Re: Problem in dump.write for vector variables
I filed https://github.com/usnistgov/fipy/issues/691 to address this
> On Jan 9, 2020, at 8:34 AM, Guyer, Jonathan E. Dr. (Fed) via fipy
> wrote:
>
> Thank you for the feedback. I'm inclined to agree.
>
> - Jon
>
>> On Jan 9, 2020, at 3:47 AM, Marcel UJI (IMAP) wrote:
>>
>> Hi Jonathan
>>
>> Sorry by my late reply
>>
>> I think that the second one would be enough as I only need to read this data
>> later for further processing. Actually this is not much an issue, as I can
>> simply save phi and later recompute phi.faceGrad, which is also much more
>> economic in terms of storage.
>>
>> Thank you anyway for spending some time on this
>>
>> Marcel
>>
>>
>>
>> El 20/12/19 a les 16:27, Guyer, Jonathan E. Dr. (Fed) via fipy ha escrit:
>>> Glad you found a solution, Marcel.
>>>
>>> The issue is that a FaceGradVariable doesn't pickle itself properly. It
>>> stores the state for a generic FaceVariable, but then it doesn't know how
>>> to rebuild itself from that.
>>>
>>> It either should
>>> - pickle the correct information, which would also involve pickling phi
>>> OR
>>> - pickle itself as a plain FaceVariable, losing connection to phi on
>>> unpickling (which is what your solution does)
>>>
>>> Do you have an opinion on which behavior you'd like?
>>>
>>>
On Dec 20, 2019, at 2:35 AM, Marcel UJI (IMAP)
wrote:
Thank you Trevor,
This works, but it saves the array values only.
I found an alternative solution with:
dump.write({'E' :
FaceVariable(mesh=mesh,value=phi.faceGrad,rank=1)},filename='prova.gz',extension='.gz')
which preserves the FaceVariable character.
Merry Christmas!
Marcel
El 19/12/19 a les 19:04, Keller, Trevor (Fed) via fipy ha escrit:
> The error message indicates that `dump.read` got something unexpected
> -- namely, a `value` field -- and threw.
>
> Naïvely, dumping `phi.faceGrad.value` instea dof `phi.faceGrad`
> appears to do the trick.
>
>
>
--
Dr. Marcel Aguilella-Arzo
Professor Titular d'Universitat, Física Aplicada
Coordinador de la Subespecialitat de CCEETT del Màster en Professor
d'Educació Secundària
Departament de Física
Escola Superior de Tecnologia i Ciències Experimentals
Universitat Jaume I
Av. Sos Baynat, s/n
12071 Castelló de la Plana (Spain)
+34 964 728 046
a...@uji.es
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>> --
>> Dr. Marcel Aguilella-Arzo
>> Professor Titular d'Universitat, Física Aplicada
>> Coordinador de la Subespecialitat de CCEETT del Màster en Professor
>> d'Educació Secundària
>> Departament de Física
>> Escola Superior de Tecnologia i Ciències Experimentals
>> Universitat Jaume I
>> Av. Sos Baynat, s/n
>> 12071 Castelló de la Plana (Spain)
>> +34 964 728 046
>>
>> a...@uji.es
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Re: Problem in dump.write for vector variables
Thank you for the feedback. I'm inclined to agree.
- Jon
> On Jan 9, 2020, at 3:47 AM, Marcel UJI (IMAP) wrote:
>
> Hi Jonathan
>
> Sorry by my late reply
>
> I think that the second one would be enough as I only need to read this data
> later for further processing. Actually this is not much an issue, as I can
> simply save phi and later recompute phi.faceGrad, which is also much more
> economic in terms of storage.
>
> Thank you anyway for spending some time on this
>
> Marcel
>
>
>
> El 20/12/19 a les 16:27, Guyer, Jonathan E. Dr. (Fed) via fipy ha escrit:
>> Glad you found a solution, Marcel.
>>
>> The issue is that a FaceGradVariable doesn't pickle itself properly. It
>> stores the state for a generic FaceVariable, but then it doesn't know how to
>> rebuild itself from that.
>>
>> It either should
>> - pickle the correct information, which would also involve pickling phi
>> OR
>> - pickle itself as a plain FaceVariable, losing connection to phi on
>> unpickling (which is what your solution does)
>>
>> Do you have an opinion on which behavior you'd like?
>>
>>
>>> On Dec 20, 2019, at 2:35 AM, Marcel UJI (IMAP)
>>> wrote:
>>>
>>> Thank you Trevor,
>>>
>>> This works, but it saves the array values only.
>>>
>>> I found an alternative solution with:
>>>
>>> dump.write({'E' :
>>> FaceVariable(mesh=mesh,value=phi.faceGrad,rank=1)},filename='prova.gz',extension='.gz')
>>>
>>> which preserves the FaceVariable character.
>>>
>>> Merry Christmas!
>>>
>>> Marcel
>>>
>>>
>>>
>>> El 19/12/19 a les 19:04, Keller, Trevor (Fed) via fipy ha escrit:
>>>
The error message indicates that `dump.read` got something unexpected
-- namely, a `value` field -- and threw.
Naïvely, dumping `phi.faceGrad.value` instea dof `phi.faceGrad`
appears to do the trick.
>>> --
>>> Dr. Marcel Aguilella-Arzo
>>> Professor Titular d'Universitat, Física Aplicada
>>> Coordinador de la Subespecialitat de CCEETT del Màster en Professor
>>> d'Educació Secundària
>>> Departament de Física
>>> Escola Superior de Tecnologia i Ciències Experimentals
>>> Universitat Jaume I
>>> Av. Sos Baynat, s/n
>>> 12071 Castelló de la Plana (Spain)
>>> +34 964 728 046
>>>
>>>
>>> a...@uji.es
>>>
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>>> ]
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>>
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>> ]
>>
> --
> Dr. Marcel Aguilella-Arzo
> Professor Titular d'Universitat, Física Aplicada
> Coordinador de la Subespecialitat de CCEETT del Màster en Professor
> d'Educació Secundària
> Departament de Física
> Escola Superior de Tecnologia i Ciències Experimentals
> Universitat Jaume I
> Av. Sos Baynat, s/n
> 12071 Castelló de la Plana (Spain)
> +34 964 728 046
>
> a...@uji.es
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Re: Problem in dump.write for vector variables
Hi Jonathan
Sorry by my late reply
I think that the second one would be enough as I only need to read this
data later for further processing. Actually this is not much an issue,
as I can simply save phi and later recompute phi.faceGrad, which is also
much more economic in terms of storage.
Thank you anyway for spending some time on this
Marcel
El 20/12/19 a les 16:27, Guyer, Jonathan E. Dr. (Fed) via fipy ha escrit:
Glad you found a solution, Marcel.
The issue is that a FaceGradVariable doesn't pickle itself properly. It stores
the state for a generic FaceVariable, but then it doesn't know how to rebuild
itself from that.
It either should
- pickle the correct information, which would also involve pickling phi
OR
- pickle itself as a plain FaceVariable, losing connection to phi on unpickling
(which is what your solution does)
Do you have an opinion on which behavior you'd like?
On Dec 20, 2019, at 2:35 AM, Marcel UJI (IMAP) wrote:
Thank you Trevor,
This works, but it saves the array values only.
I found an alternative solution with:
dump.write({'E' :
FaceVariable(mesh=mesh,value=phi.faceGrad,rank=1)},filename='prova.gz',extension='.gz')
which preserves the FaceVariable character.
Merry Christmas!
Marcel
El 19/12/19 a les 19:04, Keller, Trevor (Fed) via fipy ha escrit:
The error message indicates that `dump.read` got something unexpected
-- namely, a `value` field -- and threw.
Naïvely, dumping `phi.faceGrad.value` instea dof `phi.faceGrad`
appears to do the trick.
--
Dr. Marcel Aguilella-Arzo
Professor Titular d'Universitat, Física Aplicada
Coordinador de la Subespecialitat de CCEETT del Màster en Professor d'Educació
Secundària
Departament de Física
Escola Superior de Tecnologia i Ciències Experimentals
Universitat Jaume I
Av. Sos Baynat, s/n
12071 Castelló de la Plana (Spain)
+34 964 728 046
a...@uji.es
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--
Dr. Marcel Aguilella-Arzo
Professor Titular d'Universitat, Física Aplicada
Coordinador de la Subespecialitat de CCEETT del Màster en Professor d'Educació
Secundària
Departament de Física
Escola Superior de Tecnologia i Ciències Experimentals
Universitat Jaume I
Av. Sos Baynat, s/n
12071 Castelló de la Plana (Spain)
+34 964 728 046
a...@uji.es
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Re: Problem in dump.write for vector variables
Glad you found a solution, Marcel.
The issue is that a FaceGradVariable doesn't pickle itself properly. It stores
the state for a generic FaceVariable, but then it doesn't know how to rebuild
itself from that.
It either should
- pickle the correct information, which would also involve pickling phi
OR
- pickle itself as a plain FaceVariable, losing connection to phi on unpickling
(which is what your solution does)
Do you have an opinion on which behavior you'd like?
> On Dec 20, 2019, at 2:35 AM, Marcel UJI (IMAP) wrote:
>
> Thank you Trevor,
>
> This works, but it saves the array values only.
>
> I found an alternative solution with:
>
> dump.write({'E' :
> FaceVariable(mesh=mesh,value=phi.faceGrad,rank=1)},filename='prova.gz',extension='.gz')
>
> which preserves the FaceVariable character.
>
> Merry Christmas!
>
> Marcel
>
>
>
> El 19/12/19 a les 19:04, Keller, Trevor (Fed) via fipy ha escrit:
>> The error message indicates that `dump.read` got something unexpected
>> -- namely, a `value` field -- and threw.
>>
>> Naïvely, dumping `phi.faceGrad.value` instea dof `phi.faceGrad`
>> appears to do the trick.
>>
>>
> --
> Dr. Marcel Aguilella-Arzo
> Professor Titular d'Universitat, Física Aplicada
> Coordinador de la Subespecialitat de CCEETT del Màster en Professor
> d'Educació Secundària
> Departament de Física
> Escola Superior de Tecnologia i Ciències Experimentals
> Universitat Jaume I
> Av. Sos Baynat, s/n
> 12071 Castelló de la Plana (Spain)
> +34 964 728 046
>
> a...@uji.es
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> fipy mailing list
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> [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ]
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Re: Problem in dump.write for vector variables
Thank you Trevor,
This works, but it saves the array values only.
I found an alternative solution with:
dump.write({'E' :
FaceVariable(mesh=mesh,value=phi.faceGrad,rank=1)},filename='prova.gz',extension='.gz')
which preserves the FaceVariable character.
Merry Christmas!
Marcel
El 19/12/19 a les 19:04, Keller, Trevor (Fed) via fipy ha escrit:
The error message indicates that `dump.read` got something unexpected
-- namely, a `value` field -- and threw.
Naïvely, dumping `phi.faceGrad.value` instea dof `phi.faceGrad`
appears to do the trick.
--
Dr. Marcel Aguilella-Arzo
Professor Titular d'Universitat, Física Aplicada
Coordinador de la Subespecialitat de CCEETT del Màster en Professor d'Educació
Secundària
Departament de Física
Escola Superior de Tecnologia i Ciències Experimentals
Universitat Jaume I
Av. Sos Baynat, s/n
12071 Castelló de la Plana (Spain)
+34 964 728 046
a...@uji.es
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Re: Problem in dump.write for vector variables
The error message indicates that `dump.read` got something unexpected
-- namely, a `value` field -- and threw.
Naïvely, dumping `phi.faceGrad.value` instea dof `phi.faceGrad`
appears to do the trick.
--
Trevor Keller, Ph.D.
Materials Science and Engineering Division
National Institute of Standards and Technology
100 Bureau Dr. MS 8550; Gaithersburg, MD 20899
Office: 223/A131 or (301) 975-2889
On Thu, Dec 19, 2019 at 04:26:07PM +0100, Marcel UJI wrote:
>I'm getting errors dumping vector variables in fipy. This minimal code
>shows the problem:
>
>from fipy import *
>
>mesh=Grid3D(nx=10,ny=10,nz=10)
>
>phi=CellVariable(mesh=mesh,value=(mesh.x*mesh.y))
>
>dump.write({'E' : (phi.faceGrad)},filename='prova.gz',extension='.gz')
>
>fitxer=dump.read('prova.gz')
>
>produces:
>
>---
>
>TypeError Traceback (most recent call
>last)
> in ()
>> 1 fitxer=dump.read('prova.gz')
>/home/marcel/.local/lib/python2.7/site-packages/fipy/tools/dump.pyc in
>read(filename, fileobject, communicator, mesh_unmangle)
>123 unpickler.find_global = find_class
>124
>--> 125 return unpickler.load()
>126
>127 def _test():
>/usr/lib/python2.7/pickle.pyc in load(self)
>862 while 1:
>863 key = read(1)
>--> 864 dispatch[key](self)
>865 except _Stop, stopinst:
>866 return stopinst.value
>/usr/lib/python2.7/pickle.pyc in load_build(self)
> 1221 setstate = getattr(inst, "__setstate__", None)
> 1222 if setstate:
>-> 1223 setstate(state)
> 1224 return
> 1225 slotstate = None
>/home/marcel/.local/lib/python2.7/site-packages/fipy/variables/variable
>.pyc in __setstate__(self, dict)
> 1525 self._refcount = sys.getrefcount(self)
> 1526
>-> 1527 self.__init__(**dict)
> 1528
> 1529 def _test(self):
>TypeError: __init__() got an unexpected keyword argument 'value'
>
>Any idea on what is wrong in this code??
>
>Marcel
> --
> Dr. Marcel Aguilella-Arzo
> Professor Titular d'Universitat, Física Aplicada
> Coordinador de la Subcomissió d'Especialitat de Ciències Experimentals i
> Tecnolo
> gia
> del Màster Universitari en Professor d'Educació Secundària Obligatòria i
> Batxill
> erat,
> Formació Professional i Ensenyament d'Idiomes
> Departament de Física
> Escola Superior de Tecnologia i Ciències Experimentals
> Universitat Jaume I
> Av. Sos Baynat, s/n
> 12071 Castelló de la Plana (Spain)
> +34 964 728 046
> [1]a...@fca.uji.es
>
> References
>
>1. mailto:a...@fca.uji.es
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