[petsc-dev] PETSC's compilation
David sheehan
david.sheehanjr at gmail.com
Mon Mar 22 18:44:29 CDT 2010
When I compile it again, there is the following error for my application
code.
#error: can't find include file: include/finclude/petsc.h
My application code incudes
#include "include/finclude/petsc.h"
In my makefile, I set the path as follows
PETSC_DIR=/home/david/petsc
include $(PETSC_DIR)/conf/variables
Actually there is pestc.h in the directory, how can I fix it? thanks.
David
On Mon, Mar 22, 2010 at 6:29 PM, Satish Balay <balay at mcs.anl.gov> wrote:
> mpiexec is part of the MPI standard. The usage is dicated as:
>
> mpiexec -n 2 ./pro.ex
>
> Satish
>
> On Mon, 22 Mar 2010, David sheehan wrote:
>
> > I tried it, but it doesn't like mpirun. For example,
> > if I want to run
> > mpirun -np 2 pro.ex
> > then it would be
> > mpiexec -np 2 pro.ex
> > , right? thanks.
> >
> > David
> >
> > On Mon, Mar 22, 2010 at 5:58 PM, Satish Balay <balay at mcs.anl.gov> wrote:
> >
> > > As mentioned before - its 'mpiexec'
> > >
> > >
> > > Satish
> > >
> > >
> > > On Mon, 22 Mar 2010, David sheehan wrote:
> > >
> > > > The "bin" directory has the following files:
> > > >
> > > > adiforfix.py mpich2version mpiexec.poe
> > > > parkill taucc.py
> > > > adprocess.py mpicxx mpiexec.prun
> > > > parseargs.py TOPSGenerator.py
> > > > chibaoutput mpiexec mpiexec.sshsync
> > > > petsc_libtool TOPSInstaller.py
> > > > configVars.py mpiexec.chiba mpiexec.uni
> > > > petscmpiexec update.py
> > > > hostnames.chiba mpiexec.gmalloc mpiexec.valgrind
> > > > popup urlget
> > > > matlab mpiexec.lam mpif77
> > > > portabilitycheck.py urlget.py
> > > > mpicc mpiexec.llrun mpif90
> > > > processSummary.py win32fe
> > > > which one is "mpirun"? thanks.
> > > >
> > > > David
> > > >
> > > > On Mon, Mar 22, 2010 at 5:44 PM, Satish Balay <balay at mcs.anl.gov>
> wrote:
> > > >
> > > > >
> > > > > You should look for mpiexec. It will be in the 'bin' dir for the
> > > > > prefix used - i.ed /home/david/petscdir/bin/mpiexec
> > > > >
> > > > > Satish
> > > > >
> > > > >
> > > > > On Mon, 22 Mar 2010, David sheehan wrote:
> > > > >
> > > > > > I build up petsc successfully as follows
> > > > > > ./configure --with-cc= --prefix=/home/david/petscdir
> --with-cc=gcc
> > > > > > --with-cxx=g++ --with-fc=ifort --download-mpich=1
> --download-hypre=1
> > > > > > make
> > > > > > make install
> > > > > > make test
> > > > > >
> > > > > > Also, I can link it with my application. Now I need to run my
> > > application
> > > > > > with the petsc, where can I find "mpirun" for the mpich
> downloaded to
> > > run
> > > > > my
> > > > > > application? thanks.
> > > > > >
> > > > > > David
> > > > > >
> > > > > >
> > > > > >
> > > > > > On Mon, Mar 22, 2010 at 4:45 PM, Satish Balay <balay at mcs.anl.gov
> >
> > > wrote:
> > > > > >
> > > > > > > You can't use 2 MPIs at same time. i.e use either
> > > --download-mpich=1
> > > > > > > or --download-openmpi=1 - but not both.
> > > > > > >
> > > > > > > Satish
> > > > > > >
> > > > > > > On Mon, 22 Mar 2010, David sheehan wrote:
> > > > > > >
> > > > > > > > You mean,
> > > > > > > > ./configure --with-cc=gcc --with-cxx=g++ --with-fc=ifort
> > > > > > > --download-mpich=1
> > > > > > > > --download-hypre=1 --download-openmpi=1
> > > > > > > > thanks.
> > > > > > > >
> > > > > > > > David
> > > > > > > >
> > > > > > > > On Mon, Mar 22, 2010 at 3:58 PM, Matthew Knepley <
> > > knepley at gmail.com>
> > > > > > > wrote:
> > > > > > > >
> > > > > > > > > On Mon, Mar 22, 2010 at 3:54 PM, David sheehan <
> > > > > > > david.sheehanjr at gmail.com>wrote:
> > > > > > > > >
> > > > > > > > >> I don't have icc and icpc. I only have ifort and gnu
> compilers
> > > > > such
> > > > > > > > >> g77,gcc
> > > > > > > > >> and g++. Since my application code works very well with
> ifort,
> > > can
> > > > > I
> > > > > > > build
> > > > > > > > >>
> > > > > > > > >> up PETSC plus Hypre with ifort and gnu compilers? thanks.
> > > > > > > > >>
> > > > > > > > >
> > > > > > > > > It might be possible (though not guaranteed if ifort
> conflicts
> > > with
> > > > > GNU
> > > > > > > > > somehow). You
> > > > > > > > > jsut provide these compilers to the configure, and use
> > > > > > > --download-openmpi.
> > > > > > > > >
> > > > > > > > > Matt
> > > > > > > > >
> > > > > > > > >
> > > > > > > > >>
> > > > > > > > >> David
> > > > > > > > >>
> > > > > > > > >> On Mon, Mar 22, 2010 at 3:29 PM, Satish Balay <
> > > balay at mcs.anl.gov>
> > > > > > > wrote:
> > > > > > > > >>
> > > > > > > > >>> If you have installation issues - send the relavent logs
> [in
> > > this
> > > > > > > case
> > > > > > > > >>> configure.log] to petsc-maint.
> > > > > > > > >>>
> > > > > > > > >>> Here you appear to try too many things.. But its not
> clear if
> > > you
> > > > > are
> > > > > > > > >>> installing openmpi/lam yourself - or using default from
> Red
> > > Hat
> > > > > 3.4.
> > > > > > > > >>> [note - default openmpi will be built with gnu compilers
> - so
> > > > > > > > >>> unuseable from ifort].
> > > > > > > > >>>
> > > > > > > > >>> Thing to do:
> > > > > > > > >>>
> > > > > > > > >>> - decide on compilers you want to use.
> > > > > > > > >>> - build PETSc and mpi with these compilers
> > > > > > > > >>>
> > > > > > > > >>> [for eg: configure CC=icc CXX=icpc FC=ifort
> > > --download-mpich=1
> > > > > > > > >>> --download-hypre=1]
> > > > > > > > >>>
> > > > > > > > >>> Note: alternative f90 compilers seable on linux are
> gfortran,
> > > g95
> > > > > > > > >>>
> > > > > > > > >>> Satish
> > > > > > > > >>>
> > > > > > > > >>> On Mon, 22 Mar 2010, David sheehan wrote:
> > > > > > > > >>>
> > > > > > > > >>> > Hi,
> > > > > > > > >>> > I am trying to compile the PETSC with hypre. I have
> Intel
> > > > > FORTRAN,
> > > > > > > > >>> openmpi
> > > > > > > > >>> > and lam
> > > > > > > > >>> > MPI (gcc version 3.4.6 (Red Hat 3.4.6-3)) available.
> > > > > > > > >>> >
> > > > > > > > >>> > Since my application code is in FORTRAN with dynamic
> memory
> > > > > > > allocation
> > > > > > > > >>> in
> > > > > > > > >>> > the code,
> > > > > > > > >>> > so I have to use Intel FORTRAN(ifort) as the compiler
> to
> > > link
> > > > > PETSC
> > > > > > > > >>> with my
> > > > > > > > >>> > application
> > > > > > > > >>> > code. I can build up PETSC(petsc-3.0.0-p11) plus hypre
> with
> > > Lam
> > > > > MPI
> > > > > > > but
> > > > > > > > >>> > without ifort
> > > > > > > > >>> > successfully. However I can not use ifort to link the
> PETSC
> > > > > with my
> > > > > > > > >>> > application success-
> > > > > > > > >>> > fully. The link always shows erros about "undefined
> > > reference"
> > > > > to
> > > > > > > MPI
> > > > > > > > >>> parts
> > > > > > > > >>> > in my application
> > > > > > > > >>> > code such as 'mpi_send_', 'mpi_recv_', 'mpi_waitany_',
> > > > > > > > >>> 'mpi_get_count_',
> > > > > > > > >>> > and etc.
> > > > > > > > >>> >
> > > > > > > > >>> > Can any one help me out? thanks in advance.
> > > > > > > > >>> >
> > > > > > > > >>> > Best Regards,
> > > > > > > > >>> >
> > > > > > > > >>> > David
> > > > > > > > >>> >
> > > > > > > > >>>
> > > > > > > > >>>
> > > > > > > > >>
> > > > > > > > >
> > > > > > > > >
> > > > > > > > > --
> > > > > > > > > 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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