Thread: [OctDev] Tests fail after compiling in Octave 3.6.3.

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[OctDev] Tests fail after compiling in Octave 3.6.3.

From: <fe...@st...> - 2012-10-20 23:59:12

Attachments: config.log

Hello,

After compiling GNU Octave 3.6.3 one of the tests fails with a
segmentation fault and exits. After typing "make check" the last lines of
the output are:


  liboctave/Sparse.cc ....................................panic:
Segmentation fault -- stopping myself...
make[1]: *** [check] Segmentation fault (core dumped)
make[1]: Leaving directory `/home/fabian/Downloads/octave-3.6.3/test'
make: *** [check] Error 2


I am using the following system:

No LSB modules are available.
Distributor ID: Ubuntu
Description:    Ubuntu 12.04 LTS
Release:        12.04
Codename:       precise

The file config.log is attached.

Any help would be appreciated. Thank you very much in advance.

Kind regards,

Fabián

Re: [OctDev] Tests fail after compiling in Octave 3.6.3.

From: marco a. <mar...@gm...> - 2012-10-21 05:35:31

On 10/21/2012 1:29 AM, fe...@st... wrote:
> Hello,
>
> After compiling GNU Octave 3.6.3 one of the tests fails with a
> segmentation fault and exits. After typing "make check" the last lines of
> the output are:
>
>
>    liboctave/Sparse.cc ....................................panic:
> Segmentation fault -- stopping myself...
> make[1]: *** [check] Segmentation fault (core dumped)
> make[1]: Leaving directory `/home/fabian/Downloads/octave-3.6.3/test'
> make: *** [check] Error 2
>
>
> I am using the following system:
>
> No LSB modules are available.
> Distributor ID: Ubuntu
> Description:    Ubuntu 12.04 LTS
> Release:        12.04
> Codename:       precise
>
> The file config.log is attached.
>
> Any help would be appreciated. Thank you very much in advance.
>
> Kind regards,
>
> Fabián
>

which version of SuiteSparse library are you using ?

Re: [OctDev] Tests fail after compiling in Octave 3.6.3.

From: <fe...@st...> - 2012-10-21 06:33:21

> On 10/21/2012 1:29 AM, fe...@st... wrote:
>> Hello,
>>
>> After compiling GNU Octave 3.6.3 one of the tests fails with a
>> segmentation fault and exits. After typing "make check" the last lines
>> of
>> the output are:
>>
>>
>>    liboctave/Sparse.cc ....................................panic:
>> Segmentation fault -- stopping myself...
>> make[1]: *** [check] Segmentation fault (core dumped)
>> make[1]: Leaving directory `/home/fabian/Downloads/octave-3.6.3/test'
>> make: *** [check] Error 2
>>
>>
>> I am using the following system:
>>
>> No LSB modules are available.
>> Distributor ID: Ubuntu
>> Description:    Ubuntu 12.04 LTS
>> Release:        12.04
>> Codename:       precise
>>
>> The file config.log is attached.
>>
>> Any help would be appreciated. Thank you very much in advance.
>>
>> Kind regards,
>>
>> Fabián
>>
>
> which version of SuiteSparse library are you using ?
>
>
>
>
>
> ------------------------------------------------------------------------------
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
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> Oct...@li...
> https://lists.sourceforge.net/lists/listinfo/octave-dev
>

Hello,

Thank you for your reply.

It seems version 2.2.3. The command "sudo apt-cache search SuiteSparse"
yields the following packages:

libsuitesparse-metis-3.1.0 - collection of libraries for computations for
sparse matrices
libsuitesparse-metis-dbg - collection of libraries for computations for
sparse matrices
libsuitesparse-metis-dev - collection of libraries for computations for
sparse matrices
libamd2.2.0 - approximate minimum degree ordering library for sparse matrices
libbtf1.1.0 - permutation to block triangular form library for sparse
matrices
libcamd2.2.0 - symmetric approximate minimum degree library for sparse
matrices
libccolamd2.7.1 - constrained column approximate library for sparse matrices
libcholmod1.7.1 - sparse Cholesky factorization library for sparse matrices
libcolamd2.7.1 - column approximate minimum degree ordering library for
sparse matrices
libcsparse2.2.3 - concise sparse matrix library
libcxsparse2.2.3 - concise sparse matrix library (complex, int and long
int support)
libklu1.1.0 - circuit simulation sparse LU factorization library
libldl2.0.1 - simple LDL' factorization library for sparse matrices
libsuitesparse-dbg - libraries for sparse matrices computations (debugging
symbols)
libsuitesparse-dev - libraries for sparse matrices computations
(development files)
libsuitesparse-doc - libraries for sparse matrices computations
(documentation)
libumfpack5.4.0 - sparse LU factorization library
r-recommended - GNU R collection of recommended packages [metapackage]

Should I update, which one?

Kind regards,

Fabián

Re: [OctDev] Tests fail after compiling in Octave 3.6.3.

From: marco a. <mar...@gm...> - 2012-10-21 07:24:03

On 10/21/2012 8:33 AM, fe...@st... wrote:
>> On 10/21/2012 1:29 AM, fe...@st... wrote:
>>> Hello,
>>>
>>> After compiling GNU Octave 3.6.3 one of the tests fails with a
>>> segmentation fault and exits. After typing "make check" the last lines
>>> of
>>> the output are:
>>>
>>>
>>>     liboctave/Sparse.cc ....................................panic:
>>> Segmentation fault -- stopping myself...
>>> make[1]: *** [check] Segmentation fault (core dumped)
>>> make[1]: Leaving directory `/home/fabian/Downloads/octave-3.6.3/test'
>>> make: *** [check] Error 2
>>>

Fabian,
two points:

1) the development mailing list for octave is:
https://mailman.cae.wisc.edu/listinfo/octave-maintainers

the one you are using is for octave-forge, dedicated to add-on packages.

2)
I remember 3.6.3 had some issues and was never deployed;
could you try the next 3.4.0

https://mailman.cae.wisc.edu/pipermail/octave-maintainers/2012-October/030449.html


>>>
>>> I am using the following system:
>>>
>>> No LSB modules are available.
>>> Distributor ID: Ubuntu
>>> Description:    Ubuntu 12.04 LTS
>>> Release:        12.04
>>> Codename:       precise
>>>
>>> The file config.log is attached.
>>>
>>> Any help would be appreciated. Thank you very much in advance.
>>>
>>> Kind regards,
>>>
>>> Fabián
>>>
>>
>> which version of SuiteSparse library are you using ?
>>
>>
>
> Hello,
>
> Thank you for your reply.
>
> It seems version 2.2.3. The command "sudo apt-cache search SuiteSparse"
> yields the following packages:
>
> libsuitesparse-metis-3.1.0 - collection of libraries for computations for
> sparse matrices
> libsuitesparse-metis-dbg - collection of libraries for computations for
> sparse matrices
> libsuitesparse-metis-dev - collection of libraries for computations for
> sparse matrices
> libamd2.2.0 - approximate minimum degree ordering library for sparse matrices
> libbtf1.1.0 - permutation to block triangular form library for sparse
> matrices
> libcamd2.2.0 - symmetric approximate minimum degree library for sparse
> matrices
> libccolamd2.7.1 - constrained column approximate library for sparse matrices
> libcholmod1.7.1 - sparse Cholesky factorization library for sparse matrices
> libcolamd2.7.1 - column approximate minimum degree ordering library for
> sparse matrices
> libcsparse2.2.3 - concise sparse matrix library
> libcxsparse2.2.3 - concise sparse matrix library (complex, int and long
> int support)
> libklu1.1.0 - circuit simulation sparse LU factorization library
> libldl2.0.1 - simple LDL' factorization library for sparse matrices
> libsuitesparse-dbg - libraries for sparse matrices computations (debugging
> symbols)
> libsuitesparse-dev - libraries for sparse matrices computations
> (development files)
> libsuitesparse-doc - libraries for sparse matrices computations
> (documentation)
> libumfpack5.4.0 - sparse LU factorization library
> r-recommended - GNU R collection of recommended packages [metapackage]
>
> Should I update, which one?
>
> Kind regards,
>
> Fabián

no idea, I am using Suitesparse 3.7 that includes:

./AMD/Doc/ChangeLog
May 15, 2011: version 2.2.4
./BTF/Doc/ChangeLog
Dec 7, 2011: version 1.1.3
./CAMD/Doc/ChangeLog
May 15, 2011: version 2.2.4
./CCOLAMD/Doc/ChangeLog
Dec 7, 2011: version 2.7.4
./CHOLMOD/Doc/ChangeLog
Dec 7, 2011: version 1.7.4
./COLAMD/Doc/ChangeLog
Dec 7, 2011: version 2.7.4
./CSparse/Doc/ChangeLog
Dec 7, 2011: version 2.2.6
./CSparse3/Doc/ChangeLog
Dec 7, 2011: version 3.0.2
./CXSparse/Doc/ChangeLog
Dec 7, 2011: version 2.2.6
./KLU/Doc/ChangeLog
Jan 20, 2012: version 1.1.4
./LDL/Doc/ChangeLog
Dec 7, 2011: version 2.0.4
./RBio/Doc/ChangeLog
Dec 7, 2011: version 2.0.2
./SPQR/Doc/ChangeLog
Dec 7, 2011: version 1.2.3
./UMFPACK/Doc/ChangeLog
Dec 7, 2011, version 5.5.2


Marco

Re: [OctDev] Tests fail after compiling in Octave 3.6.3.

From: Daniel J S. <dan...@ie...> - 2012-10-21 07:32:23

On 10/21/2012 01:33 AM, fe...@st... wrote:
>> On 10/21/2012 1:29 AM, fe...@st... wrote:
>>> Hello,
>>>
>>> After compiling GNU Octave 3.6.3 one of the tests fails with a
>>> segmentation fault and exits. After typing "make check" the last lines
>>> of
>>> the output are:
>>>
>>>
>>>     liboctave/Sparse.cc ....................................panic:
>>> Segmentation fault -- stopping myself...
>>> make[1]: *** [check] Segmentation fault (core dumped)
>>> make[1]: Leaving directory `/home/fabian/Downloads/octave-3.6.3/test'
>>> make: *** [check] Error 2
>>>
>>>
>>> I am using the following system:
>>>
>>> No LSB modules are available.
>>> Distributor ID: Ubuntu
>>> Description:    Ubuntu 12.04 LTS
>>> Release:        12.04
>>> Codename:       precise
>>>
>>> The file config.log is attached.
>>>
>>> Any help would be appreciated. Thank you very much in advance.
>>>
>>> Kind regards,
>>>
>>> Fabián
>>>
>>
>> which version of SuiteSparse library are you using ?
>>
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Everyone hates slow websites. So do we.
>> Make your web apps faster with AppDynamics
>> Download AppDynamics Lite for free today:
>> http://p.sf.net/sfu/appdyn_sfd2d_oct
>> _______________________________________________
>> Octave-dev mailing list
>> Oct...@li...
>> https://lists.sourceforge.net/lists/listinfo/octave-dev
>>
>
> Hello,
>
> Thank you for your reply.
>
> It seems version 2.2.3. The command "sudo apt-cache search SuiteSparse"
> yields the following packages:
>
> libsuitesparse-metis-3.1.0 - collection of libraries for computations for
> sparse matrices
> libsuitesparse-metis-dbg - collection of libraries for computations for
> sparse matrices
> libsuitesparse-metis-dev - collection of libraries for computations for
> sparse matrices
> libamd2.2.0 - approximate minimum degree ordering library for sparse matrices
> libbtf1.1.0 - permutation to block triangular form library for sparse
> matrices
> libcamd2.2.0 - symmetric approximate minimum degree library for sparse
> matrices
> libccolamd2.7.1 - constrained column approximate library for sparse matrices
> libcholmod1.7.1 - sparse Cholesky factorization library for sparse matrices
> libcolamd2.7.1 - column approximate minimum degree ordering library for
> sparse matrices
> libcsparse2.2.3 - concise sparse matrix library
> libcxsparse2.2.3 - concise sparse matrix library (complex, int and long
> int support)
> libklu1.1.0 - circuit simulation sparse LU factorization library
> libldl2.0.1 - simple LDL' factorization library for sparse matrices
> libsuitesparse-dbg - libraries for sparse matrices computations (debugging
> symbols)
> libsuitesparse-dev - libraries for sparse matrices computations
> (development files)
> libsuitesparse-doc - libraries for sparse matrices computations
> (documentation)
> libumfpack5.4.0 - sparse LU factorization library
> r-recommended - GNU R collection of recommended packages [metapackage]
>
> Should I update, which one?


Fabián

Before digging too deep into the libraries themselves, you may want to 
get the latest version of Octave from the repository.  3.6.3 is from a 
couple months ago and there may have been some code changes related to 
sparse matrices since then.

Here is the graph at the time of 3.6.3:

http://hg.savannah.gnu.org/hgweb/octave/graph/a95432e7309c

 From there you can move forward in the graph using the +60 button on 
the right side.  Then use the browser search for "sparse".  I'm seeing 
related changesets below.  Whether any of those contain a fix, I'm not 
sure.  If the problem persists, then write back and folks can help 
isolate the problem in the library or Octave.

Dan

# Fix Octave builds with SuiteSparse >=4.0 (bug #37031)6 weeks ago

# Ensure sparse constructors have valid ridx and data indices even if 
they are zero matrices (bug #36104)

# Special-case removing rows or columns from empty sparse matricesstable

# build: Don't directly compile #included template code Sparse.cc, 
MSparse.cc5 weeks ago

# configure.ac: Fix building of Octave with ancient versions of 
SuiteSparse (3.2.X)

# when writing sparse matrices to MAT files, use nzmax of at least 1 
(bug #36603)

# error out when attempting sparse minimum solution and CXSparse is 
unavailable

Re: [OctDev] Tests fail after compiling in Octave 3.6.3.

From: nitnit <ni...@gm...> - 2012-10-21 07:21:32

This a known regression of 3.6.3

See discussion and fix in
See
http://octave.1599824.n4.nabble.com/GNU-Octave-3-6-3-Released-td4643700.html#a4643800

You can try the fix or recent octave-3.6.4-rc0.

Nitzan



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