cout-based debugging

[Dong Liang]

Hi,

I remember reading on the group that lines containing std∷cout were optimized out from the cpp file by the TMB∷compile function.
In the development stage, these std∷cout can be handy for debugging.
Is there a way to keep these std∷cout results while running the optimization (e.g. optim or nlminb)?
Please see attached a very simple example from the reference manual. How to show the trace outputs from cout in R-console after line 12?

Thanks
Dong

[Ben Bolker]

Hmm. Is Rprintf() also optimized out? (I prefer Rprintf() to cout
anyway, but I appreciate that it doesn't necessarily serve exactly the
same function)

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[Andrea Havron]

I have used Rcout before (replace std::cout with Rcout). Note that your Rcout statements will get printed four times. From my understanding, this is due to the four AD types of a TMB model that track value, 1st, 2nd, and 3rd derivatives (Kasper correct me if I'm wrong here). I haven't tried Rprintf().

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[Dong Liang]

Both Rprintf and Rcout results showed up in the R-Console after running MakeADFun, but none appeared iteratively during the optim run. How can I see the intermediate results during the iterations?

Thanks
Dong

[Andrea Havron]

I'm not sure how to get Rcout statements to print with every iteration.

If you are trying to track parameter values though, you can set tracepar = TRUE, that is:

obj <- MakeADFun(data, parameters, DLL="matern")
obj$env$tracepar <- TRUE

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[Dong Liang]

Thanks, but tracepar does not trace random effects. Neither does it trace "generated values" (functions of parameters) with every iteration.

Thanks
Dong

[Katie Paulson]

Hi all -- I'm hoping to do something similar. In R I have obj <- TMB::MakeADFun(...). I want to run obj$fn(obj$par) and have some of functions of parameters (from the middle of my .cpp code) printed to my R console to help with debugging. I added a Rcout line to my .cpp code but nothing is printed to my R console when I run obj$fn(obj$par). Please let me know if you found a solution to this, or if there's another suggestion for debugging where I want to view values from the middle of my .cpp code.

Thanks!

Katie

[Kasper Kristensen]

The tricky thing about cout based debugging is that your C++ template is only processed a few times for the initial parameters when you create the internal 'tape' of the model by running MakeADFun(...). The cout statements do not become part of the tape, so you won't see any output when running 'obj$fn()'.
Here's a workaround:

Start by running obj$fn(par) to update the internal parameters (or skip this step if you wish to debug from a state where your program stopped with an error). Then grab the corresponding full parameter vector and evaluate your C++ template for this parameter using 'double' types:

lp <- obj$env$last.par        ## Grab most recent full parameter
obj$env$f(lp, type="double")  ## Evaluate template using 'double' types to execute cout statements

[Katie Paulson]

Hmm I tried this and I'm still not getting cout statements printed to my R console. Here's the code I have in my objective function:

  std::cout<<"Matrix SigmaInv:";
  for (int i = 0; i < 2; i++) {
    for (int j = 0; j < 2; j++) {
      std::cout<<SigmaInv(i,j);
    }
  }

[Kasper Kristensen]

Please see previous answer in this thread about using Rcout rather than std::cout.

[Katie Paulson]

This in my .cpp code:  

Rcout<<"Matrix SigmaInv:";

  for (int i = 0; i < 2; i++) {
    for (int j = 0; j < 2; j++) {

      Rcout<<SigmaInv(i,j);
    }
 }

plus your suggestion from the R console:

lp <- obj$env$last.par
obj$env$f(lp, type="double")

does not print anything other than the value of the objective function at these parameter values (which for me is NaN which is why I'm trying to do some debugging).

Thank you again for your time and help on this.

Katie