petsc4py fails to configure with my own lapack/blas

Thu Jun 4 18:51:54 CDT 2009

First of all, what Fortran compilers do you have installed? g77? g95?
gfortran? all of them? two of them? just one? This is going to be a
real mess for you if more than one is installed. If you want to use
the system blas/lapack, then you should use a matching compiler, and
this dependency will apply when you build numpy and scipy.

At first look, it seems you are using blas/lapack libraries built with
g77 ?? But PETSc seems to pick gfortran as Fortran compiler ??
Moreover, libpetsc.so is linked with some f77 and f90 MPI bits... I'm
not sure if that's fine...

On Thu, Jun 4, 2009 at 8:28 PM, Ondrej Certik <ondrej at certik.cz> wrote:
> On Thu, Jun 4, 2009 at 5:18 PM, Ondrej Certik<ondrej at certik.cz> wrote:
>> On Thu, Jun 4, 2009 at 5:14 PM, Lisandro Dalcin<dalcinl at gmail.com> wrote:
>>> On Thu, Jun 4, 2009 at 7:59 PM, Ondrej Certik <ondrej at certik.cz> wrote:
>>>> On Thu, Jun 4, 2009 at 4:13 PM, Lisandro Dalcin<dalcinl at gmail.com> wrote:
>>>>> This smells to a 32/64 bit libs mismatch, or a g77/g95/gfortran
>>>>> mismatch. Addionally, could you try to run 'ldd' on core PETSc libs
>>>>> and on the PETSc.so extension module?
>>>>
>>>> So those core PETSc libs are just .a libraries (not dynamic
>>>> executables). Could that be a problem?
>>>>
>>>
>>> That could be a BIG problem. petsc4py does not "officially" support
>>> PETSc builds with static libs, though it could work on some scenarios.
>>> Moreover, even if you get it working, you will not be able to use let
>>> say slepc4py, or any other C code depending on the PETSc libraries
>>> (think of a fast, Cython-implemented Function()/Jacobian() routine for
>>> a nonlinear problem solved with SNES).
>>>
>>> I really recommend you to pass '--with-shared' to PETSc's configure.
>>
>> Ah, I didn't know I have to pass it. I thought petsc will do the right
>> thing. Let me do it right now and I'll report back.
>
> Ok, so now everything is built as an .so library, but it still fails
> in exactly the same way as here:
>
> http://code.google.com/p/femhub/issues/detail?id=30
>
> Here is the ldd on petsc libraries:
>
> $ ldd lib/libpetsc.so
>        linux-vdso.so.1 =>  (0x00007fff32bfe000)
>        libX11.so.6 => /usr/lib/libX11.so.6 (0x00007fc62a372000)
>        liblapack.so.3gf => /usr/lib/liblapack.so.3gf (0x00007fc6298ac000)
>        libcblas.so.3gf => /usr/lib/libcblas.so.3gf (0x00007fc62968e000)
>        libf77blas.so.3gf => /usr/lib/libf77blas.so.3gf (0x00007fc62946f000)
>        libatlas.so.3gf => /usr/lib/libatlas.so.3gf (0x00007fc628ae8000)
>        libdl.so.2 => /lib/libdl.so.2 (0x00007fc6288e4000)
>        libmpi.so.0 => /usr/lib/libmpi.so.0 (0x00007fc628641000)
>        libopen-rte.so.0 => /usr/lib/libopen-rte.so.0 (0x00007fc6283f8000)
>        libopen-pal.so.0 => /usr/lib/libopen-pal.so.0 (0x00007fc62818d000)
>        libnsl.so.1 => /lib/libnsl.so.1 (0x00007fc627f73000)
>        libutil.so.1 => /lib/libutil.so.1 (0x00007fc627d6f000)
>        libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x00007fc627b57000)
>        libpthread.so.0 => /lib/libpthread.so.0 (0x00007fc62793b000)
>        libmpi_f90.so.0 => /usr/lib/libmpi_f90.so.0 (0x00007fc627736000)
>        libmpi_f77.so.0 => /usr/lib/libmpi_f77.so.0 (0x00007fc6274fe000)
>        libgfortran.so.3 => /usr/lib/libgfortran.so.3 (0x00007fc627222000)
>        libm.so.6 => /lib/libm.so.6 (0x00007fc626f9c000)
>        libc.so.6 => /lib/libc.so.6 (0x00007fc626c2a000)
>        libxcb.so.1 => /usr/lib/libxcb.so.1 (0x00007fc626a0e000)
>        libblas.so.3gf => /usr/lib/libblas.so.3gf (0x00007fc62677d000)
>        /lib64/ld-linux-x86-64.so.2 (0x00007fc62a9ec000)
>        libXau.so.6 => /usr/lib/libXau.so.6 (0x00007fc62657a000)
>        libXdmcp.so.6 => /usr/lib/libXdmcp.so.6 (0x00007fc626374000)
>
>
>
> and here on the PETSc.so:
>
> $ ldd lib/python2.5/site-packages/petsc4py/lib/linux-gnu-c-debug/PETSc.so
>        linux-vdso.so.1 =>  (0x00007fff899ff000)
>        libpetscts.so =>
> /home/ondrej/ext/spd-3.4.2spd3-ubuntu-64bit/local/lib/libpetscts.so
> (0x00007f2881264000)
>        libpetscsnes.so =>
> /home/ondrej/ext/spd-3.4.2spd3-ubuntu-64bit/local/lib/libpetscsnes.so
> (0x00007f2880ffb000)
>        libpetscksp.so =>
> /home/ondrej/ext/spd-3.4.2spd3-ubuntu-64bit/local/lib/libpetscksp.so
> (0x00007f2880b68000)
>        libpetscdm.so =>
> /home/ondrej/ext/spd-3.4.2spd3-ubuntu-64bit/local/lib/libpetscdm.so
> (0x00007f28808a4000)
>        libpetscmat.so =>
> /home/ondrej/ext/spd-3.4.2spd3-ubuntu-64bit/local/lib/libpetscmat.so
> (0x00007f28802f9000)
>        libpetscvec.so =>
> /home/ondrej/ext/spd-3.4.2spd3-ubuntu-64bit/local/lib/libpetscvec.so
> (0x00007f287ffff000)
>        libpetsc.so =>
> /home/ondrej/ext/spd-3.4.2spd3-ubuntu-64bit/local/lib/libpetsc.so
> (0x00007f287fc8f000)
>        libX11.so.6 => /usr/lib/libX11.so.6 (0x00007f287f987000)
>        libcblas.so.3gf => /usr/lib/libcblas.so.3gf (0x00007f287f769000)
>        libf77blas.so.3gf => /usr/lib/libf77blas.so.3gf (0x00007f287f54a000)
>        libatlas.so.3gf => /usr/lib/libatlas.so.3gf (0x00007f287ebc3000)
>        libdl.so.2 => /lib/libdl.so.2 (0x00007f287e9bf000)
>        libmpi.so.0 => /usr/lib/libmpi.so.0 (0x00007f287e71c000)
>        libopen-rte.so.0 => /usr/lib/libopen-rte.so.0 (0x00007f287e4d3000)
>        libopen-pal.so.0 => /usr/lib/libopen-pal.so.0 (0x00007f287e268000)
>        libnsl.so.1 => /lib/libnsl.so.1 (0x00007f287e04e000)
>        libutil.so.1 => /lib/libutil.so.1 (0x00007f287de4a000)
>        libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x00007f287dc32000)
>        libpthread.so.0 => /lib/libpthread.so.0 (0x00007f287da16000)
>        libmpi_f90.so.0 => /usr/lib/libmpi_f90.so.0 (0x00007f287d811000)
>        libmpi_f77.so.0 => /usr/lib/libmpi_f77.so.0 (0x00007f287d5d9000)
>        libgfortran.so.3 => /usr/lib/libgfortran.so.3 (0x00007f287d2fd000)
>        libm.so.6 => /lib/libm.so.6 (0x00007f287d077000)
>        libc.so.6 => /lib/libc.so.6 (0x00007f287cd05000)
>        liblapack.so.3gf => /usr/lib/liblapack.so.3gf (0x00007f287c240000)
>        libxcb.so.1 => /usr/lib/libxcb.so.1 (0x00007f287c023000)
>        /lib64/ld-linux-x86-64.so.2 (0x00007f28818b0000)
>        libblas.so.3gf => /usr/lib/libblas.so.3gf (0x00007f287bd92000)
>        libXau.so.6 => /usr/lib/libXau.so.6 (0x00007f287bb8f000)
>        libXdmcp.so.6 => /usr/lib/libXdmcp.so.6 (0x00007f287b989000)
>
>
>
> I also noticed that the -fPIC flags are now put there several times,
> but I guess this can't hurt, that's not a problem for now.
>
> Ondrej
>

-- 
Lisandro Dalcín
---------------
Centro Internacional de Métodos Computacionales en Ingeniería (CIMEC)
Instituto de Desarrollo Tecnológico para la Industria Química (INTEC)
Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)
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