Just as a side idea, apt-get is *not* required in order to use the install script, so you could try running that script and see if it Just Works.

If you are concerned to make sure it never tries to run apt, you can pass the --no_package_manager option to the install script.

On Thu, 17 Sep 2015 at 12:03 Mitchell, Lawrence <lawrence.mitchell@imperial.ac.uk> wrote:
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On 17/09/15 11:57, Buesing, Henrik wrote:
>
>
>> -----Ursprüngliche Nachricht----- Von:
>> firedrake-bounces@imperial.ac.uk [mailto:firedrake-
>> bounces@imperial.ac.uk] Im Auftrag von Buesing, Henrik Gesendet:
>> 17 September 2015 12:29 An: firedrake@imperial.ac.uk Betreff: Re:
>> [firedrake] undefined symbol: kspfgmresmodifypcksp_
>>
>>
>>
>>> -----Ursprüngliche Nachricht----- Von:
>>> firedrake-bounces@imperial.ac.uk [mailto:firedrake-
>>> bounces@imperial.ac.uk] Im Auftrag von Buesing, Henrik
>>> Gesendet: 17 September 2015 11:43 An: firedrake@imperial.ac.uk
>>> Betreff: Re: [firedrake] undefined symbol:
>>> kspfgmresmodifypcksp_
>>>
>>>> -----Ursprüngliche Nachricht----- Von:
>>>> firedrake-bounces@imperial.ac.uk [mailto:firedrake-
>>>> bounces@imperial.ac.uk] Im Auftrag von Buesing, Henrik
>>>> Gesendet: 17 September 2015 10:53 An:
>>>> firedrake@imperial.ac.uk Betreff: Re: [firedrake] undefined
>>>> symbol: kspfgmresmodifypcksp_
>>>>
>>>> @Lawrence: I will go through your tests. At the moment I try
>>>> to use my own petsc version (and not the pip installed one)
>>>> for petsc4py. This crashed because I did not have
>>>> "--download-ctetgen --download-triangle - -download-chaco".
>>>> I'm doing a petsc ./configure atm. I will see how that goes.
>>>
>>> [Buesing, Henrik] This gave at least different errors (see the
>>> attached pyop2 test). I get "Import errors" No module named
>>> sparsity cannot import name plan No module named computeind
>>
>> [Buesing, Henrik] There are shared object files
>>
>> computeind.so  plan.so  sparsity.so
>>
>> in the pyop2 directory
>>
>> build/lib.linux-x86_64-2.7/pyop2
>>
>> Maybe he does not find these files somehow?
>>
>
> [Buesing, Henrik] I have added the above directory to the
> PYTHONPATH. He now does not complain about sparsity anymore. I get
> a
>
> Intel MKL FATAL ERROR: Cannot load libmkl_mc3.so or libmkl_def.so.
>
> Well, I guess that has to do with Petsc and its blas-lapack-dir. I
> will try to reconfigure with --download-fblaslapack and not set the
> directory.

I would start by trying to get petsc4py working on top of the PETSc
you built manually (rather than through pip), which I think seemed to
be working.  Then we need to build PyOP2 with the correct
PETSc/petsc4py combo.  The MKL error may be similar to this error
mentioned in the PETSc FAQ:

http://www.mcs.anl.gov/petsc/documentation/faq.html#libimf

Lawrence
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