[gpaw-users] GPAW installation through Homebrew on Mac OS X Mavericks
Jakob Schiøtz
schiotz at fysik.dtu.dk
Tue Apr 5 15:42:25 CEST 2016
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/
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