[gpaw-users] GPAW parallel installation on El Capitan

Varadharajan Srinivasan varadharajan.srinivasan at gmail.com
Sat Apr 9 14:42:15 CEST 2016 

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/
>>
>>
>>
>>
>
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