[gpaw-users] compilation help
Marcin Dulak
Marcin.Dulak at fysik.dtu.dk
Tue Apr 23 17:49:49 CEST 2013
On 04/23/2013 05:29 PM, Glen Jenness wrote:
> Marcin: That worked! I got it to compile, but I got some issue with
> my numpy installation to fight now.....
i would recommend to start with numpy built with its own blas/lapack -
you need to patch it
to be sure it does not use the first blas/lapack it finds. See for
example here:
https://wiki.fysik.dtu.dk/gpaw/install/Linux/sun_chpc.html
Install also nose and run numpy unit tests.
Marcin
>
> Jens: I did try gcc, but it didn't put the object files anywhere
> (i.e. when it came time to linking, it couldn't find any of the *.o,
> and the build directory where they're stored was empty), however I got
> no errors during compilation.
>
>
> On Tue, Apr 23, 2013 at 2:26 AM, Marcin Dulak
> <Marcin.Dulak at fysik.dtu.dk <mailto:Marcin.Dulak at fysik.dtu.dk>> wrote:
>
> Hi,
>
> some people report this is due to "-Wp,-D_FORTIFY_SOURCE=2"
> http://software.intel.com/en-us/forums/topic/294666
> Remove the "-openmp" option (GPAW won't work with that), and use:
> python setup.py build_ext --remove-default-flags
>
> Best regards,
>
> Marcin
>
>
> On 04/22/2013 05:45 PM, Glen Jenness wrote:
>> Those are still there.
>>
>> The only thing that really changed where the IPO objects i.e.
>> instead of:
>> "/tmp/ipo_iccjqCeKV.o: In function `overlap':"
>>
>> I get
>>
>> "/tmp/ipo_icc1xXXJ4.o: In function `overlap':"
>>
>> I still have all the external declaration remarks that I had before.
>>
>> I've attached my newer build.log
>>
>>
>>
>> On Mon, Apr 22, 2013 at 10:09 AM, Marcin Dulak
>> <Marcin.Dulak at fysik.dtu.dk <mailto:Marcin.Dulak at fysik.dtu.dk>> wrote:
>>
>> On 04/22/2013 04:52 PM, Glen Jenness wrote:
>>> Marcin,
>>> Sadly no. Still getting the same error.
>> but the problems with "external declaration in primary source
>> file" etc, disappeared?
>> How the complete build log looks like now, starting from
>> python setup.py clean?
>>
>> Marcin
>>
>>>
>>> Glen
>>>
>>>
>>> On Mon, Apr 22, 2013 at 9:43 AM, Marcin Dulak
>>> <Marcin.Dulak at fysik.dtu.dk
>>> <mailto:Marcin.Dulak at fysik.dtu.dk>> wrote:
>>>
>>> Hi,
>>>
>>> first, in the customize.py, try to use:
>>>
>>> include_dirs +=
>>>
>>> You are missing some includes.
>>> Does that help?
>>>
>>> Marcin
>>>
>>>
>>> On 04/20/2013 09:39 PM, Glen Jenness wrote:
>>>> Hey GPAW users!
>>>>
>>>> I recently tried compiling GPAW, but I keep getting
>>>> this error:
>>>>
>>>> /usr/lib64/python2.4/config/libpython2.4.a(posixmodule.o):
>>>> In function `posix_tmpnam':
>>>> (.text+0x725): warning: the use of `tmpnam_r' is
>>>> dangerous, better use `mkstemp'
>>>> /usr/lib64/python2.4/config/libpython2.4.a(posixmodule.o):
>>>> In function `posix_tempnam':
>>>> (.text+0x808): warning: the use of `tempnam' is
>>>> dangerous, better use `mkstemp'
>>>> /tmp/ipo_iccjqCeKV.o: warning: memset used with
>>>> constant zero length parameter; this could be due to
>>>> transposed parameters
>>>> /tmp/ipo_iccjqCeKV.o: In function `overlap':
>>>> /home/gjenness/programs/gpaw-0.9.0.8965/c/lcao.c:92:
>>>> undefined reference to `__builtin_object_size'
>>>> /home/gjenness/programs/gpaw-0.9.0.8965/c/lcao.c:92:
>>>> undefined reference to `__builtin_object_size'
>>>> /home/gjenness/programs/gpaw-0.9.0.8965/c/lcao.c:92:
>>>> undefined reference to `__builtin___memcpy_chk'
>>>> /home/gjenness/programs/gpaw-0.9.0.8965/c/lcao.c:92:
>>>> undefined reference to `__builtin_object_size'
>>>> /home/gjenness/programs/gpaw-0.9.0.8965/c/lcao.c:92:
>>>> undefined reference to `__builtin___memcpy_chk'
>>>> /home/gjenness/programs/gpaw-0.9.0.8965/c/lcao.c:138:
>>>> undefined reference to `__builtin_object_size'
>>>> /home/gjenness/programs/gpaw-0.9.0.8965/c/lcao.c:138:
>>>> undefined reference to `__builtin_object_size'
>>>> /home/gjenness/programs/gpaw-0.9.0.8965/c/lcao.c:138:
>>>> undefined reference to `__builtin___memcpy_chk'
>>>> /home/gjenness/programs/gpaw-0.9.0.8965/c/lcao.c:138:
>>>> undefined reference to `__builtin_object_size'
>>>> /home/gjenness/programs/gpaw-0.9.0.8965/c/lcao.c:138:
>>>> undefined reference to `__builtin___memcpy_chk'
>>>> /home/gjenness/programs/gpaw-0.9.0.8965/c/lcao.c:146:
>>>> undefined reference to `__builtin_object_size'
>>>> /home/gjenness/programs/gpaw-0.9.0.8965/c/lcao.c:146:
>>>> undefined reference to `__builtin_object_size'
>>>> /home/gjenness/programs/gpaw-0.9.0.8965/c/lcao.c:146:
>>>> undefined reference to `__builtin___memcpy_chk'
>>>> /home/gjenness/programs/gpaw-0.9.0.8965/c/lcao.c:146:
>>>> undefined reference to `__builtin_object_size'
>>>> /home/gjenness/programs/gpaw-0.9.0.8965/c/lcao.c:146:
>>>> undefined reference to `__builtin___memcpy_chk'
>>>> /tmp/ipo_iccjqCeKV.o: In function `bmgs_cut':
>>>> /
>>>>
>>>> It continues on (I'm including my full build.log file
>>>> and customize.py), but I can't figure out how to
>>>> correct it. I am using python2.4
>>>>
>>>> Any help would be appreciated :)
>>>>
>>>> Thanks!
>>>> Glen
>>>>
>>>> --
>>>> Dr. Glen Jenness
>>>> Schmidt Group/Morgan Group
>>>> Department of Chemistry/Materials Science and
>>>> Engineering (MSAE)
>>>> University of Wisconsin - Madison
>>>>
>>>>
>>>> _______________________________________________
>>>> gpaw-users mailing list
>>>> gpaw-users at listserv.fysik.dtu.dk <mailto: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 <tel:%28%2B45%29%204525%203157>
>>> Fax.:(+45) 4593 2399 <tel:%28%2B45%29%204593%202399>
>>> email:Marcin.Dulak at fysik.dtu.dk <mailto:Marcin.Dulak at fysik.dtu.dk>
>>>
>>> ***********************************
>>>
>>>
>>>
>>>
>>> --
>>> Dr. Glen Jenness
>>> Schmidt Group/Morgan Group
>>> Department of Chemistry/Materials Science and Engineering (MSAE)
>>> University of Wisconsin - Madison
>>
>>
>> --
>> ***********************************
>>
>> Marcin Dulak
>> Technical University of Denmark
>> Department of Physics
>> Building 307, Room 229
>> DK-2800 Kongens Lyngby
>> Denmark
>> Tel.:(+45) 4525 3157 <tel:%28%2B45%29%204525%203157>
>> Fax.:(+45) 4593 2399 <tel:%28%2B45%29%204593%202399>
>> email:Marcin.Dulak at fysik.dtu.dk <mailto:Marcin.Dulak at fysik.dtu.dk>
>>
>> ***********************************
>>
>>
>>
>>
>> --
>> Dr. Glen Jenness
>> Schmidt Group/Morgan Group
>> Department of Chemistry/Materials Science and Engineering (MSAE)
>> University of Wisconsin - Madison
>
>
> --
> ***********************************
>
> Marcin Dulak
> Technical University of Denmark
> Department of Physics
> Building 307, Room 229
> DK-2800 Kongens Lyngby
> Denmark
> Tel.:(+45) 4525 3157 <tel:%28%2B45%29%204525%203157>
> Fax.:(+45) 4593 2399 <tel:%28%2B45%29%204593%202399>
> email:Marcin.Dulak at fysik.dtu.dk <mailto:Marcin.Dulak at fysik.dtu.dk>
>
> ***********************************
>
>
>
>
> --
> Dr. Glen Jenness
> Schmidt Group/Morgan Group
> Department of Chemistry/Materials Science and Engineering (MSAE)
> University of Wisconsin - Madison
--
***********************************
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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