Re: [firedrake] undefined symbol: kspfgmresmodifypcksp_
Hi Henrik, Welcome to Firedrake. That's quite an odd error you have there. The symbol kspfgmresmodifypcksp_ should be defined in libpetsc itself, and indeed that does work in the firedrake install on my machine updated this morning. Can we just get some basic information here. Which OS is this? If Linux, which distribution and release? How did you install Firedrake? Is this using the install script (preferred, but it doesn't look like it from your log) or are you using the step by step instructions? Specifically which version of petsc is this (ie which command did you type to install petsc). Cheers, David On Thu, 17 Sep 2015 at 09:07 Buesing, Henrik <HBuesing@eonerc.rwth-aachen.de> wrote:
I tried to rebuild everything from scratch, but the error persists. It already occurs in the tests for pyop2 (see attachement).
Henrik
*Von:* firedrake-bounces@imperial.ac.uk [mailto: firedrake-bounces@imperial.ac.uk] *Im Auftrag von *Buesing, Henrik *Gesendet:* 16 September 2015 23:19 *An:* firedrake@imperial.ac.uk *Betreff:* [firedrake] undefined symbol: kspfgmresmodifypcksp_
Dear Firedrake Developers,
I tried to start the *helmholtz.py* example, but I get the following error:
* File "helmholtz.py", line 47, in <module> from firedrake import * File "/home/user/.local/lib/python2.7/site-packages/firedrake/__init__.py", line 8, in <module> import firedrake.petsc as petsc File "/home/user/.local/lib/python2.7/site-packages/firedrake/petsc.py", line 5, in <module> petsc4py.init(sys.argv) File "/home/user/.local/lib/python2.7/site-packages/petsc4py/__init__.py", line 42, in init PETSc = petsc4py.lib.ImportPETSc(arch) File "/home/user/.local/lib/python2.7/site-packages/petsc4py/lib/__init__.py", line 29, in ImportPETSc return Import('petsc4py', 'PETSc', path, arch) File "/home/user/.local/lib/python2.7/site-packages/petsc4py/lib/__init__.py", line 64, in Import module = imp.load_module(fullname, fo, fn, stuff) ImportError: /home/user/.local/lib/python2.7/site-packages/petsc/lib/libpetsc.so.3.06: undefined symbol: kspfgmresmodifypcksp_ *Is there anything I can do about it? Thank you!
Henrik
-- Dipl.-Math. Henrik Büsing Applied Geophysics and Geothermal Energy E.ON Energy Research Center RWTH Aachen University ----------------------------------------------- Mathieustr. 10 | Tel +49 (0)241 80 49907 52074 Aachen, Germany | Fax +49 (0)241 80 49889 ----------------------------------------------- http://www.eonerc.rwth-aachen.de/GGE hbuesing@eonerc.rwth-aachen.de -----------------------------------------------
Von: firedrake-bounces@imperial.ac.uk [mailto:firedrake-bounces@imperial.ac.uk] Im Auftrag von David Ham Gesendet: 17 September 2015 10:40 An: firedrake Betreff: Re: [firedrake] undefined symbol: kspfgmresmodifypcksp_ Hi Henrik, Welcome to Firedrake. That's quite an odd error you have there. The symbol kspfgmresmodifypcksp_ should be defined in libpetsc itself, and indeed that does work in the firedrake install on my machine updated this morning. Can we just get some basic information here. Which OS is this? If Linux, which distribution and release? [Buesing, Henrik] I’m on Scientific Linux release 6.6 (Carbon). How did you install Firedrake? Is this using the install script (preferred, but it doesn't look like it from your log) or are you using the step by step instructions? [Buesing, Henrik] I’m using the step by step instructions, since I have no apt-get. Specifically which version of petsc is this (ie which command did you type to install petsc). [Buesing, Henrik] I did a PETSC_CONFIGURE_OPTIONS="--with-blas-lapack-dir=/opt/intel/mkl/11.3.0.109/mkl/lib/intel64 --with-cc=mpicc --with-fc=mpif90 --with-cxx=mpicxx --download-hypre --download-ml --download-mumps --download-superlu_dist --download-suitesparse --download-scalapack --download-blacs --download-hdf5 --download-parmetis --download-metis --with-debugging=0 --download-ctetgen --download-triangle --download-chaco" \ pip install --user -U --no-deps https://bitbucket.org/mapdes/petsc/get/firedrake.tar.bz2 Cheers, David On Thu, 17 Sep 2015 at 09:07 Buesing, Henrik <HBuesing@eonerc.rwth-aachen.de<mailto:HBuesing@eonerc.rwth-aachen.de>> wrote: I tried to rebuild everything from scratch, but the error persists. It already occurs in the tests for pyop2 (see attachement). Henrik Von: firedrake-bounces@imperial.ac.uk<mailto:firedrake-bounces@imperial.ac.uk> [mailto:firedrake-bounces@imperial.ac.uk<mailto:firedrake-bounces@imperial.ac.uk>] Im Auftrag von Buesing, Henrik Gesendet: 16 September 2015 23:19 An: firedrake@imperial.ac.uk<mailto:firedrake@imperial.ac.uk> Betreff: [firedrake] undefined symbol: kspfgmresmodifypcksp_ Dear Firedrake Developers, I tried to start the helmholtz.py example, but I get the following error: File "helmholtz.py", line 47, in <module> from firedrake import * File "/home/user/.local/lib/python2.7/site-packages/firedrake/__init__.py", line 8, in <module> import firedrake.petsc as petsc File "/home/user/.local/lib/python2.7/site-packages/firedrake/petsc.py", line 5, in <module> petsc4py.init(sys.argv) File "/home/user/.local/lib/python2.7/site-packages/petsc4py/__init__.py", line 42, in init PETSc = petsc4py.lib.ImportPETSc(arch) File "/home/user/.local/lib/python2.7/site-packages/petsc4py/lib/__init__.py", line 29, in ImportPETSc return Import('petsc4py', 'PETSc', path, arch) File "/home/user/.local/lib/python2.7/site-packages/petsc4py/lib/__init__.py", line 64, in Import module = imp.load_module(fullname, fo, fn, stuff) ImportError: /home/user/.local/lib/python2.7/site-packages/petsc/lib/libpetsc.so.3.06: undefined symbol: kspfgmresmodifypcksp_ Is there anything I can do about it? Thank you! Henrik -- Dipl.-Math. Henrik Büsing Applied Geophysics and Geothermal Energy E.ON Energy Research Center RWTH Aachen University ----------------------------------------------- Mathieustr. 10 | Tel +49 (0)241 80 49907 52074 Aachen, Germany | Fax +49 (0)241 80 49889 ----------------------------------------------- http://www.eonerc.rwth-aachen.de/GGE hbuesing@eonerc.rwth-aachen.de<mailto:hbuesing@eonerc.rwth-aachen.de> -----------------------------------------------
participants (2)
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Buesing, Henrik
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David Ham