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Elizabeth Tasker

24 Mar 2011 24 Mar '11

2:54 p.m.

Hi,

Is there any way in yt to get a script to delete (or ignore) all the .yt and .harray files and clear its memory? I run into errors when I'm re-doing a plot or I've re-run the simulation and over-written the last data set I looked at with yt. I have to exit yt, delete the above files by hand and restart, which is a bit of a pain.

Elizabeth

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Matthew Turk

24 Mar 24 Mar

2:58 p.m.

Hi Elizabeth,

There should be a check in the .yt and .harray files for the modification time of the simulation using the CurrentTimeIdentifier. But if you are running into issues, this should prevent all the .yt and .harray files from being looked at:

from yt.config import ytcfg; ytcfg["yt","serialize"] = "False"

Note that this must go at the top of your script.

-Matt

On Thu, Mar 24, 2011 at 10:54 AM, Elizabeth Tasker taskere@mcmaster.ca wrote:

...

Hi,

Elizabeth

yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

Elizabeth Tasker

8:09 p.m.

Hi Matt,

So actually that didn't work. Below, I've not re-run the simulation but just updated my script to move the centre in "pc = PlotCollection(pf, center=[100,100,100])" to a new location.

bash-4.0$ ~/yt/yt-2/bin/iyt slice_yt.py

NeedsDataField Traceback (most recent call last)

/1/home/taskere/yt/scripts/iyt in <module>() 23 pf = load(fn)
24 pc = PlotCollection(pf, center=[100,100,100]) ---> 25 p = pc.add_slice("Density", 2)
26
p.modify"grids"
27 p = pc.add_projection("Density", 2)
etc

But if I do:

In [2]: exit() Do you really want to exit ([y]/n)? y bash-4.0$ rm -rf yt bash-4.0$ rm -rf harr* bash-4.0$ ~/yt/yt-2/bin/iyt slice_yt.py

Then everything works. I've attached my yt script for added excitement.

Elizabeth

Matthew Turk wrote:

...

Hi Elizabeth,

from yt.config import ytcfg; ytcfg["yt","serialize"] = "False"

Note that this must go at the top of your script.

-Matt

On Thu, Mar 24, 2011 at 10:54 AM, Elizabeth Tasker taskere@mcmaster.ca wrote:

Hi,

Elizabeth

yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

Matthew Turk

8:24 p.m.

Hi Elizabeth,

My mistake; .harrays were not respecting "serialize". Fixed in hg.

-Matt

On Thu, Mar 24, 2011 at 4:09 PM, Elizabeth Tasker taskere@mcmaster.ca wrote:

...

Hi Matt,

So actually that didn't work. Below, I've not re-run the simulation but just updated my script to move the centre in "pc = PlotCollection(pf, center=[100,100,100])" to a new location.

bash-4.0$ ~/yt/yt-2/bin/iyt slice_yt.py

NeedsDataField Traceback (most recent call last)

/1/home/taskere/yt/scripts/iyt in <module>() 23 pf = load(fn) 24 pc = PlotCollection(pf, center=[100,100,100]) ---> 25 p = pc.add_slice("Density", 2) 26 p.modify"grids" 27 p = pc.add_projection("Density", 2) etc

But if I do:

In [2]: exit() Do you really want to exit ([y]/n)? y bash-4.0$ rm -rf yt bash-4.0$ rm -rf harr* bash-4.0$ ~/yt/yt-2/bin/iyt slice_yt.py

Then everything works. I've attached my yt script for added excitement.

Elizabeth

Matthew Turk wrote: >

Hi Elizabeth,

from yt.config import ytcfg; ytcfg["yt","serialize"] = "False"

Note that this must go at the top of your script.

-Matt

On Thu, Mar 24, 2011 at 10:54 AM, Elizabeth Tasker taskere@mcmaster.ca wrote:

Hi,

Elizabeth

yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

Molly Peeples

11:17 p.m.

Hi Matt,

I think I'm getting a similar thing; I updated yt and now I'm getting "global name 'ytcfg' is not defined" when I call PlotCollection. I've tried the removing what's in ~/.yt/ and including the ytcfg["yt","serialize"] = "False" but the error is the same. I put a copy of the script and the error at http://paste.enzotools.org/show/1540/

Thanks, --Molly

On Thu, Mar 24, 2011 at 1:24 PM, Matthew Turk matthewturk@gmail.com wrote:

...

Hi Elizabeth,

My mistake; .harrays were not respecting "serialize". Fixed in hg.

-Matt

On Thu, Mar 24, 2011 at 4:09 PM, Elizabeth Tasker taskere@mcmaster.ca wrote:

Hi Matt,

So actually that didn't work. Below, I've not re-run the simulation but just updated my script to move the centre in "pc = PlotCollection(pf, center=[100,100,100])" to a new location.

bash-4.0$ ~/yt/yt-2/bin/iyt slice_yt.py

NeedsDataField Traceback (most recent call last)

/1/home/taskere/yt/scripts/iyt in <module>() 23 pf = load(fn) 24 pc = PlotCollection(pf, center=[100,100,100]) ---> 25 p = pc.add_slice("Density", 2) 26 p.modify"grids" 27 p = pc.add_projection("Density", 2) etc

But if I do:

In [2]: exit() Do you really want to exit ([y]/n)? y bash-4.0$ rm -rf yt bash-4.0$ rm -rf harr* bash-4.0$ ~/yt/yt-2/bin/iyt slice_yt.py

Then everything works. I've attached my yt script for added excitement.

Elizabeth

Matthew Turk wrote: >

Hi Elizabeth,

from yt.config import ytcfg; ytcfg["yt","serialize"] = "False"

Note that this must go at the top of your script.

-Matt

On Thu, Mar 24, 2011 at 10:54 AM, Elizabeth Tasker taskere@mcmaster.ca wrote:

Hi,

Elizabeth

yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

Sam Skillman

25 Mar 25 Mar

1:41 a.m.

Hi Molly,

Looks like there was a missing import. It should be fixed in now in 6160341d2e8f.

Best, Sam

On Thu, Mar 24, 2011 at 7:17 PM, Molly Peeples molly@astro.ucla.edu wrote:

...

Hi Matt,

Thanks, --Molly

On Thu, Mar 24, 2011 at 1:24 PM, Matthew Turk matthewturk@gmail.com wrote:

Hi Elizabeth,

My mistake; .harrays were not respecting "serialize". Fixed in hg.

-Matt

On Thu, Mar 24, 2011 at 4:09 PM, Elizabeth Tasker taskere@mcmaster.ca wrote:

Hi Matt,

So actually that didn't work. Below, I've not re-run the simulation but just updated my script to move the centre in "pc = PlotCollection(pf, center=[100,100,100])" to a new location.

bash-4.0$ ~/yt/yt-2/bin/iyt slice_yt.py

NeedsDataField Traceback (most recent call last)

/1/home/taskere/yt/scripts/iyt in <module>() 23 pf = load(fn) 24 pc = PlotCollection(pf, center=[100,100,100]) ---> 25 p = pc.add_slice("Density", 2) 26 p.modify"grids" 27 p = pc.add_projection("Density", 2) etc

But if I do:

In [2]: exit() Do you really want to exit ([y]/n)? y bash-4.0$ rm -rf yt bash-4.0$ rm -rf harr* bash-4.0$ ~/yt/yt-2/bin/iyt slice_yt.py

Then everything works. I've attached my yt script for added excitement.

Elizabeth

Matthew Turk wrote: >

Hi Elizabeth,

from yt.config import ytcfg; ytcfg["yt","serialize"] = "False"

Note that this must go at the top of your script.

-Matt

On Thu, Mar 24, 2011 at 10:54 AM, Elizabeth Tasker taskere@mcmaster.ca wrote:

Hi,

Elizabeth

yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

Molly Peeples

2:51 a.m.

Hi Sam,

It's working now; thanks!

--Molly

On Thu, Mar 24, 2011 at 6:41 PM, Sam Skillman samskillman@gmail.com wrote:

...

Hi Molly, Looks like there was a missing import. It should be fixed in now in 6160341d2e8f. Best, Sam

On Thu, Mar 24, 2011 at 7:17 PM, Molly Peeples molly@astro.ucla.edu wrote: >

Hi Matt,

Thanks, --Molly

On Thu, Mar 24, 2011 at 1:24 PM, Matthew Turk matthewturk@gmail.com wrote:

Hi Elizabeth,

My mistake; .harrays were not respecting "serialize". Fixed in hg.

-Matt

On Thu, Mar 24, 2011 at 4:09 PM, Elizabeth Tasker taskere@mcmaster.ca wrote:

Hi Matt,

So actually that didn't work. Below, I've not re-run the simulation but just updated my script to move the centre in "pc = PlotCollection(pf, center=[100,100,100])" to a new location.

bash-4.0$ ~/yt/yt-2/bin/iyt slice_yt.py

NeedsDataField Traceback (most recent call last)

/1/home/taskere/yt/scripts/iyt in <module>() 23 pf = load(fn) 24 pc = PlotCollection(pf, center=[100,100,100]) ---> 25 p = pc.add_slice("Density", 2) 26 p.modify"grids" 27 p = pc.add_projection("Density", 2) etc

But if I do:

In [2]: exit() Do you really want to exit ([y]/n)? y bash-4.0$ rm -rf yt bash-4.0$ rm -rf harr* bash-4.0$ ~/yt/yt-2/bin/iyt slice_yt.py

Then everything works. I've attached my yt script for added excitement.

Elizabeth

Matthew Turk wrote: >

Hi Elizabeth,

from yt.config import ytcfg; ytcfg["yt","serialize"] = "False"

Note that this must go at the top of your script.

-Matt

On Thu, Mar 24, 2011 at 10:54 AM, Elizabeth Tasker taskere@mcmaster.ca wrote:

Hi,

Elizabeth

yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

Elizabeth Tasker

31 Aug 31 Aug

11:40 p.m.

Hi,

I think this is a related issue, so I'm going to put it on the same thread:

My arrays do not seem to be clearing properly in that, if I repeatedly run my analysis script, I start seeing very strange features in my ray objects (made from derived fields that I create myself) that I know are wrong. If I exit yt and restart, all becomes well again. Adding in:

from yt.config import ytcfg; ytcfg["yt","serialize"] = "False"

doesn't help, so this is possibly a python memory clearing issue, not yt.

Has anyone seen this before? Is there any kind of clear cache for ipython?

Thanks!

Elizabeth

Molly Peeples wrote:

...

Hi Sam,

It's working now; thanks!

--Molly

On Thu, Mar 24, 2011 at 6:41 PM, Sam Skillman samskillman@gmail.com wrote:

Hi Molly, Looks like there was a missing import. It should be fixed in now in 6160341d2e8f. Best, Sam

On Thu, Mar 24, 2011 at 7:17 PM, Molly Peeples molly@astro.ucla.edu wrote:

Hi Matt,

Thanks, --Molly

On Thu, Mar 24, 2011 at 1:24 PM, Matthew Turk matthewturk@gmail.com wrote:

Hi Elizabeth,

My mistake; .harrays were not respecting "serialize". Fixed in hg.

-Matt

On Thu, Mar 24, 2011 at 4:09 PM, Elizabeth Tasker taskere@mcmaster.ca wrote:

Hi Matt,

So actually that didn't work. Below, I've not re-run the simulation but just updated my script to move the centre in "pc = PlotCollection(pf, center=[100,100,100])" to a new location.

bash-4.0$ ~/yt/yt-2/bin/iyt slice_yt.py

NeedsDataField Traceback (most recent call last)

/1/home/taskere/yt/scripts/iyt in <module>() 23 pf = load(fn) 24 pc = PlotCollection(pf, center=[100,100,100]) ---> 25 p = pc.add_slice("Density", 2) 26 p.modify"grids" 27 p = pc.add_projection("Density", 2) etc

But if I do:

In [2]: exit() Do you really want to exit ([y]/n)? y bash-4.0$ rm -rf yt bash-4.0$ rm -rf harr* bash-4.0$ ~/yt/yt-2/bin/iyt slice_yt.py

Then everything works. I've attached my yt script for added excitement.

Elizabeth

Matthew Turk wrote:

Hi Elizabeth,

from yt.config import ytcfg; ytcfg["yt","serialize"] = "False"

Note that this must go at the top of your script.

-Matt

On Thu, Mar 24, 2011 at 10:54 AM, Elizabeth Tasker taskere@mcmaster.ca wrote:

> Hi, > > Is there any way in yt to get a script to delete (or ignore) all the > .yt > and > .harray files and clear its memory? I run into errors when I'm > re-doing a > plot or I've re-run the simulation and over-written the last data set > I > looked at with yt. I have to exit yt, delete the above files by hand > and > restart, which is a bit of a pain. > > 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

Matthew Turk

1 Sep 1 Sep

10:45 a.m.

Hi Elizabeth,

Serialize shouldn't have much or any effect on the problems you are describing. If you can give more information, specifically which variables seem corrupted, if the derived fields use any external sources or mutable variables, if you have diagnosed things with other fields, etc etc, that may help out, however.

-Matt

On Wed, Aug 31, 2011 at 7:40 PM, Elizabeth Tasker taskere@mcmaster.ca wrote:

...

Hi,

I think this is a related issue, so I'm going to put it on the same thread:

from yt.config import ytcfg; ytcfg["yt","serialize"] = "False"

doesn't help, so this is possibly a python memory clearing issue, not yt.

Has anyone seen this before? Is there any kind of clear cache for ipython?

Thanks!

Elizabeth

Molly Peeples wrote: >

Hi Sam,

It's working now; thanks!

--Molly

On Thu, Mar 24, 2011 at 6:41 PM, Sam Skillman samskillman@gmail.com wrote:

Hi Molly, Looks like there was a missing import. It should be fixed in now in 6160341d2e8f. Best, Sam

On Thu, Mar 24, 2011 at 7:17 PM, Molly Peeples molly@astro.ucla.edu wrote:

Hi Matt,

Thanks, --Molly

On Thu, Mar 24, 2011 at 1:24 PM, Matthew Turk matthewturk@gmail.com wrote:

Hi Elizabeth,

My mistake; .harrays were not respecting "serialize". Fixed in hg.

-Matt

On Thu, Mar 24, 2011 at 4:09 PM, Elizabeth Tasker taskere@mcmaster.ca wrote:

Hi Matt,

So actually that didn't work. Below, I've not re-run the simulation but just updated my script to move the centre in "pc = PlotCollection(pf, center=[100,100,100])" to a new location.

bash-4.0$ ~/yt/yt-2/bin/iyt slice_yt.py

NeedsDataField Traceback (most recent call last)

/1/home/taskere/yt/scripts/iyt in <module>() 23 pf = load(fn) 24 pc = PlotCollection(pf, center=[100,100,100]) ---> 25 p = pc.add_slice("Density", 2) 26 p.modify"grids" 27 p = pc.add_projection("Density", 2) etc

But if I do:

In [2]: exit() Do you really want to exit ([y]/n)? y bash-4.0$ rm -rf yt bash-4.0$ rm -rf harr* bash-4.0$ ~/yt/yt-2/bin/iyt slice_yt.py

Then everything works. I've attached my yt script for added excitement.

Elizabeth

Matthew Turk wrote:

> Hi Elizabeth, > > There should be a check in the .yt and .harray files for the > modification time of the simulation using the CurrentTimeIdentifier. > But if you are running into issues, this should prevent all the .yt > and .harray files from being looked at: > > from yt.config import ytcfg; ytcfg["yt","serialize"] = "False" > > Note that this must go at the top of your script. > > -Matt > > On Thu, Mar 24, 2011 at 10:54 AM, Elizabeth Tasker > taskere@mcmaster.ca > wrote: > > >> >> Hi, >> >> Is there any way in yt to get a script to delete (or ignore) all the >> .yt >> and >> .harray files and clear its memory? I run into errors when I'm >> re-doing a >> plot or I've re-run the simulation and over-written the last data >> set >> I >> looked at with yt. I have to exit yt, delete the above files by hand >> and >> restart, which is a bit of a pain. >> >> 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 > >

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participants (4)

Elizabeth Tasker
Matthew Turk
Molly Peeples
Sam Skillman