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

[Satish Balay]

Ok - I see the issue now.

We are using --with-mpi-root option with sundials.

However - configure is not able to determine this - when configured
with CC=/path/to/mpicc

sundials.py looks complicated enough - just to work arround this
mpi/non-mpi compiler issue of sundials.

But perhaps we should always add -with-mpicc - as you suggest
[and get rid of --with-mpi-root stuff? - I'm not sure if that would work]

Namu, Can you try using:

--with-mpi-dir=/Users/namupatel/Softwares/OpenMPI/1.10.0

[in place of options: "--CC=/Users/namupatel/Softwares/OpenMPI/1.10.0/bin/mpicc --CXX=/Users/namupatel/Softwares/OpenMPI/1.10.0/bin/mpicxx --FC=/Users/namupatel/Softwares/OpenMPI/1.10.0/bin/mpif90" ]

Satish

On Sun, 29 Nov 2015, Matthew Knepley 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
> >>
> >
> >
> 
> 
>