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How to save a list to a file, with sage objects in it?

asked 2011-12-15 12:59:22 -0500

updated 2015-01-14 07:19:08 -0500

FrédéricC gravatar image

Hi, I am trying to save intermediate step of my calculation into a file, so that next time I can read the file to resume the calculation. Say, I need to save

f = function('a',var('t'))
s = [f] # together with other things in the list

How to save s to a file?

I tried two ways:

(1) Standard python module pickle cannot save sage objects, thus fails

(2) I converted s to a python object:

s = Sequence([f])

Now I can use'file_name'). However, there is a bug that I cannot load using load('file_name')

RuntimeError: unknown function 'a' in archive

It is a known bug: .

Unfortunately I am not expert enough to fix that bug, and I really want to get my work done before waiting for the fix. Is there any other way to save the list s currently?

In the bug report it is mentioned that an older version of Pynac doesn't have this bug. If there is no other work around, is it possible to downgrade Pynac within sage or I have to downgrade the whole sage?


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I don't think it's the fact that `s` is a list, it's that it contains the function `f`. If you had "s = [sin(x), 12, 'hello']", you could do "save(s, 'file_name')" and then "load('file_name.sobj')" works fine.

John Palmieri gravatar imageJohn Palmieri ( 2011-12-15 17:29:37 -0500 )edit

Hi, John: thanks a lot for your reply! I agree with you. But my actual goal is really want to save a list with a lot of functions like f. In my project, I start from an abstract form of a differential equation, and simplify it to a simpler form (here I want to save my work because the former step is slow, and I want to use it when I start Sage next time), and solve the differential equation with different additional conditions. It's a differential equation thus I have to define a general function instead of put a "sin(x)" in the list.

tririver gravatar imagetririver ( 2011-12-15 23:52:44 -0500 )edit

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answered 2011-12-17 15:02:59 -0500

DSM gravatar image

updated 2011-12-17 15:39:05 -0500

Okay, this really isn't a solution, but might serve as a temporary workaround-- you can't save formal functions, but you can convert them to maxima objects, and those can be saved.

For example:

sage: f = function('a',var('t'))
sage: parent(f)
Symbolic Ring
sage: # convert it to maxima (maxima(f) does the same thing)
sage: f._maxima_()
sage: # note the prefix ' now!
sage: parent(_)
sage: # convert forward and back
sage: (f._maxima_())._sage_()
sage: # do we have equality?
sage: bool((f._maxima_())._sage_() == f)

So while we have

sage: loads(dumps(f))
RuntimeError                              Traceback (most recent call last)
RuntimeError: unknown function 'a' in archive

we're lucky enough to have

sage: bool(loads(dumps(f._maxima_()))._sage_() == f)

It's straightforward to bundle the above technique for these guys. Not everything can be converted seamlessly between Sage and maxima, so you might want to only convert some things, but you get the idea.

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Thanks a lot! Seems a best answer before the bug is fixed.

tririver gravatar imagetririver ( 2011-12-19 02:00:23 -0500 )edit

answered 2011-12-17 12:53:37 -0500

A partial answer: in Sage 4.7.0, the above attempt (2) works. Thus it is indeed a bug brought in from either 4.7.1 or 4.7.2. I also tried 4.8 alpha 5, the bug is not fixed --looking forward to a fix.

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Asked: 2011-12-15 12:59:22 -0500

Seen: 909 times

Last updated: Dec 17 '11