[gpaw-users] gpaw-users Digest, Vol 75, Issue 22

Toma Susi toma.susi at univie.ac.at
Sat Apr 23 13:50:32 CEST 2016 

My advice would be to try what you want to try on the workstation despite the test fails, it may be likely that you won't run into issues.

Dr. Toma Susi
Principal investigator
HeQuCoG FWF project
University of Vienna, Austria

http://mostlyphysics.net

"Love is the only emotion that enhances our intelligence." 
	-Humberto Maturana

> On 23 Apr 2016, at 14:45, Varadharajan Srinivasan <varadharajan.srinivasan at gmail.com> wrote:
> 
> We are trying to install GPAW on our cluster. But I was too excited to use it so installed on my workstation :)
> 
> Vardha.
> 
>> On Sat, Apr 23, 2016 at 5:04 PM, Toma Susi <toma.susi at univie.ac.at> wrote:
>> Hi,
>> 
>> Yes, but the issue might still be related. 
>> 
>> I'm not actually sure if I ever resolved this, but I don't really run anything heavy on my desktop anyways, and all that I have used has worked fine.
>> 
>> Dr. Toma Susi
>> Principal investigator
>> HeQuCoG FWF project
>> University of Vienna, Austria
>> 
>> http://mostlyphysics.net
>> 
>> "Love is the only emotion that enhances our intelligence." 
>> 	-Humberto Maturana
>> 
>>> On 23 Apr 2016, at 12:14, Varadharajan Srinivasan <varadharajan.srinivasan at gmail.com> wrote:
>>> 
>>> Dear Toma,
>>> 
>>> Thanks for this. I checked and I have a more recent version of numpy 1.11.0 and openmpi-1.10.2 installed. If I understood corrected these were the libraries giving errors in your case right?
>>> 
>>> Best,
>>> Vardha.
>>> 
>>>> On Wed, Apr 20, 2016 at 1:17 AM, Toma Susi via gpaw-users <gpaw-users at listserv.fysik.dtu.dk> wrote:
>>>> 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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>>>> > When replying, please edit your Subject line so it is more specific
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>>>> >
>>>> > Today's Topics:
>>>> >
>>>> >   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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