[gpaw-users] gpaw-users Digest, Vol 75, Issue 22
Varadharajan Srinivasan
varadharajan.srinivasan at gmail.com
Sun Apr 24 00:12:56 CEST 2016
I am hoping the same. So far there have been no glitches.
Thanks,
Vardha.
On Sat, Apr 23, 2016 at 5:20 PM, Toma Susi <toma.susi at univie.ac.at> wrote:
> 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:
>>> >
>>> > Send gpaw-users mailing list submissions to
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>>> >
>>> > When replying, please edit your Subject line so it is more specific
>>> > than "Re: Contents of gpaw-users digest..."
>>> >
>>> >
>>> > 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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>>> >
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>>> >
>>> > End of gpaw-users Digest, Vol 75, Issue 22
>>> > ******************************************
>>>
>>>
>>> _______________________________________________
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