Re: [Boost-users] Mystery exception.

Subject: Re: [Boost-users] Mystery exception.
From: Will Mason (willchido_at_[hidden])
Date: 2012-03-25 17:04:44

Hi, Ted,

On Sun, Mar 25, 2012 at 2:06 PM, Ted Byers <r.ted.byers_at_[hidden]> wrote:

> As an aside, does anyone know how to tell MS Outlook not to top-post?****
>
> ** **
>
> Anyway,  Hi Will,****
>
> ** **
>
> Thanks, I would if I knew how to make sense of it.  Here is what is in the
> latest stackdump:****
>
> ** **
>
> Exception: STATUS_ACCESS_VIOLATION at eip=6110D500****
>
> ****
>
> eax=20024D68 ebx=00000338 ecx=3FBBDE84 edx=20022070 esi=200223A8
> edi=A9AE95F4****
>
> ****
>
> ebp=1ED48072 esp=0028BD00
> program=C:\cygwin\home\Ted\New.System\tests\test.pca.reg.gsl.exe, pid 7888,
> thread main****
>
> ****
>
> cs=0023 ds=002B es=002B fs=0053 gs=002B ss=002B****
>
> ****
>
> Stack trace:****
>
> ****
>
> Frame     Function  Args****
>
> ****
>
>       0 [main] test.pca.reg.gsl 7888 exception::handle: Error while
> dumping state (probably corrupted stack)****
>
> ** **
>
> I look at it and I don't know what to make of what it is telling me.  How
> can I turn an of those values into something meaningful?****
>
> ** **
>
> And the other one is even less intelligible:****
>
> ** **
>
> Stack trace:****
>
> ****
>
> Frame     Function  Args****
>
> ****
>
> 0028BBA4  75961194  (00000104, 0000EA60, 00000000, 0028BCD8)****
>
> ****
>
> 0028BBB8  75961148  (00000104, 0000EA60, 000000A4, 0028BCB4)****
>
> ****
>
> 0028BCD8  610D9339  (00000000, 0028BDF4, 0028BD08, 611352F4)****
>
> ****
>
> 0028BDC8  610D67CE  (00000000, 6C4F4A60, 6C4F4A60, 6C4F4A60)****
>
> ****
>
> 0028BE28  610D6C9E  (00000000, 0028BE34, 61183704, 00000006)****
>
> ****
>
> 0028BED8  610D6DF0  (00002FDC, 00000006, 00000000, 200223B0)****
>
> ****
>
> 0028BEF8  610D6E1C  (00000006, 0028CE80, 00000000, 00000064)****
>
> ****
>
> 0028BF28  610D70A5  (00000000, 00000000, 00000002, 00000001)****
>
> ****
>
> 0028BFC8  6110D4E5  (200217D0, 0028CC5C, 0028CC50, 00000000)****
>
> ****
>
> 0028CC88  00401C2D  (0000002F, 00000000, 6127390C, 61006F58)****
>
> ****
>
> 0028CD28  61006F58  (00000000, 0028CD78, 61006550, 0000000A)****
>
> ****
>
> End of stack trace****
>
> ** **
>
> How does one make sense of this?
>

I usually use gdb to help me see what's going on when I have a core file. I
assume that since you mentioned gmake before you probably have gdb. If not,
any system's normal debugger, like dbx, will make use of core files.

$ gdb prog-name core-name

Will load the core. The most useful command for me is "bt" ("where" under
dbx), which shows you the call stack of the current thread.

Cheers,
Will

> ****
>
> ** **
>
> Cheers****
>
> ** **
>
> Ted****
>
> ** **
>
> *From:* boost-users-bounces_at_[hidden] [mailto:
> boost-users-bounces_at_[hidden]] *On Behalf Of *Will Mason
> *Sent:* March-25-12 2:38 PM
>
> *To:* boost-users_at_[hidden]
> *Subject:* Re: [Boost-users] Mystery exception.****
>
> ** **
>
> Hi, Ted,****
>
> ** **
>
> 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).****
>
> ** **
>
> It sounds like you haven't looked at the core file. You don't have to
> wonder where it is crashing if it produces a core file. That's what they
> are for.****
>
> ** **
>
> Cheers,****
>
> Will****
>
> ** **
>
> On Sun, Mar 25, 2012 at 12:00 PM, Ted Byers <r.ted.byers_at_[hidden]> 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,
>
> ****
>
>
> _______________________________________________
> Boost-users mailing list
> Boost-users_at_[hidden]
> http://lists.boost.org/mailman/listinfo.cgi/boost-users****
>
> ** **
>
> _______________________________________________
> Boost-users mailing list
> Boost-users_at_[hidden]
> http://lists.boost.org/mailman/listinfo.cgi/boost-users
>