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Re: [Getfem-users] Error with the python interface


From: Konstantinos Poulios
Subject: Re: [Getfem-users] Error with the python interface
Date: Mon, 23 Jan 2017 10:43:48 +0100

Dear David

So as far I see the error from the linker is
ld: library not found for -lsmumps_seq

you can try to add the path of the mumps library manually to the configure command. E.g. on some Linux distribution I use

./configure CXXFLAGS=-g -I/..some...path.../MUMPS_5.0.2/include LDFLAGS=-L/..some...path.../MUMPS_5.0.2/lib -L/..some...path.../scotch_6.0.4/lib LIBS="-lmumps_common -lpord -lmpiseq -lmetis -lesmumps -lscotch -lscotcherr -lgfortran -lpthread" --prefix=/...installation...path --enable-boost --enable-shared --with-optimization=-O2 --with-pic --enable-python --enable-metis --disable-matlab --disable-superlu --enable-mumps --with-mumps="smumps dmumps cmumps zmumps"

you can adapt this to your case.

Best regards
Kostas


On Mon, Jan 23, 2017 at 10:22 AM, David Danan <address@hidden> wrote:
Dear Yves, Dear Kostas,

sure, please find enclosed the config.log corresponding to the error.

Thanks in advance for your help,
best regards,
David


-----E-mail d'origine-----
De : Konstantinos Poulios <address@hidden>
A: David Danan <address@hidden>
Cc: getfem-users <address@hidden>; Yves Renard <address@hidden>
Envoyé le : Lu, 23 Jan 2017 9:06

Sujet : Re: [Getfem-users] Error with the python interface

Dear David

Could you please send us your config.log file after you get the errors with "checking for library containing smumps_c... no"?

Best regards
Kostas

On Mon, Jan 23, 2017 at 9:02 AM, Yves Renard <address@hidden> wrote:

Dear David,

The detection of the configure file is probably wrong (the search of smumps_c ...) may be the names have to be adapted in configure.ac for Mac ...
Unfortunately, I have no Mac to test it.

Yves.


Le 23/01/2017 à 00:27, David Danan a écrit :
Dear Yves,

i checked, unfortunately i had installed the sequential version...The issue lies somewhere else.

I went back to the square one just to be sure and it seems that, even though mumps is found with the ./configure, i obtained the following result

[...]
checking for library containing smumps_c... no
checking for library containing dmumps_c... no
checking for library containing cmumps_c... no
checking for library containing zmumps_c... no
checking smumps_c.h usability... yes
checking smumps_c.h presence... yes
checking for smumps_c.h... yes
checking dmumps_c.h usability... yes
checking dmumps_c.h presence... yes
checking for dmumps_c.h... yes
checking cmumps_c.h usability... yes
checking cmumps_c.h presence... yes
checking for cmumps_c.h... yes
checking zmumps_c.h usability... yes
checking zmumps_c.h presence... yes
checking for zmumps_c.h... yes
[...]

Quite strange. Do you have any idea that may explain this behavior?

Thanks in advance,
David.



-----E-mail d'origine-----
De : Yves Renard <address@hidden>
A: David Danan <address@hidden>
Cc: getfem-users <address@hidden>
Envoyé le : Sa, 21 Jan 2017 17:00
Sujet : Re: [Getfem-users] Error with the python interface



Dear David,

libsmumps_seq is the sequential Mumps library. May be you installed the parallel one (libsmumps). Please check.

Yves.

----- Original Message -----
From: "David Danan" <address@hidden>
To: "getfem-users" <getfem-address@hidden>
Sent: Saturday, January 21, 2017 3:48:56 PM
Subject: Re: [Getfem-users] Error with the python interface

Dear Getfem users,

beside the interface problem, i noticed that there is another issue. When i compile the test case elastostatic.cc, for instance, i get the following error message

ld: library not found for -lsmumps_seq

And since i am on Mac, i didn't find how to obtain the missing library (as recommended on the Getfem download page, i used brew to download mumps but that's it). Is there anyone who had a similar problem on Mac?

Thank you in advance,
David.

-----E-mail d'origine-----
De : David Danan <address@hidden>
A: getfem-users <getfem-address@hidden>
Envoyé le : Ma, 17 Jan 2017 17:44
Sujet : Error with the python interface

Dear Getfem users,

I have just installed Getfem on a mac but i have trouble with the python interface.
The compilation process occur ed without major issue, but when importing python in a demo example , I get the following error

Traceback (most recent call last):
File "demo_laplacian.py", line 30, in <module>
import getfem as gf
File "/usr/local/lib/python2.7/site-packages/getfem/__init__.py", line 16, in <module>
from getfem import *
File "/usr/local/lib/python2.7/site-packages/getfem/getfem.py", line 44, in <module>
from _getfem import *
ImportError: dlopen(/usr/local/lib/python2.7/site-packages/getfem/_getfem.so, 2): Symbol not found: __ZNSt12bad_weak_ptrD1Ev
Referenced from: /usr/local/lib/python2.7/site-packages/getfem/_getfem.so
Expected in: flat namespace
in /usr/local/lib/python2.7/site-packages/getfem/_getfem.so

I had this issue with the options "-enable-python=yes --with-pic" for configure.

Do you have any clue about the cause of the problem ?

Thank you in advance,
David.

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-- 

  Yves Renard (address@hidden)       tel : (33) 04.72.43.87.08
  Pole de Mathematiques, INSA-Lyon             fax : (33) 04.72.43.85.29
  20, rue Albert Einstein
  69621 Villeurbanne Cedex, FRANCE
  http://math.univ-lyon1.fr/~renard

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