[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 15:26:11 CEST 2014
On 08/01/2014 03:10 PM, Pu ZHANG wrote:
> I'm sorry I'm not sure which script you are referring to. Do you mean
> the script used for compilation?
No, the cubeWF.py script will read a gpw-file and write cube files (I'm
guessing). To debug this, I would need your gpw-file or a script that
can calculate it.
Jens Jørgen
> Then I'm using the gpaw compiled previously by our cluster
> administrator. I don't know the details.
>
> 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, Aug 1, 2014 at 3:03 PM, Jens Jørgen Mortensen
> <jensj at fysik.dtu.dk <mailto:jensj at fysik.dtu.dk>> wrote:
>
>
> 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>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> gpaw-users mailing list
>>> gpaw-users at listserv.fysik.dtu.dk <mailto:gpaw-users at listserv.fysik.dtu.dk>
>>> https://listserv.fysik.dtu.dk/mailman/listinfo/gpaw-users
>>
>>
>
>
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