[petsc-users] petsc4py Build Problem

[Satish Balay]

If you get errors when running basic petsc examples - send us the
relavant petsc logs [configure.log, make.log, test.log etc..]

Also - note that mpich is not supported on cygwin/windows [it
generally works for us - when we try the --download-mpich build].

Unless you really need a cywin build/use of petsc4py - it might be
easier to install a linux VM - and use PETSc/petsc4py on it.

Satish

On Thu, 11 Jun 2015, Mikhail Khodak wrote:

> I added these lines to the petsc4py test files (specifically test_comm.py)
> but the error remains the same. However, I have done the standard 'which
> mpiexec', 'which mpicc', 'which mpirun' and they are all in the same
> folder. In fact it is the only MPI installed.
> The reason I thought it might be a PETSc build problem is because one of
> the PETSc 'make test' tests (ex5f) fails with the same error, even though
> the 'make streams' test works fine with MPI processes.
> Thanks,
> Mikhail
> 
> On Thu, Jun 11, 2015 at 4:21 AM, Matthew Knepley <knepley at gmail.com> wrote:
> 
> > On Thu, Jun 11, 2015 at 5:07 AM, Mikhail Khodak <mkhodak at princeton.edu>
> > wrote:
> >
> >> Thank you for your help - the install seems to work, apart from routines
> >> requiring MPI, which fail due to the "Attempting to use an MPI routine
> >> before initializing MPI" error. This seems to be an error in the PETSc
> >> build itself.
> >>
> >
> > The MPI routines will not work until after
> >
> > import petsc4py, sys
> > petsc4py.init(sys.argv)
> > from petsc4py import PETSc
> >
> > If they fail after this, it is usually a mismatch between the mpiexec
> > being used and the MPI
> > libraries being linked.
> >
> >   Thanks,
> >
> >     Matt
> >
> > Thanks again,
> >> Mikhail Khodak
> >>
> >> On Mon, Jun 8, 2015 at 5:11 AM, Lisandro Dalcin <dalcinl at gmail.com>
> >> wrote:
> >>
> >>> On 8 June 2015 at 02:50, Mikhail Khodak <mkhodak at princeton.edu> wrote:
> >>> > Hello, I am trying to build petsc4py-3.5.1 using Cygwin on 64-bit
> >>> Windows 7.
> >>> > I have built PETSc 3.5.4 with shared and dynamic libraries using
> >>> > mpich2-1.2.1 and successfully ran the installation tests. I am using
> >>> Python
> >>> > 2.7 and NumPy 1.9.2 and have installed mpi4py. However, when I attempt
> >>> to
> >>> > install petsc4py (both with pip and distutils) I get a mpicc compiler
> >>> error
> >>> > due to undefined references/symbols. I have attached the output of
> >>> running
> >>> >
> >>> > pip install petsc petsc4py --allow-external petsc --allow-external
> >>> petsc4py
> >>> >
> >>>
> >>> I've never ever built or test petsc4py under Cygwin. The errors you
> >>> see are expected.
> >>> Perhaps you can manually workaround the issues following the following
> >>> steps:
> >>>
> >>> 1) Download the petsc4py tarball and unpack it.
> >>> 2) Open the file "src/libpetsc4py/libpetsc4py.h", add remove all
> >>> occurences of DL_IMPORT, i.e, replace DL_IMPORT(XYZ) for just XYZ
> >>> 3) Use pip again:
> >>>
> >>> pip install petsc
> >>> pip install .
> >>>
> >>> The last line assumes your current working directory is the one having
> >>> petsc4py's setup.py
> >>>
> >>> Finally, I do not guarantee this will work. I'm just guessing,
> >>> petsc4py never explicitly supported Windows and/or Cygwin.
> >>>
> >>>
> >>> --
> >>> Lisandro Dalcin
> >>> ============
> >>> Research Scientist
> >>> Computer, Electrical and Mathematical Sciences & Engineering (CEMSE)
> >>> Numerical Porous Media Center (NumPor)
> >>> King Abdullah University of Science and Technology (KAUST)
> >>> http://numpor.kaust.edu.sa/
> >>>
> >>> 4700 King Abdullah University of Science and Technology
> >>> al-Khawarizmi Bldg (Bldg 1), Office # 4332
> >>> Thuwal 23955-6900, Kingdom of Saudi Arabia
> >>> http://www.kaust.edu.sa
> >>>
> >>> Office Phone: +966 12 808-0459
> >>>
> >>
> >>
> >
> >
> > --
> > 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
> >
>