[petsc-dev] PETSC's compilation
Matthew Knepley
knepley at gmail.com
Wed Mar 24 14:08:20 CDT 2010
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Matt
On Wed, Mar 24, 2010 at 2:03 PM, David sheehan <david.sheehanjr at gmail.com>wrote:
> 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
>>
>
>
--
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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