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Re: Problems with compiling DOLFIN on Redhat

To: Discussion of DOLFIN development <dolfin-dev@xxxxxxxxxx>
From: Anders Logg <logg@xxxxxxxxx>
Date: Fri, 7 Apr 2006 20:05:29 -0500
In-reply-to: <4436F417.6020309@gmail.com>
Mail-followup-to: Discussion of DOLFIN development <dolfin-dev@xxxxxxxxxx>
Reply-to: Discussion of DOLFIN development <dolfin-dev@xxxxxxxxxx>
User-agent: Mutt/1.5.9i
ok, that looks right.

The next step is to check the contents of the file

    src/config/var.tmp

which is created when dolfin-config.

If that file has the correct flags then dolfin-config should also spit
out the correct flags. If not, we can check why.

If var.tmp does not contain the correct flags, I will also know what
to check next...

/Anders


On Fri, Apr 07, 2006 at 04:21:59PM -0700, Alireza Forghani wrote:
> 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
> >>
> >>    
> >
> >  
> 
> 
> _______________________________________________
> DOLFIN-dev mailing list
> DOLFIN-dev@xxxxxxxxxx
> http://www.fenics.org/cgi-bin/mailman/listinfo/dolfin-dev
> 

-- 
Anders Logg
Research Assistant Professor
Toyota Technological Institute at Chicago
http://www.tti-c.org/logg/
Follow ups

Re: Problems with compiling DOLFIN on Redhat
From: Alireza Forghani, 2006-04-08
References

Re: Problems with compiling DOLFIN on Redhat
From: Alireza Forghani, 2006-04-07
Re: Problems with compiling DOLFIN on Redhat
From: Alireza Forghani, 2006-04-07
Re: Problems with compiling DOLFIN on Redhat
From: Anders Logg, 2006-04-07
Re: Problems with compiling DOLFIN on Redhat
From: Alireza Forghani, 2006-04-07