[gpaw-users] compilation help
Marcin Dulak
Marcin.Dulak at fysik.dtu.dk
Tue Apr 23 09:26:59 CEST 2013
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
Fax.: (+45) 4593 2399
email: Marcin.Dulak at fysik.dtu.dk
***********************************
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