[gpaw-users] GPAW installation through Homebrew on Mac OS X Mavericks

Thu Mar 31 21:39:58 CEST 2016

Dear all,

I thought I would try again for some help on a mac compilation error below.

Thanks,
Vardha.

On Wed, Mar 30, 2016 at 11:31 AM, Varadharajan Srinivasan <
varadharajan.srinivasan at gmail.com> wrote:

> Dear all,
>
> I am new to GPAW and have been trying to install it on my MacPro which
> runs Mavericks 10.9.5 (haven't had the courage to upgrade to El Capitan). I
> followed the instructions given on
> https://wiki.fysik.dtu.dk/gpaw/platforms/MacOSX/homebrew.html
>
> I also downloaded gpaw-1.0.1b1, untarred it and ran python setup.py
> install (as given in the link above). However, I got the following errors.
> mpicc -DNPY_NO_DEPRECATED_API=7 -DPARALLEL=1 -DGPAW_INTERPRETER=1 -Wall
> -std=c99ld: warning: could not create compact unwind for _dgehrd_: stack
> subq instruction is too different from dwarf stack size
> ld: warning: could not create compact unwind for _dhseqr_: stack subq
> instruction is too different from dwarf stack size
> ld: warning: could not create compact unwind for _dormlq_: stack subq
> instruction is too different from dwarf stack size
> ld: warning: could not create compact unwind for _dormqr_: stack subq
> instruction is too different from dwarf stack size
> ld: warning: could not create compact unwind for _zgbtrf_: stack subq
> instruction is too different from dwarf stack size
> ld: warning: could not create compact unwind for _dormql_: stack subq
> instruction is too different from dwarf stack size
> ld: warning: could not create compact unwind for _zunmql_: stack subq
> instruction is too different from dwarf stack size
> ld: warning: could not create compact unwind for _zunmqr_: stack subq
> instruction is too different from dwarf stack size
> Undefined symbols for architecture x86_64:
>   "__gfortran_concat_string", referenced from:
>       _dtrtri_ in liblapack.a(dtrtri.o)
>       _ztrtri_ in liblapack.a(ztrtri.o)
>       _dhseqr_ in liblapack.a(dhseqr.o)
>       _dormlq_ in liblapack.a(dormlq.o)
>       _dormqr_ in liblapack.a(dormqr.o)
>       _dormtr_ in liblapack.a(dormtr.o)
>       _zunmtr_ in liblapack.a(zunmtr.o)
>       ...
>   "__gfortran_st_write", referenced from:
>       _xerbla_ in libblas.a(xerbla.o)
>   "__gfortran_st_write_done", referenced from:
>       _xerbla_ in libblas.a(xerbla.o)
>   "__gfortran_stop_string", referenced from:
>       _xerbla_ in libblas.a(xerbla.o)
>   "__gfortran_string_len_trim", referenced from:
>       _xerbla_ in libblas.a(xerbla.o)
>   "__gfortran_transfer_character_write", referenced from:
>       _xerbla_ in libblas.a(xerbla.o)
>   "__gfortran_transfer_integer_write", referenced from:
>       _xerbla_ in libblas.a(xerbla.o)
> ld: symbol(s) not found for architecture x86_64
> clang: error: linker command failed with exit code 1 (use -v to see
> invocation)
>  -fPIC -I/usr/local/lib/python2.7/site-packages/numpy/core/include
> -I/usr/local/Cellar/python/2.7.8_2/Frameworks/Python.framework/Versions/2.7/include/python2.7
> -I/usr/local/Cellar/python/2.7.8_2/Frameworks/Python.framework/Versions/2.7/include/python2.7
> -o build/temp.macosx-10.9-x86_64-2.7/c/xc/libvdwxc.o -c c/xc/libvdwxc.c
> mpicc -o build/bin.macosx-10.9-x86_64-2.7//gpaw-python
> build/temp.macosx-10.9-x86_64-2.7/c/_gpaw.o
> build/temp.macosx-10.9-x86_64-2.7/c/bc.o
> build/temp.macosx-10.9-x86_64-2.7/c/blacs.o
> build/temp.macosx-10.9-x86_64-2.7/c/blas.o
> build/temp.macosx-10.9-x86_64-2.7/c/bmgs/bmgs.o
> build/temp.macosx-10.9-x86_64-2.7/c/cerf.o
> build/temp.macosx-10.9-x86_64-2.7/c/fftw.o
> build/temp.macosx-10.9-x86_64-2.7/c/hdf5.o
> build/temp.macosx-10.9-x86_64-2.7/c/lapack.o
> build/temp.macosx-10.9-x86_64-2.7/c/lcao.o
> build/temp.macosx-10.9-x86_64-2.7/c/lfc.o
> build/temp.macosx-10.9-x86_64-2.7/c/lfc2.o
> build/temp.macosx-10.9-x86_64-2.7/c/localized_functions.o
> build/temp.macosx-10.9-x86_64-2.7/c/mlsqr.o
> build/temp.macosx-10.9-x86_64-2.7/c/mpi.o
> build/temp.macosx-10.9-x86_64-2.7/c/operators.o
> build/temp.macosx-10.9-x86_64-2.7/c/plane_wave.o
> build/temp.macosx-10.9-x86_64-2.7/c/plt.o
> build/temp.macosx-10.9-x86_64-2.7/c/point_charges.o
> build/temp.macosx-10.9-x86_64-2.7/c/spline.o
> build/temp.macosx-10.9-x86_64-2.7/c/symmetry.o
> build/temp.macosx-10.9-x86_64-2.7/c/transformers.o
> build/temp.macosx-10.9-x86_64-2.7/c/utilities.o
> build/temp.macosx-10.9-x86_64-2.7/c/wigner_seitz.o
> build/temp.macosx-10.9-x86_64-2.7/c/woperators.o
> build/temp.macosx-10.9-x86_64-2.7/c/xc/ensemble_gga.o
> build/temp.macosx-10.9-x86_64-2.7/c/xc/libvdwxc.o
> build/temp.macosx-10.9-x86_64-2.7/c/xc/libxc.o
> build/temp.macosx-10.9-x86_64-2.7/c/xc/m06l.o
> build/temp.macosx-10.9-x86_64-2.7/c/xc/pbe.o
> build/temp.macosx-10.9-x86_64-2.7/c/xc/pw91.o
> build/temp.macosx-10.9-x86_64-2.7/c/xc/revtpss.o
> build/temp.macosx-10.9-x86_64-2.7/c/xc/revtpss_c_pbe.o
> build/temp.macosx-10.9-x86_64-2.7/c/xc/rpbe.o
> build/temp.macosx-10.9-x86_64-2.7/c/xc/tpss.o
> build/temp.macosx-10.9-x86_64-2.7/c/xc/vdw.o
> build/temp.macosx-10.9-x86_64-2.7/c/xc/xc.o
> build/temp.macosx-10.9-x86_64-2.7/c/xc/xc_mgga.o
>  -L/usr/local/Cellar/python/2.7.8_2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/config
> -lxc -lblas -llapack -lpython2.7 -ldl  -framework CoreFoundation
> -L/usr/local/lib -L/usr/local/opt/sqlite/lib
> Traceback (most recent call last):
>   File "setup.py", line 266, in <module>
>     'Topic :: Scientific/Engineering :: Physics'])
>   File
> "/usr/local/Cellar/python/2.7.8_2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/core.py",
> line 151, in setup
>     dist.run_commands()
>   File
> "/usr/local/Cellar/python/2.7.8_2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/dist.py",
> line 953, in run_commands
>     self.run_command(cmd)
>   File
> "/usr/local/Cellar/python/2.7.8_2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/dist.py",
> line 972, in run_command
>     cmd_obj.run()
>   File
> "/usr/local/Cellar/python/2.7.8_2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/command/install.py",
> line 563, in run
>     self.run_command('build')
>   File
> "/usr/local/Cellar/python/2.7.8_2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/cmd.py",
> line 326, in run_command
>     self.distribution.run_command(command)
>   File
> "/usr/local/Cellar/python/2.7.8_2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/dist.py",
> line 972, in run_command
>     cmd_obj.run()
>   File
> "/usr/local/Cellar/python/2.7.8_2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/command/build.py",
> line 127, in run
>     self.run_command(cmd_name)
>   File
> "/usr/local/Cellar/python/2.7.8_2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/cmd.py",
> line 326, in run_command
>     self.distribution.run_command(command)
>   File
> "/usr/local/Cellar/python/2.7.8_2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/dist.py",
> line 972, in run_command
>     cmd_obj.run()
>   File "setup.py", line 218, in run
>     assert error == 0
> AssertionError
>
>
>
> I compiled lapack and blas separately (using the brew installed gfortran)
> and moved the .a files to /usr/local/lib as suggested here
> https://pheiter.wordpress.com/2012/09/04/howto-installing-lapack-and-blas-on-mac-os/
>
> Looking through a lot of forums on this error I gather that there is some
> mismatch in the compilations giving rise to undefined references. But I am
> unsure what it is as I did everything under the home-brew environment. I
> have been staying up for several nights straight to try and fix this but
> have been unsuccessful. I was hoping I can get some insights from other
> users.
>
> Looking forward to your help.
>
> Best,
> Vardha.
>
> IISER Bhopal, India.
>
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