Subject: [FEniCS-users] [Fwd: Re: build issuse with dolfin on amd64 platform]

From: Andre Massing <[email-masked]>
Date: Tue, 22 Sep 2009 21:36:31 +0200

Hi Kaspar,

I just forward your email to the fenics-user list so that its member can 
also participate in this thread and you get a higher probability that 
your questions will be quickly and thoroughly answered :)
Hope your are subscribed, as it would be advisable for a serious fenics 
user ;)

Greetings,
Andre

Subject: Re: build issuse with dolfin on amd64 platform
From: Kaspar Müller <[email-masked]>
To: Andre Massing <[email-masked]>
Date: Tue, 22 Sep 2009 11:50:51 -0700

Hi Andre

Thanks for your help. I did an update to Karmic and built the packages 
with Dorsal. But first I had to replace the ginac-1.5.3 with the 
ginac-1.5.3 because the 1.5.3 has some problems with 64 bit architecture.
http://www.ginac.de/pipermail/ginac-devel/2009-July/001615.html
With this all went good.
But now when I try to run a demo I get some errors.
When I use the example pde/poisson/python and type python demo.py a get 
the following error:
------------------------------------------------------------------------------------------------------------------------------------------------------------------
muellerk@kitt:~/FEniCS/dolfin-0.9.2/demo/pde/poisson/python$ python demo.py
Traceback (most recent call last):
  File "demo.py", line 19, in <module>
    from dolfin import *
  File 
"/home/muellerk/FEniCS/build/lib/python2.6/site-packages/dolfin/__init__.py", 
line 11, in <module>
    import cpp
  File 
"/home/muellerk/FEniCS/build/lib/python2.6/site-packages/dolfin/cpp.py", 
line 22, in <module>
    _cpp = swig_import_helper()
  File 
"/home/muellerk/FEniCS/build/lib/python2.6/site-packages/dolfin/cpp.py", 
line 18, in swig_import_helper
    _mod = imp.load_module('_cpp', fp, pathname, description)
ImportError: /home/muellerk/FEniCS/build/lib/libdolfin.so.0: undefined 
symbol: 
_ZN3mtl6vector8num_rowsIdNS0_10parametersINS_3tag9col_majorENS0_9non_fixed9dimensionELb0ELb0EEEEENS0_12dense_vectorIT_T0_E9size_typeERKSB_
---------------------------------------------------------------------------------------------------------------------------------------------------------
If I try the cpp case the ffc compilation for the variational 
formulation runs through but then the program compilation with scons 
gives me the following error:
---------------------------------------------------------------------------------------------------------------------------------------------------------
muellerk@kitt:~/FEniCS/dolfin-0.9.2/demo/pde/poisson/cpp$ scons
scons: Reading SConscript files ...
scons: done reading SConscript files.
scons: Building targets ...
mpic++ -o demo -Wl,-rpath,/home/muellerk/FEniCS/build/lib -pthread 
-Wl,--export-dynamic main.o -L/home/muellerk/FEniCS/build/lib 
-L/usr/lib/atlas -L/usr/lib/lib -ldolfin -lgmp -lgmpxx -lslepc -lml 
-lifpack -lamesos -laztecoo -lteuchos -lepetra -lepetraext -lumfpack 
-lgts -lm -lxml2 -llapack -lblas -lcholmod -lamd -lcolamd -lscotch 
-lscotcherr -lparmetis -lmetis -lpetscts -lpetscsnes -lpetscksp 
-lpetscdm -lpetscmat -lpetscvec -lpetsc -lgthread-2.0 -lrt -lgmodule-2.0 
-lglib-2.0
/home/muellerk/FEniCS/build/lib/libdolfin.so: undefined reference to 
`mtl::vector::dense_vector<double, 
mtl::vector::parameters<mtl::tag::col_major, 
mtl::vector::non_fixed::dimension, false, false> >::size_type 
mtl::vector::num_rows<double, 
mtl::vector::parameters<mtl::tag::col_major, 
mtl::vector::non_fixed::dimension, false, false> 
 >(mtl::vector::dense_vector<double, 
mtl::vector::parameters<mtl::tag::col_major, 
mtl::vector::non_fixed::dimension, false, false> > const&)'
collect2: ld returned 1 exit status
scons: *** [demo] Error 1
scons: building terminated because of errors.
---------------------------------------------------------------------------------------------------------------------------------------------------------
Thanks for your help,
Cheers Kaspar

Andre Massing wrote:
> Hi Kaspar,
>
> uff, let me try to recall (good thing that you sent the link to the 
> post :))
>
> AFAIR I switched from the libsuitesparse-metis-dev package to the 
> libsuitesparse-dev package *without* libmetis support and compiled 
> everything from scratch (to be sure) with dorsal. If you recompile, 
> remember to remove all the related pkg-config files, which where 
> generated by scons. They can sometimes cause a real headache :) if you 
> switch related libraries.
> Usually they reside in DOLFIN_REPOSITORY_DIRECTORY/scons/pkgconfig, 
> and in the DOLFIN_INSTALLATION_PATH/lib/pkgconfig.
>
> I am now on karmic, and everything compiles quite smoothly.
>
> HTH, and let me know, if it worked for you.
> Good luck :)
>
> Kaspar Müller wrote:
>> Hi Andre
>>
>> I runned in the same problem as you
>> http://article.gmane.org/gmane.comp.mathematics.fenics.dolfin/7914
>> on my Ubuntu 8.10 Intrepid 64bit maschine.
>> I tried to compile the fenics packages with dorsal
>> http://www.fenics.org/pub/software/dorsal/
>> To specifie the compilation of the different packages for fenics you 
>> have the *.package files.
>> In the suitesparsewithmetis.package there was the flac -fPIC already 
>> set like Harish proposed to solve the problem.
>> http://article.gmane.org/gmane.comp.mathematics.fenics.dolfin/7916
>>
>> Could you solve your problem? If yes, how you did it? If not, do you 
>> know how to get mor help?
>>
>> Thanks for your help
>> Cheers Kaspar
>

---

From: "Garth N. Wells" <[email-masked]>
Date: Tue, 22 Sep 2009 20:39:39 +0100

This looks like the MTL4 problem again. We're thinking of removing MTL4 
from DOLFIN.

Harish: Is it an idea to disable MTL4 in Dorsal?

Garth

Andre Massing wrote:
> ------------------------------------------------------------------------
> 
> Subject:
> Re: build issuse with dolfin on amd64 platform
> From:
> ------------------------------------------------------------------------
> 
> _______________________________________________
> FEniCS-users mailing list
> [email-masked]
> http://fenics.org/mailman/listinfo/fenics-users

---

From: Harish Narayanan <[email-masked]>
Date: Tue, 22 Sep 2009 21:46:46 +0200

> Harish: Is it an idea to disable MTL4 in Dorsal?

No, but it is not difficult to do. Just comment out mtl from the list of
packages for your platform.

Once DOLFIN removes support for it, I will remove it for all platforms.

Harish

---

From: Andre Massing <[email-masked]>
Date: Tue, 22 Sep 2009 21:49:53 +0200

Since I already started top-posting (shame on me btw :))

Yepp, it is the same problem again.
@Kasper: A probably quick and dirty solution would be to comment out the 
mtl line in the

dorsal/platforms/<YOUR_PLATFORM>.platform

file, at least it seemed to work for me, but Harish is the dorsal 
wizard... But mind the spurious *.pc files :) If you insist for any 
reason to use mtl4 you can do an svn up -r 6821 (a version that worked)
comment out the line in dorsal and rely on scons option cache to still 
include mtl4. But as already decided, mtl4 will be dropped until becomes 
more stable.

Garth N. Wells wrote:
>> I just forward your email to the fenics-user list so that its member 
>> can also participate in this thread and you get a higher probability 
>> that your questions will be quickly and thoroughly answered :)
>> Hope your are subscribed, as it would be advisable for a serious 
>> fenics user ;)
>>
>> Greetings,
>> Andre
>>
>> When I use the example pde/poisson/python and type python demo.py a 
>> get the following error:
>> -lpetscdm -lpetscmat -lpetscvec -lpetsc -lgthread-2.0 -lrt 
>> -lgmodule-2.0 -lglib-2.0
>>> generated by scons. They can sometimes cause a real headache :) if 
>>> you switch related libraries.

---

From: "Garth N. Wells" <[email-masked]>
Date: Wed, 23 Sep 2009 07:35:41 +0100

> Once DOLFIN removes support for it, I will remove it for all platforms.

I'm suggesting that you disable it now in Dorsal. I won't consider 
removing it from DOLFIN until after the release.

Garth

---

From: Harish Narayanan <[email-masked]>
Date: Wed, 23 Sep 2009 08:40:32 +0200

Garth N. Wells wrote:
> 
> 
> Harish Narayanan wrote:
>> Garth N. Wells wrote:
>>> This looks like the MTL4 problem again. We're thinking of removing
>>> MTL4 from DOLFIN.
>>>

I will do that then.

Harish