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

Varadharajan Srinivasan varadharajan.srinivasan at gmail.com
Fri Apr 1 21:27:36 CEST 2016 

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.
>>
>
>
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