dolfin team mailing list archive

[Alireza Forghani <arforghani@xxxxxxxxx>]

I got:

[alireza@master dolfin-0.6.1]$ make -s -C $PETSC_DIR getincludedirs 
PETSC_DIR=$PETSC_DIR
-I/data/alireza/petsc-2.3.1-p11 
-I/data/alireza/petsc-2.3.1-p11/bmake/linux-gnu-c-real-debug 
-I/data/alireza/petsc-2.3.1-p11/include 
-I/data/alireza/petsc-2.3.1-p11/externalpackages/mpich2-1.0.3/linux-gnu-c-real-debug/include

Alireza

Anders Logg wrote:
> What do you get when you type
>
>     make -s -C $PETSC_DIR getincludedirs PETSC_DIR=$PETSC_DIR
>
> ?
>
> This is the command run by configure to find out the PETSc flags.
>
> /Anders
>
> On Fri, Apr 07, 2006 at 03:15:26PM -0700, Alireza Forghani wrote:
>   
> > I downloaded and installed locally but problem remains.
> > when I type "dolfin-config --cflags"
> >
> > it returns:
> >
> > -I/usr/local/include -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/nls 
> > -I../../src/kernel/ode -I../../src/kernel/pde 
> > -I../../src/kernel/quadrature -I../../src/kernel/parameter 
> > -I../../src/kernel/log -I/data/daan/FeNics/petsc-2.3.1-p2 
> > -I/data/daan/FeNics/petsc-2.3.1-p2/bmake/linux-gnu-intel 
> > -I/data/daan/FeNics/petsc-2.3.1-p2/include 
> > -I/data/daan/FeNics/petsc-2.3.1-p2/include/mpiuni 
> > -I/usr/local/mpich/default/include -I/usr/include/libxml2 
> > -I../../src/modules/elasticity -I../../src/modules/elasticity-updated 
> > -I../../src/modules/convdiff -I../../src/modules/navierstokes 
> > -I../../src/modules/poisson -I../../src/modules/stokes 
> > -I../../src/modules/heat -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/nls -I../../src/kernel/ode -I../../src/kernel/pde 
> > -I../../src/kernel/quadrature -I../../src/kernel/parameter 
> > -I../../src/kernel/log -I/data/daan/FeNics/petsc-2.3.1-p2 
> > -I/data/daan/FeNics/petsc-2.3.1-p2/bmake/linux-gnu-intel 
> > -I/data/daan/FeNics/petsc-2.3.1-p2/include 
> > -I/data/daan/FeNics/petsc-2.3.1-p2/include/mpiuni 
> > -I/usr/local/mpich/default/include -I/usr/include/libxml2 
> > -I../../src/modules/
> >
> >
> > also "dolfin-config --libs" returns:
> >
> > -I/usr/local/include -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/nls 
> > -I../../src/kernel/ode -I../../src/kernel/pde 
> > -I../../src/kernel/quadrature -I../../src/kernel/parameter 
> > -I../../src/kernel/log -I/data/daan/FeNics/petsc-2.3.1-p2 
> > -I/data/daan/FeNics/petsc-2.3.1-p2/bmake/linux-gnu-intel 
> > -I/data/daan/FeNics/petsc-2.3.1-p2/include 
> > -I/data/daan/FeNics/petsc-2.3.1-p2/include/mpiuni 
> > -I/usr/local/mpich/default/include -I/usr/include/libxml2 
> > -I../../src/modules/elasticity -I../../src/modules/elasticity-updated 
> > -I../../src/modules/convdiff -I../../src/modules/navierstokes 
> > -I../../src/modules/poisson -I../../src/modules/stokes 
> > -I../../src/modules/heat -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/nls -I../../src/kernel/ode -I../../src/kernel/pde 
> > -I../../src/kernel/quadrature -I../../src/kernel/parameter 
> > -I../../src/kernel/log -I/data/daan/FeNics/petsc-2.3.1-p2 
> > -I/data/daan/FeNics/petsc-2.3.1-p2/bmake/linux-gnu-intel 
> > -I/data/daan/FeNics/petsc-2.3.1-p2/include 
> > -I/data/daan/FeNics/petsc-2.3.1-p2/include/mpiuni 
> > -I/usr/local/mpich/default/include -I/usr/include/libxml2 
> > -I../../src/modules/
> >
> > As you see every thing related to PETSC is assigned to "/data/daan...." 
> > instead of "data/alireza/PETSC...."
> >
> >
> > Alireza Forghani wrote:
> >     
> > > Hi Garth,
> > >
> > > I did:
> > >
> > > [alireza@master alireza]$ env |grep PETSC_DIR
> > > PETSC_DIR=/data/alireza/petsc-2.3.1-p11
> > >
> > > It might be because I haven't installed MPI on my account and didn't 
> > > disable it during configuration of MPI. may be it uses MPI of another 
> > > account?
> > >
> > > Alireza
> > >
> > > ------------------------
> > > Date: Fri, 07 Apr 2006 21:25:12 +0200
> > > From: "Garth N. Wells" <g.n.wells@xxxxxxxxxx>
> > > Subject: Re: [DOLFIN-dev] Problems with compiling DOLFIN on Redhat
> > > To: Discussion of DOLFIN development <dolfin-dev@xxxxxxxxxx>
> > > Message-ID: <1144437912.8606.2.camel@localhost.localdomain>
> > > Content-Type: text/plain
> > >
> > > What do you see if you do
> > >
> > >       
> > > > env | grep PETSC_DIR ?
> > > >         
> > > Garth
> > >
> > >
> > > On Fri, 2006-04-07 at 10:22 -0700, Alireza Forghani wrote:
> > >
> > >       
> > > > > Hi Anders,
> > > > >           
> > > > > > Configuration says:
> > > > > > using PETSC_DIR=/data/alireza/petsc-2.3.1-p11
> > > > > >             
> > > > > disabling compilation of PyDOLFIN
> > > > > checking for configarch... yes
> > > > >           
> > > > > > but exactly after that when I try to compile demo the error appears:
> > > > > >             
> > > > > > > /data/daan/FeNics/petsc-2.3.1-p2: Permission denied
> > > > > > >               
> > > > > /data/daan/FeNics/petsc-2.3.1-p2/bmake/linux-gnu-intel: Permission 
> > > > >           
> > > > denied
> > > >         
> > > > > /data/daan/FeNics/petsc-2.3.1-p2/include: Permission denied
> > > > > /data/daan/FeNics/petsc-2.3.1-p2/include/mpiuni: Permission denied
> > > > > /data/daan/FeNics/petsc-2.3.1-p2: Permission denied
> > > > > /data/daan/FeNics/petsc-2.3.1-p2/bmake/linux-gnu-intel: Permission 
> > > > >           
> > > > denied
> > > >         
> > > > > /data/daan/FeNics/petsc-2.3.1-p2/include: Permission denied
> > > > > /data/daan/FeNics/petsc-2.3.1-p2/include/mpiuni: Permission denied
> > > > > make[3]: *** [main.o] Error 1
> > > > >           
> > > > > > As you see it tries to use another library.
> > > > > > I also used:
> > > > > > export PATH="data/alireza/dolfin0.6.1/local/bin:$PATH"
> > > > > > and these are what exactly PETSc says after configuration:
> > > > > >
> > > > > >             
> > > > ================================================================================= 
> > > >
> > > >         
> > > > >              Configuring PETSc to compile on your 
> > > > >           
> > > > system                         > 
> > > > ================================================================================= 
> > > >
> > > >         
> > > > Compilers:                                                                
> > > >         
> > > > >   C Compiler:         mpicc  -fPIC -Wall -Wshadow -Wwrite-strings 
> > > > >           
> > > > -fomit-frame-pointer -g3 >   Fortran Compiler:   mpif77  -fPIC -Wall 
> > > > -g  > Linkers:
> > > >         
> > > > >   Shared linker:   mpicc  -shared  -fPIC -Wall -Wshadow 
> > > > >           
> > > > -Wwrite-strings -fomit-frame-pointer -g3 >   Dynamic linker:   mpicc  
> > > > -shared  -fPIC -Wall -Wshadow -Wwrite-strings -fomit-frame-pointer 
> > > > -g3 > PETSc:
> > > >         
> > > > >   **
> > > > >   ** Before running "make" your PETSC_ARCH must be specified with:
> > > > >   **  ** setenv PETSC_ARCH linux-gnu-c-real-debug (csh/tcsh)
> > > > >   **  ** PETSC_ARCH=linux-gnu-c-real-debug; export PETSC_ARCH 
> > > > >           
> > > > (sh/bash)
> > > >         
> > > > >   **
> > > > >   PETSC_DIR: /data/alireza/petsc-2.3.1-p11
> > > > >   **
> > > > >   ** Now build and test the libraries with "make all test"
> > > > >   **
> > > > >   Scalar type:real
> > > > >   Clanguage: C
> > > > > MPI:
> > > > >   PETSc shared libraries: disabled
> > > > >   PETSc dynamic libraries: disabled
> > > > > X11:
> > > > >   Includes: ['-I/usr/X11R6/include']
> > > > >   Library: ['-L/usr/X11R6/lib -lX11']
> > > > > BLAS/LAPACK: 
> > > > >           
> > > > -Wl,-rpath,/data/alireza/petsc-2.3.1-p11/externalpackages/fblaslapack/linux-gnu-c-real-debug 
> > > > -L/data/alireza/petsc-2.3.1-p11/externalpackages/fblaslapack/linux-gnu-c-real-debug 
> > > > -lflapack 
> > > > -Wl,-rpath,/data/alireza/petsc-2.3.1-p11/externalpackages/fblaslapack/linux-gnu-c-real-debug 
> > > > -L/data/alireza/petsc-2.3.1-p11/externalpackages/fblaslapack/linux-gnu-c-real-debug 
> > > > -lfblas
> > > >         
> > > > > > > Thank You,
> > > > > > >               
> > > > > Alireza
> > > > >           
> > > _______________________________________________
> > > DOLFIN-dev mailing list
> > > DOLFIN-dev@xxxxxxxxxx
> > > http://www.fenics.org/cgi-bin/mailman/listinfo/dolfin-dev
> > >
> > >       
> > _______________________________________________
> > DOLFIN-dev mailing list
> > DOLFIN-dev@xxxxxxxxxx
> > http://www.fenics.org/cgi-bin/mailman/listinfo/dolfin-dev
> >
> >     
>
>