dolfin team mailing list archive

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Re: FW: Install Dolfin

To: "Naboulsi, Samir K CTR USAF ASC/HP" <Samir.Naboulsi@xxxxxxxxxxxx>
From: "Garth N. Wells" <g.n.wells@xxxxxxxxxx>
Date: Mon, 23 Oct 2006 17:33:12 +0200
Cc: dolfin@xxxxxxxxxx, Discussion of DOLFIN development <dolfin-dev@xxxxxxxxxx>
Delivered-to: dolfin-dev@xxxxxxxxxx
In-reply-to: <16FE85BAFD4AF347AC9946480F8424D1165D50@VFOHMLAO03.Enterprise.afmc.ds.af.mil>
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Naboulsi, Samir K CTR USAF ASC/HP wrote:
> I submitted this e-mail to the dolfin-dev@xxxxxxxxxx however, I recieved an automated e-mail stating 
> 
> Your mail to 'DOLFIN-dev' with the subject
> 
>     Install Dolfin
> 
> 
> is being held until the list moderator can review it for deletion or
> approval. Don't expect this to happen very soon.
> 
> 
> It also state that the size is too big, since I have submitted the config and make files to give you more detail of the problem. The original message is shown below. I am new to FEnics and not sure how things are normally done. Please advise.
> 
> Thank you and best regards
> Sam
> 
> 
> -----Original Message-----
> From: Naboulsi, Samir K CTR USAF ASC/HP
> Sent: Thu 10/19/2006 4:02 PM
> To: dolfin-dev@xxxxxxxxxx
> Subject: Install Dolfin
>  
> 
> 
> I am having difficulties installing dolfin on my machine. I do not have root privileges, and I have done the following:
> 
> 1- installed Python-2.4.1 and tested it (roots has version 2.3)
> 2- installed Numeric-24.2 numarray-1.5.2 and numpy-1.0b5 and tested them 
> 3- installed FIAT-0.2.5 FErari-0.0.1 and ffc-0.3.3 and tested them
> 4- installed boost_1_33_1 lib locally 
> 5- Libxml2 and PETSc are installed on the machine by root, also an older version of boost lib exist
> 6 tried to installed Dolfin using the options:
> 
>>> ./configure --prefix=/workspace/naboulsk/FX/local --with-boost-include=/workspace/naboulsk/FX/local/include/boost-1_33_1/boost 
> 

Assuming that you're using dolfin-0.6.2-1, try

> ./configure.local
--with-boost-include=/workspace/naboulsk/FX/local/include/boost-1_33_1
--disable-pydolfin

Garth

> However I get errors running the configure if I use the python2.4 version but not python2.3. 
> If I use python2.3 I get errors during make that I think it has to do with the root installed boost version even though I am using the --with-boost-include?
> 
> I am including the files  config.status Makefile config.log
> 
> Could you please advise of a solution to my problem.
> Thanks and best regards
> Sam
> 
> 
> ERRORS USING PYTHON2.4
> 
> checking for xml2-config... /usr/bin/xml2-config
> checking for libxml - version >= 2.0.0... yes (version 2.6.16)
> checking boost/version.hpp usability... yes
> checking boost/version.hpp presence... yes
> checking for boost/version.hpp... yes
> checking for amd_info in -lamd... no
> Cannot find amd library (part of umfpack). Umfpack will be disabled
> checking for a Python interpreter with version >= 2.3... python2.4
> checking for python2.4... /workspace/naboulsk/FX/local/bin/python2.4
> checking for python2.4 version... 2.4
> checking for python2.4 platform... linux2
> checking for python2.4 script directory... ${prefix}/lib/python2.4/site-packages
> checking for python2.4 extension module directory... ${exec_prefix}/lib/python2.4/site-packages
> checking for Python include path... /workspace/naboulsk/FX/local/include/python2.4
> checking for Python library path... /workspace/naboulsk/FX/local/lib/python2.4/config
> checking python extra libraries...
> checking python2.4/Python.h usability... no
> checking python2.4/Python.h presence... no
> checking for python2.4/Python.h... no
> *** Cannot find Python development files on your system.
> *** Perhaps you need to install the package python2.4-dev?
> 
> 
> ERRORS IN MAKE FILE
> 
> /workspace/naboulsk/FX/dolfin-0.6.2-1> make
> Making all in src
> make[1]: Entering directory `/workspace/naboulsk/FX/dolfin-0.6.2-1/src'
> Making all in pre
> make[2]: Entering directory `/workspace/naboulsk/FX/dolfin-0.6.2-1/src/pre'
> rm -f ../config/dolfin-config
> make[2]: Leaving directory `/workspace/naboulsk/FX/dolfin-0.6.2-1/src/pre'
> Making all in kernel
> make[2]: Entering directory `/workspace/naboulsk/FX/dolfin-0.6.2-1/src/kernel'
> Making all in common
> make[3]: Entering directory `/workspace/naboulsk/FX/dolfin-0.6.2-1/src/kernel/common'
> Making all in dolfin
> make[4]: Entering directory `/workspace/naboulsk/FX/dolfin-0.6.2-1/src/kernel/common/dolfin'
> make[4]: Nothing to be done for `all'.
> make[4]: Leaving directory `/workspace/naboulsk/FX/dolfin-0.6.2-1/src/kernel/common/dolfin'
> make[4]: Entering directory `/workspace/naboulsk/FX/dolfin-0.6.2-1/src/kernel/common'
> make[4]: Nothing to be done for `all-am'.
> make[4]: Leaving directory `/workspace/naboulsk/FX/dolfin-0.6.2-1/src/kernel/common'
> make[3]: Leaving directory `/workspace/naboulsk/FX/dolfin-0.6.2-1/src/kernel/common'
> Making all in fem
> make[3]: Entering directory `/workspace/naboulsk/FX/dolfin-0.6.2-1/src/kernel/fem'
> Making all in dolfin
> make[4]: Entering directory `/workspace/naboulsk/FX/dolfin-0.6.2-1/src/kernel/fem/dolfin'
> make[4]: Nothing to be done for `all'.
> make[4]: Leaving directory `/workspace/naboulsk/FX/dolfin-0.6.2-1/src/kernel/fem/dolfin'
> make[4]: Entering directory `/workspace/naboulsk/FX/dolfin-0.6.2-1/src/kernel/fem'
> if /bin/sh ../../../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"DOLFIN\" -DPACKAGE_TARNAME=\"dolfin\" -DPACKAGE_VERSION=\"0.6.2-1\" -DPACKAGE_STRING=\"DOLFIN\ 0.6.2-1\" -DPACKAGE_BUGREPORT=\"dolfin@xxxxxxxxxx\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1  -I. -I. -I../../../src/kernel/common -I../../../src/kernel/fem -I../../../src/kernel/form -I../../../src/kernel/function -I../../../src/kernel/io -I../../../src/kernel/la -I../../../src/kernel/main -I../../../src/kernel/math -I../../../src/kernel/mesh -I../../../src/kernel/mf -I../../../src/kernel/nls -I../../../src/kernel/ode -I../../../src/kernel/pde -I../../../src/kernel/quadrature -I../../../src/kernel/parameter -I../../../src/kernel/log   -I/usr/include/libxml2      -g -O2 -DNDEBUG -pedantic -Wno-long-long -std=c++98 -fPIC -MT FEM.lo -MD -MP -MF ".dep
s/FEM.Tpo" -c -o FEM.lo FEM.cpp; \
> then mv -f ".deps/FEM.Tpo" ".deps/FEM.Plo"; else rm -f ".deps/FEM.Tpo"; exit 1; fi
>  g++ -DPACKAGE_NAME=\"DOLFIN\" -DPACKAGE_TARNAME=\"dolfin\" -DPACKAGE_VERSION=\"0.6.2-1\" "-DPACKAGE_STRING=\"DOLFIN 0.6.2-1\"" -DPACKAGE_BUGREPORT=\"dolfin@xxxxxxxxxx\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -I. -I. -I../../../src/kernel/common -I../../../src/kernel/fem -I../../../src/kernel/form -I../../../src/kernel/function -I../../../src/kernel/io -I../../../src/kernel/la -I../../../src/kernel/main -I../../../src/kernel/math -I../../../src/kernel/mesh -I../../../src/kernel/mf -I../../../src/kernel/nls -I../../../src/kernel/ode -I../../../src/kernel/pde -I../../../src/kernel/quadrature -I../../../src/kernel/parameter -I../../../src/kernel/log -I/usr/include/libxml2 -g -O2 -DNDEBUG -pedantic -Wno-long-long -std=c++98 -fPIC -MT FEM.lo -MD -MP -MF .deps/FEM.Tpo -c FEM.cpp  -fPIC -DPIC -o .libs/FEM.o
> In file included from ../../../src/kernel/la/dolfin/ublas.h:12,
>                  from ../../../src/kernel/la/dolfin/uBlasMatrix.h:18,
>                  from ../../../src/kernel/la/dolfin/uBlasDenseMatrix.h:10,
>                  from ../../../src/kernel/la/dolfin/DenseMatrix.h:12,
>                  from ./dolfin/FEM.h:18,
>                  from FEM.cpp:10:
> /usr/include/boost/numeric/ublas/vector_of_vector.hpp:17:2: #error class generalized_vector_of_vector is experiment and currently does not work
> In file included from ../../../src/kernel/la/dolfin/ublas.h:12,
>                  from ../../../src/kernel/la/dolfin/uBlasMatrix.h:18,
>                  from ../../../src/kernel/la/dolfin/uBlasDenseMatrix.h:10,
>                  from ../../../src/kernel/la/dolfin/DenseMatrix.h:12,
>                  from ./dolfin/FEM.h:18,
>                  from FEM.cpp:10:
> /usr/include/boost/numeric/ublas/vector_of_vector.hpp:1203: error: declaration of `class T'
> /usr/include/boost/numeric/ublas/vector_of_vector.hpp:32: error:  shadows template parm `class T'
> /usr/include/boost/numeric/ublas/vector_of_vector.hpp:1203: error: declaration of `class F'
> /usr/include/boost/numeric/ublas/vector_of_vector.hpp:32: error:  shadows template parm `class F'
> /usr/include/boost/numeric/ublas/vector_of_vector.hpp:1203: error: declaration of `class A'
> /usr/include/boost/numeric/ublas/vector_of_vector.hpp:32: error:  shadows template parm `class A'
> /usr/include/boost/numeric/ublas/vector_of_vector.hpp:1208: error: type `boost::numeric::ublas::generalized_vector_of_vector<T, F, A>' is not derived from type `boost::numeric::ublas::generalized_vector_of_vector<T, F, A>'
> /usr/include/boost/numeric/ublas/vector_of_vector.hpp:1208: error: ISO C++ forbids initialization of member 
> ....................
> ...............
> .........FEM.cpp:216: error: 'const class boost::numeric::dolfin::LinearForm' has no member named 'test'
> FEM.cpp:217: error: `boost::numeric::dolfin::LogManager' has not been declared
> FEM.cpp:217: error: request for member `error' in `log', which is of non-class type `double ()(double) throw ()'
> FEM.cpp:220: error: 'const class boost::numeric::dolfin::LinearForm' has no member named 'test'
> FEM.cpp:221: error: `boost::numeric::dolfin::LogManager' has not been declared
> FEM.cpp:221: error: request for member `error' in `log', which is of non-class type `double ()(double) throw ()'
> FEM.cpp:224: error: `boost::numeric::dolfin::LogManager' has not been declared
> FEM.cpp:224: error: request for member `error' in `log', which is of non-class type `double ()(double) throw ()'
> FEM.cpp: At global scope:
> FEM.cpp:228: error: expected constructor, destructor, or type conversion before "FEM"
> FEM.cpp:238: error: expected `,' or `...' before '&' token
> FEM.cpp:239: error: ISO C++ forbids declaration of `GenericMatrix' with no type
> FEM.cpp: In static member function `static void boost::numeric::dolfin::FEM::countNonZeros(int)':
> FEM.cpp:240: error: `A' was not declared in this scope
> FEM.cpp:241: error: `nz' was not declared in this scope
> FEM.cpp:242: error: `boost::numeric::dolfin::LogManager' has not been declared
> FEM.cpp:242: error: request for member `warning' in `log', which is of non-class type `double ()(double) throw ()'
> FEM.cpp:245: error: `dolfin_info' was not declared in this scope
> FEM.cpp: At global scope:
> FEM.cpp:246: error: expected `}' at end of input
> FEM.cpp:246: error: expected `}' at end of input
> make[4]: *** [FEM.lo] Error 1
> make[4]: Leaving directory `/workspace/naboulsk/FX/dolfin-0.6.2-1/src/kernel/fem'
> make[3]: *** [all-recursive] Error 1
> make[3]: Leaving directory `/workspace/naboulsk/FX/dolfin-0.6.2-1/src/kernel/fem'
> make[2]: *** [all-recursive] Error 1
> make[2]: Leaving directory `/workspace/naboulsk/FX/dolfin-0.6.2-1/src/kernel'
> make[1]: *** [all-recursive] Error 1
> make[1]: Leaving directory `/workspace/naboulsk/FX/dolfin-0.6.2-1/src'
> make: *** [all-recursive] Error 1
> 
> 
> 
> 
> 

-- 

Dr. Garth N. Wells
Faculty of Civil Engineering and Geosciences
Delft University of Technology
Stevinweg 1
2628 CN Delft
Netherlands

tel.   +31 15 278 7922
fax.   +31 15 278 6383
e-mail g.n.wells@xxxxxxxxxx
url    http://www.mechanics.citg.tudelft.nl/~garth