I tried ['io', 'particle_position_x'] on my Flash data, and it seemed to work just fine. I use the latest yt. Yuan On Sat, May 9, 2015 at 7:51 PM, Nathan Goldbaum wrote:

I'm not able to reproduce this using the Orbit dataset on yt-project.org/data. Unfortunately I don't think we have any other flash test datasets that use particles.

It would also help to see the full error traceback you're getting.

On Sat, May 9, 2015 at 4:32 PM, Matthew Turk wrote:

...

Hi Jason,

Don't worry about posting the data -- that's completely fine, and I think in general we should do all we can to reproduce without the dataset! I'm wondering if perhaps there's something funny about the "io" particle field. If you try "all" instead of "io", does it work any better?

-Matt

On Fri, May 8, 2015 at 1:01 PM, Jason Galyardt wrote:

...

Hi all,

Has anyone had success accessing deposited particle data generated with FLASH? It appears in the dataset derived field list, but when I go to access it (via ds.all_data()['deposit', 'io_mass']), I get an error concerning zero-length selection. I get the same error when I try to access the 'standard' particle data (from ds.field_list), such as ds.all_data()['io', 'particle_mass'].

Does this ring any bells? This very well could be user error, so please let me know if that seems to be the case. I've pasted a basic script to reproduce the error here:

http://paste.yt-project.org/show/5538/

I'd rather not post the dataset publicly, but I can send you a link, if you're interested.

Cheers, Jason Galyardt

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If I had access to the dataset, I would put a breakpoint before line 76 in your traceback here: /home/jeg/yt/yt/frontends/flash/io.pyc in _read_particle_coords(self, chunks, ptf) 74 start = p_ind[g1.id - g1._id_offset] 75 end = p_ind[g2.id - g2._id_offset + 1] ---> 76 x = np.asarray(p_fields[start:end, px], dtype="=f8") 77 y = np.asarray(p_fields[start:end, py], dtype="=f8") 78 z = np.asarray(p_fields[start:end, pz], dtype="=f8") I would try to print out start and end, as well as g1.id, g1._id_offset, g2.id,and g2._id_offset. This is the last frame before we leave yt and enter h5py. For some reason start = end here, and we'd need to look at how the dataset is being read in to figure out why. On Mon, May 11, 2015 at 6:38 AM, Jason Galyardt wrote:

Hi all,

Per Matt's suggestion, I've tried accessing the FLASH particles via ['all', 'particle_mass'], to no avail. The traceback can be found here:

http://paste.yt-project.org/show/5541/

I get the same zero-length selection exception when I use ['io', 'particle_position_x'] or ['all', 'particle_position_x'], as Yuan suggests.

To further check the input particle file format, I used the low-level h5py interface. I was able to read both particle position and mass. This script doesn't know about the grid, however.

Any other ideas?

Thanks, Jason

On Sat, May 9, 2015 at 9:59 PM, Yuan Li wrote:

...

I tried ['io', 'particle_position_x'] on my Flash data, and it seemed to work just fine. I use the latest yt.

Yuan

On Sat, May 9, 2015 at 7:51 PM, Nathan Goldbaum wrote:

...

I'm not able to reproduce this using the Orbit dataset on yt-project.org/data. Unfortunately I don't think we have any other flash test datasets that use particles.

It would also help to see the full error traceback you're getting.

On Sat, May 9, 2015 at 4:32 PM, Matthew Turk wrote:

...

Hi Jason,

Don't worry about posting the data -- that's completely fine, and I think in general we should do all we can to reproduce without the dataset! I'm wondering if perhaps there's something funny about the "io" particle field. If you try "all" instead of "io", does it work any better?

-Matt

...

Hi all,

Has anyone had success accessing deposited particle data generated with FLASH? It appears in the dataset derived field list, but when I go to access it (via ds.all_data()['deposit', 'io_mass']), I get an error concerning zero-length selection. I get the same error when I try to access the 'standard' particle data (from ds.field_list), such as ds.all_data()['io', 'particle_mass'].

Does this ring any bells? This very well could be user error, so

On Fri, May 8, 2015 at 1:01 PM, Jason Galyardt < jason.galyardt@gmail.com> wrote: please let

...

me know if that seems to be the case. I've pasted a basic script to reproduce the error here:

http://paste.yt-project.org/show/5538/

I'd rather not post the dataset publicly, but I can send you a link, if you're interested.

Cheers, Jason Galyardt

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Hi Jason, That does look odd; the way the particle mappings are constructed may not be valid for your data. How many species of particles do you have, and of what types? -Matt On Mon, May 11, 2015 at 2:36 PM, Jason Galyardt wrote:

It seems that the problem is in the evaluation of 'end', which gets set to 0. I don't know how the ds.index._particle_indices container (which p_ind is set to) is supposed to look, but it's got an awful lot of zeros packed in front. In fact, of the 8017 elements, 5655 of them are exactly 0.

Looking at line 76 with the debugger, p_ind[g2.id - g2._id_offset + 1] = p_ind[1000 - 1 + 1] = p_ind[1000] = 0.

Is this normal? Doesn't make sense to me, since there are 9000+ particles in this time step.

Jason

On Mon, May 11, 2015 at 1:17 PM, Nathan Goldbaum wrote:

...

If I had access to the dataset, I would put a breakpoint before line 76 in your traceback here:

/home/jeg/yt/yt/frontends/flash/io.pyc in _read_particle_coords(self, chunks, ptf) 74 start = p_ind[g1.id - g1._id_offset] 75 end = p_ind[g2.id - g2._id_offset + 1] ---> 76 x = np.asarray(p_fields[start:end, px], dtype="=f8") 77 y = np.asarray(p_fields[start:end, py], dtype="=f8") 78 z = np.asarray(p_fields[start:end, pz], dtype="=f8")

I would try to print out start and end, as well as g1.id, g1._id_offset, g2.id,and g2._id_offset.

This is the last frame before we leave yt and enter h5py. For some reason start = end here, and we'd need to look at how the dataset is being read in to figure out why.

On Mon, May 11, 2015 at 6:38 AM, Jason Galyardt wrote:

...

Hi all,

Per Matt's suggestion, I've tried accessing the FLASH particles via ['all', 'particle_mass'], to no avail. The traceback can be found here:

http://paste.yt-project.org/show/5541/

I get the same zero-length selection exception when I use ['io', 'particle_position_x'] or ['all', 'particle_position_x'], as Yuan suggests.

To further check the input particle file format, I used the low-level h5py interface. I was able to read both particle position and mass. This script doesn't know about the grid, however.

Any other ideas?

Thanks, Jason

On Sat, May 9, 2015 at 9:59 PM, Yuan Li wrote:

...

I tried ['io', 'particle_position_x'] on my Flash data, and it seemed to work just fine. I use the latest yt.

Yuan

On Sat, May 9, 2015 at 7:51 PM, Nathan Goldbaum wrote:

...

I'm not able to reproduce this using the Orbit dataset on yt-project.org/data. Unfortunately I don't think we have any other flash test datasets that use particles.

It would also help to see the full error traceback you're getting.

On Sat, May 9, 2015 at 4:32 PM, Matthew Turk wrote:

...

Hi Jason,

Don't worry about posting the data -- that's completely fine, and I think in general we should do all we can to reproduce without the dataset! I'm wondering if perhaps there's something funny about the "io" particle field. If you try "all" instead of "io", does it work any better?

-Matt

On Fri, May 8, 2015 at 1:01 PM, Jason Galyardt wrote: > Hi all, > > Has anyone had success accessing deposited particle data generated > with > FLASH? It appears in the dataset derived field list, but when I go > to access > it (via ds.all_data()['deposit', 'io_mass']), I get an error > concerning > zero-length selection. I get the same error when I try to access the > 'standard' particle data (from ds.field_list), such as > ds.all_data()['io', > 'particle_mass']. > > Does this ring any bells? This very well could be user error, so > please let > me know if that seems to be the case. I've pasted a basic script to > reproduce the error here: > > http://paste.yt-project.org/show/5538/ > > I'd rather not post the dataset publicly, but I can send you a link, > if > you're interested. > > Cheers, > Jason Galyardt > > > > _______________________________________________ > 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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By the way, I'm working on a bug report, currently. Jason On Mon, May 11, 2015 at 3:51 PM, Matthew Turk wrote:

Hi Jason,

That does look odd; the way the particle mappings are constructed may not be valid for your data. How many species of particles do you have, and of what types?

-Matt

...

It seems that the problem is in the evaluation of 'end', which gets set to 0. I don't know how the ds.index._particle_indices container (which

...

is set to) is supposed to look, but it's got an awful lot of zeros

...

front. In fact, of the 8017 elements, 5655 of them are exactly 0.

Looking at line 76 with the debugger, p_ind[g2.id - g2._id_offset + 1] = p_ind[1000 - 1 + 1] = p_ind[1000] = 0.

Is this normal? Doesn't make sense to me, since there are 9000+

...

this time step.

Jason

On Mon, May 11, 2015 at 1:17 PM, Nathan Goldbaum wrote:

...

If I had access to the dataset, I would put a breakpoint before line 76

in

...

your traceback here:

/home/jeg/yt/yt/frontends/flash/io.pyc in _read_particle_coords(self, chunks, ptf) 74 start = p_ind[g1.id - g1._id_offset] 75 end = p_ind[g2.id - g2._id_offset + 1] ---> 76 x = np.asarray(p_fields[start:end, px], dtype="=f8") 77 y = np.asarray(p_fields[start:end, py], dtype="=f8") 78 z = np.asarray(p_fields[start:end, pz], dtype="=f8")

I would try to print out start and end, as well as g1.id, g1._id_offset, g2.id,and g2._id_offset.

This is the last frame before we leave yt and enter h5py. For some reason start = end here, and we'd need to look at how the dataset is being read in to figure out why.

On Mon, May 11, 2015 at 6:38 AM, Jason Galyardt < jason.galyardt@gmail.com> wrote:

...

Hi all,

Per Matt's suggestion, I've tried accessing the FLASH particles via ['all', 'particle_mass'], to no avail. The traceback can be found here:

http://paste.yt-project.org/show/5541/

I get the same zero-length selection exception when I use ['io', 'particle_position_x'] or ['all', 'particle_position_x'], as Yuan

suggests.

...

To further check the input particle file format, I used the low-level h5py interface. I was able to read both particle position and mass.

This

...

script doesn't know about the grid, however.

Any other ideas?

Thanks, Jason

On Sat, May 9, 2015 at 9:59 PM, Yuan Li wrote:

...

I tried ['io', 'particle_position_x'] on my Flash data, and it seemed

to

...

work just fine. I use the latest yt.

Yuan

On Sat, May 9, 2015 at 7:51 PM, Nathan Goldbaum < nathan12343@gmail.com> wrote:

...

I'm not able to reproduce this using the Orbit dataset on yt-project.org/data. Unfortunately I don't think we have any other

flash

...

test datasets that use particles.

It would also help to see the full error traceback you're getting.

On Sat, May 9, 2015 at 4:32 PM, Matthew Turk wrote: > > Hi Jason, > > Don't worry about posting the data -- that's completely fine, and I > think in general we should do all we can to reproduce without the > dataset! I'm wondering if perhaps there's something funny about the > "io" particle field. If you try "all" instead of "io", does it work > any better? > > -Matt > > On Fri, May 8, 2015 at 1:01 PM, Jason Galyardt > wrote: > > Hi all, > > > > Has anyone had success accessing deposited particle data generated > > with > > FLASH? It appears in the dataset derived field list, but when I go > > to access > > it (via ds.all_data()['deposit', 'io_mass']), I get an error > > concerning > > zero-length selection. I get the same error when I try to access

...

...

...

...

...

> > 'standard' particle data (from ds.field_list), such as > > ds.all_data()['io', > > 'particle_mass']. > > > > Does this ring any bells? This very well could be user error, so > > please let > > me know if that seems to be the case. I've pasted a basic script to > > reproduce the error here: > > > > http://paste.yt-project.org/show/5538/ > > > > I'd rather not post the dataset publicly, but I can send you a

On Mon, May 11, 2015 at 2:36 PM, Jason Galyardt wrote: p_ind packed in particles in the link,

...

...

...

...

...

> > if > > you're interested. > > > > Cheers, > > Jason Galyardt > > > > > > > > _______________________________________________ > > 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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