[gpaw-users] GPAW parallel installation on El Capitan

Varadharajan Srinivasan varadharajan.srinivasan at gmail.com
Sat Apr 23 11:07:48 CEST 2016 

Dear Tristan,

Sorry for the late reply. I just saw your email. I am giving below the
configuration log. I didn't save the build log. If needed I can try
building it again and save the log. Let me know if the information below is
useful.

Current configuration
libraries ['xc', 'scalapack', 'openblas']
library_dirs ['/usr/local/opt/openblas/lib', '/usr/local/lib']
include_dirs ['/usr/local/lib/python2.7/site-packages/numpy/core/include']
define_macros [('NPY_NO_DEPRECATED_API', 7), ('GPAW_NO_UNDERSCORE_CBLACS',
'1'), ('GPAW_NO_UNDERSCORE_CSCALAPACK', '1'), ('GPAW_WITH_SL', '1')]
extra_link_args []
extra_compile_args ['-Wall', '-std=c99']
runtime_library_dirs []
extra_objects []

Parallel configuration
mpicompiler mpicc
mpi_libraries []
mpi_library_dirs []
mpi_include_dirs []
mpi_define_macros []
mpi_runtime_library_dirs []

Best,
Vardha.

On Wed, Apr 20, 2016 at 1:12 AM, Tristan Maxson <tgmaxson at gmail.com> wrote:

> On Apr 19, 2016 3:41 PM, tgmaxson at gmail.com wrote:
>
>> Can you possibly attach your build log for what you are using?  that
>> could shed some light on the issue.
>> On Apr 19, 2016 3:37 PM, "Varadharajan Srinivasan via gpaw-users" <
>> gpaw-users at listserv.fysik.dtu.dk> wrote:
>>
>>> Dear Ask,
>>>
>>> I did try both with 2 and 4 cores and indeed I get segmentation faults.
>>> I attach the log file for the tests run with 4 cores.
>>> So far in my trial runs (on the tutorials) I haven't faced any problem
>>> but your insight into this issue would be very helpful.
>>>
>>> Best,
>>> Vardha.
>>>
>>> On Mon, Apr 18, 2016 at 2:13 PM, Ask Hjorth Larsen <asklarsen at gmail.com>
>>> wrote:
>>>
>>>> The test suite is designed for 1, 2, 4, or 8 cores.  Definitely there
>>>> will be some tests that do not run on 12.  However the segmentation
>>>> fault should never happen.  Can you reproduce that with 2, 4 or 8
>>>> cores?
>>>>
>>>> Best regards
>>>> Ask
>>>>
>>>> 2016-04-09 14:42 GMT+02:00 Varadharajan Srinivasan
>>>> <varadharajan.srinivasan at gmail.com>:
>>>> > Dear Jakob,
>>>> >
>>>> > I installed ASE and GPAW without using virtualenvs. gnaw-python
>>>> $(which paw)
>>>> > info  gives:
>>>> > python-2.7.11   /usr/local/bin/gpaw-python
>>>> > gpaw-1.0.1b1
>>>> >
>>>> /usr/local/opt/python/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/gpaw/
>>>> > ase-3.11.0b1    /Users/vardha/SWARE/ase/ase/
>>>> > numpy-1.11.0
>>>> >
>>>> /usr/local/opt/python/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/
>>>> > scipy-0.17.0
>>>> >
>>>> /usr/local/opt/python/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/
>>>> > _gpaw           built-in
>>>> > parallel        /usr/local/bin/gpaw-python
>>>> > FFTW            no
>>>> > scalapack       yes
>>>> > libvdwxc        no
>>>> > PAW-datasets    /usr/local/share/gpaw-setups:
>>>> >                 /usr/share/gpaw-setups
>>>> >
>>>> >
>>>> > Serial tests run fine. However, on running parallel tests several
>>>> tests fail
>>>> > complaining of errors like :
>>>> > (a) ValueError: Cannot construct interpolator.  Grid 12 x 12 x 12 may
>>>> be too
>>>> > small
>>>> > (b) RuntimeError: Cannot distribute 80 bands to 12 processors
>>>> > (c) RuntimeError: use fewer bands or more basis functions
>>>> >
>>>> > I think most of these errors are because I got greedy and used 12
>>>> cores
>>>> > which might be too much for the tests. But one error was from
>>>> xc/atomize.py
>>>> > which was a segmentation fault :
>>>> > xc/atomize.py                            [helios:47447] *** Process
>>>> received
>>>> > signal ***
>>>> > [helios:47447] Signal: Segmentation fault: 11 (11)
>>>> > [helios:47447] Signal code: Address not mapped (1)
>>>> > [helios:47447] Failing at address: 0x1230ea000
>>>> > [helios:47447] [ 0] 0   libsystem_platform.dylib
>>>> > 0x00007fff9371352a _sigtramp + 26
>>>> > [helios:47447] [ 1] 0   ???
>>>> > 0x00000000000003e8 0x0 + 1000
>>>> > [helios:47447] [ 2] 0   gpaw-python
>>>> > 0x000000010b8ed035 calc_mgga + 581
>>>> > [helios:47447] [ 3] 0   gpaw-python
>>>> > 0x000000010b8ec613 XCFunctional_calculate + 435
>>>> > [helios:47447] [ 4] 0   Python
>>>> > 0x000000011051dbcd PyEval_EvalFrameEx + 26858
>>>> > [helios:47447] [ 5] 0   Python
>>>> > 0x00000001105170f1 PyEval_EvalCodeEx + 1583
>>>> > [helios:47447] [ 6] 0   Python
>>>> > 0x000000011052169a fast_function + 117
>>>> > [helios:47447] [ 7] 0   Python
>>>> > 0x000000011051daf3 PyEval_EvalFrameEx + 26640
>>>> > [helios:47447] [ 8] 0   Python
>>>> > 0x000000011052172d fast_function + 264
>>>> > [helios:47447] [ 9] 0   Python
>>>> > 0x000000011051daf3 PyEval_EvalFrameEx + 26640
>>>> > [helios:47447] [10] 0   Python
>>>> > 0x000000011052172d fast_function + 264
>>>> > [helios:47447] [11] 0   Python
>>>> > 0x000000011051daf3 PyEval_EvalFrameEx + 26640
>>>> > [helios:47447] [12] 0   Python
>>>> > 0x00000001105170f1 PyEval_EvalCodeEx + 1583
>>>> > [helios:47447] [13] 0   Python
>>>> > 0x000000011052169a fast_function + 117
>>>> > [helios:47447] [14] 0   Python
>>>> > 0x000000011051daf3 PyEval_EvalFrameEx + 26640
>>>> > [helios:47447] [15] 0   Python
>>>> > 0x000000011052172d fast_function + 264
>>>> > [helios:47447] [16] 0   Python
>>>> > 0x000000011051daf3 PyEval_EvalFrameEx + 26640
>>>> > [helios:47447] [17] 0   Python
>>>> > 0x000000011052172d fast_function + 264
>>>> > [helios:47447] [18] 0   Python
>>>> > 0x000000011051daf3 PyEval_EvalFrameEx + 26640
>>>> > [helios:47447] [19] 0   Python
>>>> > 0x00000001105170f1 PyEval_EvalCodeEx + 1583
>>>> > [helios:47447] [20] 0   Python
>>>> > 0x00000001105174fc PyEval_EvalFrameEx + 537
>>>> > [helios:47447] [21] 0   Python
>>>> > 0x00000001105170f1 PyEval_EvalCodeEx + 1583
>>>> > [helios:47447] [22] 0   Python
>>>> > 0x000000011052169a fast_function + 117
>>>> > [helios:47447] [23] 0   Python
>>>> > 0x000000011051daf3 PyEval_EvalFrameEx + 26640
>>>> > [helios:47447] [24] 0   Python
>>>> > 0x000000011052172d fast_function + 264
>>>> > [helios:47447] [25] 0   Python
>>>> > 0x000000011051daf3 PyEval_EvalFrameEx + 26640
>>>> > [helios:47447] [26] 0   Python
>>>> > 0x000000011052172d fast_function + 264
>>>> > [helios:47447] [27] 0   Python
>>>> > 0x000000011051daf3 PyEval_EvalFrameEx + 26640
>>>> > [helios:47447] [28] 0   Python
>>>> > 0x00000001105170f1 PyEval_EvalCodeEx + 1583
>>>> > [helios:47447] [29] 0   Python
>>>> > 0x00000001104bbfb1 function_call + 352
>>>> > [helios:47447] *** End of error message ***
>>>> >
>>>> >
>>>> > And that's where the tests stopped. I will try with lesser processors
>>>> but do
>>>> > you think this is a compilation/installation issue ?
>>>> >
>>>> > Thanks,
>>>> > Vardha.
>>>> >
>>>> >
>>>> > On Sat, Apr 9, 2016 at 2:07 AM, Varadharajan Srinivasan
>>>> > <varadharajan.srinivasan at gmail.com> wrote:
>>>> >>
>>>> >> Dear Jakob,
>>>> >>
>>>> >> Thank you very much for your suggestion. I will try it and report
>>>> back.
>>>> >>
>>>> >> Best,
>>>> >> Vardha.
>>>> >>
>>>> >> On Sat, Apr 9, 2016 at 1:38 AM, Jakob Schiøtz <schiotz at fysik.dtu.dk>
>>>> >> wrote:
>>>> >>>
>>>> >>> This is VirtualEnv doing its “magic”.  I was never able to get gpaw
>>>> or
>>>> >>> asap to work with virtualenv, because they use their own python
>>>> interpreter
>>>> >>> (which breaks virtualenv).  But strangely, it always worked for
>>>> Marcin who
>>>> >>> wrote the instructions.  I think it was a difference between using
>>>> the
>>>> >>> build-in python or the homebrew python.
>>>> >>>
>>>> >>> Try without using virtualenv.  But in that case it is essential to
>>>> use
>>>> >>> the homebrew Python, so you can clean up if something goes horribly
>>>> wrong.
>>>> >>> Try for example to follow these instructions:
>>>> >>>
>>>> https://wiki.fysik.dtu.dk/asap/Installing%20ASE%2C%20Asap%20and%20GPAW%20on%20a%20Mac
>>>> >>> Just skip the installation of Asap, you do not need it.
>>>> >>>
>>>> >>> Best regards
>>>> >>>
>>>> >>> Jakob
>>>> >>>
>>>> >>>
>>>> >>> > On 08 Apr 2016, at 13:43, Varadharajan Srinivasan via gpaw-users
>>>> >>> > <gpaw-users at listserv.fysik.dtu.dk> wrote:
>>>> >>> >
>>>> >>> > Dear Ask,
>>>> >>> >
>>>> >>> > Thank you for the prompt reply.
>>>> >>> >
>>>> >>> > You run "gpaw info" in serial, so it has no scalapack.
>>>> >>> >
>>>> >>> > Try "gpaw-python $(which gpaw) info".
>>>> >>> >
>>>> >>> > I ran this and got an error :
>>>> >>> >  gpaw-python $(which gpaw) info
>>>> >>> > Traceback (most recent call last):
>>>> >>> >   File "/Users/vardha/Virtualenvs/gpaw-trunk/bin/gpaw", line 2, in
>>>> >>> > <module>
>>>> >>> >     from gpaw.cli.main import main
>>>> >>> > ImportError: No module named gpaw.cli.main
>>>> >>> >
>>>> >>> > In fact, someone should probably add that trick to the web page
>>>> if it
>>>> >>> > isn't there already.
>>>> >>> >
>>>> >>> > They don't find ASE installed.  Please check that you can import
>>>> ase
>>>> >>> > from gpaw-python, e.g. gpaw-python -c "import ase"
>>>> >>> >
>>>> >>> > I then tried  gpaw-python -c "import ase" and got :
>>>> >>> > Traceback (most recent call last):
>>>> >>> >   File "<string>", line 1, in <module>
>>>> >>> > ImportError: No module named ase
>>>> >>> >
>>>> >>> > Is there something wrong with my paths? I installed GPAW in
>>>> virtualenvs
>>>> >>> > and used  the .bash_profile  below.
>>>> >>> >
>>>> >>> > Thanks,
>>>> >>> > Vardha.
>>>> >>> >
>>>> >>> > # Set architecture flags
>>>> >>> > export ARCHFLAGS="-arch x86_64"
>>>> >>> >
>>>> >>> > # personal installation of pip
>>>> >>> > export PATH=/Users/$USER/pip_latest:$PATH
>>>> >>> > export PYTHONPATH=/Users/$USER/pip_latest:$PYTHONPATH
>>>> >>> >
>>>> >>> > pyver=`python -c "from distutils import sysconfig; print
>>>> >>> > sysconfig.get_python_version()"`
>>>> >>> >
>>>> >>> > # pip --user installations of packages
>>>> >>> > export PATH=/Users/$USER/Library/Python/${pyver}/bin:$PATH
>>>> >>> > export
>>>> >>> >
>>>> PYTHONPATH=/Users/$USER/Library/Python/${pyver}/lib/python/site-packages:$PYTHONPATH
>>>> >>> >
>>>> >>> > # homebrew
>>>> >>> > # Ensure user-installed binaries take precedence
>>>> >>> > export PATH=/usr/local/bin:$PATH
>>>> >>> > export
>>>> >>> > PYTHONPATH=/usr/local/lib/python${pyver}/site-packages:$PYTHONPATH
>>>> >>> > # hack gtk-2.0
>>>> >>> > export
>>>> >>> >
>>>> PYTHONPATH=/usr/local/lib/python${pyver}/site-packages/gtk-2.0:$PYTHONPATH
>>>> >>> > # https://github.com/mxcl/homebrew/issues/16891
>>>> >>> > export PKG_CONFIG_PATH=`brew --prefix
>>>> >>> > libffi`/lib/pkgconfig:$PKG_CONFIG_PATH
>>>> >>> > export PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:$PKG_CONFIG_PATH
>>>> >>> > export PKG_CONFIG_PATH=/usr/local/lib/pkgconfig:$PKG_CONFIG_PATH
>>>> >>> >
>>>> >>> > # virtualenv
>>>> >>> > # virtualenv should use Distribute instead of legacy setuptools
>>>> >>> > export VIRTUALENV_DISTRIBUTE=true
>>>> >>> > # Centralized location for new virtual environments
>>>> >>> > export PIP_VIRTUALENV_BASE=$HOME/Virtualenvs
>>>> >>> > # pip should only run if there is a virtualenv currently activated
>>>> >>> > export PIP_REQUIRE_VIRTUALENV=true
>>>> >>> > # cache pip-installed packages to avoid re-downloading
>>>> >>> > export PIP_DOWNLOAD_CACHE=$HOME/.pip/cache
>>>> >>> >
>>>> >>> > Then try within mpirun.
>>>> >>> >
>>>> >>> > Best regards
>>>> >>> > Ask
>>>> >>> >
>>>> >>> > > Thanks,
>>>> >>> > > Vardha.
>>>> >>> > >
>>>> >>> > > _______________________________________________
>>>> >>> > > gpaw-users mailing list
>>>> >>> > > gpaw-users at listserv.fysik.dtu.dk
>>>> >>> > > https://listserv.fysik.dtu.dk/mailman/listinfo/gpaw-users
>>>> >>> >
>>>> >>> > _______________________________________________
>>>> >>> > gpaw-users mailing list
>>>> >>> > gpaw-users at listserv.fysik.dtu.dk
>>>> >>> > https://listserv.fysik.dtu.dk/mailman/listinfo/gpaw-users
>>>> >>>
>>>> >>> --
>>>> >>> 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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