Quantcast

problem with "pkg -forge fem-fenics"

Previous Topic Next Topic
 
classic Classic list List threaded Threaded
6 messages Options
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

problem with "pkg -forge fem-fenics"

arnaudl
Hello,

I am working on:
-> Linux version 4.4.0-67-generic (buildd@lgw01-46) (gcc version 5.4.0 20160609 (Ubuntu 5.4.0-6ubuntu1~16.04.4) )
-> Octave version 4.0.0

Trying to install fem-fenics using
 "pkg -forge fem-fenics"

lead to the following error
*********************************************************
ar: création de libfemfenics_factories.a
Mesh.cc: In function ‘octave_value compute_facet_markers(std::shared_ptr<const dolfin::Mesh>, const Array<int>&, std::size_t)’:
Mesh.cc:430:38: error: invalid initialization of reference of type ‘const std::vector<long unsigned int>&’ from expression of type ‘const std::vector<long int>’
     _msh->topology ().global_indices (0);
                                      ^
Mesh.cc:432:38: error: invalid initialization of reference of type ‘const std::vector<long unsigned int>&’ from expression of type ‘const std::vector<long int>’
     _msh->topology ().global_indices (D - 1);
                                      ^
Mesh.cc: In function ‘octave_value compute_cell_markers(std::shared_ptr<const dolfin::Mesh>, const Array<int>&, std::size_t)’:
Mesh.cc:530:38: error: invalid initialization of reference of type ‘const std::vector<long unsigned int>&’ from expression of type ‘const std::vector<long int>’
     _msh->topology ().global_indices (0);
                                      ^
Mesh.cc:532:38: error: invalid initialization of reference of type ‘const std::vector<long unsigned int>&’ from expression of type ‘const std::vector<long int>’
     _msh->topology ().global_indices (D);
                                      ^
make: *** [Mesh.o] Erreur 1
************************************************************************************************************************

Has anyone ever solved this issue ?

Thanks for your answer (and sorry for my poor english)

Arnaud

Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Re: problem with "pkg -forge fem-fenics"

NJank


On Mon, Mar 27, 2017 at 5:25 AM, arnaudl <[hidden email]> wrote:
Hello,

I am working on:
-> Linux version 4.4.0-67-generic (buildd@lgw01-46) (gcc version 5.4.0
20160609 (Ubuntu 5.4.0-6ubuntu1~16.04.4) )
-> Octave version 4.0.0

Trying to install fem-fenics using
 "pkg -forge fem-fenics"

first question, did you mean:

pkg install -forge fem-fenics

?

_______________________________________________
Help-octave mailing list
[hidden email]
https://lists.gnu.org/mailman/listinfo/help-octave
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Re: problem with "pkg -forge fem-fenics"

NJank
On Mon, Mar 27, 2017 at 11:18 AM, Arnaud Lejeune <[hidden email]> wrote:
Yes
Le 27/03/2017 16:54, Nicholas Jankowski a écrit :


On Mon, Mar 27, 2017 at 5:25 AM, arnaudl <[hidden email]> wrote:
Hello,

I am working on:
-> Linux version 4.4.0-67-generic (buildd@lgw01-46) (gcc version 5.4.0
20160609 (Ubuntu 5.4.0-6ubuntu1~16.04.4) )
-> Octave version 4.0.0

Trying to install fem-fenics using
 "pkg -forge fem-fenics"

first question, did you mean:

pkg install -forge fem-fenics

?
Yes I mean
pkg install -forge fem-fenics

Downloading fem-fenics sources and looking at Mesh.cc, perhaps could it be a problem with "size_t" as "_msh" seems to be a dolfin::mesh shared_ptr ?

Dolfin version is the stable one installed with "apt-get".

Note that during the fem-fenis installation, compilation of fem-fenics sources uses the following CPPFLAGS options:
-DDOLFIN_VERSION=\"2016.2.0" -DDOLFIN_SIZE_T=8 -DDOLFIN_LA_INDEX_SIZE=4

Thanks for your help.


please keep the help list on the replies, as I'm not familiar enough with this package to help further myself.

_______________________________________________
Help-octave mailing list
[hidden email]
https://lists.gnu.org/mailman/listinfo/help-octave
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Re: problem with "pkg -forge fem-fenics"

arnaudl

Le 27/03/2017 17:20, Nicholas Jankowski a écrit :
On Mon, Mar 27, 2017 at 11:18 AM, Arnaud Lejeune <[hidden email]> wrote:
Yes
Le 27/03/2017 16:54, Nicholas Jankowski a écrit :


On Mon, Mar 27, 2017 at 5:25 AM, arnaudl <[hidden email]> wrote:
Hello,

I am working on:
-> Linux version 4.4.0-67-generic (buildd@lgw01-46) (gcc version 5.4.0
20160609 (Ubuntu 5.4.0-6ubuntu1~16.04.4) )
-> Octave version 4.0.0

Trying to install fem-fenics using
 "pkg -forge fem-fenics"

first question, did you mean:

pkg install -forge fem-fenics

?
Yes I mean
pkg install -forge fem-fenics

Downloading fem-fenics sources and looking at Mesh.cc, perhaps could it be a problem with "size_t" as "_msh" seems to be a dolfin::mesh shared_ptr ?

Dolfin version is the stable one installed with "apt-get".

Note that during the fem-fenis installation, compilation of fem-fenics sources uses the following CPPFLAGS options:
-DDOLFIN_VERSION=\"2016.2.0" -DDOLFIN_SIZE_T=8 -DDOLFIN_LA_INDEX_SIZE=4

Thanks for your help.


please keep the help list on the replies, as I'm not familiar enough with this package to help further myself.

Ok,

looking at the source file "MeshTopology.h" from Dolfin package, one could see that  :
_msh->topology ().global_indices(std::size_t d) 

returns a 

const std::vector< std::int64_t > &

The compilation seems to fail as std::int64_t is not equivalent to std::size_t.

Is there a way to change fem-fenics options to solve this problem ?

Thanks

-- 
Arnaud LEJEUNE
Ingénieur de Recherche
Responsable Pôle Calcul Scientifique
Departement Mec'Appli/Institut FEMTO-ST

24 chemin de l'epitaphe
25000 BESANCON
tel : +(33)3 81 66 60 24
fax : +(33)3 81 66 67 00
mail: [hidden email]

_______________________________________________
Help-octave mailing list
[hidden email]
https://lists.gnu.org/mailman/listinfo/help-octave
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Re: problem with "pkg -forge fem-fenics"

arnaudl
Le 27/03/2017 17:33, Arnaud Lejeune a écrit :

Le 27/03/2017 17:20, Nicholas Jankowski a écrit :
On Mon, Mar 27, 2017 at 11:18 AM, Arnaud Lejeune <[hidden email]> wrote:
Yes
Le 27/03/2017 16:54, Nicholas Jankowski a écrit :


On Mon, Mar 27, 2017 at 5:25 AM, arnaudl <[hidden email]> wrote:
Hello,

I am working on:
-> Linux version 4.4.0-67-generic (buildd@lgw01-46) (gcc version 5.4.0
20160609 (Ubuntu 5.4.0-6ubuntu1~16.04.4) )
-> Octave version 4.0.0

Trying to install fem-fenics using
 "pkg -forge fem-fenics"

first question, did you mean:

pkg install -forge fem-fenics

?
Yes I mean
pkg install -forge fem-fenics

Downloading fem-fenics sources and looking at Mesh.cc, perhaps could it be a problem with "size_t" as "_msh" seems to be a dolfin::mesh shared_ptr ?

Dolfin version is the stable one installed with "apt-get".

Note that during the fem-fenis installation, compilation of fem-fenics sources uses the following CPPFLAGS options:
-DDOLFIN_VERSION=\"2016.2.0" -DDOLFIN_SIZE_T=8 -DDOLFIN_LA_INDEX_SIZE=4

Thanks for your help.


please keep the help list on the replies, as I'm not familiar enough with this package to help further myself.

Ok,

looking at the source file "MeshTopology.h" from Dolfin package, one could see that  :
_msh->topology ().global_indices(std::size_t d) 

returns a 

const std::vector< std::int64_t > &

The compilation seems to fail as std::int64_t is not equivalent to std::size_t.

Is there a way to change fem-fenics options to solve this problem ?

Thanks

Trying to find a solution, I found a change between dolfin version 1.3.0 (required for last fem-fenics package ) and the stable one  installed with apt-get (2016.2.0).
MeshTopology.h :
--> dolfin version 1.3.0 untl version 2016.1.0
const std::vector< std::size_t > & global_indices(std::size_t d) const

--> dolfin version 2016.2.0

const std::vector< std::int64_t > & global_indices(std::size_t d) const
***************************************************************************

Then I think it's really a bug and one has to change Mesh.cc in the fem-fenics sources.

So I go back to 2016.1.0


Arnaud





_______________________________________________
Help-octave mailing list
[hidden email]
https://lists.gnu.org/mailman/listinfo/help-octave
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Re: problem with "pkg -forge fem-fenics"

NJank
On Mar 28, 2017 9:03 AM, "Arnaud Lejeune" <[hidden email]> wrote:
Le 27/03/2017 17:33, Arnaud Lejeune a écrit :
...

relaying an offline note from the package maintainer:

This is not the first time fem-fenics breaks due to a change in DOLFIN's API, yet if this is the only issue it should be a quick fix.
The build system and code already support multiple versions via macros, hence a similar solution could do the trick even in this case.
For instance, when they released version 1.3.0 all the shared_ptrs were migrated from boost:: to std::, and fem-fenics handles this by conditionally defining a SHARED_PTR macro.
Unfortunately, I do not expect to be able to devote time to such a fix before next week.

Kind regards,
Eugenio

_______________________________________________
Help-octave mailing list
[hidden email]
https://lists.gnu.org/mailman/listinfo/help-octave
Loading...