[gpaw-users] New stable release: 1.1

Sun Jun 26 14:47:59 CEST 2016

This is a follow up to my message. A custom build of the stable version
(1.1.0) included the scalapack correctly. However, the following parallel
test failed:

parallel/realspace_blacs.py              [helios:98266] *** Process
received signal ***
[helios:98266] Signal: Bus error: 10 (10)
[helios:98266] Signal code: Non-existant physical address (2)
[helios:98266] Failing at address: 0x10f57db88
[helios:98268] *** Process received signal ***
[helios:98268] Signal: Bus error: 10 (10)
[helios:98268] Signal code: Non-existant physical address (2)
[helios:98268] Failing at address: 0x10e11eb88
[helios:98266] [ 0] [helios:98268] [ 0] 0   libsystem_platform.dylib
     0x00007fff86a0c52a _sigtramp + 26
[helios:98266] [ 1] 0   ???
0x0000000123ba56e0 0x0 + 4894381792
[helios:98266] [ 2] 0   libsystem_platform.dylib
 0x00007fff86a0c52a _sigtramp + 26
[helios:98268] [ 1] 0   mca_pml_ob1.so
 0x00000001190d0db1 mca_pml_ob1_recv_frag_callback_match + 433
[helios:98268] [ 2] 0   libscalapack.dylib
 0x000000010e0bc06d pzlarfg_ + 1885
0   libscalapack.dylib                  0x000000010f51b06d pzlarfg_ + 1885
[helios:98266] *** End of error message ***
[helios:98268] *** End of error message ***
--------------------------------------------------------------------------
mpirun noticed that process rank 3 with PID 98268 on node helios exited on
signal 10 (Bus error: 10).

Even the home-brew version gave many failed tests mostly related to
parallel runs. I will try the serial tests and see if the error is only
happening in the parallel mode.

Best,
Vardha.

On Sun, Jun 26, 2016 at 5:05 PM, Varadharajan Srinivasan <
varadharajan.srinivasan at gmail.com> wrote:

> Hi Jens,
>
> Thank you for the update. I upgraded it on my Mac (El Capitan) using
> home-brew and added the new setup files.
> On running the gpaw info I realised that it wasn't installed with
> scalapack and fftw although I have already installed both using home-brew.
> Below is the info output.
>
> gpaw-python $(which gpaw) info
> python-2.7.11   /usr/local/bin/gpaw-python
> gpaw-1.1.0
>  /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       no
> libvdwxc        no
> PAW-datasets    1: /usr/local/share/gpaw-setups/gpaw-setups-0.9.20000
>                 2: /usr/local/share/gpaw-setups
>                 3: /usr/share/gpaw-setups
>
> I also tried a custom installation of the trunk version using python
> setup.py install but got a bunch of errors with "Undefined reference".
> Please find attached the log file for the errors during the build. The
> configuration I used was
>
> Current configuration
> libraries ['xc', 'scalapack', 'openblas']
> library_dirs ['/usr/local/opt/openblas/lib', '/usr/local/lib']
> include_dirs ['/usr/local/lib/python2.7/site-packages/numpy/core/include']
> define_macros [('NPY_NO_DEPRECATED_API', 7), ('GPAW_NO_UNDERSCORE_CBLACS',
> '1'), ('GPAW_NO_UNDERSCORE_CSCALAPACK', '1'), ('GPAW_WITH_SL', '1')]
> extra_link_args []
> extra_compile_args ['-Wall', '-std=c99']
> runtime_library_dirs []
> extra_objects []
>
> Parallel configuration
> mpicompiler mpicc
> mpi_libraries []
> mpi_library_dirs []
> mpi_include_dirs []
> mpi_define_macros []
> mpi_runtime_library_dirs []
>
> Any help would be really appreciated.
>
> Thanks,
> Vardha.
>
>
>
> On Wed, Jun 22, 2016 at 1:28 PM, Jens Jørgen Mortensen <
> gpaw-users at listserv.fysik.dtu.dk> wrote:
>
>> Hi!
>>
>> There is a new stable GPAW release: 1.1.0.  You can clone it from
>> https://gitlab.com/gpaw/gpaw.git, pip install it from PyPI or download a
>> tar-file from PyPI.  More details here:
>>
>>     https://wiki.fysik.dtu.dk/gpaw/install.html
>>
>> You will need to update your ASE to version 3.11.0 or later.
>>
>> *This release fixes a bug in the recently added spin-orbit module*.
>>
>> Other news since 1.0:
>>
>> The default Davidson eigensolver can now parallelize over bands.
>>
>> Jellium calculations can now be done in plane-wave mode and there is a
>> new *background_charge* keyword.
>>
>> New band structure unfolding tool.
>>
>> The get_pseudo_wave_function() method has a new keyword:  Use
>> periodic=True to get the periodic part of the wave function.
>>
>> New tool for interpolating the pseudo wave functions to a fine real-space
>> grids and for adding PAW-corrections in order to obtain all-electron wave
>> functions.
>>
>> New and improved dataset pages.  Now shows convergence of absolute and
>> relative energies with respect to plane-wave cut-off.
>>
>> New Wannier90 interface.
>>
>> Updated MacOSX installation guide for homebrew users.
>>
>> There is a new PAW-dataset file available: gpaw-setup-0.9.20000.tar.gz.
>> It's identical to the previous one except for one new data-file which is
>> needed for doing vdW-DF calculations with Python 3.
>>
>> See the release notes for more details:
>>
>>     https://wiki.fysik.dtu.dk/gpaw/releasenotes.html
>>
>> Thanks a lot to everyone who contributed to this release.
>>
>> Please update and let us know if you encounter any problems.
>>
>> Jens Jørgen
>>
>> _______________________________________________
>> gpaw-users mailing list
>> gpaw-users at listserv.fysik.dtu.dk
>> https://listserv.fysik.dtu.dk/mailman/listinfo/gpaw-users
>
>
>
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