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 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

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 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 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 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

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

Hi Sam, It's working now; thanks! --Molly On Thu, Mar 24, 2011 at 6:41 PM, Sam Skillman 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 wrote:

...

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 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 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 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

_______________________________________________ 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 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 wrote:

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 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 wrote:

...

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 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 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 > > 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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