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Subject: Re: [Boost-users] Mystery exception.
From: Ted Byers (r.ted.byers_at_[hidden])
Date: 2012-03-25 16:33:36


I have heard of it, but the last I checked, it didn't support Windows. I'll
do a quick search and see if that has changed at all.

 

 

Cheers

 

Ted

 

From: Sven Steckmann [mailto:sven_at_[hidden]]
Sent: March-25-12 4:27 PM
To: boost-users_at_[hidden]
Cc: Ted Byers
Subject: Re: [Boost-users] Mystery exception.

 

Hi Ted,

I had a long look to your sources, but I am unable to find any problems
there. But I think there is still one, maybe also inside the gsl if
something has the wrong size. Speaking from my experience, I would not look
for problems with the shared_ptr stuff. I am using it very often and as long
as I had problems, these problems had their source in my program :)

Do you know valgrind? In cases of memory corruption, this can be a valuable
tool too.

Cheers,
    Sven

On 03/25/2012 08:00 PM, Ted Byers wrote:

Hi Sven,

 

Thanks for this.

 

 

Second, in my first post, the problem was due to some unpleasant behaviour
of Gnu make I wasn't aware of that resulting in a certain object file not
being remade even though the source for it had changed (actually, I don't
know if it is in make itself or a bug in my suite of make files - something
to be investigated further - doing make realclean followed by make solved
that). My current problem is something else, probably due to how memory is
handled either in GSL or in boost::shared_array, but maybe something more
subtle.

 

I had left the comments in place to show alternatives I had tried. It is no
surprise that compiling would fail if they were uncommented.

 

I have now changed regressionPCA back to the way I had intended it to be in
the first place.

 

Here is the header:

 

#ifndef REG_CLASS_H

#define REG_CLASS_H

 

#include <iosfwd>

#include <vector>

#include <gsl/gsl_linalg.h>

#include <boost/smart_ptr/shared_array.hpp>

 

class regressionPCA {

private:

  unsigned int nrows, ncols;

  boost::shared_array<double> B, Y, U, V, S;

  regressionPCA(void) {}; // makes default construction impossible

public:

  regressionPCA(const std::vector<std::vector<double> >&, const
std::vector<double>&);

  void Reset(const std::vector<std::vector<double> >&, const
std::vector<double>&);

  inline void setNrows(unsigned int v) { nrows = v;};

  inline void setNcols(unsigned int v) { ncols = v;};

  inline unsigned int getNrows(void) const { return nrows; };

  inline unsigned int getNcols(void) const { return ncols; };

};

 

#endif

 

And here is the implementation:

 

#include "reg.class.h"

 

#include <iostream>

#include <algorithm>

#include <gsl/gsl_linalg.h>

 

regressionPCA::regressionPCA(const std::vector<std::vector<double> >&data,

                             const std::vector<double>& Ydata) {

  Reset(data,Ydata);

}

 

void regressionPCA::Reset(const std::vector<std::vector<double> >&data,

                             const std::vector<double>& Ydata) {

  unsigned int r(0),c(0),n(0);

  std::cout << "r: " << r << "\tc: " << c << "\tn: " << n << std::endl;

  r = data.size();

  std::cout << "r: " << r << "\tc: " << c << "\tn: " << n << std::endl;

  c = data[0].size();

  std::cout << "r: " << r << "\tc: " << c << "\tn: " << n << std::endl;

  setNrows(r);

  setNcols(c);

  n = r * c;

  std::cout << "r: " << r << "\tc: " << c << "\tn: " << n << std::endl;

  B.reset(new double[c]);

  Y.reset(new double[r]);

  U.reset(new double[n]);

  V.reset(new double[c*c]);

  S.reset(new double[c]);

  double* Btmp = B.get();

  double* Ytmp = Y.get();

  double* Utmp = U.get();

  double* Vtmp = V.get();

  double* Stmp = S.get();

  double *bptr = Utmp;

  std::vector<std::vector<double> >::const_iterator it = data.begin(), end =
data.end();

  while (it != end) {

    bptr = std::copy(it->begin(), it->end(),bptr);

    ++it;

  }

  bptr = Ytmp;

  std::copy(Ydata.begin(),Ydata.end(),bptr);

  gsl_matrix_view Um = gsl_matrix_view_array(Utmp, getNrows(), getNcols());

  gsl_vector_view Ym = gsl_vector_view_array(Ytmp, getNrows());

  gsl_vector_view Bm = gsl_vector_view_array(Btmp, getNcols());

  gsl_vector_view Sm = gsl_vector_view_array(Stmp, getNcols());

  gsl_matrix_view Vm = gsl_matrix_view_array(Vtmp, getNcols(), getNcols());

  gsl_linalg_SV_decomp_jacobi(&Um.matrix,&Vm.matrix,&Sm.vector);

 
gsl_linalg_SV_solve(&Um.matrix,&Vm.matrix,&Sm.vector,&Ym.vector,&Bm.vector);

  std::cout << std::endl << std::endl << "Sv = " <<
gsl_vector_get(&Sm.vector,0) << "\t" << gsl_vector_get(&Sm.vector,1) <<
std::endl;

  std::cout << std::endl << std::endl << "V = " << std::endl;

  std::cout << "\t" << gsl_matrix_get(&Vm.matrix,0,0) << "\t" <<
gsl_matrix_get(&Vm.matrix,0,1) << std::endl;

  std::cout << "\t" << gsl_matrix_get(&Vm.matrix,1,0) << "\t" <<
gsl_matrix_get(&Vm.matrix,1,1) << std::endl;

  std::cout << std::endl << std::endl << "Beta = " <<
gsl_vector_get(&Bm.vector,0) << "\t" << gsl_vector_get(&Bm.vector,1) <<
std::endl;

};

 

Obviously a work in progress as I need to create data members to store the
result of the analysis, and member functions to pass the results back to the
calling code. I also need to get and analyse the residuals..

 

Here is function main:

 

#include <iostream>

#include <vector>

#include "data.generator.h"

#include "reg.class.h"

#include <boost/smart_ptr/shared_ptr.hpp>

 

int main(int argc, char* argv[]) {

  basicGenerator bg;

  std::cout << "Sample size: " << bg.get_sampleSize() << std::endl;

  bg.makeData();

  std::vector<std::vector<double> > x;

  std::vector<double> y;

  bg.getDataForRegression(x,y);

  unsigned int imax = y.size();

  for (unsigned int i = 0 ; i < imax ; i++) {

    std::cout << i << "\t" << y[i] << "\t" << x[i][0] << "\t" << x[i][1] <<
std::endl;

  }

  std::cout <<
"==================================================================" <<
std::endl;

  regressionPCA rpca(x,y);

  std::cout <<
"==================================================================" <<
std::endl;

  boost::shared_ptr<regressionPCA> prpca;

  for (unsigned int j = 0 ; j < 25 ; j++) {

    std::cout << std::endl << std::endl << "Run #: " << (j + 1) <<
std::endl;

    bg.makeData();

    bg.getDataForRegression(x,y);

    /* for (unsigned int i = 0 ; i < imax ; i++) {

      std::cout << i << "\t" << y[i] << "\t" << x[i][0] << "\t" << x[i][1]
<< std::endl;

      }*/

    prpca.reset(new regressionPCA(x,y));

    std::cout <<
"==================================================================" <<
std::endl;

  }

  return 0;

}

 

The following output shows that cleaning up the declaration and definition
has not changed anything:

 

94 -1.86323 -1.90867 -1.35118

95 0.907604 1.14917 0.621669

96 2.1166 1.06194 1.1703

97 0.159543 0.14446 -0.665135

98 -0.508617 -0.370597 -0.703225

99 2.69086 2.75267 1.40633

==================================================================

r: 0 c: 0 n: 0

r: 100 c: 0 n: 0

r: 100 c: 2 n: 0

r: 100 c: 2 n: 200

 

Sv = 18.3225 4.69155

 

V =

        0.695362 -0.718659

        0.718659 0.695362

 

Beta = 0.693195 0.627794

==================================================================

Run #: 1

r: 0 c: 0 n: 0

r: 100 c: 0 n: 0

r: 100 c: 2 n: 0

r: 100 c: 2 n: 200

 

Sv = 14.1699 10.7091

 

V =

        0.49497 -0.86891

        0.86891 0.49497

 

Beta = 0.476181 0.391545

==================================================================

 

Run #: 2

r: 0 c: 0 n: 0

r: 100 c: 0 n: 0

r: 100 c: 2 n: 0

r: 100 c: 2 n: 200

 

Sv = 18.3225 4.69155

 

V =

        0.695362 -0.718659

        0.718659 0.695362

 

Beta = 0.693195 0.627794

Aborted (core dumped)

 

Ted_at_Ted-acer-i7w7 ~/New.System/tests

$

 

There are a couple things I see.

 

1) the last statement successfully executed was the last statement of my
Reset function. It then returns to function main, and it's nect statement
produces the line of '+' symbols, and this is not successfully executed.
So, something bad is happening between the end of the function and the
return to function main.

2) if I uncomment the inner loop, over I, and comment out ' prpca.reset(new
regressionPCA(x,y));', that loop runs to completion. Thus, we can exclude
bg from having any role in this core dump. It must be something in either
gsl or boost::shared_array, or maybe boost::shared_ptr (but the core dump
happens too soon to be in shared_ptr's reset, unless the output to std::cout
is buffered and contents of the buffer are lost in the core dump before they
can be printed, but this is unlikely).

3) It must be something subtle, as I get one execution of the analysis done
in Reset, as shown in the first analysis reported by 'rpca', and then I get
two complete passes through my loop over j before it crashes. I am baffled
as to even how I determine whether it is something I have done wrong with
GSL or with boost::shared_array.

 

But here is an experiment I tried, let's see what you make of this. I
changed my main loop to use:

 

    rpca.Reset(x,y);

 

instead of

 

    prpca.reset(new regressionPCA(x,y));

 

That is, I used the object I'd made on the stack, instead of the one(s) made
on the heap. I then added " std::cout << "Flag 1" << std::endl <<
std::flush;" right after I invoked boost::shared_array's reset, and "
std::cout << "Flag 2" << std::endl << std::flush;" right after I copy new
data to these arrays. Here is the result:

 

98 -0.508617 -0.370597 -0.703225

99 2.69086 2.75267 1.40633

==================================================================

r: 0 c: 0 n: 0

r: 100 c: 0 n: 0

r: 100 c: 2 n: 0

r: 100 c: 2 n: 200

Flag 1

Flag 2

 

 

Sv = 18.3225 4.69155

 

 

V =

        0.695362 -0.718659

        0.718659 0.695362

 

 

Beta = 0.693195 0.627794

==================================================================

 

 

Run #: 1

r: 0 c: 0 n: 0

r: 100 c: 0 n: 0

r: 100 c: 2 n: 0

r: 100 c: 2 n: 200

Flag 1

Flag 2

 

 

Sv = 14.1699 10.7091

 

 

V =

        0.49497 -0.86891

        0.86891 0.49497

 

 

Beta = 0.476181 0.391545

==================================================================

 

 

Run #: 2

r: 0 c: 0 n: 0

r: 100 c: 0 n: 0

r: 100 c: 2 n: 0

r: 100 c: 2 n: 200

      0 [main] test.pca.reg.gsl 7888 exception::handle: Error while dumping
state (probably corrupted stack)

Segmentation fault (core dumped)

 

Ted_at_Ted-acer-i7w7 ~/New.System/tests

$

 

 

Do you notice the change?

 

Instead of finishing the second analysis in the loop, it crashes after I
print the dimensions of the input matrix and vector, at some point in
resetting one of the boost::shared_array objects. How do I determine
whether this is a bug in boost::shared_array or some bad interaction between
boost::shared_array and GSL?

 

 

Cheers

 

Ted

 

From: boost-users-bounces_at_[hidden]
[mailto:boost-users-bounces_at_[hidden]] On Behalf Of Sven Steckmann
Sent: March-25-12 4:13 AM
To: boost-users_at_[hidden]
Subject: Re: [Boost-users] Mystery exception.

 

Hi Ted,

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