[gpaw-users] Import Error After Installation
Marcin Dulak
Marcin.Dulak at fysik.dtu.dk
Thu Nov 11 08:58:36 CET 2010
Hi,
Jibiao Li wrote:
> The sripts are run by mpirun -np 2 gpaw-python, and the problem
> remains standing there with mpicompiler='mpicc'
> the output of mpif90 -showme:
> gfortran -I/home/jibiaoli/Install/openmpi-1.3.4/include -pthread
> -I/home/jibiaoli/Install/openmpi-1.3.4/lib
> -L/home/jibiaoli/Install/openmpi-1.3.4/lib -lmpi_f90 -lmpi_f77 -lmpi
> -lopen-rte -lopen-pal -ldl -Wl,--export-dynamic -lnsl -lutil -lm -ldl
>
you use your own installation of openmpi, do you also use your own gcc?
What about:
rpm -q gcc && gcc -v
ldd `find /home/jibiaoli/Install/gpaw-0.7.2.6974/gpaw -name _gpaw.so`
Marcin
>
> On Wed, Nov 10, 2010 at 1:18 PM, Christian Glinsvad <chlg at fysik.dtu.dk
> <mailto:chlg at fysik.dtu.dk>> wrote:
>
>
> Hi
>
> I think the fact that you're using gcc for the serial compile and
> mpif90
> for the parallel compile might lead to conflicts. The undefined
> __divdc3
> is a very basic math function (computes quotient of two complex
> numbers).
> How are you running your scripts - with the python or gpaw-python
> binary?
>
> Also, could you try compiling mpicompiler='mpicc' or is that out
> of the
> question? Alternatively, please post the output of the command:
> mpif90 -showme
>
> Regards
> Christian Glinsvad
>
>
> On Wed, 10 Nov 2010, Jibiao Li wrote:
>
> Hi, Marcin Dulak
> Python scripts can now be run quite successfully with your
> suggestions. But the import error still there when I try to
> generate xes1s file by
> gpaw-setup command. Could you please provide further suggestions?
>
> File "/usr/bin/gpaw-setup", line 60, in <module>
> from gpaw.atom.generator import Generator, parameters
> File
> "/home/jibiaoli/Install/gpaw-0.7.2.6974/gpaw/lib/python/gpaw/__init__.py",
> line 255, in <module>
> from gpaw.aseinterface import GPAW
> File
> "/home/jibiaoli/Install/gpaw-0.7.2.6974/gpaw/lib/python/gpaw/aseinterface.py",
> line 11, in <module>
> from gpaw.paw import PAW
> File
> "/home/jibiaoli/Install/gpaw-0.7.2.6974/gpaw/lib/python/gpaw/paw.py",
> line 14, in <module>
> import gpaw.io <http://gpaw.io>
> File
> "/home/jibiaoli/Install/gpaw-0.7.2.6974/gpaw/lib/python/gpaw/io/__init__.py",
> line 10, in <module>
> import gpaw.mpi as mpi
> File
> "/home/jibiaoli/Install/gpaw-0.7.2.6974/gpaw/lib/python/gpaw/mpi/__init__.py",
> line 13, in <module>
> from gpaw.utilities import is_contiguous
> File
> "/home/jibiaoli/Install/gpaw-0.7.2.6974/gpaw/lib/python/gpaw/utilities/__init__.py",
> line 13, in <module>
> import _gpaw
> ImportError:
> /home/jibiaoli/Install/gpaw-0.7.2.6974/gpaw/lib/python/_gpaw.so:
> undefined symbol: __divdc3
>
> In the customize.py file, I specify the following parameters
> while all others are commented. (the path of gcclib.so was
> specified in my .bashrc file.)
> compiler = 'gcc'
> mpicompiler = 'mpif90'
> mpi_library_dirs = ['../openmpi-1.3.4/lib']
> mpi_include_dirs = ['../openmpi-1.3.4/include']
>
>
>
> On Sat, Oct 16, 2010 at 1:17 PM, Jibiao Li <jibiaoli at gmail.com
> <mailto:jibiaoli at gmail.com>> wrote:
> Hi, Marcin Dulak
> The problem has been solved with your suggestions. Thanks
>
> On Sat, Oct 16, 2010 at 12:00 PM, Marcin Dulak
> <Marcin.Dulak at fysik.dtu.dk <mailto:Marcin.Dulak at fysik.dtu.dk>>
> wrote:
> Hi,
>
> first thing i would recommend is to update to Fedora 13,
> and then install GPAW using RPMS as described at
> https://wiki.fysik.dtu.dk/gpaw/install/Linux/Fedora.html#fedora
> If you prefer not to update then please post the
> customize.py that you used for building.
> Do you use a custom gcc installation, as __divdc3 comes
> from libgcc.a?
> What is the output of
> rpm -q gcc && gcc -v
> What is the output of
> ldd `find /home/jibiaoli/Install/gpaw-0.7.2.6974/gpaw
> -name _gpaw.so`
> Anyway, maybe it's better to choose the root of
> installation to a different location and keep the source
> directory untouched, like:
> /home/jibiaoli/Install/gpaw-0.7.2.6974-1 (first build of
> gpaw-0.7.2.6974)
>
> Marcin
>
> Jibiao Li wrote:
> Hi All
> An import error appeared as I test GPAW after a new
> intallation on my laptop(with Fedora 10), Could you tell me
> how to
> tackle this trival problem? $ gpaw-setup
> Traceback (most recent call last):
> File
> "/home/jibiaoli/Install/gpaw-0.7.2.6974/gpaw/bin/gpaw-setup",
> line 5, in <module>
> from gpaw.atom.gpaw_setup import main
> File
> "/home/jibiaoli/Install/gpaw-0.7.2.6974/gpaw/lib/python/gpaw/__init__.py",
> line 255, in <module>
> from gpaw.aseinterface import GPAW
> File
> "/home/jibiaoli/Install/gpaw-0.7.2.6974/gpaw/lib/python/gpaw/aseinterface.py",
> line 11, in <module>
> from gpaw.paw import PAW
> File
> "/home/jibiaoli/Install/gpaw-0.7.2.6974/gpaw/lib/python/gpaw/paw.py",
> line 14, in <module>
> import gpaw.io <http://gpaw.io> <http://gpaw.io>
> File
> "/home/jibiaoli/Install/gpaw-0.7.2.6974/gpaw/lib/python/gpaw/io/__init__.py",
> line 10, in <module>
> import gpaw.mpi as mpi
> File
> "/home/jibiaoli/Install/gpaw-0.7.2.6974/gpaw/lib/python/gpaw/mpi/__init__.py",
> line 13, in <module>
> from gpaw.utilities import is_contiguous
> File
> "/home/jibiaoli/Install/gpaw-0.7.2.6974/gpaw/lib/python/gpaw/utilities/__init__.py",
> line 13, in <module>
> import _gpaw
> ImportError:
> /home/jibiaoli/Install/gpaw-0.7.2.6974/gpaw/lib/python/_gpaw.so:
> undefined symbol: __divdc3
> ------------------------------------------------------------------------
>
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>
> --
> ***********************************
>
> Marcin Dulak
> Technical University of Denmark
> Department of Physics
> Building 307, Room 229
> DK-2800 Kongens Lyngby
> Denmark
> Tel.: (+45) 4525 3157
> Fax.: (+45) 4593 2399
> email: Marcin.Dulak at fysik.dtu.dk
> <mailto:Marcin.Dulak at fysik.dtu.dk>
>
> ***********************************
>
>
>
>
>
--
***********************************
Marcin Dulak
Technical University of Denmark
Department of Physics
Building 307, Room 229
DK-2800 Kongens Lyngby
Denmark
Tel.: (+45) 4525 3157
Fax.: (+45) 4593 2399
email: Marcin.Dulak at fysik.dtu.dk
***********************************
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