[gpaw-users] GPAW parallel installation on El Capitan
Tristan Maxson
tgmaxson at gmail.com
Tue Apr 19 21:42:06 CEST 2016
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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