Slice Plot Gadget Problem
Hello! I have a vanilla gadget snapshot (one from the lcdm sample run that the code comes with) that I was able to plot by following the instructions given here: http://yt-project.org/docs/3.0/cookbook/tipsy_notebook.html#tipsy-notebook I then moved on to the 'Making Smoothed Images' section of that page and tried the SlicePlot command. However, I get the following error: IndexError: index 32767 is out of bounds for axis 0 with size 32767 Basically, I'm not really sure what that means. It seems like it's overstepping the bounds of an array, as, for a zero-indexed array of size 32767, index 32767 would be out of bounds by one. I just wanted to see if anyone else has had this problem, and if so, how they fixed it? Thank you very much! -Jared
Hi Jared, Would you mind pasting the full error traceback? We use paste.yt-project.org for this purpose. -Nathan On Thu, Aug 7, 2014 at 1:16 PM, Jared Coughlin <Jared.W.Coughlin.29@nd.edu> wrote:
Hello! I have a vanilla gadget snapshot (one from the lcdm sample run that the code comes with) that I was able to plot by following the instructions given here: http://yt-project.org/docs/3.0/cookbook/tipsy_notebook.html#tipsy-notebook
I then moved on to the 'Making Smoothed Images' section of that page and tried the SlicePlot command. However, I get the following error: IndexError: index 32767 is out of bounds for axis 0 with size 32767
Basically, I'm not really sure what that means. It seems like it's overstepping the bounds of an array, as, for a zero-indexed array of size 32767, index 32767 would be out of bounds by one. I just wanted to see if anyone else has had this problem, and if so, how they fixed it? Thank you very much! -Jared
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Hi Nathan, I pasted the traceback here: http://paste.yt-project.org/show/4998/ -Jared On Thu, Aug 7, 2014 at 4:16 PM, Jared Coughlin <Jared.W.Coughlin.29@nd.edu> wrote:
Hello! I have a vanilla gadget snapshot (one from the lcdm sample run that the code comes with) that I was able to plot by following the instructions given here: http://yt-project.org/docs/3.0/cookbook/tipsy_notebook.html#tipsy-notebook
I then moved on to the 'Making Smoothed Images' section of that page and tried the SlicePlot command. However, I get the following error: IndexError: index 32767 is out of bounds for axis 0 with size 32767
Basically, I'm not really sure what that means. It seems like it's overstepping the bounds of an array, as, for a zero-indexed array of size 32767, index 32767 would be out of bounds by one. I just wanted to see if anyone else has had this problem, and if so, how they fixed it? Thank you very much! -Jared
Hi Jared, Try instead: yt.SlicePlot(ds, 'z', ('gas', 'density'), width=(10000., 'kpc'), center ='m') (note the lower-case). ('Gas', 'Density') is a particle field, i.e. the Density values associated with each of the Gas particles in your simulation. ('gas', 'density') is a mesh field - for SPH it is the smoothed gas density, taken from the original Gas particles. Particle fields are unstructured, the field is only defined at the positions where particles exist. Mesh fields are defined over the whole simulation domain. Unfortunately there's some name collision here for gadget binary files so I can see how this is confusing. At the very least we should catch that you're trying to create a SlicePlot of a particle field and crash with a nicer, more understandable error. More detail on the difference between particle and mesh fields as well as fields in yt in general here: http://yt-project.org/docs/3.0/analyzing/fields.html Hope that helps, -Nathan On Thu, Aug 7, 2014 at 2:08 PM, Jared Coughlin <Jared.W.Coughlin.29@nd.edu> wrote:
Hi Nathan, I pasted the traceback here: http://paste.yt-project.org/show/4998/ -Jared
On Thu, Aug 7, 2014 at 4:16 PM, Jared Coughlin <Jared.W.Coughlin.29@nd.edu
wrote:
Hello! I have a vanilla gadget snapshot (one from the lcdm sample run that the code comes with) that I was able to plot by following the instructions given here: http://yt-project.org/docs/3.0/cookbook/tipsy_notebook.html#tipsy-notebook
I then moved on to the 'Making Smoothed Images' section of that page and tried the SlicePlot command. However, I get the following error: IndexError: index 32767 is out of bounds for axis 0 with size 32767
Basically, I'm not really sure what that means. It seems like it's overstepping the bounds of an array, as, for a zero-indexed array of size 32767, index 32767 would be out of bounds by one. I just wanted to see if anyone else has had this problem, and if so, how they fixed it? Thank you very much! -Jared
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Hi Nathan, Thank you for responding! I tried what you suggested, but still no luck. I'm still getting the index out of bounds error. I've copied the traceback to the paste bin at: http://paste.yt-project.org/show/5001/ I've included how I loaded the snapshot as well as the call to yt.SlicePlot, in case that helps. Thank you very much for all the help! -Jared On Thu, Aug 7, 2014 at 5:12 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
Hi Jared,
Try instead:
yt.SlicePlot(ds, 'z', ('gas', 'density'), width=(10000., 'kpc'), center ='m')
(note the lower-case).
('Gas', 'Density') is a particle field, i.e. the Density values associated with each of the Gas particles in your simulation. ('gas', 'density') is a mesh field - for SPH it is the smoothed gas density, taken from the original Gas particles. Particle fields are unstructured, the field is only defined at the positions where particles exist. Mesh fields are defined over the whole simulation domain.
Unfortunately there's some name collision here for gadget binary files so I can see how this is confusing. At the very least we should catch that you're trying to create a SlicePlot of a particle field and crash with a nicer, more understandable error.
More detail on the difference between particle and mesh fields as well as fields in yt in general here: http://yt-project.org/docs/3.0/analyzing/fields.html
Hope that helps,
-Nathan
On Thu, Aug 7, 2014 at 2:08 PM, Jared Coughlin <Jared.W.Coughlin.29@nd.edu
wrote:
Hi Nathan, I pasted the traceback here: http://paste.yt-project.org/show/4998/ -Jared
On Thu, Aug 7, 2014 at 4:16 PM, Jared Coughlin < Jared.W.Coughlin.29@nd.edu> wrote:
Hello! I have a vanilla gadget snapshot (one from the lcdm sample run that the code comes with) that I was able to plot by following the instructions given here:
http://yt-project.org/docs/3.0/cookbook/tipsy_notebook.html#tipsy-notebook
I then moved on to the 'Making Smoothed Images' section of that page and tried the SlicePlot command. However, I get the following error: IndexError: index 32767 is out of bounds for axis 0 with size 32767
Basically, I'm not really sure what that means. It seems like it's overstepping the bounds of an array, as, for a zero-indexed array of size 32767, index 32767 would be out of bounds by one. I just wanted to see if anyone else has had this problem, and if so, how they fixed it? Thank you very much! -Jared
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I'm not sure if this is the main cause of the problem, but the units for that simulation should be kpc/h not Mpc/h. It looks like yt is assuming the box is 50,000 Mpc/h on a side. You can set the units in the yt.GadgetDataset command ( http://yt-project.org/doc/examining/loading_data.html?highlight=gadget#units...). Try something like this, ds = GadgetDataset("snap_005", unit_base = {'length': ('kpccm/h', 1.0)}) best, -Gabriel On Fri, Aug 8, 2014 at 12:39 PM, Jared Coughlin <Jared.W.Coughlin.29@nd.edu> wrote:
Hi Nathan, Thank you for responding! I tried what you suggested, but still no luck. I'm still getting the index out of bounds error. I've copied the traceback to the paste bin at: http://paste.yt-project.org/show/5001/ I've included how I loaded the snapshot as well as the call to yt.SlicePlot, in case that helps. Thank you very much for all the help! -Jared
On Thu, Aug 7, 2014 at 5:12 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
Hi Jared,
Try instead:
yt.SlicePlot(ds, 'z', ('gas', 'density'), width=(10000., 'kpc'), center ='m')
(note the lower-case).
('Gas', 'Density') is a particle field, i.e. the Density values associated with each of the Gas particles in your simulation. ('gas', 'density') is a mesh field - for SPH it is the smoothed gas density, taken from the original Gas particles. Particle fields are unstructured, the field is only defined at the positions where particles exist. Mesh fields are defined over the whole simulation domain.
Unfortunately there's some name collision here for gadget binary files so I can see how this is confusing. At the very least we should catch that you're trying to create a SlicePlot of a particle field and crash with a nicer, more understandable error.
More detail on the difference between particle and mesh fields as well as fields in yt in general here: http://yt-project.org/docs/3.0/analyzing/fields.html
Hope that helps,
-Nathan
On Thu, Aug 7, 2014 at 2:08 PM, Jared Coughlin < Jared.W.Coughlin.29@nd.edu> wrote:
Hi Nathan, I pasted the traceback here: http://paste.yt-project.org/show/4998/ -Jared
On Thu, Aug 7, 2014 at 4:16 PM, Jared Coughlin < Jared.W.Coughlin.29@nd.edu> wrote:
Hello! I have a vanilla gadget snapshot (one from the lcdm sample run that the code comes with) that I was able to plot by following the instructions given here:
http://yt-project.org/docs/3.0/cookbook/tipsy_notebook.html#tipsy-notebook
I then moved on to the 'Making Smoothed Images' section of that page and tried the SlicePlot command. However, I get the following error: IndexError: index 32767 is out of bounds for axis 0 with size 32767
Basically, I'm not really sure what that means. It seems like it's overstepping the bounds of an array, as, for a zero-indexed array of size 32767, index 32767 would be out of bounds by one. I just wanted to see if anyone else has had this problem, and if so, how they fixed it? Thank you very much! -Jared
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-- -- Gabriel Altay, PhD Center for Relativistic Astrophysics Georgia Institute of Technology, Physics Department 837 State Street, Atlanta, GA, 30332 phone: +01 404 205 9795 url: http://cosmo.gatech.edu/?page_id=1075
Hi Jared, Looking at the traceback, it seems the issue is in calculating the maximum gas density in the simulation. I'm not sure why this is failing, but to see if we can create a plot at all, can you try supplying 'c' as the plot center instead of 'm'? Can you also paste the contents of 'ds.field_list' and 'ds.derived_field_list'? Additionally, can you create a SlicePlot of one of the following fields: ('deposit', 'Gas_smoothed_Density') ('deposit', 'all_cic') The first is another name for the SPH smoothed gas density - I'm checking here whether the ('gas', 'density') alias is misbehaving. The second is the cloud-in-cell deposited density for all particles in the simulation - I want to make sure that deposition isn't completely broken for your dataset. Lastly, if the dataset isn't enormous and it is ok to share it, it would be helpful if you could share the actual dataset so one of us can reproduce your problem locally. We've had a lot of success using dropbox and google drive for this purpose in the past. Hopefully we'll be able to get to the bottom of this, Nathan On Fri, Aug 8, 2014 at 9:39 AM, Jared Coughlin <Jared.W.Coughlin.29@nd.edu> wrote:
Hi Nathan, Thank you for responding! I tried what you suggested, but still no luck. I'm still getting the index out of bounds error. I've copied the traceback to the paste bin at: http://paste.yt-project.org/show/5001/ I've included how I loaded the snapshot as well as the call to yt.SlicePlot, in case that helps. Thank you very much for all the help! -Jared
On Thu, Aug 7, 2014 at 5:12 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
Hi Jared,
Try instead:
yt.SlicePlot(ds, 'z', ('gas', 'density'), width=(10000., 'kpc'), center ='m')
(note the lower-case).
('Gas', 'Density') is a particle field, i.e. the Density values associated with each of the Gas particles in your simulation. ('gas', 'density') is a mesh field - for SPH it is the smoothed gas density, taken from the original Gas particles. Particle fields are unstructured, the field is only defined at the positions where particles exist. Mesh fields are defined over the whole simulation domain.
Unfortunately there's some name collision here for gadget binary files so I can see how this is confusing. At the very least we should catch that you're trying to create a SlicePlot of a particle field and crash with a nicer, more understandable error.
More detail on the difference between particle and mesh fields as well as fields in yt in general here: http://yt-project.org/docs/3.0/analyzing/fields.html
Hope that helps,
-Nathan
On Thu, Aug 7, 2014 at 2:08 PM, Jared Coughlin < Jared.W.Coughlin.29@nd.edu> wrote:
Hi Nathan, I pasted the traceback here: http://paste.yt-project.org/show/4998/ -Jared
On Thu, Aug 7, 2014 at 4:16 PM, Jared Coughlin < Jared.W.Coughlin.29@nd.edu> wrote:
Hello! I have a vanilla gadget snapshot (one from the lcdm sample run that the code comes with) that I was able to plot by following the instructions given here:
http://yt-project.org/docs/3.0/cookbook/tipsy_notebook.html#tipsy-notebook
I then moved on to the 'Making Smoothed Images' section of that page and tried the SlicePlot command. However, I get the following error: IndexError: index 32767 is out of bounds for axis 0 with size 32767
Basically, I'm not really sure what that means. It seems like it's overstepping the bounds of an array, as, for a zero-indexed array of size 32767, index 32767 would be out of bounds by one. I just wanted to see if anyone else has had this problem, and if so, how they fixed it? Thank you very much! -Jared
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Hi, I tried changing the units, and that gave the same error. I also tried changing the center to 'c', and same thing. I've posted the contents of ds.field_list and ds.derived_field_list here: http://paste.yt-project.org/show/5003/ The plot of ('deposit'', 'Gas_smoothed_Density') also didn't work. The traceback is here: http://paste.yt-project.org/show/5004/ The plot of ('deposit', 'all_cic') worked, however. At least, it ran and produced an image without throwing any errors. I can upload the image to google drive, if you'd like? As for the snapshot, it's not very big, only 2.2M. I can put that on google drive as well. Also, it's little endian. I can upload the parameter file and ic file, as well, if you'd like. -Jared On Fri, Aug 8, 2014 at 1:51 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
Hi Jared,
Looking at the traceback, it seems the issue is in calculating the maximum gas density in the simulation. I'm not sure why this is failing, but to see if we can create a plot at all, can you try supplying 'c' as the plot center instead of 'm'?
Can you also paste the contents of 'ds.field_list' and 'ds.derived_field_list'?
Additionally, can you create a SlicePlot of one of the following fields:
('deposit', 'Gas_smoothed_Density') ('deposit', 'all_cic')
The first is another name for the SPH smoothed gas density - I'm checking here whether the ('gas', 'density') alias is misbehaving. The second is the cloud-in-cell deposited density for all particles in the simulation - I want to make sure that deposition isn't completely broken for your dataset.
Lastly, if the dataset isn't enormous and it is ok to share it, it would be helpful if you could share the actual dataset so one of us can reproduce your problem locally. We've had a lot of success using dropbox and google drive for this purpose in the past.
Hopefully we'll be able to get to the bottom of this,
Nathan
On Fri, Aug 8, 2014 at 9:39 AM, Jared Coughlin <Jared.W.Coughlin.29@nd.edu
wrote:
Hi Nathan, Thank you for responding! I tried what you suggested, but still no luck. I'm still getting the index out of bounds error. I've copied the traceback to the paste bin at: http://paste.yt-project.org/show/5001/ I've included how I loaded the snapshot as well as the call to yt.SlicePlot, in case that helps. Thank you very much for all the help! -Jared
On Thu, Aug 7, 2014 at 5:12 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
Hi Jared,
Try instead:
yt.SlicePlot(ds, 'z', ('gas', 'density'), width=(10000., 'kpc'), center ='m')
(note the lower-case).
('Gas', 'Density') is a particle field, i.e. the Density values associated with each of the Gas particles in your simulation. ('gas', 'density') is a mesh field - for SPH it is the smoothed gas density, taken from the original Gas particles. Particle fields are unstructured, the field is only defined at the positions where particles exist. Mesh fields are defined over the whole simulation domain.
Unfortunately there's some name collision here for gadget binary files so I can see how this is confusing. At the very least we should catch that you're trying to create a SlicePlot of a particle field and crash with a nicer, more understandable error.
More detail on the difference between particle and mesh fields as well as fields in yt in general here: http://yt-project.org/docs/3.0/analyzing/fields.html
Hope that helps,
-Nathan
On Thu, Aug 7, 2014 at 2:08 PM, Jared Coughlin < Jared.W.Coughlin.29@nd.edu> wrote:
Hi Nathan, I pasted the traceback here: http://paste.yt-project.org/show/4998/ -Jared
On Thu, Aug 7, 2014 at 4:16 PM, Jared Coughlin < Jared.W.Coughlin.29@nd.edu> wrote:
Hello! I have a vanilla gadget snapshot (one from the lcdm sample run that the code comes with) that I was able to plot by following the instructions given here:
http://yt-project.org/docs/3.0/cookbook/tipsy_notebook.html#tipsy-notebook
I then moved on to the 'Making Smoothed Images' section of that page and tried the SlicePlot command. However, I get the following error: IndexError: index 32767 is out of bounds for axis 0 with size 32767
Basically, I'm not really sure what that means. It seems like it's overstepping the bounds of an array, as, for a zero-indexed array of size 32767, index 32767 would be out of bounds by one. I just wanted to see if anyone else has had this problem, and if so, how they fixed it? Thank you very much! -Jared
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Ok, I can trigger the error you're seeing locally. I've passed this on to Matt who can take a closer look at what's happening and hopefully fix the issue you're running into. Sorry for the difficulties, hopefully we'll have this cleared up soon. Thanks also for reporting this and working with us. On Fri, Aug 8, 2014 at 12:55 PM, Jared Coughlin <Jared.W.Coughlin.29@nd.edu> wrote:
Hi, I tried changing the units, and that gave the same error. I also tried changing the center to 'c', and same thing. I've posted the contents of ds.field_list and ds.derived_field_list here: http://paste.yt-project.org/show/5003/
The plot of ('deposit'', 'Gas_smoothed_Density') also didn't work. The traceback is here: http://paste.yt-project.org/show/5004/
The plot of ('deposit', 'all_cic') worked, however. At least, it ran and produced an image without throwing any errors. I can upload the image to google drive, if you'd like?
As for the snapshot, it's not very big, only 2.2M. I can put that on google drive as well. Also, it's little endian. I can upload the parameter file and ic file, as well, if you'd like. -Jared
On Fri, Aug 8, 2014 at 1:51 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
Hi Jared,
Looking at the traceback, it seems the issue is in calculating the maximum gas density in the simulation. I'm not sure why this is failing, but to see if we can create a plot at all, can you try supplying 'c' as the plot center instead of 'm'?
Can you also paste the contents of 'ds.field_list' and 'ds.derived_field_list'?
Additionally, can you create a SlicePlot of one of the following fields:
('deposit', 'Gas_smoothed_Density') ('deposit', 'all_cic')
The first is another name for the SPH smoothed gas density - I'm checking here whether the ('gas', 'density') alias is misbehaving. The second is the cloud-in-cell deposited density for all particles in the simulation - I want to make sure that deposition isn't completely broken for your dataset.
Lastly, if the dataset isn't enormous and it is ok to share it, it would be helpful if you could share the actual dataset so one of us can reproduce your problem locally. We've had a lot of success using dropbox and google drive for this purpose in the past.
Hopefully we'll be able to get to the bottom of this,
Nathan
On Fri, Aug 8, 2014 at 9:39 AM, Jared Coughlin < Jared.W.Coughlin.29@nd.edu> wrote:
Hi Nathan, Thank you for responding! I tried what you suggested, but still no luck. I'm still getting the index out of bounds error. I've copied the traceback to the paste bin at: http://paste.yt-project.org/show/5001/ I've included how I loaded the snapshot as well as the call to yt.SlicePlot, in case that helps. Thank you very much for all the help! -Jared
On Thu, Aug 7, 2014 at 5:12 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
Hi Jared,
Try instead:
yt.SlicePlot(ds, 'z', ('gas', 'density'), width=(10000., 'kpc'), center ='m')
(note the lower-case).
('Gas', 'Density') is a particle field, i.e. the Density values associated with each of the Gas particles in your simulation. ('gas', 'density') is a mesh field - for SPH it is the smoothed gas density, taken from the original Gas particles. Particle fields are unstructured, the field is only defined at the positions where particles exist. Mesh fields are defined over the whole simulation domain.
Unfortunately there's some name collision here for gadget binary files so I can see how this is confusing. At the very least we should catch that you're trying to create a SlicePlot of a particle field and crash with a nicer, more understandable error.
More detail on the difference between particle and mesh fields as well as fields in yt in general here: http://yt-project.org/docs/3.0/analyzing/fields.html
Hope that helps,
-Nathan
On Thu, Aug 7, 2014 at 2:08 PM, Jared Coughlin < Jared.W.Coughlin.29@nd.edu> wrote:
Hi Nathan, I pasted the traceback here: http://paste.yt-project.org/show/4998/ -Jared
On Thu, Aug 7, 2014 at 4:16 PM, Jared Coughlin < Jared.W.Coughlin.29@nd.edu> wrote:
Hello! I have a vanilla gadget snapshot (one from the lcdm sample run that the code comes with) that I was able to plot by following the instructions given here:
http://yt-project.org/docs/3.0/cookbook/tipsy_notebook.html#tipsy-notebook
I then moved on to the 'Making Smoothed Images' section of that page and tried the SlicePlot command. However, I get the following error: IndexError: index 32767 is out of bounds for axis 0 with size 32767
Basically, I'm not really sure what that means. It seems like it's overstepping the bounds of an array, as, for a zero-indexed array of size 32767, index 32767 would be out of bounds by one. I just wanted to see if anyone else has had this problem, and if so, how they fixed it? Thank you very much! -Jared
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No problem, thank you very much for all your help, I really appreciate it! -Jared On Aug 8, 2014 5:48 PM, "Nathan Goldbaum" <nathan12343@gmail.com> wrote:
Ok, I can trigger the error you're seeing locally. I've passed this on to Matt who can take a closer look at what's happening and hopefully fix the issue you're running into.
Sorry for the difficulties, hopefully we'll have this cleared up soon. Thanks also for reporting this and working with us.
On Fri, Aug 8, 2014 at 12:55 PM, Jared Coughlin < Jared.W.Coughlin.29@nd.edu> wrote:
Hi, I tried changing the units, and that gave the same error. I also tried changing the center to 'c', and same thing. I've posted the contents of ds.field_list and ds.derived_field_list here: http://paste.yt-project.org/show/5003/
The plot of ('deposit'', 'Gas_smoothed_Density') also didn't work. The traceback is here: http://paste.yt-project.org/show/5004/
The plot of ('deposit', 'all_cic') worked, however. At least, it ran and produced an image without throwing any errors. I can upload the image to google drive, if you'd like?
As for the snapshot, it's not very big, only 2.2M. I can put that on google drive as well. Also, it's little endian. I can upload the parameter file and ic file, as well, if you'd like. -Jared
On Fri, Aug 8, 2014 at 1:51 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
Hi Jared,
Looking at the traceback, it seems the issue is in calculating the maximum gas density in the simulation. I'm not sure why this is failing, but to see if we can create a plot at all, can you try supplying 'c' as the plot center instead of 'm'?
Can you also paste the contents of 'ds.field_list' and 'ds.derived_field_list'?
Additionally, can you create a SlicePlot of one of the following fields:
('deposit', 'Gas_smoothed_Density') ('deposit', 'all_cic')
The first is another name for the SPH smoothed gas density - I'm checking here whether the ('gas', 'density') alias is misbehaving. The second is the cloud-in-cell deposited density for all particles in the simulation - I want to make sure that deposition isn't completely broken for your dataset.
Lastly, if the dataset isn't enormous and it is ok to share it, it would be helpful if you could share the actual dataset so one of us can reproduce your problem locally. We've had a lot of success using dropbox and google drive for this purpose in the past.
Hopefully we'll be able to get to the bottom of this,
Nathan
On Fri, Aug 8, 2014 at 9:39 AM, Jared Coughlin < Jared.W.Coughlin.29@nd.edu> wrote:
Hi Nathan, Thank you for responding! I tried what you suggested, but still no luck. I'm still getting the index out of bounds error. I've copied the traceback to the paste bin at: http://paste.yt-project.org/show/5001/ I've included how I loaded the snapshot as well as the call to yt.SlicePlot, in case that helps. Thank you very much for all the help! -Jared
On Thu, Aug 7, 2014 at 5:12 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
Hi Jared,
Try instead:
yt.SlicePlot(ds, 'z', ('gas', 'density'), width=(10000., 'kpc'), center ='m')
(note the lower-case).
('Gas', 'Density') is a particle field, i.e. the Density values associated with each of the Gas particles in your simulation. ('gas', 'density') is a mesh field - for SPH it is the smoothed gas density, taken from the original Gas particles. Particle fields are unstructured, the field is only defined at the positions where particles exist. Mesh fields are defined over the whole simulation domain.
Unfortunately there's some name collision here for gadget binary files so I can see how this is confusing. At the very least we should catch that you're trying to create a SlicePlot of a particle field and crash with a nicer, more understandable error.
More detail on the difference between particle and mesh fields as well as fields in yt in general here: http://yt-project.org/docs/3.0/analyzing/fields.html
Hope that helps,
-Nathan
On Thu, Aug 7, 2014 at 2:08 PM, Jared Coughlin < Jared.W.Coughlin.29@nd.edu> wrote:
Hi Nathan, I pasted the traceback here: http://paste.yt-project.org/show/4998/ -Jared
On Thu, Aug 7, 2014 at 4:16 PM, Jared Coughlin < Jared.W.Coughlin.29@nd.edu> wrote:
> Hello! I have a vanilla gadget snapshot (one from the lcdm sample > run that the code comes with) that I was able to plot by following the > instructions given here: > > http://yt-project.org/docs/3.0/cookbook/tipsy_notebook.html#tipsy-notebook > > I then moved on to the 'Making Smoothed Images' section of that page > and tried the SlicePlot command. However, I get the following error: > IndexError: index 32767 is out of bounds for axis 0 with size 32767 > > Basically, I'm not really sure what that means. It seems like it's > overstepping the bounds of an array, as, for a zero-indexed array of size > 32767, index 32767 would be out of bounds by one. I just wanted to see if > anyone else has had this problem, and if so, how they fixed it? Thank you > very much! > -Jared >
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Hi Jared, I've found the bug and issued a fix, here: https://bitbucket.org/yt_analysis/yt/pull-request/1140/adding-check-for-no-f... Should go in shortly. (I put up a projection just for fun.) -Matt On Fri, Aug 8, 2014 at 5:21 PM, Jared Coughlin <Jared.W.Coughlin.29@nd.edu> wrote:
No problem, thank you very much for all your help, I really appreciate it! -Jared
On Aug 8, 2014 5:48 PM, "Nathan Goldbaum" <nathan12343@gmail.com> wrote:
Ok, I can trigger the error you're seeing locally. I've passed this on to Matt who can take a closer look at what's happening and hopefully fix the issue you're running into.
Sorry for the difficulties, hopefully we'll have this cleared up soon. Thanks also for reporting this and working with us.
On Fri, Aug 8, 2014 at 12:55 PM, Jared Coughlin <Jared.W.Coughlin.29@nd.edu> wrote:
Hi, I tried changing the units, and that gave the same error. I also tried changing the center to 'c', and same thing. I've posted the contents of ds.field_list and ds.derived_field_list here: http://paste.yt-project.org/show/5003/
The plot of ('deposit'', 'Gas_smoothed_Density') also didn't work. The traceback is here: http://paste.yt-project.org/show/5004/
The plot of ('deposit', 'all_cic') worked, however. At least, it ran and produced an image without throwing any errors. I can upload the image to google drive, if you'd like?
As for the snapshot, it's not very big, only 2.2M. I can put that on google drive as well. Also, it's little endian. I can upload the parameter file and ic file, as well, if you'd like. -Jared
On Fri, Aug 8, 2014 at 1:51 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
Hi Jared,
Looking at the traceback, it seems the issue is in calculating the maximum gas density in the simulation. I'm not sure why this is failing, but to see if we can create a plot at all, can you try supplying 'c' as the plot center instead of 'm'?
Can you also paste the contents of 'ds.field_list' and 'ds.derived_field_list'?
Additionally, can you create a SlicePlot of one of the following fields:
('deposit', 'Gas_smoothed_Density') ('deposit', 'all_cic')
The first is another name for the SPH smoothed gas density - I'm checking here whether the ('gas', 'density') alias is misbehaving. The second is the cloud-in-cell deposited density for all particles in the simulation - I want to make sure that deposition isn't completely broken for your dataset.
Lastly, if the dataset isn't enormous and it is ok to share it, it would be helpful if you could share the actual dataset so one of us can reproduce your problem locally. We've had a lot of success using dropbox and google drive for this purpose in the past.
Hopefully we'll be able to get to the bottom of this,
Nathan
On Fri, Aug 8, 2014 at 9:39 AM, Jared Coughlin <Jared.W.Coughlin.29@nd.edu> wrote:
Hi Nathan, Thank you for responding! I tried what you suggested, but still no luck. I'm still getting the index out of bounds error. I've copied the traceback to the paste bin at: http://paste.yt-project.org/show/5001/ I've included how I loaded the snapshot as well as the call to yt.SlicePlot, in case that helps. Thank you very much for all the help! -Jared
On Thu, Aug 7, 2014 at 5:12 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
Hi Jared,
Try instead:
yt.SlicePlot(ds, 'z', ('gas', 'density'), width=(10000., 'kpc'), center ='m')
(note the lower-case).
('Gas', 'Density') is a particle field, i.e. the Density values associated with each of the Gas particles in your simulation. ('gas', 'density') is a mesh field - for SPH it is the smoothed gas density, taken from the original Gas particles. Particle fields are unstructured, the field is only defined at the positions where particles exist. Mesh fields are defined over the whole simulation domain.
Unfortunately there's some name collision here for gadget binary files so I can see how this is confusing. At the very least we should catch that you're trying to create a SlicePlot of a particle field and crash with a nicer, more understandable error.
More detail on the difference between particle and mesh fields as well as fields in yt in general here: http://yt-project.org/docs/3.0/analyzing/fields.html
Hope that helps,
-Nathan
On Thu, Aug 7, 2014 at 2:08 PM, Jared Coughlin <Jared.W.Coughlin.29@nd.edu> wrote: > > Hi Nathan, I pasted the traceback here: > http://paste.yt-project.org/show/4998/ > -Jared > > > On Thu, Aug 7, 2014 at 4:16 PM, Jared Coughlin > <Jared.W.Coughlin.29@nd.edu> wrote: >> >> Hello! I have a vanilla gadget snapshot (one from the lcdm sample >> run that the code comes with) that I was able to plot by following the >> instructions given here: >> >> http://yt-project.org/docs/3.0/cookbook/tipsy_notebook.html#tipsy-notebook >> >> I then moved on to the 'Making Smoothed Images' section of that page >> and tried the SlicePlot command. However, I get the following error: >> IndexError: index 32767 is out of bounds for axis 0 with size 32767 >> >> Basically, I'm not really sure what that means. It seems like it's >> overstepping the bounds of an array, as, for a zero-indexed array of size >> 32767, index 32767 would be out of bounds by one. I just wanted to see if >> anyone else has had this problem, and if so, how they fixed it? Thank you >> very much! >> -Jared > > > > _______________________________________________ > yt-users mailing list > yt-users@lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >
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Thank you very much, I really appreciate the help! -Jared On Aug 11, 2014 9:44 AM, "Matthew Turk" <matthewturk@gmail.com> wrote:
Hi Jared,
I've found the bug and issued a fix, here:
https://bitbucket.org/yt_analysis/yt/pull-request/1140/adding-check-for-no-f...
Should go in shortly. (I put up a projection just for fun.)
-Matt
No problem, thank you very much for all your help, I really appreciate it! -Jared
On Aug 8, 2014 5:48 PM, "Nathan Goldbaum" <nathan12343@gmail.com> wrote:
Ok, I can trigger the error you're seeing locally. I've passed this on
to
Matt who can take a closer look at what's happening and hopefully fix
issue you're running into.
Sorry for the difficulties, hopefully we'll have this cleared up soon. Thanks also for reporting this and working with us.
On Fri, Aug 8, 2014 at 12:55 PM, Jared Coughlin <Jared.W.Coughlin.29@nd.edu> wrote:
Hi, I tried changing the units, and that gave the same error. I also tried changing the center to 'c', and same thing. I've posted the contents
of
ds.field_list and ds.derived_field_list here: http://paste.yt-project.org/show/5003/
The plot of ('deposit'', 'Gas_smoothed_Density') also didn't work. The traceback is here: http://paste.yt-project.org/show/5004/
The plot of ('deposit', 'all_cic') worked, however. At least, it ran and produced an image without throwing any errors. I can upload the image to google drive, if you'd like?
As for the snapshot, it's not very big, only 2.2M. I can put that on google drive as well. Also, it's little endian. I can upload the
file and ic file, as well, if you'd like. -Jared
On Fri, Aug 8, 2014 at 1:51 PM, Nathan Goldbaum <nathan12343@gmail.com
wrote:
Hi Jared,
Looking at the traceback, it seems the issue is in calculating the maximum gas density in the simulation. I'm not sure why this is
failing,
but to see if we can create a plot at all, can you try supplying 'c' as the plot center instead of 'm'?
Can you also paste the contents of 'ds.field_list' and 'ds.derived_field_list'?
Additionally, can you create a SlicePlot of one of the following fields:
('deposit', 'Gas_smoothed_Density') ('deposit', 'all_cic')
The first is another name for the SPH smoothed gas density - I'm checking here whether the ('gas', 'density') alias is misbehaving. The second is the cloud-in-cell deposited density for all particles in the simulation - I want to make sure that deposition isn't completely broken for your dataset.
Lastly, if the dataset isn't enormous and it is ok to share it, it would be helpful if you could share the actual dataset so one of us can reproduce your problem locally. We've had a lot of success using dropbox and google drive for this purpose in the past.
Hopefully we'll be able to get to the bottom of this,
Nathan
On Fri, Aug 8, 2014 at 9:39 AM, Jared Coughlin <Jared.W.Coughlin.29@nd.edu> wrote:
Hi Nathan, Thank you for responding! I tried what you suggested, but still no luck. I'm still getting the index out of bounds error. I've copied
traceback to the paste bin at: http://paste.yt-project.org/show/5001/ I've included how I loaded the snapshot as well as the call to yt.SlicePlot, in case that helps. Thank you very much for all the help! -Jared
On Thu, Aug 7, 2014 at 5:12 PM, Nathan Goldbaum < nathan12343@gmail.com> wrote: > > Hi Jared, > > Try instead: > > yt.SlicePlot(ds, 'z', ('gas', 'density'), width=(10000., 'kpc'), > center ='m') > > (note the lower-case). > > ('Gas', 'Density') is a particle field, i.e. the Density values > associated with each of the Gas particles in your simulation. ('gas', > 'density') is a mesh field - for SPH it is the smoothed gas density, taken > from the original Gas particles. Particle fields are unstructured,
> field is only defined at the positions where particles exist. Mesh fields > are defined over the whole simulation domain. > > Unfortunately there's some name collision here for gadget binary files > so I can see how this is confusing. At the very least we should catch that > you're trying to create a SlicePlot of a particle field and crash with a > nicer, more understandable error. > > More detail on the difference between particle and mesh fields as well > as fields in yt in general here: > http://yt-project.org/docs/3.0/analyzing/fields.html > > Hope that helps, > > -Nathan > > > On Thu, Aug 7, 2014 at 2:08 PM, Jared Coughlin > <Jared.W.Coughlin.29@nd.edu> wrote: >> >> Hi Nathan, I pasted the traceback here: >> http://paste.yt-project.org/show/4998/ >> -Jared >> >> >> On Thu, Aug 7, 2014 at 4:16 PM, Jared Coughlin >> <Jared.W.Coughlin.29@nd.edu> wrote: >>> >>> Hello! I have a vanilla gadget snapshot (one from the lcdm sample >>> run that the code comes with) that I was able to plot by following the >>> instructions given here: >>> >>> http://yt-project.org/docs/3.0/cookbook/tipsy_notebook.html#tipsy-notebook >>> >>> I then moved on to the 'Making Smoothed Images' section of that
On Fri, Aug 8, 2014 at 5:21 PM, Jared Coughlin <Jared.W.Coughlin.29@nd.edu> wrote: the parameter the the page
>>> and tried the SlicePlot command. However, I get the following error: >>> IndexError: index 32767 is out of bounds for axis 0 with size 32767 >>> >>> Basically, I'm not really sure what that means. It seems like it's >>> overstepping the bounds of an array, as, for a zero-indexed array of size >>> 32767, index 32767 would be out of bounds by one. I just wanted to see if >>> anyone else has had this problem, and if so, how they fixed it? Thank you >>> very much! >>> -Jared >> >> >> >> _______________________________________________ >> 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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participants (4)
-
Gabriel Altay -
Jared Coughlin -
Matthew Turk -
Nathan Goldbaum