[petsc-dev] PETSC's compilation
David sheehan
david.sheehanjr at gmail.com
Wed Mar 24 14:03:09 CDT 2010
How can I be added in the list of petsc-maint? thanks.
David
On Wed, Mar 24, 2010 at 12:45 PM, Matthew Knepley <knepley at gmail.com> wrote:
> 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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