How can I define coverage bin for transition that might have many repetitions in it? What I'm trying to do is something like this:
bins st = (2=> 3[* 1:$] => 2);
Of course, this doesn't work. Simulators give error messages when compiling this line.
Edit: Simulators complain about $ symbol, they don't recognize it as "unbounded maximum". However when writing sequences, it is legal to use consecutive repetition operator as [* 1:$]. I hope next version of SystemVerilog makes it legal for covergroups too.
As a crude workaround, I substituted $ with a large number so it works fine for my case.
bins st = (2=> 3[* 1:1000] => 2);
SystemVerilog transition bins were not designed to handle anything but simple transitions. Anything more complex should be modeled using a cover directive, or some combination of sequence.triggered() method and covergroup.
Related
I have a constrained nonlinear optimization problem, "A". Inside the computation is an om.Group which I'll call "B" that requires a nonlinear solve. Whether "B" finds a solution or crashes seems to depend on its initial conditions. So far I've found that some of the initial conditions given to "B" are inconsistent with the constraints on "A", and that this seems to be contributing to its propensity for crashing. The constraints on "A" can be computed before "B".
If the objective of "A" could be computed before "B" then I would put "A" in its own group and have it pass its known-good solution to "B". However, the objective of "A" can only be computed as a result of the converged solution of "B". Is there a way to tell OpenMDAO or the optimizer (right now I'm using ScipyOptimizerDriver and the SLSQP method) that when it chooses a new point in design-variable space, it should check that the constraints of "A" hold before proceeding to "B"?
A slightly simpler example (without the complication of an initial guess) might be:
There are two design variables 0 < x1 < 1, 0 < x2 < 1.
There is a constraint that x2 >= x1.
Minimize f(sqrt(x2 - x1), x1) where f crashes if given imaginary inputs. How can I make sure that the driver explores the design space without giving f a bad input?
I have two proposed solutions. The best one is highly problem dependent. You can either raise an AnalysisError or use numerical clipping.
import numpy as np
import openmdao.api as om
class SafeComponent(om.ExplicitComponent):
def setup(self):
self.add_input('x1')
self.add_input('x2')
self.add_output('y')
def compute(self, inputs, outputs):
x1 = inputs['x1']
x2 = inputs['x2']
diff = x1 - x2
######################################################
# option 1: raise an error, which causes the
# optimizer line search to backtrack
######################################################
# if (diff < 0):
# raise om.AnalysisError('invalid inputs: x2 > x1')
######################################################
# option 2: use numerical clipping
######################################################
if (diff < 0):
diff = 0.
outputs['y'] = np.sqrt(diff)
# build the model
prob = om.Problem()
prob.model.add_subsystem('sc', SafeComponent(), promotes=['*'])
prob.setup()
prob['x1'] = 10
prob['x2'] = 20
prob.run_model()
print(prob['y'])
Option 1: raise an AnalysisError
Some optimizers are set up to handle this well. Others are not.
As of V3.7.0, the OpenMDAO wrappers for SLSQP from scipy and pyoptsparse, and the SNOPT/IPOPT wrappers from pyoptsparse all handle AnalysisErrors gracefully.
When the error is raised, the execution stops and the optimizer recognizes a failed case. It backtracks on the linesearch a bit to try and get out of the situation. It will usually try a few steps backwards, but at some point it will give up. So the success of this situation depends a bit on why you ended up in the bad part of the space and how much the gradients are pushing you back into it.
This solution works very well with fully analytic derivatives. The reason is that (most) gradient based optimizers will only ever ask for function evaluations along a line search operation. So that means that, as long as a clean point is found, you're always able to be able to compute derivatives at that point as well.
If you're using finite-differences, you could end a line search right near the error condition, but not violating it (e.g. x1=1, x2=.9999999). Then during the FD step to compute derivatives, you might end up tripping the error condition and raising the error. The optimizer is not going to be able to recover from this condition. Errors during FD steps will effectively kill the whole opt.
So, for this reason I never recommend the AnalysisError approach if you're suing FD.
Option 2: Numerical Clipping
If you optimizer wrapper does not have the ability to handle an AnalysisError, you can try some numerical clipping instead. You can add a filter in your calcs to to keep the values numerically safe. However, you obviously need to use this very carefully. You should at least add an additional constraint that forces the optimizer to keep away from the error condition when converged (e.g. x1 >= x2).
One important note: if you provide analytic derivatives, include the clipping in them!
Sometimes the optimizer just wants to pass through this bad region on its way to the answer. In that case, the simple clipping I show here is probably fine. Other times it wants to ride the constraint (be sure you add that constraint!!!) and then you probably want a more smoothly varying type of clipping. In other words don't use a simple if-condition. Smooth the round corner a bit, and maybe make the value asymptotically approach 0 from a very small value. This way you have a c1 continuous function and the derivatives won't got to exactly 0 for these inputs.
I have a lengthy symbolic expression that involves rational polynomials (basic arithmetic and integer powers). I'd like to simplify it into a single (simple) rational polynomial.
numden does it, but it seems to use some expensive optimization, which probably addresses a more general case. When tried on my example below, it crashed after a few hours--out of memory (32GB).
I believe something more efficient is possible even if I don't have a cpp access to matlab functionality (e.g. children).
Motivation: I have an objective function that involves polynomials. I manually derived it, and I'd like to verify and compare the derivatives: I subtract the two expressions, and the result should vanish.
Currently, my interest in this is academic since practically, I simply substitute some random expression, get zero, and it's enough for me.
I'll try to find the time to play with this as some point, and I'll update here about it, but I posted in case someone finds it interesting and would like to give it a try before that.
To run my function:
x = sym('x', [1 32], 'real')
e = func(x)
The function (and believe it or not, this is just the Jacobian, and I also have the Hessian) can't be pasted here since the text limit is 30K:
https://drive.google.com/open?id=1imOAa4VS87WDkOwAK0NoFCJPTK_2QIRj
I’m running RStudio Version 1.1.419 with R-3.4.3 on Windows 10. I am trying to fit an (f)arima model and setting the fractional differencing parameter during the optimization process to be between (-0.5,0.5), i.e. allowing for antipersistence (d < 0), short memory (d = 0) and long memory (d > 0). I have tried multiple functions to accomplish that. I am aware that the default of fracdiff$drange is (0,0.5). Therefore this ...
> result <- fracdiff(MeanPrice, nar = 2, nma = 1, drange = c(-0.5,0.5))
sadly returns this..
Warning: C fracdf() optimization failure
Warning message: unable to compute correlation matrix; maybe change 'h'
Is there a way to fit fracdiff or other models (maybe arfima::arfima()?) with that drange? Your help is very much appreciated.
If you look at the package documentation, it states that the h argument for fracdiff "is used to compute a finite difference approximation to the Hessian, and
hence only influences the cov, cor, and std.error computations." However, as they are referring to the Hessian, I would assume that this affects the results of the MLE. There are other functions in that package that may be helpful: fdGHP for estimating the order of fractional differencing based on the Geweke and Porter-Hudak method, and similarly fdSperio.
Take a look at the forecast package. If you estimate the order of fractional differencing using the above mentioned functions, you might be able to use the same method described in the details of the arfima function.
There is one thing I do not like on Matlab: It tries sometimes to be too smart. For instance, if I have a negative square root like
a = -1; sqrt(a)
Matlab does not throw an error but switches silently to complex numbers. The same happens for negative logarithms. This can lead to hard to find errors in a more complicated algorithm.
A similar problem is that Matlab "solves" silently non quadratic linear systems like in the following example:
A=eye(3,2); b=ones(3,1); x = A \ b
Obviously x does not satisfy A*x==b (It solves a least square problem instead).
Is there any possibility to turn that "features" off, or at least let Matlab print a warning message in this cases? That would really helps a lot in many situations.
I don't think there is anything like "being smart" in your examples. The square root of a negative number is complex. Similarly, the left-division operator is defined in Matlab as calculating the pseudoinverse for non-square inputs.
If you have an application that should not return complex numbers (beware of floating point errors!), then you can use isreal to test for that. If you do not want the left division operator to calculate the pseudoinverse, test for whether A is square.
Alternatively, if for some reason you are really unable to do input validation, you can overload both sqrt and \ to only work on positive numbers, and to not calculate the pseudoinverse.
You need to understand all of the implications of what you're writing and make sure that you use the right functions if you're going to guarantee good code. For example:
For the first case, use realsqrt instead
For the second case, use inv(A) * b instead
Or alternatively, include the appropriate checks before/after you call the built-in functions. If you need to do this every time, then you can always write your own functions.
I have a function which does the following loop many, many times:
for cluster=1:max(bins), % bins is a list in the same format as kmeans() IDX output
select=bins==cluster; % find group of values
means(select,:)=repmat_fast_spec(meanOneIn(x(select,:)),sum(select),1);
% (*, above) for each point, write the mean of all points in x that
% share its label in bins to the equivalent row of means
delta_x(select,:)=x(select,:)-(means(select,:));
%subtract out the mean from each point
end
Noting that repmat_fast_spec and meanOneIn are stripped-down versions of repmat() and mean(), respectively, I'm wondering if there's a way to do the assignment in the line labeled (*) that avoids repmat entirely.
Any other thoughts on how to squeeze performance out of this thing would also be welcome.
Here is a possible improvement to avoid REPMAT:
x = rand(20,4);
bins = randi(3,[20 1]);
d = zeros(size(x));
for i=1:max(bins)
idx = (bins==i);
d(idx,:) = bsxfun(#minus, x(idx,:), mean(x(idx,:)));
end
Another possibility:
x = rand(20,4);
bins = randi(3,[20 1]);
m = zeros(max(bins),size(x,2));
for i=1:max(bins)
m(i,:) = mean( x(bins==i,:) );
end
dd = x - m(bins,:);
One obvious way to speed up calculation in MATLAB is to make a MEX file. You can compile C code and perform any operations you want. If you're searching for the fastest-possible performance, turning the operation into a custom MEX file would likely be the way to go.
You may be able to get some improvement by using ACCUMARRAY.
%# gather array sizes
[nPts,nDims] = size(x);
nBins = max(bins);
%# calculate means. Not sure whether it might be faster to loop over nDims
meansCell = accumarray(bins,1:nPts,[nBins,1],#(idx){mean(x(idx,:),1)},{NaN(1,nDims)});
means = cell2mat(meansCell);
%# subtract cluster means from x - this is how you can avoid repmat in your code, btw.
%# all you need is the array with cluster means.
delta_x = x - means(bins,:);
First of all: format your code properly, surround any operator or assignment by whitespace. I find your code very hard to comprehend as it looks like a big blob of characters.
Next of all, you could follow the other responses and convert the code to C (mex) or Java, automatically or manually, but in my humble opinion this is a last resort. You should only do such things when your performance is not there yet by a small margin. On the other hand, your algorithm doesn't show obvious flaws.
But the first thing you should do when trying to improve performance: profile. Use the MATLAB profiler to determine which part of your code is causing your problems. How much would you need to improve this to meet your expectations? If you don't know: first determine this boundary, otherwise you will be looking for a needle in a hay stack which might not even be in there in the first place. MATLAB will never be the fastest kid on the block with respect to runtime, but it might be the fastest with respect to development time for certain kinds of operations. In that respect, it might prove useful to sacrifice the clarity of MATLAB over the execution speed of other languages (C or even Java). But in the same respect, you might as well code everything in assembler to squeeze all of the performance out of the code.
Another obvious way to speed up calculation in MATLAB is to make a Java library (similar to #aardvarkk's answer) since MATLAB is built on Java and has very good integration with user Java libraries.
Java's easier to interface and compile than C. It might be slower than C in some cases, but the just-in-time (JIT) compiler in the Java virtual machine generally speeds things up very well.