[gpaw-users] Problems with calculating all electron wave functions in parallel mode
Jens Jørgen Mortensen
jjmo at dtu.dk
Fri Sep 15 07:31:29 CEST 2017
On 09/14/2017 09:08 PM, Varadharajan Srinivasan wrote:
> Dear Jens,
>
> I am actually interested in computing projections of time-propagated
> Kohn-Sham states with the initial KS states. Does a tool for this
> already exist? I wasn't aware so I wanted to code one. However, I was
> not sure if pseudo wave functions in PAW would be useful for this. So
> I am trying to get all-electron wave functions along my
> time-propagated simulation. Since that is parallel I also wanted the
> PS2AE to work in the same framework.
>
> This might be a very round about way of getting the projections and
> would be unnecessary if such a tool is already in existence. If not, I
> guess my trials might eventually contribute to making one. I would
> really appreciate any help in this regard.
Do your atoms move?
Jens Jørgen
>
> Vardha.
>
> On Thu, Sep 14, 2017 at 1:46 PM, Jens Jørgen Mortensen <jjmo at dtu.dk
> <mailto:jjmo at dtu.dk>> wrote:
>
> On 09/13/2017 08:16 PM, Varadharajan Srinivasan wrote:
>
> Hi Jens,
>
> I installed and tried out the development version and am
> getting it to work in parallel mode as well.
>
>
> Thanks for checking. Note that the current implementation will
> not run any faster in parallel!
>
> Jens Jørgen
>
>
> Thanks,
> Vardha.
>
> On Tue, Sep 12, 2017 at 7:32 PM, Varadharajan Srinivasan
> <varadharajan.srinivasan at gmail.com
> <mailto:varadharajan.srinivasan at gmail.com>
> <mailto:varadharajan.srinivasan at gmail.com
> <mailto:varadharajan.srinivasan at gmail.com>>> wrote:
>
> Ok I will try and report.
>
> Vardha.
>
> On Tue, Sep 12, 2017 at 3:02 PM, Jens Jørgen Mortensen
> <jjmo at dtu.dk <mailto:jjmo at dtu.dk> <mailto:jjmo at dtu.dk
> <mailto:jjmo at dtu.dk>>> wrote:
>
> On 09/11/2017 07:44 PM, Varadharajan Srinivasan wrote:
>
> Yes it does. I am sorry I had forgotten to add
> that. It
> only fails when run in parallel.
>
>
> It should work Ok in parallel also. Can you try the
> latest
> development version of ASE+GPAW?
>
> Jens Jørgen
>
>
> Vardha.
>
>
> On Mon, Sep 11, 2017 at 3:02 PM, Jens Jørgen Mortensen
> <jjmo at dtu.dk <mailto:jjmo at dtu.dk>
> <mailto:jjmo at dtu.dk <mailto:jjmo at dtu.dk>> <mailto:jjmo at dtu.dk
> <mailto:jjmo at dtu.dk>
>
> <mailto:jjmo at dtu.dk <mailto:jjmo at dtu.dk>>>> wrote:
>
> On 09/10/2017 02:26 PM, Varadharajan
> Srinivasan via
> gpaw-users wrote:
>
> Dear all,
>
> I am trying to obtain all electron wave
> functions
> from a
> ground-state calculation on guanine. Having
> performed the GS
> calculation in domain parallel mode, I wrote a
> script to get
> the all electron wave function using the ps2ae
> utility. The
> code used is attached below. However, I
> get the
> following
> error. I have seen some similar posts in
> the forum
> but there
> was no response. I would greatly
> appreciate some
> advice on
> this issue.
>
>
> Does the script work OK when you run it in serial?
>
> Jens Jørgen
>
>
> Vardha.
> IISER Bhopal
> India
>
> Number of Atomic Orbitals: 49
>
> Number of Bands in Calculation: 50
>
> Bands to Converge: 40 Lowest Bands
>
> Number of Valence Electrons: 56
>
> rank=0 L00: Traceback (most recent call last):
>
> rank=0 L01: File "trial.py", line 19, in
> <module>
>
> rank=0 L02: wf =
> twf_gs.get_wave_function(band, ae=False)
>
> rank=0 L03: File
> "/opt/gpaw-intelmpi/lib/python2.7/site-packages/gpaw/utilities/ps2ae.py",
> line 97, in get_wave_function
>
> rank=0 L04: pad=True, periodic=True)
>
> rank=0 L05: File
> "/opt/gpaw-intelmpi/lib/python2.7/site-packages/gpaw/aseinterface.py",
> line 458, in get_pseudo_wave_function
>
> rank=0 L06: periodic=periodic)
>
> rank=0 L07: File
> "/opt/gpaw-intelmpi/lib/python2.7/site-packages/gpaw/aseinterface.py",
> line 465, in get_pseudo_wave_function
>
> rank=0 L08: periodic=periodic)
>
> rank=0 L09: File
> "/opt/gpaw-intelmpi/lib/python2.7/site-packages/gpaw/wavefunctions/base.py",
> line 404, in get_wave_function_array
>
> rank=0 L10: psit_G =
> self.gd.collect(psit_G)
>
> rank=0 L11: File
> "/opt/gpaw-intelmpi/lib/python2.7/site-packages/gpaw/grid_descriptor.py",
> line 502, in collect
>
> rank=0 L12: A_xg[..., b0:e0, b1:e1,
> b2:e2] = a_xg
>
> rank=0 L13: ValueError: could not
> broadcast input
> array from
> shape (115,107,83) into shape (23,53,83)
>
> GPAW CLEANUP (node 0): <type
> 'exceptions.ValueError'>
> occurred. Calling MPI_Abort!
>
> application called
> MPI_Abort(MPI_COMM_WORLD, 42) -
> process 0
>
>
>
>
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