Re: [firedrake] undefined symbol: kspfgmresmodifypcksp_
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 -----BEGIN PGP SIGNATURE----- Version: GnuPG v1
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Von: firedrake-bounces@imperial.ac.uk [mailto:firedrake-bounces@imperial.ac.uk] Im Auftrag von David Ham Gesendet: 17 September 2015 13:07 An: firedrake Betreff: Re: [firedrake] undefined symbol: kspfgmresmodifypcksp_ 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. [Buesing, Henrik] Also a good idea. I will keep that in mind. I ran the script without –no_package_manager and then he aborted and complained about not finding apt-get. That’s why I assumed it’s needed. On Thu, 17 Sep 2015 at 12:03 Mitchell, Lawrence <lawrence.mitchell@imperial.ac.uk<mailto:lawrence.mitchell@imperial.ac.uk>> wrote: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 On 17/09/15 11:57, Buesing, Henrik wrote:
-----Ursprüngliche Nachricht----- Von: firedrake-bounces@imperial.ac.uk<mailto:firedrake-bounces@imperial.ac.uk> [mailto:firedrake-<mailto:firedrake-> bounces@imperial.ac.uk<mailto:bounces@imperial.ac.uk>] Im Auftrag von Buesing, Henrik Gesendet: 17 September 2015 12:29 An: firedrake@imperial.ac.uk<mailto:firedrake@imperial.ac.uk> Betreff: Re: [firedrake] undefined symbol: kspfgmresmodifypcksp_
-----Ursprüngliche Nachricht----- Von: firedrake-bounces@imperial.ac.uk<mailto:firedrake-bounces@imperial.ac.uk> [mailto:firedrake-<mailto:firedrake-> bounces@imperial.ac.uk<mailto:bounces@imperial.ac.uk>] Im Auftrag von Buesing, Henrik Gesendet: 17 September 2015 11:43 An: firedrake@imperial.ac.uk<mailto:firedrake@imperial.ac.uk> Betreff: Re: [firedrake] undefined symbol: kspfgmresmodifypcksp_
-----Ursprüngliche Nachricht----- Von: firedrake-bounces@imperial.ac.uk<mailto:firedrake-bounces@imperial.ac.uk> [mailto:firedrake-<mailto:firedrake-> bounces@imperial.ac.uk<mailto:bounces@imperial.ac.uk>] Im Auftrag von Buesing, Henrik Gesendet: 17 September 2015 10:53 An: firedrake@imperial.ac.uk<mailto: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 -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQEcBAEBAgAGBQJV+p3UAAoJECOc1kQ8PEYvNuwH/iuTymdAT0MofwrnwRV1iRwe kNj9tC3mN3E3pXVnCml8Wc4IvdGYGM0wgdlk8glUtQSyJNu+YoNuK7KRRTUhsNUr GLwxX61SV9kuwXfk5XjXjmvLGoJlxn4275jslNlUz8vXRAgajY46pPqXlb7v4D/H Et5jkHirDVC29lM42P9KmtCmX4zxjZGUpNrUAGQxRm6nbAeA+cplifHJ6zlb1Pf0 ewU4adl2ywxagtvX8Nxy5uIQt3pJmF6QX+nJBsei1OjVsoFMGMz869nEZuG6jqN9 yxkbno5PBS8LsLTAyVYsYScRo1pxWE8uaq7T4TMWrQSE+/j/85l5ZapOKuoUvmo= =WUld -----END PGP SIGNATURE----- _______________________________________________ firedrake mailing list firedrake@imperial.ac.uk<mailto:firedrake@imperial.ac.uk> https://mailman.ic.ac.uk/mailman/listinfo/firedrake
participants (2)
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                Buesing, Henrik
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                David Ham