[gpaw-users] Import Error After Installation

[Jibiao Li]

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


On Wed, Nov 10, 2010 at 1:18 PM, Christian Glinsvad <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
>>   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> 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>
>> 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>
>>  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
>> ------------------------------------------------------------------------
>>
>> _______________________________________________
>> gpaw-users mailing list
>> gpaw-users at listserv.fysik.dtu.dk
>> https://listserv.fysik.dtu.dk/mailman/listinfo/gpaw-users
>>
>>
>> --
>> ***********************************
>>
>> 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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