[gpaw-users] calc.get_pseudo_wave_function error in tutorial "Creating wave function cube files"
Jens Jørgen Mortensen
jensj at fysik.dtu.dk
Fri Aug 1 15:03:18 CEST 2014
On 08/01/2014 02:56 PM, Pu ZHANG wrote:
> 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:
To fix this when it runs in parallel, we would need to see the script
that generated the gpw-file.
Jens Jørgen
>
> 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 <mailto: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 <mailto: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 <mailto: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
>> <mailto: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 <mailto:puzha at fotonik.dtu.dk>
>> Homepage:
>> http://www.dtu.dk/Service/Telefonbog/Person?id=91944&tab=0
>> Phone: 45 25 36 43 <tel:45%2025%2036%2043>
>> Fax: 45 93 65 81 <tel:45%2093%2065%2081>
>>
>>
>>
>>
>> _______________________________________________
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>
>
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