[petsc-users] Error configuring PETSc with SUNDIALS (to solve stiff PDE)

[Satish Balay]

> --LDFLAGS="-L/Users/namupatel/Softwares/OpenMPI/1.10.0/lib -Wl,-rpath,/Users/namupatel/Softwares/OpenMPI/1.10.0/lib"

Try:

export LD_LIBRARY_PATH=/Users/namupatel/Softwares/OpenMPI/1.10.0/lib

And then rerun configure

Satish

On Sun, 29 Nov 2015, namu patel wrote:

> I didn't try the --with-mpicc flag, however, the configuration is
> successful for PETSc 3.5.4.
> 
> On Sun, Nov 29, 2015 at 11:56 AM, Matthew Knepley <knepley at gmail.com> wrote:
> 
> > On Sun, Nov 29, 2015 at 11:50 AM, namu patel <namu.patel7 at gmail.com>
> > wrote:
> >
> >> Attached is my configuration log file.
> >>
> >
> > Satish, the idiotic Sundials configure cannot find mpicc even when its
> > passed in as the C compiler:
> >
> > MPI-C Settings
> > --------------
> > checking if using MPI-C script... yes
> > checking if absolute path to mpicc was given... no
> > checking for mpicc... none
> >    Unable to find a functional MPI-C compiler.
> >    Try using --with-mpicc to specify a MPI-C compiler script,
> >    --with-mpi-incdir, --with-mpi-libdir and --with-mpi-libs
> >    to specify the locations of all relevant MPI files, or
> >    --with-mpi-root to specify the base installation directory
> >    of the MPI implementation to be used.
> >    Disabling the parallel NVECTOR module and all parallel examples...
> >
> > Do we have to give -with-mpicc as an argument?
> >
> >   Thanks,
> >
> >      Matt
> >
> >
> >> Thanks,
> >> Namu
> >>
> >> On Sun, Nov 29, 2015 at 11:48 AM, Matthew Knepley <knepley at gmail.com>
> >> wrote:
> >>
> >>> You must send configure.log
> >>>
> >>>   Thanks,
> >>>
> >>>     Matt
> >>>
> >>> On Sun, Nov 29, 2015 at 11:42 AM, namu patel <namu.patel7 at gmail.com>
> >>> wrote:
> >>>
> >>>> Hello All,
> >>>>
> >>>> I was trying to configure PETSc with SUNDIALS so that I may use PVODE
> >>>> to solve a stiff hyperbolic PDE of the form
> >>>>
> >>>> A(x) u_tt = K [B(x) u_x - F(x, u, u_x, t)]_x ,  t > 0,  0 < x < L ,
> >>>> u_x(0, t) = u_x(L, t) = 0 ,
> >>>> u(x, 0) = u_t(x, 0) = 0 ,
> >>>>
> >>>> where K >> 1. I was reading around to see what may be a good numerical
> >>>> implementation for such a problem and it can be tricky here because the
> >>>> stiffness is both in the linear part and the nonlinear forcing term.
> >>>>
> >>>> I want to try PVODE availble in the SUNDIALS package. When I try to
> >>>> configure PETSc with SUNDIALS, I get the message:
> >>>>
> >>>> Downloaded sundials could not be used. Please check install in
> >>>> /Users/namupatel/Softwares/PETSc/3.6.2/linux-dbg
> >>>>
> >>>>
> >>>> *******************************************************************************
> >>>>
> >>>>   File "./config/configure.py", line 363, in petsc_configure
> >>>>
> >>>>     framework.configure(out = sys.stdout)
> >>>>
> >>>>   File
> >>>> "/Users/namupatel/Softwares/PETSc/3.6.2/config/BuildSystem/config/framework.py",
> >>>> line 1081, in configure
> >>>>
> >>>>     self.processChildren()
> >>>>
> >>>>   File
> >>>> "/Users/namupatel/Softwares/PETSc/3.6.2/config/BuildSystem/config/framework.py",
> >>>> line 1070, in processChildren
> >>>>
> >>>>     self.serialEvaluation(self.childGraph)
> >>>>
> >>>>   File
> >>>> "/Users/namupatel/Softwares/PETSc/3.6.2/config/BuildSystem/config/framework.py",
> >>>> line 1051, in serialEvaluation
> >>>>
> >>>>     child.configure()
> >>>>
> >>>>   File
> >>>> "/Users/namupatel/Softwares/PETSc/3.6.2/config/BuildSystem/config/package.py",
> >>>> line 677, in configure
> >>>>
> >>>>     self.executeTest(self.configureLibrary)
> >>>>
> >>>>   File
> >>>> "/Users/namupatel/Softwares/PETSc/3.6.2/config/BuildSystem/config/base.py",
> >>>> line 126, in executeTest
> >>>>
> >>>>     ret = test(*args,**kargs)
> >>>>
> >>>>   File
> >>>> "/Users/namupatel/Softwares/PETSc/3.6.2/config/BuildSystem/config/package.py",
> >>>> line 592, in configureLibrary
> >>>>
> >>>>     for location, directory, lib, incl in self.generateGuesses():
> >>>>
> >>>>   File
> >>>> "/Users/namupatel/Softwares/PETSc/3.6.2/config/BuildSystem/config/package.py",
> >>>> line 332, in generateGuesses
> >>>>
> >>>>     raise RuntimeError('Downloaded '+self.package+' could not be used.
> >>>> Please check install in '+d+'\n')
> >>>>
> >>>> Two questions:
> >>>>
> >>>> 1. How can I resolve the above error?
> >>>>
> >>>> 2. Are there any recommendations to solving the stiff PDE stated above
> >>>> so that I can experiment to see what may be an efficient implementation?
> >>>>
> >>>> Thank you,
> >>>>
> >>>> Namu
> >>>>
> >>>>
> >>>>
> >>>
> >>>
> >>> --
> >>> 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
> >
>