New subject: undefined symbol: kspfgmresmodifypcksp_

17 Sep 2015

      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:
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-----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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Re: [firedrake] undefined symbol: kspfgmresmodifypcksp_

David Ham

Buesing, Henrik

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