[yt-users] Ramses without hydro
Marcelo Vargas dos Santos
marcelovsrj at gmail.com
Tue Apr 15 08:56:28 PDT 2014
I thinking that is almost well. I recieved the error message that you
espected.
Do you know how i can fix it?
Thank you
yt : [WARNING ] 2014-04-15 12:53:57,895 RAMSES frontend assumes all
simulations are cosmological!
yt : [INFO ] 2014-04-15 12:53:57,916 Parameters: current_time
= -3.65552566796e+15
yt : [INFO ] 2014-04-15 12:53:57,916 Parameters: domain_dimensions
= [128 128 128]
yt : [INFO ] 2014-04-15 12:53:57,917 Parameters: domain_left_edge
= [ 0. 0. 0.]
yt : [INFO ] 2014-04-15 12:53:57,917 Parameters: domain_right_edge
= [ 1. 1. 1.]
yt : [INFO ] 2014-04-15 12:53:57,918 Parameters:
cosmological_simulation = 1
yt : [INFO ] 2014-04-15 12:53:57,918 Parameters: current_redshift
= 49.9999981951
yt : [INFO ] 2014-04-15 12:53:57,918 Parameters: omega_lambda
= 0.723999977112
yt : [INFO ] 2014-04-15 12:53:57,918 Parameters: omega_matter
= 0.275999993086
yt : [INFO ] 2014-04-15 12:53:57,918 Parameters: hubble_constant
= 0.738000030518
yt : [INFO ] 2014-04-15 12:53:58,300 Loading field plugins.
yt : [INFO ] 2014-04-15 12:53:58,300 Loaded angular_momentum (8 new
fields)
yt : [INFO ] 2014-04-15 12:53:58,302 Loaded astro (14 new fields)
yt : [INFO ] 2014-04-15 12:53:58,302 Loaded cosmology (20 new fields)
yt : [INFO ] 2014-04-15 12:53:58,302 Loaded fluid (56 new fields)
yt : [INFO ] 2014-04-15 12:53:58,303 Loaded fluid_vector (88 new fields)
yt : [INFO ] 2014-04-15 12:53:58,303 Loaded geometric (103 new fields)
yt : [INFO ] 2014-04-15 12:53:58,303 Loaded local (103 new fields)
yt : [INFO ] 2014-04-15 12:53:58,303 Loaded magnetic_field (109 new
fields)
yt : [WARNING ] 2014-04-15 12:53:58,391 No particle_type, no
creation_time, so not distinguishing.
---------------------------------------------------------------------------
YTFieldNotFound Traceback (most recent call last)
/home/marcelo/anaconda/lib/python2.7/site-packages/IPython/utils/py3compat.pyc
in execfile(fname, *where)
202 else:
203 filename = fname
--> 204 __builtin__.execfile(filename, *where)
/home/marcelo/Simulations/NBody/Ramses/branches/ramses_omp/run1/plot.py in
<module>()
12
13 ds = load(files[0])
---> 14 halos = HaloFinder(ds)
15 #print ds.parameters
16 #print "\n"
/home/marcelo/yt/yt/analysis_modules/halo_finding/halo_objects.pyc in
__init__(self, pf, subvolume, threshold, dm_only, padding, total_mass)
2387 select = self._get_dm_indices()
2388 total_mass = \
-> 2389
self.comm.mpi_allreduce((self._data_source['all',
"ParticleMassMsun"][select]).sum(dtype='float64'), op='sum')
2390 else:
2391 total_mass =
self.comm.mpi_allreduce(self._data_source.quantities["TotalQuantity"]("ParticleMassMsun")[0],
op='sum')
/home/marcelo/yt/yt/data_objects/data_containers.pyc in __getitem__(self,
key)
203 Returns a single field. Will add if necessary.
204 """
--> 205 f = self._determine_fields([key])[0]
206 if f not in self.field_data and key not in self.field_data:
207 if f in self._container_fields:
/home/marcelo/yt/yt/data_objects/data_containers.pyc in
_determine_fields(self, fields)
451 raise YTFieldNotParseable(field)
452 ftype, fname = field
--> 453 finfo = self.pf._get_field_info(ftype, fname)
454 else:
455 fname = field
/home/marcelo/yt/yt/data_objects/static_output.pyc in _get_field_info(self,
ftype, fname)
487 self._last_finfo = self.field_info[(ftype,
fname)]
488 return self._last_finfo
--> 489 raise YTFieldNotFound((ftype, fname), self)
490
491 def _setup_classes(self):
YTFieldNotFound: Could not find field '('all', 'ParticleMassMsun')' in
info_00001.
On 15 April 2014 10:24, Sam Geen <samgeen at astro.ox.ac.uk> wrote:
> Hi Marcelo,
>
> I believe a fix has been merged into the branch yt-3.0 of the yt
> repository, i.e. call:
>
> hg pull && hg update yt-3.0
>
> Let me know if this works for you or if it throws an exception again. Note
> that I believe the particle field names have been updated recently (e.g.
> particle_mass instead of ParticleMassMsun), so be careful with that.
>
> Cheers,
>
> Sam
>
>
> On 14/04/2014 23:19, Sam Geen wrote:
>
> OK, my local version wasn't up to date, which is why I was confused
> before. There seems to be a check for a hydro file (line 370 of
> data_structures.py) but I don't think it'd work (it's a check against a
> string, not against an os.path.exists call), and it'd only run if you're
> checking for fields. I suspect it's a bug in the latest version of the
> RAMSES frontend, and we should check that yt doesn't throw an error if you
> try to feed it a particle-only dataset, i.e. do a check for a
> "hydro_?????.out00001" file, and only read if it exists. If I get time
> tomorrow I might try to take a look.
>
> On 14/04/14 22:59, Marcelo Vargas dos Santos wrote:
>
> yt module located at:
> /home/marcelo/Downloads/yt-x86_64/src/yt-hg
> The supplemental repositories are located at:
> /home/marcelo/Downloads/yt-x86_64/src/yt-supplemental
> aviso: ignorando pai desconhecido do diretório de trabalho '794b2beb2c48'!
>
> The current version of the code is:
>
> ---
> 000000000000
> ---
>
> This installation CAN be automatically updated.
> yt dependencies were last updated on
> Qui Abr 10 19:15:16 BRT 2014
>
> To update all dependencies, run "yt update --all".
>
>
>
> On 14 April 2014 17:57, Nathan Goldbaum <nathan12343 at gmail.com> wrote:
>
>> Hi Marcelo,
>>
>> Can you tell us the output of 'yt instinfo' run from the command line?
>> That will give more precise version information.
>>
>> -Nathan
>>
>>
>> On Mon, Apr 14, 2014 at 1:56 PM, Marcelo Vargas dos Santos <
>> marcelovsrj at gmail.com> wrote:
>>
>>> Sorry, i'm using the Bleeding Edge version. There's no 4.0.0
>>>
>>>
>>> On 14 April 2014 17:55, Marcelo Vargas dos Santos <marcelovsrj at gmail.com
>>> > wrote:
>>>
>>>> I'm using the yt-4.0.0.
>>>>
>>>>
>>>> On 14 April 2014 17:53, Sam Geen <samgeen at astro.ox.ac.uk> wrote:
>>>>
>>>>> Out of interest, Marcelo, what version are you using? I just looked at
>>>>> the yt-3.0 code and it looks a little different, and doesn't seem to rely
>>>>> on hydro files existing as your log suggests. If you're not using yt-3.0
>>>>> it's definitely worth trying it for the RAMSES module.
>>>>>
>>>>>
>>>>> On 14/04/14 22:17, Kim, Ji-hoon wrote:
>>>>>
>>>>>> Dear Marcelo,
>>>>>>
>>>>>> As noted by Matt, you may want to take a look at the yt script that
>>>>>> was developed and used by the AGORA collaboration, to analyze the dark
>>>>>> matter-only simulations of various astrophysical codes including Ramses.
>>>>>>
>>>>>> https://bitbucket.org/mornkr/agora-analysis-script/src/655e46d0b3a06d2e6da222a0f50f79ca5da3b48f/script-Flagship-DM.py?at=default
>>>>>>
>>>>>> Thank you very much.
>>>>>>
>>>>>> Best wishes,
>>>>>> Ji-hoon
>>>>>>
>>>>>>
>>>>>>
>>>>>> -------------------------------------------------------------------------
>>>>>> Ji-hoon Kim
>>>>>> Postdoctoral Scholar in Astrophysics at Caltech
>>>>>> www.jihoonkim.org
>>>>>> me at jihoonkim.org / 1(650)714-2879
>>>>>>
>>>>>> -------------------------------------------------------------------------
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Apr 14, 2014, at 12:57 PM, Matthew Turk <matthewturk at gmail.com>
>>>>>> wrote:
>>>>>>
>>>>>> Hi Marcelo,
>>>>>>>
>>>>>>> Sorry to hear you're having trouble. I haven't done much with RAMSES
>>>>>>> dark matter only simulations, but I think that Ji-hoon Kim may have
>>>>>>> in
>>>>>>> support of the AGORA project. Additionally, others here might have
>>>>>>> some experience.
>>>>>>>
>>>>>>> In general, we are happy to help get things working and running --
>>>>>>> this seems like a genuine bug which we will need to address. Can you
>>>>>>> post the full traceback?
>>>>>>>
>>>>>>> -Matt
>>>>>>>
>>>>>>> On Mon, Apr 14, 2014 at 3:45 PM, Marcelo Vargas dos Santos
>>>>>>> <marcelovsrj at gmail.com> wrote:
>>>>>>>
>>>>>>>> I'm trying to use HaloFinders on a ramses simulation without hydro.
>>>>>>>> but it's
>>>>>>>> not working. Tha error message is:
>>>>>>>>
>>>>>>>> No such file or directory:
>>>>>>>>
>>>>>>>> '/home/marcelo/Simulations/NBody/Ramses/branches/ramses_omp/run1/output_00001/hydro_00001.out00001'
>>>>>>>>
>>>>>>>> someone know how to fix it?
>>>>>>>>
>>>>>>>> Best.
>>>>>>>>
>>>>>>>> --
>>>>>>>> Marcelo Vargas dos Santos
>>>>>>>> Professor e Doutorando
>>>>>>>>
>>>>>>>> Sala A 318-05
>>>>>>>> Tel.: (21) 2562-7276 <%2821%29%202562-7276>
>>>>>>>> E-mails: vargas at if.ufrj.br, marcelovsrj at gmail.com
>>>>>>>> Departamento de Física Teórica - Instituto de Física
>>>>>>>> Universidade Federal do Rio de Janeiro
>>>>>>>>
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>>>>
>>>> --
>>>> Marcelo Vargas dos Santos
>>>> Professor e Doutorando
>>>>
>>>> Sala A 318-05
>>>> Tel.: (21) 2562-7276 <%2821%29%202562-7276>
>>>> E-mails: vargas at if.ufrj.br, marcelovsrj at gmail.com
>>>> Departamento de Física Teórica - Instituto de Física
>>>> Universidade Federal do Rio de Janeiro
>>>>
>>>
>>>
>>>
>>> --
>>> Marcelo Vargas dos Santos
>>> Professor e Doutorando
>>>
>>> Sala A 318-05
>>> Tel.: (21) 2562-7276 <%2821%29%202562-7276>
>>> E-mails: vargas at if.ufrj.br, marcelovsrj at gmail.com
>>> Departamento de Física Teórica - Instituto de Física
>>> Universidade Federal do Rio de Janeiro
>>>
>>> _______________________________________________
>>> yt-users mailing list
>>> yt-users at lists.spacepope.org
>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>
>>>
>>
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>
>
> --
> Marcelo Vargas dos Santos
> Professor e Doutorando
>
> Sala A 318-05
> Tel.: (21) 2562-7276
> E-mails: vargas at if.ufrj.br, marcelovsrj at gmail.com
> Departamento de Física Teórica - Instituto de Física
> Universidade Federal do Rio de Janeiro
>
>
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--
Marcelo Vargas dos Santos
Professor e Doutorando
Sala A 318-05
Tel.: (21) 2562-7276
E-mails: vargas at if.ufrj.br, marcelovsrj at gmail.com
Departamento de Física Teórica - Instituto de Física
Universidade Federal do Rio de Janeiro
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