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 E-mails: vargas@if.ufrj.br, marcelovsrj@gmail.com Departamento de Física Teórica - Instituto de Física Universidade Federal do Rio de Janeiro
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@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 E-mails: vargas@if.ufrj.br, marcelovsrj@gmail.com Departamento de Física Teórica - Instituto de Física Universidade Federal do Rio de Janeiro
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
Attached. Good luck On 14 April 2014 16:57, Matthew Turk <matthewturk@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@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 E-mails: vargas@if.ufrj.br, marcelovsrj@gmail.com Departamento de Física Teórica - Instituto de Física Universidade Federal do Rio de Janeiro
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
-- Marcelo Vargas dos Santos Professor e Doutorando Sala A 318-05 Tel.: (21) 2562-7276 E-mails: vargas@if.ufrj.br, marcelovsrj@gmail.com Departamento de Física Teórica - Instituto de Física Universidade Federal do Rio de Janeiro
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/655e46d0b3a06d2e6da22... Thank you very much. Best wishes, Ji-hoon ------------------------------------------------------------------------- Ji-hoon Kim Postdoctoral Scholar in Astrophysics at Caltech www.jihoonkim.org me@jihoonkim.org / 1(650)714-2879 ------------------------------------------------------------------------- On Apr 14, 2014, at 12:57 PM, Matthew Turk <matthewturk@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@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 E-mails: vargas@if.ufrj.br, marcelovsrj@gmail.com Departamento de Física Teórica - Instituto de Física Universidade Federal do Rio de Janeiro
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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/655e46d0b3a06d2e6da22...
Thank you very much.
Best wishes, Ji-hoon
------------------------------------------------------------------------- Ji-hoon Kim Postdoctoral Scholar in Astrophysics at Caltech www.jihoonkim.org me@jihoonkim.org / 1(650)714-2879 -------------------------------------------------------------------------
On Apr 14, 2014, at 12:57 PM, Matthew Turk <matthewturk@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@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 E-mails: vargas@if.ufrj.br, marcelovsrj@gmail.com Departamento de Física Teórica - Instituto de Física Universidade Federal do Rio de Janeiro
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
I'm using the yt-4.0.0. On 14 April 2014 17:53, Sam Geen <samgeen@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@jihoonkim.org / 1(650)714-2879 -------------------------------------------------------------------------
On Apr 14, 2014, at 12:57 PM, Matthew Turk <matthewturk@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@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 E-mails: vargas@if.ufrj.br, marcelovsrj@gmail.com Departamento de Física Teórica - Instituto de Física Universidade Federal do Rio de Janeiro
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
-- Marcelo Vargas dos Santos Professor e Doutorando Sala A 318-05 Tel.: (21) 2562-7276 E-mails: vargas@if.ufrj.br, marcelovsrj@gmail.com Departamento de Física Teórica - Instituto de Física Universidade Federal do Rio de Janeiro
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@gmail.com>wrote:
I'm using the yt-4.0.0.
On 14 April 2014 17:53, Sam Geen <samgeen@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@jihoonkim.org / 1(650)714-2879 ------------------------------------------------------------ -------------
On Apr 14, 2014, at 12:57 PM, Matthew Turk <matthewturk@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@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 E-mails: vargas@if.ufrj.br, marcelovsrj@gmail.com Departamento de Física Teórica - Instituto de Física Universidade Federal do Rio de Janeiro
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
-- Marcelo Vargas dos Santos Professor e Doutorando
Sala A 318-05 Tel.: (21) 2562-7276 E-mails: vargas@if.ufrj.br, marcelovsrj@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 E-mails: vargas@if.ufrj.br, marcelovsrj@gmail.com Departamento de Física Teórica - Instituto de Física Universidade Federal do Rio de Janeiro
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@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@gmail.com>wrote:
I'm using the yt-4.0.0.
On 14 April 2014 17:53, Sam Geen <samgeen@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@jihoonkim.org / 1(650)714-2879 ------------------------------------------------------------ -------------
On Apr 14, 2014, at 12:57 PM, Matthew Turk <matthewturk@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@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 E-mails: vargas@if.ufrj.br, marcelovsrj@gmail.com Departamento de Física Teórica - Instituto de Física Universidade Federal do Rio de Janeiro
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
-- Marcelo Vargas dos Santos Professor e Doutorando
Sala A 318-05 Tel.: (21) 2562-7276 E-mails: vargas@if.ufrj.br, marcelovsrj@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 E-mails: vargas@if.ufrj.br, marcelovsrj@gmail.com Departamento de Física Teórica - Instituto de Física Universidade Federal do Rio de Janeiro
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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@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@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@gmail.com>wrote:
I'm using the yt-4.0.0.
On 14 April 2014 17:53, Sam Geen <samgeen@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@jihoonkim.org / 1(650)714-2879 ------------------------------------------------------------ -------------
On Apr 14, 2014, at 12:57 PM, Matthew Turk <matthewturk@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@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 > E-mails: vargas@if.ufrj.br, marcelovsrj@gmail.com > Departamento de Física Teórica - Instituto de Física > Universidade Federal do Rio de Janeiro > > _______________________________________________ > yt-users mailing list > yt-users@lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
-- Marcelo Vargas dos Santos Professor e Doutorando
Sala A 318-05 Tel.: (21) 2562-7276 E-mails: vargas@if.ufrj.br, marcelovsrj@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 E-mails: vargas@if.ufrj.br, marcelovsrj@gmail.com Departamento de Física Teórica - Instituto de Física Universidade Federal do Rio de Janeiro
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
-- Marcelo Vargas dos Santos Professor e Doutorando Sala A 318-05 Tel.: (21) 2562-7276 E-mails: vargas@if.ufrj.br, marcelovsrj@gmail.com Departamento de Física Teórica - Instituto de Física Universidade Federal do Rio de Janeiro
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@gmail.com <mailto:nathan12343@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@gmail.com <mailto:marcelovsrj@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@gmail.com <mailto:marcelovsrj@gmail.com>> wrote:
I'm using the yt-4.0.0.
On 14 April 2014 17:53, Sam Geen <samgeen@astro.ox.ac.uk <mailto:samgeen@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/655e46d0b3a06d2e6da22...
Thank you very much.
Best wishes, Ji-hoon
------------------------------------------------------------------------- Ji-hoon Kim Postdoctoral Scholar in Astrophysics at Caltech www.jihoonkim.org <http://www.jihoonkim.org> me@jihoonkim.org <mailto:me@jihoonkim.org> / 1(650)714-2879 <tel:1%28650%29714-2879> -------------------------------------------------------------------------
On Apr 14, 2014, at 12:57 PM, Matthew Turk <matthewturk@gmail.com <mailto:matthewturk@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@gmail.com <mailto:marcelovsrj@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 <tel:%2821%29%202562-7276> E-mails: vargas@if.ufrj.br <mailto:vargas@if.ufrj.br>, marcelovsrj@gmail.com <mailto:marcelovsrj@gmail.com> Departamento de Física Teórica - Instituto de Física Universidade Federal do Rio de Janeiro
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Sala A 318-05 Tel.: (21) 2562-7276 <tel:%2821%29%202562-7276> E-mails: vargas@if.ufrj.br <mailto:vargas@if.ufrj.br>, marcelovsrj@gmail.com <mailto:marcelovsrj@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 <tel:%2821%29%202562-7276> E-mails: vargas@if.ufrj.br <mailto:vargas@if.ufrj.br>, marcelovsrj@gmail.com <mailto:marcelovsrj@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@if.ufrj.br <mailto:vargas@if.ufrj.br>, marcelovsrj@gmail.com <mailto:marcelovsrj@gmail.com> Departamento de Física Teórica - Instituto de Física Universidade Federal do Rio de Janeiro
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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@gmail.com <mailto:nathan12343@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@gmail.com <mailto:marcelovsrj@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@gmail.com <mailto:marcelovsrj@gmail.com>> wrote:
I'm using the yt-4.0.0.
On 14 April 2014 17:53, Sam Geen <samgeen@astro.ox.ac.uk <mailto:samgeen@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/655e46d0b3a06d2e6da22...
Thank you very much.
Best wishes, Ji-hoon
------------------------------------------------------------------------- Ji-hoon Kim Postdoctoral Scholar in Astrophysics at Caltech www.jihoonkim.org <http://www.jihoonkim.org> me@jihoonkim.org <mailto:me@jihoonkim.org> / 1(650)714-2879 <tel:1%28650%29714-2879> -------------------------------------------------------------------------
On Apr 14, 2014, at 12:57 PM, Matthew Turk <matthewturk@gmail.com <mailto:matthewturk@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@gmail.com <mailto:marcelovsrj@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 <tel:%2821%29%202562-7276> E-mails: vargas@if.ufrj.br <mailto:vargas@if.ufrj.br>, marcelovsrj@gmail.com <mailto:marcelovsrj@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 <tel:%2821%29%202562-7276> E-mails: vargas@if.ufrj.br <mailto:vargas@if.ufrj.br>, marcelovsrj@gmail.com <mailto:marcelovsrj@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 <tel:%2821%29%202562-7276> E-mails: vargas@if.ufrj.br <mailto:vargas@if.ufrj.br>, marcelovsrj@gmail.com <mailto:marcelovsrj@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@if.ufrj.br <mailto:vargas@if.ufrj.br>, marcelovsrj@gmail.com <mailto:marcelovsrj@gmail.com> Departamento de Física Teórica - Instituto de Física Universidade Federal do Rio de Janeiro
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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@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@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@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@gmail.com
wrote:
I'm using the yt-4.0.0.
On 14 April 2014 17:53, Sam Geen <samgeen@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/655e46d0b3a06d2e6da22...
Thank you very much.
Best wishes, Ji-hoon
------------------------------------------------------------------------- Ji-hoon Kim Postdoctoral Scholar in Astrophysics at Caltech www.jihoonkim.org me@jihoonkim.org / 1(650)714-2879
-------------------------------------------------------------------------
On Apr 14, 2014, at 12:57 PM, Matthew Turk <matthewturk@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@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@if.ufrj.br, marcelovsrj@gmail.com >> Departamento de Física Teórica - Instituto de Física >> Universidade Federal do Rio de Janeiro >> >> _______________________________________________ >> yt-users mailing list >> yt-users@lists.spacepope.org >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >> >> _______________________________________________ > yt-users mailing list > yt-users@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 <%2821%29%202562-7276> E-mails: vargas@if.ufrj.br, marcelovsrj@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@if.ufrj.br, marcelovsrj@gmail.com Departamento de Física Teórica - Instituto de Física Universidade Federal do Rio de Janeiro
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_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
-- Marcelo Vargas dos Santos Professor e Doutorando
Sala A 318-05 Tel.: (21) 2562-7276 E-mails: vargas@if.ufrj.br, marcelovsrj@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@if.ufrj.br, marcelovsrj@gmail.com Departamento de Física Teórica - Instituto de Física Universidade Federal do Rio de Janeiro
Hi Marcelo, You need to replace "ParticleMassMsun" with "particle_mass". With yt 3.0 we've switched to a new field naming scheme that we think is much nicer to work with and more rational. Basically, CamelCase field names like ParticleMass are replaced with lower_case_underscore names like particle_mass. With the new unit system we've also eliminated redundant field names that are only different in units. So, ParticleMassMsun gets replaced with particle_mass. We're working on the documentation for all of this - sorry it's a bit confusing to use right now while it's still under active development. There will definitely be documentation to cover all of this when we do the stable release for yt 3.0. -Nathan On Tue, Apr 15, 2014 at 8:56 AM, Marcelo Vargas dos Santos < marcelovsrj@gmail.com> wrote:
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@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@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@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@gmail.com> wrote:
I'm using the yt-4.0.0.
On 14 April 2014 17:53, Sam Geen <samgeen@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/655e46d0b3a06d2e6da22... > > Thank you very much. > > Best wishes, > Ji-hoon > > > > ------------------------------------------------------------------------- > Ji-hoon Kim > Postdoctoral Scholar in Astrophysics at Caltech > www.jihoonkim.org > me@jihoonkim.org / 1(650)714-2879 > > ------------------------------------------------------------------------- > > > > > On Apr 14, 2014, at 12:57 PM, Matthew Turk <matthewturk@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@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@if.ufrj.br, marcelovsrj@gmail.com >>> Departamento de Física Teórica - Instituto de Física >>> Universidade Federal do Rio de Janeiro >>> >>> _______________________________________________ >>> yt-users mailing list >>> yt-users@lists.spacepope.org >>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >>> >>> _______________________________________________ >> yt-users mailing list >> yt-users@lists.spacepope.org >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >> > > > _______________________________________________ > yt-users mailing list > yt-users@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 <%2821%29%202562-7276> E-mails: vargas@if.ufrj.br, marcelovsrj@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@if.ufrj.br, marcelovsrj@gmail.com Departamento de Física Teórica - Instituto de Física Universidade Federal do Rio de Janeiro
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_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
-- Marcelo Vargas dos Santos Professor e Doutorando
Sala A 318-05 Tel.: (21) 2562-7276 E-mails: vargas@if.ufrj.br, marcelovsrj@gmail.com Departamento de Física Teórica - Instituto de Física Universidade Federal do Rio de Janeiro
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_______________________________________________ yt-users mailing listyt-users@lists.spacepope.orghttp://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
-- Marcelo Vargas dos Santos Professor e Doutorando
Sala A 318-05 Tel.: (21) 2562-7276 E-mails: vargas@if.ufrj.br, marcelovsrj@gmail.com Departamento de Física Teórica - Instituto de Física Universidade Federal do Rio de Janeiro
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participants (5)
-
Kim, Ji-hoon -
Marcelo Vargas dos Santos -
Matthew Turk -
Nathan Goldbaum -
Sam Geen