[gpaw-users] calc.get_pseudo_wave_function error in tutorial "Creating wave function cube files"

[Pu ZHANG]

Hi, Jens!

Thanks a lot for the reply!

Yes, I was running in parallel. And it does work if I use only one
processor. The script is as follows:

job script
-------------
#!/bin/bash
#PBS -N cubeWF
#PBS -e $PBS_JOBNAME.$PBS_JOBID.err
#PBS -o $PBS_JOBNAME.$PBS_JOBID.log
#PBS -q fotonano
#PBS -A fotonano
#PBS -l nodes=1:ppn=2
#PBS -l walltime=02:00:00

source $PBS_O_HOME/.bashrc
module purge
module load npa-cluster-setup

ulimit -s unlimited
cd $PBS_O_WORKDIR

module load python2.7.numpy.scipy.scientific.ase.gpaw.inelastica
module load gpaw-setups/0.9.9672
xc=`which xc-info`
xc_h=$(dirname $(dirname $xc))
export LD_LIBRARY_PATH=$xc_h/lib:$LD_LIBRARY_PATH

m=`which mpirun`
m_h=$(dirname $(dirname $m))
export LD_LIBRARY_PATH=$m_h/lib:$LD_LIBRARY_PATH

export GPAW_FFTWSO="libmkl_intel_lp64.so"

mpirun -np $PBS_NP gpaw-python "cubeWF.py" > RUN.out
-------------

Best regards, Pu Zhang
--
Postdoc
The group of Structured Electromagnetic Materials
Department of Photonics Engineering
Technical University of Denmark
Ørsteds Plads, Building 345v, 166
2800, Kgs. Lyngby
E-mail: puzha at fotonik.dtu.dk
Homepage: http://www.dtu.dk/Service/Telefonbog/Person?id=91944&tab=0
Phone: 45 25 36 43
Fax: 45 93 65 81


On Fri, Aug 1, 2014 at 2:38 PM, Jens Jørgen Mortensen <jensj at fysik.dtu.dk>
wrote:

>  On 07/28/2014 05:13 PM, Pu ZHANG wrote:
>
> From the error information it seems something's wrong with the argument
> when calling the function get_pseudo_wave_function. But I searched around
> and couldn't figure out the problem. Have anyone ever had such a problem?
>
>
> Are you running this in parallel?  If yes - then try running it in serial.
> Could you show us your input script?
>
> Jens Jørgen
>
>
>  Thanks!
>
>   Best regards, Pu Zhang
>  --
> Postdoc
> The group of Structured Electromagnetic Materials
>  Department of Photonics Engineering
> Technical University of Denmark
> Ørsteds Plads, Building 345v, 166
>  2800, Kgs. Lyngby
> E-mail: puzha at fotonik.dtu.dk
> Homepage: http://www.dtu.dk/Service/Telefonbog/Person?id=91944&tab=0
> Phone: 45 25 36 43
> Fax: 45 93 65 81
>
>
> On Fri, Jul 25, 2014 at 3:06 PM, Pu ZHANG <puzhang0702 at gmail.com> wrote:
>
>>  Dear all,
>>
>>  Execution of the tutorial example "Creating wave function cube files"
>> leads to error related to calc.get_pseudo_wave_function.
>>
>>  The script is
>> https://wiki.fysik.dtu.dk/gpaw/tutorials/plotting/plot_wave_functions.html,
>> and the error message looks like:
>>
>>  Traceback (most recent call last):
>>   File "cubeWF.py", line 14, in <module>
>>     wf = calc.get_pseudo_wave_function(band=band)
>>   File
>> "/zdata/groups/common/nicpa/2014-may/XeonX5550/python/2.7.6/packages/gpaw/0.10.0.11364/intel-14.0.1/lib/python2.7/site-packages/gpaw/aseinterface.py",
>> line 407, in get_pseudo_wave_function
>>     pad=False)
>>   File
>> "/zdata/groups/common/nicpa/2014-may/XeonX5550/python/2.7.6/packages/gpaw/0.10.0.11364/intel-14.0.1/lib/python2.7/site-packages/gpaw/aseinterface.py",
>> line 412, in get_pseudo_wave_function
>>     psit_G = self.wfs.get_wave_function_array(band, kpt, spin)
>>   File
>> "/zdata/groups/common/nicpa/2014-may/XeonX5550/python/2.7.6/packages/gpaw/0.10.0.11364/intel-14.0.1/lib/python2.7/site-packages/gpaw/wavefunctions/base.py",
>> line 401, in get_wave_function_array
>>     psit_G = self.gd.collect(psit_G)
>>   File
>> "/zdata/groups/common/nicpa/2014-may/XeonX5550/python/2.7.6/packages/gpaw/0.10.0.11364/intel-14.0.1/lib/python2.7/site-packages/gpaw/grid_descriptor.py",
>> line 459, in collect
>>     A_xg[..., b0:e0, b1:e1, b2:e2] = a_xg
>> ValueError: could not broadcast input array from shape (23,23,23) into
>> shape (11,23,23)
>> GPAW CLEANUP (node 0): <type 'exceptions.ValueError'> occurred.  Calling
>> MPI_Abort!
>> [n-62-13-7:00605] 1 more process has sent help message
>> help-mpi-runtime.txt / mpi_init:warn-fork
>> [n-62-13-7:00605] Set MCA parameter "orte_base_help_aggregate" to 0 to
>> see all help / error messages
>>
>>  Any idea? Is there extra information shall I provide to help diagnose
>> the problem?
>>
>>  Thanks!
>>   Best regards, Pu Zhang
>>  --
>> Postdoc
>> The group of Structured Electromagnetic Materials
>>  Department of Photonics Engineering
>> Technical University of Denmark
>> Ørsteds Plads, Building 345v, 166
>>  2800, Kgs. Lyngby
>> E-mail: puzha at fotonik.dtu.dk
>> Homepage: http://www.dtu.dk/Service/Telefonbog/Person?id=91944&tab=0
>> Phone: 45 25 36 43 <45%2025%2036%2043>
>> Fax: 45 93 65 81 <45%2093%2065%2081>
>>
>
>
>
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