Hi, I'm having some problems with clump finder. Specifically, it gets to this point: yt : [INFO ] 2012-06-13 02:10:34,119 Getting field TotalEnergy from 1 yt : [INFO ] 2012-06-13 02:10:34,139 Getting field x from 1 yt : [INFO ] 2012-06-13 02:10:34,147 Getting field y from 1 yt : [INFO ] 2012-06-13 02:10:34,155 Getting field z from 1 yt : [INFO ] 2012-06-13 02:10:34,159 Adjusting clump for periodic boundaries in dim z and then stops (no error). My region actually isn't periodic and this must be a memory intensive step that isn't appropriate. Does the clump find tools/wrapper have a switch for non-periodic regions? Thanks! Elizabeth
Hi Elizabeth, On Tue, Jun 12, 2012 at 7:34 PM, Elizabeth Tasker <tasker@astro1.sci.hokudai.ac.jp> wrote:
Hi,
I'm having some problems with clump finder.
Specifically, it gets to this point:
yt : [INFO ] 2012-06-13 02:10:34,119 Getting field TotalEnergy from 1 yt : [INFO ] 2012-06-13 02:10:34,139 Getting field x from 1 yt : [INFO ] 2012-06-13 02:10:34,147 Getting field y from 1 yt : [INFO ] 2012-06-13 02:10:34,155 Getting field z from 1 yt : [INFO ] 2012-06-13 02:10:34,159 Adjusting clump for periodic boundaries in dim z
and then stops (no error).
My region actually isn't periodic and this must be a memory intensive step that isn't appropriate. Does the clump find tools/wrapper have a switch for non-periodic regions?
Are you sure this is a memory problem? Does it OOM error, does it segfault, etc etc? As for turning off periodicity, this is possible but not currently implemented. -Matt
Thanks!
Elizabeth _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
Hi Matt,
Are you sure this is a memory problem? Does it OOM error, does it segfault, etc etc?
As for turning off periodicity, this is possible but not currently implemented.
I'm not totally sure, no. It just says "Forced termination" and stops. (Actually, it says '強制終了' but that translated to forced termination.) Elizabeth
I should maybe add that I'm running this on a disk object and I was previously using connected sets on its own without the clump find wrapper, and that was no problem. I think that means that either it's the periodic nature that's an issue or it's a memory issue because the number of iterations clump find is doing? Elizabeth On 2012-06-13, at 9:09 AM, Matthew Turk wrote:
Hi Elizabeth,
On Tue, Jun 12, 2012 at 7:34 PM, Elizabeth Tasker <tasker@astro1.sci.hokudai.ac.jp> wrote:
Hi,
I'm having some problems with clump finder.
Specifically, it gets to this point:
yt : [INFO ] 2012-06-13 02:10:34,119 Getting field TotalEnergy from 1 yt : [INFO ] 2012-06-13 02:10:34,139 Getting field x from 1 yt : [INFO ] 2012-06-13 02:10:34,147 Getting field y from 1 yt : [INFO ] 2012-06-13 02:10:34,155 Getting field z from 1 yt : [INFO ] 2012-06-13 02:10:34,159 Adjusting clump for periodic boundaries in dim z
and then stops (no error).
My region actually isn't periodic and this must be a memory intensive step that isn't appropriate. Does the clump find tools/wrapper have a switch for non-periodic regions?
Are you sure this is a memory problem? Does it OOM error, does it segfault, etc etc?
As for turning off periodicity, this is possible but not currently implemented.
-Matt
Thanks!
Elizabeth _______________________________________________ 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
On Tue, Jun 12, 2012 at 8:18 PM, Elizabeth Tasker <tasker@astro1.sci.hokudai.ac.jp> wrote:
I should maybe add that I'm running this on a disk object and I was previously using connected sets on its own without the clump find wrapper, and that was no problem.
I think that means that either it's the periodic nature that's an issue or it's a memory issue because the number of iterations clump find is doing?
It will output each time it does another iteration, which leads me to believe something is going wrong the first time. How have you changed between the clump and the connected set calls? Are they operating on the same data object? A thought occurs: Stephen, Britton, do you have the binding energy calculation on by default?
Elizabeth
On 2012-06-13, at 9:09 AM, Matthew Turk wrote:
Hi Elizabeth,
On Tue, Jun 12, 2012 at 7:34 PM, Elizabeth Tasker <tasker@astro1.sci.hokudai.ac.jp> wrote:
Hi,
I'm having some problems with clump finder.
Specifically, it gets to this point:
yt : [INFO ] 2012-06-13 02:10:34,119 Getting field TotalEnergy from 1 yt : [INFO ] 2012-06-13 02:10:34,139 Getting field x from 1 yt : [INFO ] 2012-06-13 02:10:34,147 Getting field y from 1 yt : [INFO ] 2012-06-13 02:10:34,155 Getting field z from 1 yt : [INFO ] 2012-06-13 02:10:34,159 Adjusting clump for periodic boundaries in dim z
and then stops (no error).
My region actually isn't periodic and this must be a memory intensive step that isn't appropriate. Does the clump find tools/wrapper have a switch for non-periodic regions?
Are you sure this is a memory problem? Does it OOM error, does it segfault, etc etc?
As for turning off periodicity, this is possible but not currently implemented.
-Matt
Thanks!
Elizabeth _______________________________________________ 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
Hi,
A thought occurs: Stephen, Britton, do you have the binding energy calculation on by default?
Yes, that is the default. -- Stephen Skory s@skory.us http://stephenskory.com/ 510.621.3687 (google voice)
Hi Stephen, Is there an easy switch for that? It's actually not a check I need for my data. Elizabeth On Jun 13, 2012, at 11:38 PM, Stephen Skory wrote:
Hi,
A thought occurs: Stephen, Britton, do you have the binding energy calculation on by default?
Yes, that is the default.
-- Stephen Skory s@skory.us http://stephenskory.com/ 510.621.3687 (google voice) _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
Hi Elizabeth,
Is there an easy switch for that? It's actually not a check I need for my data.
I have done something like this in the past: fname = 'len([1])' master_clump = amods.level_sets.Clump(sp, None, field, function=fname) fname just needs to be something that evaluates to 1 or True. There are probably more elegant functions, but this is short and sweet. Let me know if that doesn't make sense. -- Stephen Skory s@skory.us http://stephenskory.com/ 510.621.3687 (google voice)
Hi Elizabeth, You can also just do: function='True' Just make sure to put it in quotes like that. Britton On Wed, Jun 13, 2012 at 11:34 AM, Stephen Skory <s@skory.us> wrote:
Hi Elizabeth,
Is there an easy switch for that? It's actually not a check I need for my data.
I have done something like this in the past:
fname = 'len([1])' master_clump = amods.level_sets.Clump(sp, None, field, function=fname)
fname just needs to be something that evaluates to 1 or True. There are probably more elegant functions, but this is short and sweet. Let me know if that doesn't make sense.
-- Stephen Skory s@skory.us http://stephenskory.com/ 510.621.3687 (google voice) _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
You can also just do: function='True' Just make sure to put it in quotes like that.
Even shorter and sweeter! -- Stephen Skory s@skory.us http://stephenskory.com/ 510.621.3687 (google voice)
That fixed my problem -- thank you! Elizabeth On Jun 14, 2012, at 12:36 AM, Stephen Skory wrote:
You can also just do: function='True' Just make sure to put it in quotes like that.
Even shorter and sweeter!
-- Stephen Skory s@skory.us http://stephenskory.com/ 510.621.3687 (google voice) _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
Hi, Still hitting some problems with clump find. The clump object doesn't accept field parameters: In [14]: cloudcores[0].set_field_parameter("thiscore_omega", core_omega[c1]) --------------------------------------------------------------------------- AttributeError Traceback (most recent call last) /home/tasker/yt/src/yt-hg/scripts/iyt in <module>() ----> 1 cloudcores[0].set_field_parameter("thiscore_omega", core_omega[c1]) AttributeError: 'Clump' object has no attribute 'set_field_parameter' Can the clump find wrapper be adjusted to fix this? The individual connected sets definitely can accept field parameters. Elizabeth On 14 June 2012 16:06, Elizabeth Tasker <tasker@astro1.sci.hokudai.ac.jp> wrote:
That fixed my problem -- thank you!
Elizabeth
On Jun 14, 2012, at 12:36 AM, Stephen Skory wrote:
You can also just do: function='True' Just make sure to put it in quotes like that.
Even shorter and sweeter!
-- Stephen Skory s@skory.us http://stephenskory.com/ 510.621.3687 (google voice) _______________________________________________ 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
The Clump object has a .data object, which should be your familiar extracted region. On Thu, Jun 14, 2012 at 4:11 AM, Elizabeth Tasker <tasker@astro1.sci.hokudai.ac.jp> wrote:
Hi,
Still hitting some problems with clump find.
The clump object doesn't accept field parameters:
In [14]: cloudcores[0].set_field_parameter("thiscore_omega", core_omega[c1]) --------------------------------------------------------------------------- AttributeError Traceback (most recent call last) /home/tasker/yt/src/yt-hg/scripts/iyt in <module>() ----> 1 cloudcores[0].set_field_parameter("thiscore_omega", core_omega[c1])
AttributeError: 'Clump' object has no attribute 'set_field_parameter'
Can the clump find wrapper be adjusted to fix this? The individual connected sets definitely can accept field parameters.
Elizabeth
On 14 June 2012 16:06, Elizabeth Tasker <tasker@astro1.sci.hokudai.ac.jp> wrote:
That fixed my problem -- thank you!
Elizabeth
On Jun 14, 2012, at 12:36 AM, Stephen Skory wrote:
You can also just do: function='True' Just make sure to put it in quotes like that.
Even shorter and sweeter!
-- Stephen Skory s@skory.us http://stephenskory.com/ 510.621.3687 (google voice) _______________________________________________ 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
Hi Matt, Great - thanks! Elizabeth On Jun 14, 2012, at 7:08 PM, Matthew Turk wrote:
The Clump object has a .data object, which should be your familiar extracted region.
On Thu, Jun 14, 2012 at 4:11 AM, Elizabeth Tasker <tasker@astro1.sci.hokudai.ac.jp> wrote:
Hi,
Still hitting some problems with clump find.
The clump object doesn't accept field parameters:
In [14]: cloudcores[0].set_field_parameter("thiscore_omega", core_omega[c1]) --------------------------------------------------------------------------- AttributeError Traceback (most recent call last) /home/tasker/yt/src/yt-hg/scripts/iyt in <module>() ----> 1 cloudcores[0].set_field_parameter("thiscore_omega", core_omega[c1])
AttributeError: 'Clump' object has no attribute 'set_field_parameter'
Can the clump find wrapper be adjusted to fix this? The individual connected sets definitely can accept field parameters.
Elizabeth
On 14 June 2012 16:06, Elizabeth Tasker <tasker@astro1.sci.hokudai.ac.jp> wrote:
That fixed my problem -- thank you!
Elizabeth
On Jun 14, 2012, at 12:36 AM, Stephen Skory wrote:
You can also just do: function='True' Just make sure to put it in quotes like that.
Even shorter and sweeter!
-- Stephen Skory s@skory.us http://stephenskory.com/ 510.621.3687 (google voice) _______________________________________________ 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
participants (4)
-
Britton Smith -
Elizabeth Tasker -
Matthew Turk -
Stephen Skory