[petsc-dev] PETSC's compilation

Matthew Knepley knepley at gmail.com
Wed Mar 24 12:45:32 CDT 2010 

On Wed, Mar 24, 2010 at 12:35 PM, David sheehan
<david.sheehanjr at gmail.com>wrote:

> Matt already moved it to petsc-maint before.
> can you help me to fix the build-up of PETSC and HYPRE? thanks in advance.
>

This is the last time I will tell you this before removing you from the
list. Do not post
these questions here.

   Matt


>
> David
>
> On Wed, Mar 24, 2010 at 12:09 PM, Satish Balay <balay at mcs.anl.gov> wrote:
>
>> moving this discussion to petsc-maint. Not appropriate for petsc-dev
>>
>> satish
>>
>> On Wed, 24 Mar 2010, David sheehan wrote:
>>
>> > That was an old try.
>> >
>> > My new try including all output information is the following. Everything
>> is
>> > OK except for "make test"  has one error.
>> > I checked the library of HYPRE. All HYPRE libs have been created, but
>> they
>> > cannot be installed with PETSC libs.
>> > And I manually copy all HYPRE libs into the directory of the
>> final-installed
>> > PETSC's libs, but "make test" still has
>> > the same problem.
>> >
>> > Please fix it, thanks.
>> >
>> > David
>> > -----------------------------------------------the final installed
>> >
>> libs-------------------------------------------------------------------------------------------------
>> > [ petsc-2.3.3-p15]$ ls /home/David/petsc233-p15/lib/linux-gnu-c-debug/
>> > libpetsc.a         libpetscdm.a   libpetscmat.a   libpetscts.a
>> > libpetsccontrib.a  libpetscksp.a  libpetscsnes.a  libpetscvec.a
>> > ------------------------------------------------PETSC
>> >
>> libs---------------------------------------------------------------------------------------------------
>> > [ petsc-2.3.3-p15]$ ls lib/linux-gnu-c-debug/
>> > libpetsc.a         libpetscdm.a   libpetscmat.a   libpetscts.a
>> > libpetsccontrib.a  libpetscksp.a  libpetscsnes.a  libpetscvec.a
>> >
>> > --------------------------------------------------HYPRE
>> >
>> libs-------------------------------------------------------------------------------------------------
>> >
>> >
>> > [ petsc-2.3.3-p15]$ ls
>> externalpackages/hypre-2.0.0/linux-gnu-c-debug/lib/
>> > libHYPRE.a                               libHYPRE_MatrixMatrix.a
>> > libHYPRE_sstruct_ls.a
>> > libHYPRE_DistributedMatrix.a             libHYPRE_multivector.a
>> > libHYPRE_sstruct_mv.a
>> > libHYPRE_DistributedMatrixPilutSolver.a  libHYPRE_ParaSails.a
>> > libHYPRE_struct_ls.a
>> > libHYPRE_Euclid.a                        libHYPRE_parcsr_block_mv.a
>> > libHYPRE_struct_mv.a
>> > libHYPRE_IJ_mv.a                         libHYPRE_parcsr_ls.a
>> > libHYPRE_utilities.a
>> > libHYPRE_krylov.a                        libHYPRE_parcsr_mv.a
>> > libHYPRE_LSI.a                           libHYPRE_seq_mv.a
>> >
>> ----------------------------------------configure------------------------------------------------------------------------------------------------------
>> > [ petsc-2.3.3-p15]$ export PETSC_DIR=$PWD
>> > [ petsc-2.3.3-p15]$  ./config/configure.py
>> --prefix=/home/David/petsc233-p15
>> > --with-cc=gcc --with-cxx=g++ --with-fc=ifort --with-mpi-dir=/opt/openmpi
>> > --with-hypre=1 --download-hypre=ifneeded
>> >
>> =================================================================================
>> >              Configuring PETSc to compile on your system
>> >
>> =================================================================================
>> > TESTING: configureLibrary from
>> > PETSc.packages.hypre(python/PETSc/packages/hypre.py:120)
>> > using: --with-MPI-include="/opt/openmpi/include"
>> > Compilers:
>> >   C Compiler:         gcc  -fPIC -Wall -Wwrite-strings
>> -Wno-strict-aliasing
>> > -g3
>> >   C++ Compiler:       g++  -Wall -Wwrite-strings -Wno-strict-aliasing -g
>> > -fPIC
>> >   Fortran Compiler:   ifort  -fPIC -g
>> > Linkers:
>> >   Shared linker:   gcc  -shared  -fPIC -Wall -Wwrite-strings
>> > -Wno-strict-aliasing -g3
>> >   Dynamic linker:   gcc  -shared  -fPIC -Wall -Wwrite-strings
>> > -Wno-strict-aliasing -g3
>> > PETSc:
>> >   **
>> >   ** Before running "make" your PETSC_ARCH must be specified with:
>> >   **  ** setenv PETSC_ARCH linux-gnu-c-debug (csh/tcsh)
>> >   **  ** PETSC_ARCH=linux-gnu-c-debug; export PETSC_ARCH (sh/bash)
>> >   **
>> >   PETSC_DIR: /home/David/petsc/petsc-2.3.3-p15
>> >   **
>> >   ** Now build and test the libraries with "make all test"
>> >   **
>> >   Clanguage: C
>> >   PETSc shared libraries: disabled
>> >   PETSc dynamic libraries: disabled
>> >   Scalar type:real
>> > MPI:
>> >   Includes: ['/opt/openmpi/include']
>> >   Library:  ['/opt/openmpi/lib/libmpi.a']
>> > X11:
>> >   Includes: ['-I/usr/X11R6/include']
>> >   Library: ['-L/usr/X11R6/lib -lX11']
>> > BLAS/LAPACK: -llapack -lblas
>> > hypre:
>> >   Includes:
>> >
>> ['/home/David/petsc/petsc-2.3.3-p15/externalpackages/hypre-2.0.0/linux-gnu-c-debug/include']
>> >   Library:
>> >
>> ['/home/David/petsc/petsc-2.3.3-p15/externalpackages/hypre-2.0.0/linux-gnu-c-debug/lib/libHYPRE.a',
>> > '-Wl,-rpath,/usr/lib/gcc/i386-redhat-linux/3.4.6',
>> > '-Wl,-rpath,/usr/lib/gcc/i386-redhat-linux/3.4.6/../../..', '-lstdc++']
>> > ---------------------------------------------------make
>> >
>> install---------------------------------------------------------------------------------
>> > Installing PETSc at /home/David/petsc233-p15
>> > Shared libraries disabled
>> > sh/bash: PETSC_DIR=/home/David/petsc233-p15; export PETSC_DIR
>> > csh/tcsh: setenv PETSC_DIR /home/David/petsc233-p15
>> > Then do make test to verify correct install
>> > ---------------------------------------------------make
>> >
>> test-------------------------------------------------------------------------------------
>> > Running test examples to verify correct installation
>> > C/C++ example src/snes/examples/tutorials/ex19 run successfully with 1
>> MPI
>> > process
>> > C/C++ example src/snes/examples/tutorials/ex19 run successfully with 2
>> MPI
>> > processes
>> > Possible error running Graphics examples
>> src/snes/examples/tutorials/ex19 1
>> > MPI process
>> > See
>> http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html
>> > lid velocity = 0.0016, prandtl # = 1, grashof # = 1
>> > [0]PETSC ERROR: --------------------- Error Message
>> > ------------------------------------
>> > [0]PETSC ERROR: Error in external library!
>> > [0]PETSC ERROR: Unable to open display on apmachine:0.0
>> > .  Make sure your COMPUTE NODES are authorized to connect
>> >     to this X server and either your DISPLAY variable
>> >     is set or you use the -display name option
>> > !
>> > [0]PETSC ERROR:
>> > ------------------------------------------------------------------------
>> > [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 15, Tue Sep 23
>> 10:02:49
>> > CDT 2008 HG revision: 31306062cd1a6f6a2496fccb4878f485c9b91760
>> > [0]PETSC ERROR: See docs/changes/index.html for recent updates.
>> > [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
>> > [0]PETSC ERROR: See docs/index.html for manual pages.
>> > [0]PETSC ERROR:
>> > ------------------------------------------------------------------------
>> > [0]PETSC ERROR: ./ex19 on a linux-gnu named apmachine by David Wed Mar
>> 24
>> > 11:41:48 2010
>> > [0]PETSC ERROR: Libraries linked from
>> > /home/David/petsc233-p15/lib/linux-gnu-c-debug
>> > [0]PETSC ERROR: Configure run at Wed Mar 24 11:21:40 2010
>> > [0]PETSC ERROR: Configure options --prefix=/home/David/petsc233-p15
>> > --with-cc=gcc --with-cxx=g++ --with-fc=ifort --with-mpi-dir=/opt/openmpi
>> > --with-hypre=1 --download-hypre=ifneeded --with-shared=0
>> > [0]PETSC ERROR:
>> > ------------------------------------------------------------------------
>> > [0]PETSC ERROR: PetscDrawXGetDisplaySize_Private() line 618 in
>> > src/sys/draw/impls/x/xops.c
>> > [0]PETSC ERROR: PETSc unable to use X windows
>> > proceeding without graphics
>> > Number of Newton iterations = 2
>> > lid velocity = 0.0016, prandtl # = 1, grashof # = 1
>> > Number of Newton iterations = 2
>> > Fortran example src/snes/examples/tutorials/ex5f run successfully with 1
>> MPI
>> > process
>> > Completed test examples
>> >
>> > On Wed, Mar 24, 2010 at 9:35 AM, Satish Balay <balay at mcs.anl.gov>
>> wrote:
>> >
>> > > On Tue, 23 Mar 2010, David sheehan wrote:
>> > >
>> > > > I try openmpi, there are the following error,
>> > > >
>> > > > ./configure --prefix=/home/David/petsc300p11_openmpi --with-cc=gcc
>> > > > --with-cxx=g++ --with-fc=ifort --download-openmpi=1
>> --download-hypre=1
>> > > >
>> > >
>> =================================================================================
>> > > >              Configuring PETSc to compile on your system
>> > > >
>> > >
>> =================================================================================
>> > > > TESTING: check from
>> > > > config.libraries(config/BuildSystem/config/libraries.py:126)
>> > > >
>> > >
>> *********************************************************************************
>> > > >          UNABLE to CONFIGURE with GIVEN OPTIONS    (see
>> configure.log for
>> > > > details):
>> > > >
>> > >
>> ---------------------------------------------------------------------------------------
>> > > > Currently --download-openmpi option does not work with --prefix
>> install.
>> > > > Suggest installing OpenMPI separately, and then configuring PETSc
>> with
>> > > > --with-mpi-dir option.
>> > > >
>> > >
>> *********************************************************************************
>> > > >
>> > > > How to fix it? thanks.
>> > >
>> > > configure already gave the answer to your question
>> > >
>> > > satish
>> > >
>> >
>>
>>
>


-- 
What most experimenters take for granted before they begin their experiments
is infinitely more interesting than any results to which their experiments
lead.
-- Norbert Wiener
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