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/
>>>
>>>
>>>
>>
>