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

Varadharajan Srinivasan varadharajan.srinivasan at gmail.com
Tue Apr 5 20:40:45 CEST 2016


Dear Jakob,

Thanks for your reply. I am also using El Capitan now. Mavericks gave me
other problems (see my first email). I suppose I could install without
virtualenvs. I will try that too.

Thanks,
Vardha.

On Tue, Apr 5, 2016 at 7:12 PM, Jakob Schiøtz <
gpaw-users at listserv.fysik.dtu.dk> wrote:

> Hi Vardha,
>
> I tried on my mac, but do not see the problem.  One difference is that I
> do not use virtualenv.  Another is that I use El Capitan.  I have no clue
> if that is related to the problem.
>
> $ gpaw info
> python-2.7.11   /usr/local/opt/python/bin/python2.7
> gpaw-1.0.1b1    /Users/schiotz/development/gpaw/gpaw/
> ase-3.11.0b1    /Users/schiotz/development/ase/ase/
> numpy-1.10.4    /usr/local/lib/python2.7/site-packages/numpy/
> scipy-0.17.0    /usr/local/lib/python2.7/site-packages/scipy/
> _gpaw
>  /Users/schiotz/development/gpaw/build/lib.macosx-10.11-x86_64-2.7/_gpaw.so
> parallel
> /Users/schiotz/development/gpaw/build/bin.macosx-10.11-x86_64-2.7/gpaw-python
> FFTW            no
> scalapack       no
> libvdwxc        no
> PAW-datasets    1: /Users/schiotz/gpaw-setups
>
>
> Best regards
>
> Jakob
>
>
>
>
> > -------- Forwarded Message --------
> > Subject:      Re: [gpaw-users] GPAW installation through Homebrew on Mac
> OS X Mavericks
> > Date: Sat, 2 Apr 2016 00:57:36 +0530
> > From: Varadharajan Srinivasan via gpaw-users <
> gpaw-users at listserv.fysik.dtu.dk>
> > Reply-To:     Varadharajan Srinivasan <varadharajan.srinivasan at gmail.com
> >
> > To:   gpaw-users at listserv.fysik.dtu.dk
> >
> > Dear all,
> >
> > After trying in vain to fix the error on my Mavericks installation I
> tried to check if I could install GPAW on my MacbookPro which runs El
> Capitan. Everything went smoothly and I could install GPAW and ASE (using
> the home-brew instructions and virtualenvs). I ran gpaw info and it gave me
> the following :
> >
> > python-2.7.10   /Users/apple/Virtualenvs/gpaw-trunk/bin/python
> > gpaw-1.0.1b1
> /Users/apple/Virtualenvs/gpaw-trunk/lib/python2.7/site-packages/gpaw/
> > ase-3.10.0
> /Users/apple/Virtualenvs/gpaw-trunk/lib/python2.7/site-packages/ase/
> > numpy-1.10.4    /usr/local/lib/python2.7/site-packages/numpy/
> > scipy-0.17.0    /usr/local/lib/python2.7/site-packages/scipy/
> > _gpaw
>  /Users/apple/Virtualenvs/gpaw-trunk/lib/python2.7/site-packages/_gpaw.so
> > parallel        /Users/apple/Virtualenvs/gpaw-trunk/bin/gpaw-python
> > FFTW            no
> > scalapack       no
> > libvdwxc        no
> > PAW-datasets    /usr/local/share/gpaw-setups:
> >                 /usr/share/gpaw-setups
> >
> > I tried running    gpaw --verbose install-data and got the following
> error :
> > Traceback (most recent call last):
> >   File "/Users/apple/Virtualenvs/gpaw-trunk/bin/gpaw", line 3, in
> <module>
> >     main()
> >   File
> "/Users/apple/Virtualenvs/gpaw-trunk/lib/python2.7/site-packages/gpaw/cli/main.py",
> line 75, in main
> >     func(*args, **kwargs)
> >   File
> "/Users/apple/Virtualenvs/gpaw-trunk/lib/python2.7/site-packages/gpaw/cli/install_data.py",
> line 73, in main
> >     urls = get_urls(opts.source)
> >   File
> "/Users/apple/Virtualenvs/gpaw-trunk/lib/python2.7/site-packages/gpaw/cli/install_data.py",
> line 215, in get_urls
> >     response = urllib2.urlopen(page)
> >   File
> "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib2.py",
> line 154, in urlopen
> >     return opener.open(url, data, timeout)
> >   File
> "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib2.py",
> line 431, in open
> >     response = self._open(req, data)
> >   File
> "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib2.py",
> line 449, in _open
> >     '_open', req)
> >   File
> "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib2.py",
> line 409, in _call_chain
> >     result = func(*args)
> >   File
> "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib2.py",
> line 1240, in https_open
> >     context=self._context)
> >   File
> "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib2.py",
> line 1197, in do_open
> >     raise URLError(err)
> > urllib2.URLError: <urlopen error EOF occurred in violation of protocol
> (_ssl.c:590)>
> >
> > Has anybody faced this error? If so how do I fix it?
> >
> > Looking forward for some help.
> >
> > Best,
> > Vardha.
> >
> >
> > On Fri, Apr 1, 2016 at 1:09 AM, Varadharajan Srinivasan <
> varadharajan.srinivasan at gmail.com> wrote:
> > 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.
> >
> >
> >
> >
> > <Attached Message Part.txt>
>
> --
> Jakob Schiøtz, professor, Ph.D.
> Department of Physics
> Technical University of Denmark
> DK-2800 Kongens Lyngby, Denmark
> http://www.fysik.dtu.dk/~schiotz/
>
>
>
>
> _______________________________________________
> gpaw-users mailing list
> gpaw-users at listserv.fysik.dtu.dk
> https://listserv.fysik.dtu.dk/mailman/listinfo/gpaw-users
>
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