Opened 13 years ago
Last modified 2 years ago
#8321 needs_work defect
numerical integration with arbitrary precision
Reported by: | Burcin Erocal | Owned by: | |
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Priority: | major | Milestone: | sage-6.4 |
Component: | symbolics | Keywords: | numerics, integration, sd32 |
Cc: | Stefan Reiterer, Fredrik Johansson, Karl-Dieter Crisman, Mariah Lennox, Jonathan Bober, Eviatar Bach, Marcelo Forets | Merged in: | |
Authors: | Stefan Reiterer | Reviewers: | Paul Zimmermann |
Report Upstream: | N/A | Work issues: | add more arbitrary precision tests |
Branch: | Commit: | ||
Dependencies: | Stopgaps: |
Description (last modified by )
From the sage-devel:
On Feb 20, 2010, at 12:40 PM, John H Palmieri wrote: ... > I was curious about this, so I tried specifying the number of digits: > > sage: h = integral(sin(x)/x^2, (x, 1, pi/2)); h > integrate(sin(x)/x^2, x, 1, 1/2*pi) > sage: h.n() > 0.33944794097891573 > sage: h.n(digits=14) > 0.33944794097891573 > sage: h.n(digits=600) > 0.33944794097891573 > sage: h.n(digits=600) == h.n(digits=14) > True > sage: h.n(prec=50) == h.n(prec=1000) > True > > Is there an inherit limit in Sage on the accuracy of numerical > integrals?
The _evalf_
function defined on line 179 of sage/symbolic/integration/integral.py
calls the gsl numerical_integral()
function and ignores the precision.
We should raise a NotImplementedError
for high precision, or find a way to do arbitrary precision numerical integration.
Attachments (2)
Change History (62)
comment:1 follow-up: 50 Changed 13 years ago by
comment:2 Changed 13 years ago by
There is an example-doctest in the file interfaces/maxima.py
, for the method nintegral
. It says:
Note that GP also does numerical integration, and can do so to very high precision very quickly:: sage: gp('intnum(x=0,1,exp(-sqrt(x)))') 0.5284822353142307136179049194 # 32-bit 0.52848223531423071361790491935415653021 # 64-bit sage: _ = gp.set_precision(80) sage: gp('intnum(x=0,1,exp(-sqrt(x)))') 0.52848223531423071361790491935415653021675547587292866196865279321015401702040079
comment:4 Changed 12 years ago by
I think I have the solution for this trac with mpmath:
def _evalf_(self, f, x, a, b, parent = None): """ Returns numerical approximation of the integral EXAMPLES:: sage: from sage.symbolic.integration.integral import definite_integral sage: h = definite_integral(sin(x)/x^2, x, 1, 2); h integrate(sin(x)/x^2, x, 1, 2) sage: h.n() # indirect doctest 0.4723991772689525... TESTS: Check if #3863 is fixed:: sage: integrate(x^2.7 * e^(-2.4*x), x, 0, 3).n() 0.154572952320790 #Check if #8321 is fixed: sage: d = definite_integral(sin(x)/x^2, x, 1, 2) sage: d.n(77) 0.4723991772689525199904 """ #from sage.gsl.integration import numerical_integral # The gsl routine returns a tuple, which also contains the error. # We only return the result. #return numerical_integral(f, a, b)[0] #Lets try mpmath instead: import sage.libs.mpmath.all as mpmath try: precision = parent.prec() mpmath.mp.prec = precision except AttributeError: precision = mpmath.mp.prec mp_f = lambda z: \ f(x = mpmath.mpmath_to_sage(z,precision)) return mpmath.call(mpmath.quad,mp_f,[a,b])
The tests just run fine:
sage: sage: sage: from sage.symbolic.integration.integral import definite_integral sage: sage: h = definite_integral(sin(x)/x^2, x, 1, 2); h integrate(sin(x)/x^2, x, 1, 2) sage: h.n() 0.472399177268953 sage: h.n(77) 0.4723991772689525199904 sage: h.n(100) 0.47239917726895251999041133798
greez maldun
comment:5 Changed 12 years ago by
Owner: | changed from Burcin Erocal to Stefan Reiterer |
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comment:6 Changed 12 years ago by
Owner: | changed from Stefan Reiterer to Burcin Erocal |
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Changed 12 years ago by
Attachment: | trac_8321_numeric_int_mpmath.patch added |
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Numerical evaluation of symbolic integration with arbitrary precision with help of mpmath
comment:7 Changed 12 years ago by
Cc: | Stefan Reiterer added |
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Status: | new → needs_review |
comment:8 follow-up: 10 Changed 12 years ago by
Thanks, Maldun, this is a good addition to have. I don't have time to review this immediately, but it would be helpful to know if you detected any errors, compared this with symbolic integrals and their evaluation, etc. Basically, that the results from this really are as accurate as advertised.
Also, you might as well leave the GSL stuff in as comments, as in the patch you posted above, or even as an optional argument, though that may not be compatible with _evalf_
elsewhere...
comment:10 follow-up: 12 Changed 12 years ago by
Replying to kcrisman:
Thanks, Maldun, this is a good addition to have. I don't have time to review this immediately, but it would be helpful to know if you detected any errors, compared this with symbolic integrals and their evaluation, etc. Basically, that the results from this really are as accurate as advertised.
Also, you might as well leave the GSL stuff in as comments, as in the patch you posted above, or even as an optional argument, though that may not be compatible with
_evalf_
elsewhere...
I will consider this, but hopefully it is not necessary, and mpmath will do the whole thing. If I understood that right, burcin wants to change the numerical evaluation completly to mpmath, because it supports arbitrary prescision.
I plyed arround a little, and I didn't find any differences between the other evaluation methods. In some cases it works even better (I had an example recently in ask sage, which motivated me to switch to this form ov _evalf_)
comment:11 Changed 12 years ago by
Replying to mhansen:
Does this work for double integrals?
mpmath does, this function doesn't, but the current version in sage didn't either, so it's no prob. If we want to support double integrals, one had to change the base class.
comment:12 follow-up: 13 Changed 12 years ago by
Authors: | → Stefan Reiterer |
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Cc: | Fredrik Johansson added |
Keywords: | numerics integration added |
Thank you for the patch Stefan. This was much needed for quite a while now.
Replying to maldun:
Replying to kcrisman:
Thanks, Maldun, this is a good addition to have. I don't have time to review this immediately, but it would be helpful to know if you detected any errors, compared this with symbolic integrals and their evaluation, etc. Basically, that the results from this really are as accurate as advertised.
I agree. I like how the patch looks overall. It would be good to see comparisons on
- error margins
- speed
Maybe Fredrik can comment on this as well.
Using fast_callable()
for mp_f
could help improve the speed.
Does anyone know of good examples to add as tests for numerical integration?
Also, you might as well leave the GSL stuff in as comments, as in the patch you posted above, or even as an optional argument, though that may not be compatible with
_evalf_
elsewhere...
Unfortunately, ATM, the numerical evaluation framework for symbolic expressions doesn't support specifying different methods. This could (probably, I didn't check the code) be done by changing the interpretation of the python object we pass around to keep the algorithm parameter and the parent, instead of just the parent. Is this a desirable change? Shall we open a ticket for this?
I will consider this, but hopefully it is not necessary, and mpmath will do the whole thing. If I understood that right, burcin wants to change the numerical evaluation completly to mpmath, because it supports arbitrary prescision.
I guess this is based on a comment I made in the context of orthogonal polynomials and scipy vs. mpmath. Instead of a general policy, I'd like to consider each function separately.
Overall, I'd lean toward using mpfr
if it supports the given function. Otherwise, choosing between pari
, mpmath
, etc. can be difficult, since on many examples one implementation doesn't beat the other uniformly for different precision or domains.
comment:13 follow-up: 15 Changed 12 years ago by
Replying to burcin:
Thank you for the patch Stefan. This was much needed for quite a while now.
Replying to maldun:
Replying to kcrisman:
Thanks, Maldun, this is a good addition to have. I don't have time to review this immediately, but it would be helpful to know if you detected any errors, compared this with symbolic integrals and their evaluation, etc. Basically, that the results from this really are as accurate as advertised.
I agree. I like how the patch looks overall. It would be good to see comparisons on
- error margins
- speed
Maybe Fredrik can comment on this as well.
Using
fast_callable()
formp_f
could help improve the speed.
Ok I will try this + do some tests in the near future!
Does anyone know of good examples to add as tests for numerical integration?
I think I should find some, since I did/do a lot of work with finite element, spectral methods, and boundary elements. I hope I can do this in the coming weeks.
Also, you might as well leave the GSL stuff in as comments, as in the patch you posted above, or even as an optional argument, though that may not be compatible with
_evalf_
elsewhere...Unfortunately, ATM, the numerical evaluation framework for symbolic expressions doesn't support specifying different methods. This could (probably, I didn't check the code) be done by changing the interpretation of the python object we pass around to keep the algorithm parameter and the parent, instead of just the parent. Is this a desirable change? Shall we open a ticket for this?
I personally would highly recommend this. Consider for example highly oscillating integrals like
\int_0^pi f(x) sin(n*x) dx
for large n
's or the example from Runge:
http://en.wikipedia.org/wiki/Runge%27s_phenomenon.
I would also suggest to take SciPy into consideration to provide indiviual data points.
On Friday, I and a colleague of mine had a simple example of a piecewise function, that only ScipPy could do properly while mpmath failed, (even MATLAB had problems) because I handled individual data points (mpath also provides different quadrature rules).
If you would like I could work on this.
I guess this is based on a comment I made in the context of orthogonal polynomials and SciPy vs. mpmath. Instead of a general policy, I'd like to consider each function separately.
Overall, I'd lean toward using
mpfr
if it supports the given function. Otherwise, choosing betweenpari
,mpmath
, etc. can be difficult, since on many examples one implementation doesn't beat the other uniformly for different precision or domains.
That's true. I think we should provide, like mentioned above, method parameters.
But I don't think we have to fear compability problems, because if I understood the documentation of
mpmath correctly it only evals the function on a data grid, and returns the \sum weigth_i * data_i
.
greez maldun
comment:14 Changed 12 years ago by
Status: | needs_review → needs_work |
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comment:15 Changed 12 years ago by
Replying to maldun:
Replying to burcin:
Replying to kcrisman:
Also, you might as well leave the GSL stuff in as comments, as in the patch you posted above, or even as an optional argument, though that may not be compatible with
_evalf_
elsewhere...Unfortunately, ATM, the numerical evaluation framework for symbolic expressions doesn't support specifying different methods. This could (probably, I didn't check the code) be done by changing the interpretation of the python object we pass around to keep the algorithm parameter and the parent, instead of just the parent. Is this a desirable change? Shall we open a ticket for this?
I personally would highly recommand this. Consider for example highly oscillating integrals like \int_0^{pi f(x) sin(n*x) dx for large n's or the example from Runge: http://en.wikipedia.org/wiki/Runge%27s_phenomenon. I would also suggest to take scipy into consideration to provide indiviual data points. On friday, I and a colleague of mine had a simple example of a piecewise function, that only scipy could do properly while mpmath failed, (even matlab had problems) because I handled individual data points.(mpath also provides different quadrature rules) If you would like I could work on this }
That would be great. I suggest making that a new enhancement ticket though. Let's fix this bug first and use mpmath for numerical evaluation.
We should also open a new ticket for numerical integration of double integrals as Mike was asking in comment:9.
comment:16 Changed 12 years ago by
Does anyone know of good examples to add as tests for numerical integration?
on page 132 of http://cannelle.lateralis.org/sagebook-1.0.pdf you'll find 10 examples.
Paul
comment:17 Changed 12 years ago by
I suggest the following doctests for integral.py:
#Testing Runge's example: sage: f(x) = 1/(1+25*x^2) sage: f x |--> 1/(25*x^2 + 1) sage: integrate(f(x),x,-1,1) 2/5*arctan(5) sage: integrate(1/(1+10^10*x^2),x,0,1) 1/100000*arctan(100000) sage: integrate(1/(1+10^10*x^2),x,0,1).n() 0.0000157078632679490 #Highly oscillating integrals: sage: integrate(exp(x)*sin(1000*x),x,0,pi/2) -1000/1000001*e^(1/2*pi) + 1000/1000001 sage: integrate(exp(x)*sin(1000*x),x,0,pi/2).n() -0.00381047357049178 sage: from sage.symbolic.integration.integral import definite_integral sage: definite_integral(exp(10*x)*sin(10000*x), x, 0, 1) 1/10000010*e^10*sin(10000) - 100/1000001*e^10*cos(10000) + 100/1000001 sage: definite_integral(exp(10*x)*sin(10000*x), x, 0, 1).n() 2.09668650785505 #Different tests: sage: integrate(sin(x^3)*x^2,x,0,10) -1/3*cos(1000) + 1/3 sage: integrate(sin(x^3)*x^2,x,0,10).n() 0.145873641236432 sage: integrate(sin(x)*exp(cos(x)), x, 0, pi) -e^(-1) + e sage: integrate(sin(x)*exp(cos(x)), x, 0, pi).n() 2.35040238728760 sage: integrate(x*log(1+x),x,0,1) 1/4 sage: integrate(x*log(1+x),x,0,1).n() 0.250000000000000 """
Further Ideas?
comment:18 Changed 12 years ago by
I suggest the following doctests for integral.py: [...]
those doctests are not in arbitrary precision (or do you suggest to take them as a basis for arbitrary precision examples?).
comment:19 Changed 12 years ago by
I had now a little time to think about it, and I suggest to add even more tests. I initially used this tests, because the analytical solution is known so they would form a good basis.
But yesterday I found out that if sage knows the analytical solution it just evaluate this, and I don't think this is the best way I gave it to discussion on sage devel: see http://groups.google.com/group/sage-devel/browse_thread/thread/886efb8ca8bdcff2
Why do I have this concern? just try this:
integrate(sin(x^2),x,0,pi).n()
I will give more examples today or tomorrow.
comment:20 Changed 12 years ago by
Cc: | Karl-Dieter Crisman added |
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comment:21 Changed 12 years ago by
See also #7763. We continue to get support requests because of the non-unified nature of our options.
comment:22 Changed 11 years ago by
#10550 should be closed as a duplicate of this ticket. The discussion there includes some examples that might be useful here.
comment:23 Changed 11 years ago by
Cc: | Mariah Lennox added |
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comment:24 follow-up: 25 Changed 11 years ago by
Here is another example from http://openopt.org/IP
sigma = 1e-4 ff = exp(-x**2/(2*sigma)) / sqrt(2*pi*sigma) bounds_x = (-20, 10)
comment:25 Changed 11 years ago by
Replying to burcin:
Here is another example [...]
Burcin, please can you be more specific, for example with a complete Sage command?
Paul
comment:26 follow-up: 27 Changed 11 years ago by
I hadn't actually done the computation in Sage. I just wanted to note that web site here. :)
With the patch attached to this ticket:
sage: sigma = 1e-4 sage: ff = exp(-x**2/(2*sigma)) / sqrt(2*pi*sigma) sage: from sage.symbolic.integration.integral import definite_integral sage: definite_integral(ff, x, -20, 10, hold=True) integrate(70.7106781186548*e^(-5000.00000000000*x^2)/sqrt(pi), x, -20, 10) sage: definite_integral(ff, x, -20, 10, hold=True).n() 5.38249970415053e-939
Without the patch:
sage: definite_integral(ff, x, -20, 10, hold=True).n() 2.1074458151264474e-45
We get a better result if we allow maxima to evaluate the integral symbolically:
sage: definite_integral(ff, x, -20, 10).n() 1.00000000000000 sage: definite_integral(ff, x, -20, 10) 0.353553390593*(sqrt(2)*sqrt(pi)*erf(500*sqrt(2)) + sqrt(2)*sqrt(pi)*erf(1000*sqrt(2)))/sqrt(pi)
The web site I linked to in comment:24 links to this page, where i got the example from:
Here is an excerpt from that file:
'''interalg result: 1.000006 (usually solution, obtained by interalg, has real residual 10-100-1000 times less than required tolerance, because interalg works with "most worst case" that extremely rarely occurs. Unfortunately, real obtained residual cannot be revealed). Now let's ensure scipy.integrate quad fails to solve the problem and mere lies about obtained residual: '''
comment:27 Changed 11 years ago by
Description: | modified (diff) |
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Replying to burcin:
I hadn't actually done the computation in Sage. I just wanted to note that web site here. :)
With the patch attached to this ticket:
sage: sigma = 1e-4 sage: ff = exp(-x**2/(2*sigma)) / sqrt(2*pi*sigma) sage: from sage.symbolic.integration.integral import definite_integral sage: definite_integral(ff, x, -20, 10, hold=True) integrate(70.7106781186548*e^(-5000.00000000000*x^2)/sqrt(pi), x, -20, 10) sage: definite_integral(ff, x, -20, 10, hold=True).n() 5.38249970415053e-939Without the patch:
sage: definite_integral(ff, x, -20, 10, hold=True).n() 2.1074458151264474e-45We get a better result if we allow maxima to evaluate the integral symbolically:
sage: definite_integral(ff, x, -20, 10).n() 1.00000000000000 sage: definite_integral(ff, x, -20, 10) 0.353553390593*(sqrt(2)*sqrt(pi)*erf(500*sqrt(2)) + sqrt(2)*sqrt(pi)*erf(1000*sqrt(2)))/sqrt(pi)
This is indeed a great example!
This is again a grid problem and not a precision problem. If you make trapezoidal or gauss rule on finer grids you get also better results.
sage: from numpy import * sage: from scipy.integrate import trapz sage: sigma = 1e-4 sage: def ff(x): return exp(-x**2/(2*sigma))/sqrt(2*pi*sigma) ....: sage: ffv = vectorize(ff) sage: x = arange(-20,10,1) sage: y = ffv(x) sage: trapz(y,x) 39.894228040143268 sage: x = arange(-20,10,0.5) sage: y = ffv(x) sage: trapz(y,x) 19.947114020071634 sage: x = arange(-20,10,0.05) sage: y = ffv(x) sage: trapz(y,x) 1.9947262692023391 sage: x = arange(-20,10,0.005) sage: y = ffv(x) sage: trapz(y,x) 1.0 from scipy.integrate import fixed_quad sage: fixed_quad(ff,-20,10,n=int(10)) (0.0, None) sage: fixed_quad(ff,-20,10,n=int(100)) (2.6290056634068843e-58, None) sage: fixed_quad(ff,-20,10,n=int(1000)) (0.8616135058547989, None)
The reason for this is simply that the function is approximately 1 in a small region arround zero and nearly zero elsewhere. Thats also the reason why maxima works so well here: The main part is included in the analytical solution.
comment:28 follow-up: 29 Changed 11 years ago by
This should really be finished and fixed. Does anyone have any objection to something that does what Stefan implements (using mpmath) but then has lots of examples in numerical integration and integrate
warning people not to trust floating-point, even with high precision, calculations? Otherwise this ticket could get doomed by the "must be perfect" problem.
Are there specific places where this patch is causing incorrect or worse behavior? Burcin's example seems to be equally bad for both, and I disagree with maldun that we shouldn't return symbolic answers. At some point you have to make a decision, and the definite integral should naturally be symbolic if at all possible.
comment:29 Changed 11 years ago by
Replying to kcrisman:
This should really be finished and fixed. Does anyone have any objection to something that does what Stefan implements (using mpmath) but then has lots of examples in numerical integration and
integrate
warning people not to trust floating-point, even with high precision, calculations? Otherwise this ticket could get doomed by the "must be perfect" problem.
we are still waiting for comparison figures for errors and timings (see comment 12). In those comparisons, I'd like to have arbitrary precision examples (say 20, 50, 100, 200, 500 and 1000 digits).
Are there specific places where this patch is causing incorrect or worse behavior? Burcin's example seems to be equally bad for both, and I disagree with maldun that we shouldn't return symbolic answers. At some point you have to make a decision, and the definite integral should naturally be symbolic if at all possible.
of course integrate(...)
will first give a symbolic result if any, then integrate(...).n()
will evaluate numerically this symbolic value.
We should explain in the documentation of integrate
how to avoid the symbolic evaluation
(for example adding the hold
option). Anyway this is a different issue than this ticket.
Paul
comment:30 Changed 11 years ago by
I'm working on adding numerical integration examples, in the meantime I've posted a rebase of the previously uploaded patch to sage-4.7.1.
comment:31 Changed 11 years ago by
I wrote a small function to compare errors and timings of the GSL implementation (of numerical_integral
) and the mpmath implementation provided by the patch. Here is the testing code:
def num_int_test(f, a, b): """ Input: `f` should be a function of a single variable, [a, b] is a domain of integration """ LJ = 25 # left justification from sage.symbolic.integration.integral import definite_integral exact_I = definite_integral(f, f.variables()[0], a, b) print "Exact ".ljust(LJ) + " = %s" % exact_I print "Exact .n()".ljust(LJ) + " = %s" % exact_I.n() print "GSL".ljust(LJ) + " = %s" % numerical_integral(f, a, b)[0] print "mpmath".ljust(LJ) + " = %s" % definite_integral(f, f.variables()[0], a, b, hold=True).n() num_I = definite_integral(f, f.variables()[0], a, b, hold=True) for p in [53, 64, 100, 200, 500, 1000]: s = "mpmath (prec=%d)" % p print s.ljust(LJ) + " = %s" % num_I.n(p) print "Timings at prec=53:" print " GSL: ", timeit('numerical_integral(%s, %s, %s)' % (f, a, b)) print " mpmath: ", timeit('definite_integral(%s, %s, %s, %s, hold=True).n()' % (f, f.variables()[0], a, b))
Now I took 3 examples from pg. 132 of the PDF suggested above at http://cannelle.lateralis.org/sagebook-1.0.pdf and tested them using num_int_test
:
# applied patch http://trac.sagemath.org/sage_trac/raw-attachment/ticket/8321/trac_8321_rebase.patch sage: x = var('x') sage: from sage.symbolic.integration.integral import definite_integral # f = e^(-x^2)*log(x) on [17, 42] sage: num_int_test(e^(-x^2)*log(x), 17, 42) Exact = integrate(e^(-x^2)*log(x), x, 17, 42) Exact .n() = 2.59225286296247e-127 GSL = 2.5657285007e-127 mpmath = 2.59225286296247e-127 mpmath (prec=53) = 2.59225286296247e-127 mpmath (prec=64) = 2.59225286296226841e-127 mpmath (prec=100) = 2.5922528629622683570941971829e-127 mpmath (prec=200) = 2.5922528629622683570941971813123497913329093314031958452707e-127 mpmath (prec=500) = 2.56572850056105148291735639613047859001477095540203266250504462960653767523831161390072264481216550025343198689835357618681873598023026225266716067780e-127 mpmath (prec=1000) = 2.56572850056105148291735639613047859001477095540203266250504462960653767360416188079136395575326953119218247602307727367985551096000368640359367812179070686479198046287233104280204937504901221620134046153583613193738177820412122516350777255525035947116513676784199592200655526485894447669230515221776e-127 Timings at prec=53: GSL: 625 loops, best of 3: 971 µs per loop mpmath: 25 loops, best of 3: 26.9 ms per loop # f = sqrt(1-x^2) on [0, 1] sage: num_int_test(sqrt(1-x^2), 0, 1) Exact = 1/4*pi Exact .n() = 0.785398163397448 GSL = 0.785398167726 mpmath = 0.785398163397448 mpmath (prec=53) = 0.785398163397448 mpmath (prec=64) = 0.785398163397448310 mpmath (prec=100) = 0.78539816339744830961566084582 mpmath (prec=200) = 0.78539816339744830961566084581987572104929234984377645524374 mpmath (prec=500) = 0.785398163397448309615660845819875721049292349843776455243736148076954101571552249657008706335529266995537021628320576661773461152387645557931339852032 mpmath (prec=1000) = 0.785398163397448309615660845819875721049292349843776455243736148076954101571552249657008706335529266995537021628320576661773461152387645557931339852032120279362571025675484630276389911155737238732595491107202743916483361532118912058446695791317800477286412141730865087152613581662053348401815062285318 Timings at prec=53: GSL: 625 loops, best of 3: 652 µs per loop mpmath: 25 loops, best of 3: 12 ms per loop # f = sin(sin(x)) on [0, 1] sage: num_int_test(sin(sin(x)), 0, 1) Exact = integrate(sin(sin(x)), x, 0, 1) Exact .n() = 0.430606103120691 GSL = 0.430606103121 mpmath = 0.430606103120691 mpmath (prec=53) = 0.430606103120691 mpmath (prec=64) = 0.430606103120690605 mpmath (prec=100) = 0.43060610312069060491237735525 mpmath (prec=200) = 0.43060610312069060491237735524846578643360804182199746950463 mpmath (prec=500) = 0.430606103120690604912377355248465786433608041821997469504633350750892193636074792502000332212863495547968512886769444385260392350928954849458834511854 mpmath (prec=1000) = 0.430606103120690604912377355248465786433608041821997469504633350750892193636074792502000332212863495547968512886769444385260392350928954849458834511854394326788473583253436780737313870079328121429092122005425057044706514198162061316772646582265252772251628205725432156943890956907988745419355505731945 Timings at prec=53: GSL: 625 loops, best of 3: 134 µs per loop mpmath: 25 loops, best of 3: 11.2 ms per loop
In the second example, GSL's answer compared to the numerically evaluated exact symbolic answer is significantly off. The mpmath answer at default precision matches the numerically evaluated exact symbolic answer perfectly.
As for the timings, as you can see GSL is *much* faster than the patch code using mpmath. I tried using fast_callable
in the case where the domain precision is the same as RDF and that gives a big speedup, though still not as fast as GSL:
def _evalf( ... ): ... try: precision = parent.prec() mpmath.mp.prec = precision if precision == RDF.precision(): mp_f = fast_callable(f, vars=[x], domain=RDF) else: mp_f = lambda z: f(x = mpmath.mpmath_to_sage(z, precision)) except AttributeError: mp_f = fast_callable(f, vars=[x], domain=RDF) return mpmath.call(mpmath.quad, mp_f, [a,b])
New timings using fast_callable
:
# Testing: added fast_callable to _evalf_ # results: definite_integral( ... ) is around 5x faster when called at RDF precision sage: timeit('numerical_integral(e^(-x^2)*log(x), 17, 42)') # base case using GSL at float precision 625 loops, best of 3: 959 µs per loop sage: timeit('definite_integral(e^(-x^2)*log(x), x, 17, 42, hold=True).n()') # using fast_callable 125 loops, best of 3: 5.41 ms per loop sage: timeit('definite_integral(e^(-x^2)*log(x), x, 17, 42, hold=True).n(53)') # using fast_callable 125 loops, best of 3: 5.41 ms per loop sage: timeit('definite_integral(e^(-x^2)*log(x), x, 17, 42, hold=True).n(54)') # *not* using fast_callable 25 loops, best of 3: 28.1 ms per loop sage: timeit('definite_integral(e^(-x^2)*log(x), x, 17, 42, hold=True).n(64)') # *not* using fast_callable 25 loops, best of 3: 26.3 ms per loop sage: timeit('definite_integral(e^(-x^2)*log(x), x, 17, 42, hold=True).n(100)') # *not* using fast_callable 25 loops, best of 3: 32.2 ms per loop
comment:32 follow-up: 34 Changed 11 years ago by
# f = e^(-x^2)*log(x) on [17, 42] sage: num_int_test(e^(-x^2)*log(x), 17, 42) Exact = integrate(e^(-x^2)*log(x), x, 17, 42) Exact .n() = 2.59225286296247e-127 GSL = 2.5657285007e-127 mpmath = 2.59225286296247e-127
Gee, I don't like this at all. So do you think this is a bug? (And if so, in which program?) GSL is pretty stable, though...
try: precision = parent.prec() mpmath.mp.prec = precision if precision == RDF.precision(): mp_f = fast_callable(f, vars=[x], domain=RDF)
What if we called GSL for precisely this use case, not fast_callable
? Also, what does Maxima (.nintegrate()
) do?
Good analysis!
comment:33 Changed 11 years ago by
Maybe GSL targets absolute rather than relative error? mpmath uses the absolute error (which is something of a bug), but gives an accurate relative value here more or less by accident.
comment:34 follow-up: 35 Changed 11 years ago by
Replying to kcrisman:
Gee, I don't like this at all. So do you think this is a bug? (And if so, in which program?) GSL is pretty stable, though...
the correct result is 2.56...e-127, i.e., GSL's result.
Paul
comment:35 Changed 11 years ago by
Replying to zimmerma:
Replying to kcrisman:
Gee, I don't like this at all. So do you think this is a bug? (And if so, in which program?) GSL is pretty stable, though...
the correct result is 2.56...e-127, i.e., GSL's result.
Paul
Oh, indeed it is. I was confused by the "exact" result. That makes more sense.
comment:36 Changed 11 years ago by
Owner: | Burcin Erocal deleted |
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Obviously mpmath should support a relative tolerance out of the box, but there's a not-so-hackish workaround which Sage could use. The quadrature rules are implemented as classes, and can be subclassed:
from mpmath import * from mpmath.calculus.quadrature import TanhSinh, GaussLegendre class RelativeErrorMixin(object): def estimate_error(self, results, prec, epsilon): mag = abs(results[-1]) if len(results) == 2: return abs(results[0]-results[1]) / mag try: if results[-1] == results[-2] == results[-3]: return self.ctx.zero D1 = self.ctx.log(abs(results[-1]-results[-2])/mag, 10) D2 = self.ctx.log(abs(results[-1]-results[-3])/mag, 10) if D2 == 0: D2 = self.ctx.inf else: D2 = self.ctx.one / D2 except ValueError: return epsilon D3 = -prec D4 = min(0, max(D1**2 * D2, 2*D1, D3)) return self.ctx.mpf(10) ** int(D4) class TanhSinhRel(RelativeErrorMixin, TanhSinh): pass class GaussLegendreRel(RelativeErrorMixin, GaussLegendre): pass
With this change:
>>> quad(lambda x: exp(-x**2)*log(x), [17,42], method=TanhSinhRel) mpf('2.5657285005610513e-127') >>> >>> quad(lambda x: exp(-x**2)*log(x), [17,42], method=GaussLegendreRel) mpf('2.5657285005610513e-127')
BTW, I think the class will be instantiated every time this way, so the init method should be overwritten as well to create a singleton. Alternatively Sage could call the summation() method directly, which would remove some overhead.
The estimate_error method should be changed to something better and should be tested on many examples. The input "results" is a list of results generated at successive levels of refinement. The code above attempts to extrapolate the error estimate (in a rather convoluted way that should be fixed in mpmath :). One could be more conservative (and slower) by just comparing the two last results.
comment:37 Changed 11 years ago by
I've run some more comparisons which include Burcin's relative error for mpmath's quad. Here are some results for 6 test functions. The code that runs the tests is here: https://gist.github.com/1166436
In the output below:
- GSL means we call
numerical_integral
- mpmath means we call
mpmath.call(mpmath.quad, mp_f, [a, b])
for an appropriate functionmp_f
- mpmath_rel means we call
mpmath.call(mpmath.quad, mp_f, [a, b], method=GaussLegendreRel)
All of the times are listed in seconds.
function: e^(-x^2)*log(x) on [17, 42] GSL: 2.5657285007e-127 time: 0.001216173172 mpmath: 2.59225286296247e-127 time: 0.0308299064636 mpmath_rel (prec=64): 2.56572850056105156e-127 time: 0.7594602108 mpmath_rel (prec=100): 2.5657285005610514829173563974e-127 time: 0.894016981125 function: sqrt(-x^2 + 1) on [0, 1] GSL: 0.785398167726 time: 0.000615119934082 mpmath: 0.785398163397448 time: 0.011482000351 mpmath_rel (prec=64): 0.785398183809260289 time: 0.50303196907 mpmath_rel (prec=100): 0.78539818380926028913861331848 time: 0.57284116745 function: sin(sin(x)) on [0, 1] GSL: 0.430606103121 time: 0.00026798248291 mpmath: 0.430606103120691 time: 0.0110800266266 mpmath_rel (prec=64): 0.430606103120690605 time: 0.00665020942688 mpmath_rel (prec=100): 0.43060610312069060491237735525 time: 0.0202469825745 function: max(sin(x), cos(x)) on [0, pi] GSL: 2.41421356237 time: 0.012158870697 mpmath: 2.41413598800040 time: 0.102693796158 mpmath_rel (prec=64): 2.41424024561759656 time: 0.514449834824 mpmath_rel (prec=100): 2.4142402456175965601829446506 time: 0.583966970444 function: e^cos(x)*sin(x) on [0, pi] GSL: 2.35040238729 time: 0.000401973724365 mpmath: 2.35040238728760 time: 0.103391170502 mpmath_rel (prec=64): 2.35040238728760291 time: 0.0510699748993 mpmath_rel (prec=100): 2.3504023872876029137647637012 time: 0.132436037064 function: e^(-x^100) on [0, 1.1] GSL: 0.994325851192 time: 0.000550031661987 mpmath: 0.994325851192472 time: 0.390738010406 mpmath_rel (prec=64): 0.994325851192555258 time: 0.75753903389 mpmath_rel (prec=100): 0.99432585119255525754634686152 time: 0.875532865524
It looks like mpmath is now just as accurate as GSL but the times are obviously a lot longer. I agree with @kcrisman 's suggestion for calling GSL when the precision is default (float or RDF or 53 bits?) and calling mpmath with relative errors when the precision is higher. Perhaps adding the mpmath relative errors should be on a different ticket which this one will depend on?
comment:38 follow-up: 39 Changed 11 years ago by
The singleton trick definitely needs to be implemented; it can save a factor 4x or more.
Then there is the question of whether to use GaussLegendreRel or TanhSinhRel by default. Gauss-Legendre is somewhat faster for smooth integrands; Tanh-Sinh is much better for something like sqrt(-x^2 + 1)
on [0,1]
(note that the values with mpmath_rel above are wrong!) or almost anything on an infinite interval (this should be tested as well!). I would favor TanhSinhRel.
Anyway, I agree that it would be sensible to use GSL by default.
comment:39 follow-up: 40 Changed 11 years ago by
Replying to fredrik.johansson:
The singleton trick definitely needs to be implemented; it can save a factor 4x or more.
I understand what you are saying about the class being instantiated on every call. Can you explain what you mean by the "singleton trick"?
Then there is the question of whether to use GaussLegendreRel or TanhSinhRel by default. Gauss-Legendre is somewhat faster for smooth integrands; Tanh-Sinh is much better for something like
sqrt(-x^2 + 1)
on[0,1]
(note that the values with mpmath_rel above are wrong!) or almost anything on an infinite interval (this should be tested as well!). I would favor TanhSinhRel.Anyway, I agree that it would be sensible to use GSL by default.
For mp_f = sqrt(1-x**2)
, here is what TanhSinhRel? gives in comparison with GaussLengendreRel? and with absolute errors, as well as the approx. of the exact answer pi/4:
sage: mp_f = lambda z: f(x = mpmath.mpmath_to_sage(z, 53)) sage: mpmath.call(mpmath.quad, mp_f, [a, b]) 0.785398163397448 sage: mpmath.call(mpmath.quad, mp_f, [a, b], method=GaussLegendreRel) 0.785398325435763 sage: mpmath.call(mpmath.quad, mp_f, [a, b], method=TanhSinhRel) 0.785398163397448 sage: N(pi/4) 0.785398163397448
ps. somehow I read your second to last comment (about the relative error) and thought it was written by Burcin (hence my reference to his name in my reply). Sorry :)
comment:40 Changed 11 years ago by
Replying to benjaminfjones:
Replying to fredrik.johansson:
The singleton trick definitely needs to be implemented; it can save a factor 4x or more.
I understand what you are saying about the class being instantiated on every call. Can you explain what you mean by the "singleton trick"?
To make a class singleton, add something like this (warning: untested):
instance = None def __new__(cls, *args, **kwargs): if not cls.instance: cls.instance = super(ThisClass, cls).__new__(cls, *args, **kwargs) return cls.instance
comment:41 Changed 11 years ago by
I tried making TanhSinhRel the default and including the singleton __new__
code you gave. Here is the resulting class definition:
class TanhSinhRel(TanhSinh): instance = None def __new__(cls, *args, **kwds): if not cls.instance: cls.instance = super(TanhSinhRel, cls).__new__(cls, *args, **kwds) return cls.instance def estimate_error(self, results, prec, epsilon): mag = abs(results[-1]) if len(results) == 2: return abs(results[0]-results[1]) / mag try: if results[-1] == results[-2] == results[-3]: return self.ctx.zero D1 = self.ctx.log(abs(results[-1]-results[-2])/mag, 10) D2 = self.ctx.log(abs(results[-1]-results[-3])/mag, 10) if D2 == 0: D2 = self.ctx.inf else: D2 = self.ctx.one / D2 except ValueError: return epsilon D3 = -prec D4 = min(0, max(D1**2 * D2, 2*D1, D3)) return self.ctx.mpf(10) ** int(D4)
I couldn't see a timing difference by adding that code to TanhSinhRel (but maybe this isn't the right place to add it?). Also, I get a deprecation warning about arguments passed to __new__
Here are two tests in a row, one shows the deprecation warning, the second doesn't:
sage: num_int_test_v2(e**(-x**2)*log(x), 17, 42) GSL: 2.5657285007e-127 time: 0.0059130191803 mpmath: 2.59225286296247e-127 time: 0.0680160522461 /Users/jonesbe/sage/latest/local/bin/sage-ipython:66: DeprecationWarning: object.__new__() takes no parameters mpmath_rel_tanh (prec=64): 2.56572850056105156e-127 time: 0.310777187347 mpmath_rel_tanh (prec=100): 2.5657285005610514829173563973e-127 time: 0.541303157806
and again in the same session to check if timings have improved:
sage: num_int_test_v2(e**(-x**2)*log(x), 17, 42) GSL: 2.5657285007e-127 time: 0.00131511688232 mpmath: 2.59225286296247e-127 time: 0.0299959182739 mpmath_rel_tanh (prec=64): 2.56572850056105156e-127 time: 0.211745023727 mpmath_rel_tanh (prec=100): 2.5657285005610514829173563973e-127 time: 0.513824939728
The timings do improve after the first call which includes method=TanhSinhRel
, but not dramatically. Am I missing something?
comment:42 Changed 11 years ago by
Ugh, I should clearly have tested this feature properly in mpmath. The problem is that the __init__
method clears the caches. This definitely needs to be changed in mpmath. Anyway, a workaround is to move the initialization to the __new__
method, like this:
def __new__(cls): if not cls.instance: cls.instance = object.__new__(cls) cls.instance.standard_cache = {} cls.instance.transformed_cache = {} cls.instance.interval_count = {} return cls.instance def __init__(self, ctx): self.ctx = ctx
This ought to work. The speedup of doing this should be greater for GaussLegendre than for TanhSinh, since the node generation is more expensive for the former.
Some further speedup would be possible by overriding the transform_nodes and sum_next methods so that Sage numbers are used most of the time. This way most of the calls to sage_to_mpmath and mpmath_to_sage could be avoided when an interval is reused.
transform_nodes would just have to be replaced by a simple wrapper function that takes the output (a list of pairs of numbers) from the transform_nodes method of the parent class and converts it to Sage numbers.
sum_next computes the sum over weight[i]*f(node[i])
. This is trivial and could just be changed to a simple loop to work optimally with Sage numbers. (Only the return value needs to be converted back to an mpmath number).
This should all just require a few lines of code. One just needs to be careful to get the precision right in the conversions, and to support both real and complex numbers. Unless someone else is extremely eager to implement this, I could look at this tomorrow.
comment:43 Changed 11 years ago by
Sorry, make that
def __new__(cls, ctx): if not cls.instance: cls.instance = object.__new__(cls) cls.instance.ctx = ctx cls.instance.standard_cache = {} cls.instance.transformed_cache = {} cls.instance.interval_count = {} return cls.instance def __init__(self, ctx): pass
comment:44 Changed 11 years ago by
Keywords: | sd32 added |
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comment:45 Changed 11 years ago by
OK, here's a version also avoiding type conversions:
from mpmath.calculus.quadrature import TanhSinh from mpmath import quad, mp from sage.libs.mpmath.all import call, sage_to_mpmath, mpmath_to_sage class TanhSinhRel(TanhSinh): instance = None def __new__(cls, ctx): if not cls.instance: cls.instance = object.__new__(cls) cls.instance.ctx = ctx cls.instance.standard_cache = {} cls.instance.transformed_cache = {} cls.instance.interval_count = {} return cls.instance def estimate_error(self, results, prec, epsilon): mag = abs(results[-1]) if len(results) == 2: return abs(results[0]-results[1]) / mag try: if results[-1] == results[-2] == results[-3]: return self.ctx.zero D1 = self.ctx.log(abs(results[-1]-results[-2])/mag, 10) D2 = self.ctx.log(abs(results[-1]-results[-3])/mag, 10) if D2 == 0: D2 = self.ctx.inf else: D2 = self.ctx.one / D2 except ValueError: print factorial(1000000) return epsilon D3 = -prec D4 = min(0, max(D1**2 * D2, 2*D1, D3)) return self.ctx.mpf(10) ** int(D4) class TanhSinhRel2(TanhSinhRel): instance = None def __init__(self, ctx): pass class TanhSinhRel3(TanhSinhRel2): instance = None def transform_nodes(self, nodes, a, b, verbose=False): nodes = TanhSinh.transform_nodes(self, nodes, a, b, verbose) prec = self.ctx.prec nodes = [(mpmath_to_sage(x, prec), mpmath_to_sage(w, prec)) for (x, w) in nodes] return nodes def sum_next(self, f, nodes, degree, prec, previous, verbose=False): h = self.ctx.mpf(2)**(-degree) if previous: S = previous[-1]/(h*2) else: S = self.ctx.zero s = 0 for (x, w) in nodes: s += w * f(x) return h * (S + sage_to_mpmath(s, prec)) def f(x): return exp(-x**2) * log(x) def g(x): x = mpmath_to_sage(x, mp.prec) y = exp(-x**2) * log(x) return sage_to_mpmath(y, mp.prec) mp.prec = 100 timeit("mp.quad(g, [17, 42], method=TanhSinhRel)") timeit("mp.quad(g, [17, 42], method=TanhSinhRel2)") timeit("mp.quad(f, [17, 42], method=TanhSinhRel3)") print mp.quad(g, [17, 42], method=TanhSinhRel) print mp.quad(g, [17, 42], method=TanhSinhRel2) print mp.quad(f, [17, 42], method=TanhSinhRel3)
This prints:
5 loops, best of 3: 82.1 ms per loop 5 loops, best of 3: 72.5 ms per loop 5 loops, best of 3: 38.2 ms per loop 2.5657285005610514829173563961e-127 2.5657285005610514829173563961e-127 2.5657285005610514829173563961e-127
The estimate_error method still needs some work, though...
comment:46 Changed 11 years ago by
It turns out that the current top-level function, numerical_integral, isn't even in the reference manual. See #11916. I don't think this is addressed here yet, though if it eventually is then that ticket would be closed as a dup.
comment:47 follow-up: 48 Changed 11 years ago by
Just FYI - the Maxima list has a similar discussion going on right now, starting here in the archives. We should continue to allow access to their methods as optional, of course :)
comment:48 Changed 11 years ago by
Replying to kcrisman:
Just FYI - the Maxima list has a similar discussion going on right now, starting here in the archives. We should continue to allow access to their methods as optional, of course :)
I especially like this quote. I think it is a better way forward than trying to guess what the user needs - maybe just allowing many options is better.
In my opinion, an interface simplifying the use of packages like QUADPACK should not attempt to guess which method is more appropriate for a given problem. This should be left to the user. Otherwise we are going to have an "all-purpose" Maxima function supposed to do everything, like Mathematica's function "NIntegrate", which, however, not only fails to do what is supposed to do in many cases, but also encourages the "blind use" of Numerical Analysis. There is no "perfect" numerical method, able to solve any problem efficiently; this is true for any numerical problem, such as numerical quadrature, solution of initial or boundary value problems etc. Two simple examples: (1) consider integrating a "sawtooth" function. Romberg integration, which is generally very fast and accurate for smooth functions would have a hard time integrating a sawtooth function, while a simple trapezoidal method would be much faster in that particular case. (2) Most people use "natural" cubic splines for interpolation, just because of their name I guess, or maybe because Computer Algebra Systems use natural cubic splines by default for interpolation. However, "natural" splines are not natural at all, and should be used only if there is a reason to assume second derivative is zero at the end points of the interpolation interval. Otherwise, "not-a-knot" splines should be used instead. I doubt there is a way to make a function which automatically selects the best method to solve a numerical problem. Mathematica tries that and the result is disappointing. I am very suspicious about such attempts, and I believe none should trust them, no matter how sophisticated they are. Everyone who needs to use numerical methods should have a basic knowledge of what (s)he is doing, and should be able to pick the numerical method most appropriate method for a given problem.
comment:49 Changed 11 years ago by
Cc: | Jonathan Bober added |
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comment:50 Changed 11 years ago by
Replying to zimmerma:
I don't know why it does not work from Sage:
sage: gp.intnum(x=1,2,sin(x)/x^2) ------------------------------------------------------------ File "<ipython console>", line 1 SyntaxError: non-keyword arg after keyword arg (<ipython console>, line 1)
It does not work for two reasons:
gp.intnum
does not accept python keyword arguments (it would be very painful and error prone to transform that to the appropriate string input togp
- formula transformation to gp is very limited:
sage: gp(sin(x)/x^2) x^-1 - 1/6*x + 1/120*x^3 - 1/5040*x^5 + 1/362880*x^7 - 1/39916800*x^9 + 1/6227020800*x^11 - 1/1307674368000*x^13 + O(x^15)
The latter point seems the most fundamental to me. For arbitrary precision numerical integration, GP/PARI is probably our best bet, though, and it seems that the PARI C api should be quite usable, because the integrand gets passed as a black box function. From PARI handbook, we get the signature:
intnum(void *E, GEN (*eval)(void*,GEN), GEN a,GEN b,GEN tab, long prec)
so as long as we can provide a way to evaluate our integrand (say) f
at a value x
with precision prec
, we can wrap that up into a C function that takes a GEN
, converts it to x
, evaluates f
there and converts the result to a GEN
and passes it back. We could pass a pointer to that function in as eval
and then everything should work.
Pari's high precision numerical integration is supposed to be of quite high quality.
This approach would be much easier than trying to symbolically translate any arbitrary Sage symbolic expression to GP (plus more general, because we would be able to use any python callable, provided we find a way to provide the desired precision)
comment:51 follow-up: 53 Changed 11 years ago by
Sage 4.8 can now integrate the formula in this ticket, thus I propose to change it to:
sage: h = integral(sin(sin(x)), (x, 1, 2)); h integrate(sin(sin(x)), x, 1, 2) sage: h.n() 0.81644995512331231 sage: h.n(digits=14) 0.81644995512331231 sage: h.n(digits=600) 0.81644995512331231 sage: h.n(digits=600) == h.n(digits=14) True sage: h.n(prec=50) == h.n(prec=1000) True
Paul
comment:52 Changed 11 years ago by
Reviewers: | → Paul Zimmermann |
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Work issues: | → add more arbitrary precision tests |
comment:53 Changed 11 years ago by
Replying to zimmerma:
Sage 4.8 can now integrate the formula in this ticket
You are right that for this ticket, the original example doesn't test generic numerical integration. The numerical approximation of the resulting expressions in gamma functions seems suspect, though:
sage: h = integral(sin(x)/x^2, (x, 1, pi/2)); sage: H1=h.n(digits=20) sage: H2=h.n(digits=100) sage: delta=parent(H2)(H1)-H2 sage: delta 0 sage: parent(delta) Complex Field with 336 bits of precision sage: H2.imag_part() 5.421010862427522170037264004349708557128906250000000000000000000000000000000000000000000000000000000e-20
Also note that the equality tests as stated in the examples are not direct evidence that something is going wrong:
sage: a=RealField(10)(1) sage: b=RealField(20)(1)+RealField(20)(2)^(-14) sage: a,b (1.0, 1.0001) sage: a == b True
I guess the numbers are coerced into the parent with least precision before being compared ...
comment:54 Changed 9 years ago by
Cc: | Eviatar Bach added |
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comment:55 Changed 9 years ago by
Milestone: | sage-5.11 → sage-5.12 |
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comment:56 Changed 9 years ago by
Milestone: | sage-6.1 → sage-6.2 |
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comment:57 Changed 9 years ago by
Milestone: | sage-6.2 → sage-6.3 |
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comment:58 Changed 8 years ago by
Milestone: | sage-6.3 → sage-6.4 |
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comment:59 Changed 5 years ago by
Cc: | Marcelo Forets added |
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is there current interest in adding the functionality of this ticket?
i read through the benchmarks in this thread, but on the other hand i didn't understand what is the proposed way to plug this into sage. how about the following: does it make sense to have the numerical integration algorithms to be called via a new keyword argument in numerical_integral
? that would use the current default GSL, the one from PARI, and the one from mpmath.
comment:60 Changed 5 years ago by
for reference one will find on https://members.loria.fr/PZimmermann/sagebook/english.html a translation into english of the book "Calcul mathematique avec Sage", which was also updated to Sage 7.6. Chapter 14 discusses numerical integration, in particular with arbitrary precision. (We have also added a section about multiple integrals.)
Note that PARI/GP can do (arbitrary precision) numerical integration:
I don't know why it does not work from Sage: