You'll need this patch: https://github.com/sympy/sympy/pull/2358 to run my code and you need theano latest dev version.
Jason moorepants.info +01 530-601-9791 On Tue, Aug 6, 2013 at 9:37 AM, Jason Moore <moorepa...@gmail.com> wrote: > Fred, > > I think on_used_input=ignore should be a default in Matthew's theano > printing code or that arg needs to be pushed up to his layer. I hit that > issue too. > > The code I have is here: https://github.com/PythonDynamics/pydy-code-gen > > See the results.txt file for basic speed comparisons. I'm generating the > ODEs for an n-link pendulum with mechanics and then see how fast it > generates and simulates with scipy.odeint. > > The code doesn't work at the moment. I haven't touched it in a month and > looks like some things have changed in sympy and/or theano. I'll work on > the bugs now. > > But "python benchmark.py" should run it with sympy master and ?some? > version of Theano. > > > Jason > moorepants.info > +01 530-601-9791 > > > On Tue, Aug 6, 2013 at 9:25 AM, Frédéric Bastien <no...@nouiz.org> wrote: > >> Hi, >> >> I don't know what is sympy.functions.elementary.piecewise. Do Jason >> answered that part? If not, I'll look into it to know how to make Theano >> reproduce it. About converting any Sympy symbol to Theano symbol, when >> there isn't a one to one matching, you can create a one to a full Theano >> graph conversion. When this is possible, it is probably the best, as if you >> make a new Theano op, it work work on the GPU. But if you make a Theano >> graph, there is good change that the graph will already work on the GPU. >> >> If it is not possible to make a Theano graph for a sympy symbol, it is >> possible to make a new Theano op that just wrap the sympy implementation. >> Also, if this is a bottleneck, I recently added an example that show how to >> use numba with Theano so speed up the python code in a Theano op. >> >> >> Theano do not parallelize on the CPU, except for the call to BLAS, when >> the BLAS library is parallel. On the GPU, it is parallel. >> >> Having on_unused_input=ignore is normal for complicated generated code. >> That is why it was added. But when the code is simpler and not generated, >> but all user manually coded, most of time it mean the user didn't do what >> he wanted. If you know it is normal that you have unused input, there is no >> problem to use that flag. >> >> >> Jason, about the case where Theano is slower, can you send me the Theano >> code? I would like to look at it. I'm very surprised that Theano is slower >> then Sympy in this case and would like to know why it is like this. >> >> Fred >> >> >> On Mon, Aug 5, 2013 at 9:03 PM, Jason Moore <moorepa...@gmail.com> wrote: >> >>> Guy, >>> >>> We're working on the same problem for sympy.physics.mechanics. Matthew >>> Rocklin added support for matrix conversions in the theano code that is in >>> SymPy and I used that, but found that theano was slower that lambdify for >>> most of my cases (I only have two cores, so I'm not taking advantage of the >>> Theano parallel stuff). I think writing specific code gen for ode >>> integration is going to be the best bet. I'm happy to collaborate on this >>> with you. >>> >>> >>> Jason >>> moorepants.info >>> +01 530-601-9791 >>> >>> >>> On Mon, Aug 5, 2013 at 3:13 PM, Guy Parsey <guy.par...@gmail.com> wrote: >>> >>>> Hello Everyone, >>>> Thank you in advance for reading through my problem and for any input >>>> you may have. I must say that I still feel like a novice programmer and my >>>> problems may be easily solvable from a different mindset. My present >>>> project entails time-integration of extremely stiff and non-linear ODEs >>>> with regards to chemical kinetics (one derivative equation for each >>>> variable species) and energy equations. Initially we were planning on using >>>> the sympy.lambdify function to create callable functions for the main >>>> function along with the jacobian and passing said functions to >>>> scipy.integrate.odeint, however this method only works for easier test >>>> cases (fewer species and/or no energy equations) before being limited by >>>> either the list recursion limit or segfaulting due to the limited stack >>>> size. I know that both of these limits can be edited, but that fact that I >>>> am reaching them makes me feel as though I am doing something extremely >>>> inefficiently. Outside of the documentation of SymPy and Theano, I have >>>> also been heavily using the BlogPost by Matthew Rocklin >>>> http://matthewrocklin.com/blog/work/2013/03/19/SymPy-Theano-part-1/ . >>>> >>>> Presently I am trying to use the mapping between Theano and SymPy >>>> (sympy.printing.theanocode theano_function) to make my callable functions >>>> and take advantage of the optimization routines. I have two major problems >>>> and a few questions: >>>> >>>> 1st major problem: Though piecewise functions exist in SymPy >>>> (sympy.functions.elementary.piecewise) there is no counterpart in Theano. >>>> Looking at the source of the inspiration for theanocode ( >>>> https://github.com/nouiz/theano_sympy/ graph_translation.py) I see >>>> that some of the SymPy equivalents were defined as lambda functions. Is >>>> there an equivalent way to add Theano conditional expressions wrapped into >>>> a function to add to the mapping dictionary in theanocode.py? >>>> >>>> 2nd major problem: Similar to the problem above in that I am not sure >>>> that the Theano counterpart is; some of the terms that I use are >>>> interpolated functions (with one ODE variable as input) that we have >>>> wrapped symbolically while providing a numerical implementation (so that >>>> symbolic derivatives can be made, resulting in their own interpolations). >>>> Is it possible to recreate the interpolation function as a Theano operation >>>> for use within the system of ODEs? >>>> >>>> Remain questions: >>>> I presently have to flatten my input to theano_function to a list of >>>> expressions and then wrap to return to a form (Jacobian is a matrix not a >>>> vector); is it possible to have a matrix of different expressions as an >>>> input to theano_function with a vector output? >>>> >>>> I know that a huge amount of Theano speed up is due to parallelization >>>> of matrix operations (which I do not have), should I be focusing on SymPy >>>> Autowrap/Ufuncify or my own code generation instead of trying to get Theano >>>> to play nicely? >>>> >>>> Stupid questions: >>>> Does sympy.printing.theanocode.theano_function automatically optimize >>>> the compiled graph? >>>> >>>> Minor comment: >>>> Perhaps unnecessary for most uses of the theano_function, but I needed >>>> to modify function inputs so as to be able to use the keyword argument >>>> 'on_unused_input=ignore' as opposed to 'raise' so that I did not need to >>>> have all symbols in all equations. This may be avoided by having the unused >>>> symbols somehow (I don't know how) included in each expression. >>>> >>>> Thank you again for your time in reading my problems and any potential >>>> help you may think of. I can attach code if necessary, I just didn't want >>>> to make my post more confusing. >>>> Have an excellent day. >>>> Sincerely, >>>> Guy Parsey >>>> >>>> -- >>>> You received this message because you are subscribed to the Google >>>> Groups "sympy" group. >>>> To unsubscribe from this group and stop receiving emails from it, send >>>> an email to sympy+unsubscr...@googlegroups.com. >>>> To post to this group, send email to sympy@googlegroups.com. >>>> Visit this group at http://groups.google.com/group/sympy. >>>> For more options, visit https://groups.google.com/groups/opt_out. >>>> >>>> >>>> >>> >>> -- >>> You received this message because you are subscribed to the Google >>> Groups "sympy" group. >>> To unsubscribe from this group and stop receiving emails from it, send >>> an email to sympy+unsubscr...@googlegroups.com. >>> To post to this group, send email to sympy@googlegroups.com. >>> Visit this group at http://groups.google.com/group/sympy. >>> For more options, visit https://groups.google.com/groups/opt_out. >>> >>> >>> >> >> -- >> You received this message because you are subscribed to the Google Groups >> "sympy" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to sympy+unsubscr...@googlegroups.com. >> To post to this group, send email to sympy@googlegroups.com. >> Visit this group at http://groups.google.com/group/sympy. >> For more options, visit https://groups.google.com/groups/opt_out. >> >> >> > > -- You received this message because you are subscribed to the Google Groups "sympy" group. To unsubscribe from this group and stop receiving emails from it, send an email to sympy+unsubscr...@googlegroups.com. To post to this group, send email to sympy@googlegroups.com. Visit this group at http://groups.google.com/group/sympy. For more options, visit https://groups.google.com/groups/opt_out.
