2006 08:06:26 -0700
Subject: [IPython-dev] Missing Import in pspersistence.py
In-Reply-To: <200604151618.51918.hans_meine@gmx.net>
References: <200604151618.51918.hans_meine@gmx.net>
Message-ID: <46cb515a0604160806x35531a05ud0795403c71b7591@mail.gmail.com>

On 4/15/06, Hans Meine <hans_meine at gmx.net> wrote:
> Hi!
>
> I could not start IPython because I got crash log; The reason is a missing
> import of sys in pspersistence.py:

Good catch, thank for the patch!

> BTW: Isn't the %store per-profile, analoguous to the history?

Not anymore, I overhauled the whole persistence system a while ago and
thought it's better to share the variables across profiles.

> Greetings and a happy easter!

Indeed!

--
Ville Vainio - vivainio.googlepages.com
vainio.blogspot.com - g[mail | talk]='vivainio'



From jorgen.stenarson at bostream.nu  Wed Apr 19 15:32:23 2006
From: jorgen.stenarson at bostream.nu (=?ISO-8859-1?Q?J=F6rgen_Stenarson?=)
Date: Wed, 19 Apr 2006 21:32:23 +0200
Subject: [IPython-dev] Patch for wildcard
Message-ID: <44469047.8090707@bostream.nu>

Ville,

attached is a patch to allow using ? as a wildcard for a single 
character (as in filename globbing). I have also included a file with 
some tests for the wildcard functionality. The test_wildcard.py is meant 
to be put in a directory such as IPython/tests. Run the test by using 
python test_wildcard.py


/J?rgen
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From jorgen.stenarson at bostream.nu  Wed Apr 19 15:41:54 2006
From: jorgen.stenarson at bostream.nu (=?ISO-8859-1?Q?J=F6rgen_Stenarson?=)
Date: Wed, 19 Apr 2006 21:41:54 +0200
Subject: [IPython-dev] more patches for flush
Message-ID: <44469282.80702@bostream.nu>

Ville,

in the CachedOutput cache_size_min is set to 20 which seems strange, why 
put in a hardcoded lower limit on the cache_size? Perhaps my change to 3 
should be 1 instead but I thought the lower limit maybe should include 
_, __, and ___.

Then there was a bug in the warning message that the cache is being 
flushed. It referenced a non existent attribute.

This message can become very annoying if you have a low cache limit I 
would prefer to remove it or at least be able to disable it in the 
config file.


/J?rgen


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From jorgen.stenarson at bostream.nu  Wed Apr 19 16:12:11 2006
From: jorgen.stenarson at bostream.nu (=?ISO-8859-1?Q?J=F6rgen_Stenarson?=)
Date: Wed, 19 Apr 2006 22:12:11 +0200
Subject: [IPython-dev] pyreadline question
In-Reply-To: <46cb515a0604030750l2f9c6f10k9a78afa8cdbf1bf9@mail.gmail.com>
References: <442CFEE7.6020000@voidspace.org.uk>
	<442D0205.9020205@voidspace.org.uk> <442D9160.2090405@bostream.nu>
	<46cb515a0604030750l2f9c6f10k9a78afa8cdbf1bf9@mail.gmail.com>
Message-ID: <4446999B.8080101@bostream.nu>

Moved from a thread in ipython-user.

I tried to add this to ipy_user_conf.py. But I believe that file is 
executed after readline is imported which won't work.

But perhaps we could apply the patch and continue to think about how to 
best expose the configuration.

/J?rgen

Ville Vainio skrev:
> On 3/31/06, J?rgen Stenarson <jorgen.stenarson at bostream.nu> wrote:
> 
>> I had to make some backwards incompatible changes to how pyreadline is
>> started. Now the recommended way is to "import readline" to initialize
>> pyreadline, if you want to set the config_path do:
>>
>> import pyreadline.rlmain
>> pyreadline.rlmain.config_path=r"c:\xxx\pyreadlineconfig.ini"
>>
>> before "import readline".
>>
>> Ville will have to decide on how he wants to expose this in ipython. A
>> workaround for now is to add those two lines before "import IPython" in
>> the ipython.py startup script.
> 
> Perhaps we should put the lines you suggest in
> UserConfig/ipy_user_conf.py, in comments? That's the first place the
> user *should* look for personal config options...
> 
> Extensions/ipy_system_conf.py is ok as well, considering that
> pyreadline is only used on Windows ATM.
> 
> --
> Ville Vainio - vivainio.googlepages.com
> vainio.blogspot.com - g[mail | talk]='vivainio'
> 

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