[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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