dolfin team mailing list archive

[Aron Wahlberg <aron.wahlberg@xxxxxxxxx>]

On 21 okt 2009, at 11.32, Harish Narayanan wrote:

> Aron Wahlberg wrote:
> > I just built dolfin (without parmetis, swiginac, trillinos or syfi).
> > After sourcing I ended up a missing symbol:
> >
> > Symbol not found: _camd_calloc
> >
> > The error does not make sense to me. Mabybe to sombody else?
>
> This is a problem with the pkgconfiggenerator for suitesparse when one
> builds a recent suitesparse by hand.
>
> You need to make sure the following modifications are made to the
> corresponding files:
>
> diff -r 0e4d88def193
> scons/simula-scons/simula_scons/pkgconfiggenerators/cholmod.py
> --- a/scons/simula-scons/simula_scons/pkgconfiggenerators/cholmod.py	 
> Mon
> Oct 19 11:41:27 2009 +0100
> +++ b/scons/simula-scons/simula_scons/pkgconfiggenerators/cholmod.py	 
> Wed
> Oct 21 11:31:23 2009 +0200
> @@ -225,8 +225,8 @@
>     libs += "-L%s -llapack -L%s -lblas" % \
>             (getLapackDir(sconsEnv=sconsEnv),
> getBlasDir(sconsEnv=sconsEnv))
>   libs += " -L%s -lcholmod" % getCholmodLibDir(sconsEnv)
> -  libs += " -L%s -lamd" % getAmdLibDir(sconsEnv)
> -  libs += " -L%s -lcolamd" % getColamdLibDir(sconsEnv)
> +  libs += " -L%s -lamd -lcamd" % getAmdLibDir(sconsEnv)
> +  libs += " -L%s -lcolamd -lccolamd" % getColamdLibDir(sconsEnv)
>   return libs
>
> def pkgTests(forceCompiler=None, sconsEnv=None,
> diff -r 0e4d88def193
> scons/simula-scons/simula_scons/pkgconfiggenerators/petsc.py
> --- a/scons/simula-scons/simula_scons/pkgconfiggenerators/petsc.py	Mon
> Oct 19 11:41:27 2009 +0100
> +++ b/scons/simula-scons/simula_scons/pkgconfiggenerators/petsc.py	Wed
> Oct 21 11:31:23 2009 +0200
> @@ -31,7 +31,7 @@
> 	-@echo -I${PETSC_DIR}/%s${PETSC_ARCH}%s -I${PETSC_DIR}/include
> ${MPI_INCLUDE}
>
> get_petsc_libs:
> -	-@echo   ${C_SH_LIB_PATH} -L${PETSC_LIB_DIR} ${PETSC_LIB_BASIC}
> +	-@echo   ${C_SH_LIB_PATH} -L${PETSC_LIB_DIR} ${PETSC_LIB_BASIC} - 
> lX11
> -L/usr/X11R6/lib
>
> get_petsc_cc:
> 	-@echo ${PCC}
> diff -r 0e4d88def193
> scons/simula-scons/simula_scons/pkgconfiggenerators/umfpack.py
> --- a/scons/simula-scons/simula_scons/pkgconfiggenerators/umfpack.py	 
> Mon
> Oct 19 11:41:27 2009 +0100
> +++ b/scons/simula-scons/simula_scons/pkgconfiggenerators/umfpack.py	 
> Wed
> Oct 21 11:31:23 2009 +0200
> @@ -225,7 +225,7 @@
>     libs += "-framework vecLib"
>   else:
>     libs += "-L%s -lblas" % getBlasDir(sconsEnv=sconsEnv)
> -  libs += " -L%s -lumfpack" % getUmfpackLibDir(sconsEnv)
> +  libs += " -L%s -lumfpack -lmetis" % getUmfpackLibDir(sconsEnv)
>   if needAMD(sconsEnv):
>     libs += " -L%s -lamd" % getAMDLibDir(sconsEnv)
>   return libs
>
> Harish

Thank you Harish. That fixed it!
However there is a new very similar problem. This time it is the  
symbol _XAllocColor that's missing. I can't see how you knew where to  
change, and to what, to fix the last problem? I expect  a similar  
change in any of the files in pkggenerator (?).

Do you have the same easy fix this time?

This time it is the development version btw (although same problem  
holds in the stable version).

Aron

from dolfin import *
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Users/aron/Work/FEniCS/unstable/build/lib/python2.6/site- 
packages/dolfin/__init__.py", line 11, in <module>
    import cpp
  File "/Users/aron/Work/FEniCS/unstable/build/lib/python2.6/site- 
packages/dolfin/cpp.py", line 28, in <module>
    _cpp = swig_import_helper()
  File "/Users/aron/Work/FEniCS/unstable/build/lib/python2.6/site- 
packages/dolfin/cpp.py", line 24, in swig_import_helper
    _mod = imp.load_module('_cpp', fp, pathname, description)
ImportError: dlopen(/Users/aron/Work/FEniCS/unstable/build/lib/ 
python2.6/site-packages/dolfin/_cpp.so, 2): Symbol not found:  
_XAllocColor
  Referenced from: /Users/aron/Work/FEniCS/unstable/build/lib/ 
libdolfin.dylib
  Expected in: flat namespace
 in /Users/aron/Work/FEniCS/unstable/build/lib/libdolfin.dylib