[gpaw-users] gpaw-users Digest, Vol 75, Issue 22
Toma Susi
toma.susi at univie.ac.at
Tue Apr 19 21:47:48 CEST 2016
Hi,
I reported segmentation faults on El Capitan 10.11.1. in November 2015:
https://listserv.fysik.dtu.dk/pipermail/gpaw-developers/2015-November/006007.html
Contains some info on mpirun crashes; I guess we decided it might be a problem with other libraries on my system.
-Toma
> On 19 Apr 2016, at 21:42, gpaw-users-request at listserv.fysik.dtu.dk wrote:
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> 1. Re: GPAW parallel installation on El Capitan (Tristan Maxson)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 19 Apr 2016 15:42:06 -0400
> From: Tristan Maxson <tgmaxson at gmail.com>
> To: Varadharajan Srinivasan <varadharajan.srinivasan at gmail.com>,
> gpaw-users <gpaw-users at listserv.fysik.dtu.dk>
> Subject: Re: [gpaw-users] GPAW parallel installation on El Capitan
> Message-ID:
> <CAGZ-oeqnc2iNRZUWqt7nyQa1uv=qQF8cB9pAnQDBip36CRcwQA at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> 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 Schi?tz <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 Schi?tz, 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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