[gpaw-users] Import Error After Installation
Jibiao Li
jibiaoli at gmail.com
Thu Nov 11 13:59:59 CET 2010
Hi, Marcin
Thanks a lot. The suggestion would be very helpful, and I will consider to
update the Fedora after my current project.
On Thu, Nov 11, 2010 at 8:50 PM, Marcin Dulak <Marcin.Dulak at fysik.dtu.dk>wrote:
> Hi,
>
> then you could use also the openmpi coming from Fedora instead of your own
> build?
> As root: yum install openmpi openmpi-devel
> I don't remember if I asked you already if this is a cluster?
> If it's a laptop then you could update it to Fedora 13 and install from
> RPMS:
>
> https://wiki.fysik.dtu.dk/gpaw/install/Linux/Fedora.html#fedora
> Fedora 10 is unsupported - that means unsafe
>
> Marcin
>
> Jibiao Li wrote:
>
>> Hi, I used the in-built gcc in Fedora 10
>>
>> On Thu, Nov 11, 2010 at 3:58 PM, Marcin Dulak <Marcin.Dulak at fysik.dtu.dk<mailto:
>> Marcin.Dulak at fysik.dtu.dk>> wrote:
>>
>> 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>
>> <mailto: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/> <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
>>
>> 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>
>> <mailto: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>
>> <mailto: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
>> <http://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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>>
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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>
>> <mailto: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 <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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