[gpaw-users] compilation help

[Glen Jenness]

Marcin:  That worked!  I got it to compile, but I got some issue with my
numpy installation to fight now.....

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>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>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>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 listgpaw-users at listserv.fysik.dtu.dkhttps://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
>>>
>>> ***********************************
>>>
>>>
>>
>>
>>  --
>> 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
>>
>> ***********************************
>>
>>
>
>
>  --
> 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
>
> ***********************************
>
>


-- 
Dr. Glen Jenness
Schmidt Group/Morgan Group
Department of Chemistry/Materials Science and Engineering (MSAE)
University of Wisconsin - Madison
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