Dear yt users, I have a problem when trying to make a SlicePlot along the y-axis of any data, for any field. yt just hangs and no plot is created. For the x- and z-axes everything works fine, and a ProjectionPlot along the y-axis is also not a problem. I have tried updating yt and installing the current development version, but to no avail. Any help is much appreciated! Best regards, Caroline
Hi Caroline, Sorry to hear you're having trouble. Can you let us know what code generated the dataset you're trying to plot? Have you been able to visualize data produced by this code in the past? If you feel comfortable sharing your data and if it is small enough to be hosted on the web somewhere, it would be great if you could upload your dataset and either reply with a link to the list or send it to me privately so that one of us could try to take a look and see what exactly is going wrong. I understand that datasets can sometimes be sensitive, however it can be slow and difficult to debug problems like this over e-mail. Cheers, Nathan On Apr 16, 2013, at 6:43 AM, Caroline Van Borm <borm@astro.rug.nl> wrote:
Dear yt users,
I have a problem when trying to make a SlicePlot along the y-axis of any data, for any field. yt just hangs and no plot is created. For the x- and z-axes everything works fine, and a ProjectionPlot along the y-axis is also not a problem. I have tried updating yt and installing the current development version, but to no avail.
Any help is much appreciated!
Best regards, Caroline _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
Hi Nathan, I used the Enzo code (version 2.2) and was just running some of the included test problems. There is some example data available at http://lca.ucsd.edu/software/enzo/data/cookbook/ (I believe this is from an earlier version of Enzo), the plotting of which also results in the described problem. This is the first time I'm using yt. Thanks, Caroline On 04/16/2013 11:03 PM, Nathan Goldbaum wrote:
Hi Caroline,
Sorry to hear you're having trouble.
Can you let us know what code generated the dataset you're trying to plot? Have you been able to visualize data produced by this code in the past?
If you feel comfortable sharing your data and if it is small enough to be hosted on the web somewhere, it would be great if you could upload your dataset and either reply with a link to the list or send it to me privately so that one of us could try to take a look and see what exactly is going wrong. I understand that datasets can sometimes be sensitive, however it can be slow and difficult to debug problems like this over e-mail.
Cheers,
Nathan
On Apr 16, 2013, at 6:43 AM, Caroline Van Borm<borm@astro.rug.nl> wrote:
Dear yt users,
I have a problem when trying to make a SlicePlot along the y-axis of any data, for any field. yt just hangs and no plot is created. For the x- and z-axes everything works fine, and a ProjectionPlot along the y-axis is also not a problem. I have tried updating yt and installing the current development version, but to no avail.
Any help is much appreciated!
Best regards, Caroline _______________________________________________ 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 Caroline, Thanks for writing, and sorry that it's not working. Don't worry too much about sending the data. I'm sorry to hear that it's hanging and not responding, which isn't behavior we have often seen. Here are a couple questions that will help us figure out how things might have gone wrong. * Did you run this via a script that you wrote? If you, could you run the command: yt pastebin that_script.py where "that_script.py" is the filename? That will give a URL, which you can include in a reply so we can see it. * What output do you see on screen up to the point where the execution hangs? * How did you install yt? * Is there one particular piece of sample data that we can run the script you paste'd (above) on to see the behavior? * Have you made any changes to your installation -- for instance, to your matplotlib installation? * When it's hung, if you press Ctrl-C so that execution terminates, what is output to the screen? It should look like a traceback, where various functions and routines are listed in order and at the bottom it will say something like "KeyboardInterrupt" Thanks very much, and let's see if we can get this working for you. :) -Matt On Wed, Apr 17, 2013 at 5:51 AM, Caroline Van Borm <borm@astro.rug.nl> wrote:
Hi Nathan,
I used the Enzo code (version 2.2) and was just running some of the included test problems. There is some example data available at http://lca.ucsd.edu/software/enzo/data/cookbook/ (I believe this is from an earlier version of Enzo), the plotting of which also results in the described problem. This is the first time I'm using yt.
Thanks, Caroline
On 04/16/2013 11:03 PM, Nathan Goldbaum wrote:
Hi Caroline,
Sorry to hear you're having trouble.
Can you let us know what code generated the dataset you're trying to plot? Have you been able to visualize data produced by this code in the past?
If you feel comfortable sharing your data and if it is small enough to be hosted on the web somewhere, it would be great if you could upload your dataset and either reply with a link to the list or send it to me privately so that one of us could try to take a look and see what exactly is going wrong. I understand that datasets can sometimes be sensitive, however it can be slow and difficult to debug problems like this over e-mail.
Cheers,
Nathan
On Apr 16, 2013, at 6:43 AM, Caroline Van Borm<borm@astro.rug.nl> wrote:
Dear yt users,
I have a problem when trying to make a SlicePlot along the y-axis of any data, for any field. yt just hangs and no plot is created. For the x- and z-axes everything works fine, and a ProjectionPlot along the y-axis is also not a problem. I have tried updating yt and installing the current development version, but to no avail.
Any help is much appreciated!
Best regards, Caroline _______________________________________________ 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 Matthew, I tried both running it from a script and interactively (with iyt). I really only used a minimum of code: from yt.mods import * pf = EnzoStaticOutput("RD0007/RedshiftOutput0007") #I also tried: pf = load("RD0007/RedshiftOutput0007") SlicePlot(pf, 'y', 'Density').save() Sample data to run this on can be found on http://lca.ucsd.edu/software/enzo/data/cookbook/ Just download and unpack any of the RD000* folders, for instance RD0007 for the example code above. On the screen, after the SlicePlot command it says yt : [INFO ] 2013-04-18 12:16:59,830 Getting the binary hierarchy yt : [INFO ] 2013-04-18 12:16:59,838 Finished with binary hierarchy reading and there it hangs. Pressing Ctrl-C doesn't do anything, I have to kill the process manually from another terminal. I installed yt using the installation script from the website, I don't think I changed any of the settings, or anything after the installation. The only thing I did before installing was "/export CC/=/icc//" ///to get HDF5 to install properly. Thank you very much! Cheers, Caroline On 04/17/2013 01:42 PM, Matthew Turk wrote:
Hi Caroline,
Thanks for writing, and sorry that it's not working. Don't worry too much about sending the data. I'm sorry to hear that it's hanging and not responding, which isn't behavior we have often seen. Here are a couple questions that will help us figure out how things might have gone wrong.
* Did you run this via a script that you wrote? If you, could you run the command:
yt pastebin that_script.py
where "that_script.py" is the filename? That will give a URL, which you can include in a reply so we can see it.
* What output do you see on screen up to the point where the execution hangs? * How did you install yt? * Is there one particular piece of sample data that we can run the script you paste'd (above) on to see the behavior? * Have you made any changes to your installation -- for instance, to your matplotlib installation? * When it's hung, if you press Ctrl-C so that execution terminates, what is output to the screen? It should look like a traceback, where various functions and routines are listed in order and at the bottom it will say something like "KeyboardInterrupt"
Thanks very much, and let's see if we can get this working for you. :)
-Matt
On Wed, Apr 17, 2013 at 5:51 AM, Caroline Van Borm<borm@astro.rug.nl> wrote:
Hi Nathan,
I used the Enzo code (version 2.2) and was just running some of the included test problems. There is some example data available at http://lca.ucsd.edu/software/enzo/data/cookbook/ (I believe this is from an earlier version of Enzo), the plotting of which also results in the described problem. This is the first time I'm using yt.
Thanks, Caroline
On 04/16/2013 11:03 PM, Nathan Goldbaum wrote:
Hi Caroline,
Sorry to hear you're having trouble.
Can you let us know what code generated the dataset you're trying to plot? Have you been able to visualize data produced by this code in the past?
If you feel comfortable sharing your data and if it is small enough to be hosted on the web somewhere, it would be great if you could upload your dataset and either reply with a link to the list or send it to me privately so that one of us could try to take a look and see what exactly is going wrong. I understand that datasets can sometimes be sensitive, however it can be slow and difficult to debug problems like this over e-mail.
Cheers,
Nathan
On Apr 16, 2013, at 6:43 AM, Caroline Van Borm<borm@astro.rug.nl> wrote:
Dear yt users,
I have a problem when trying to make a SlicePlot along the y-axis of any data, for any field. yt just hangs and no plot is created. For the x- and z-axes everything works fine, and a ProjectionPlot along the y-axis is also not a problem. I have tried updating yt and installing the current development version, but to no avail.
Any help is much appreciated!
Best regards, Caroline _______________________________________________ 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 Caroline, On Thu, Apr 18, 2013 at 6:29 AM, Caroline Van Borm <borm@astro.rug.nl> wrote:
Hi Matthew,
I tried both running it from a script and interactively (with iyt). I really only used a minimum of code:
from yt.mods import * pf = EnzoStaticOutput("RD0007/RedshiftOutput0007") #I also tried: pf = load("RD0007/RedshiftOutput0007") SlicePlot(pf, 'y', 'Density').save()
Sample data to run this on can be found on
http://lca.ucsd.edu/software/enzo/data/cookbook/
Just download and unpack any of the RD000* folders, for instance RD0007 for the example code above.
On the screen, after the SlicePlot command it says
yt : [INFO ] 2013-04-18 12:16:59,830 Getting the binary hierarchy yt : [INFO ] 2013-04-18 12:16:59,838 Finished with binary hierarchy reading
and there it hangs. Pressing Ctrl-C doesn't do anything, I have to kill the process manually from another terminal.
Interesting. I've never seen this behavior, and particularly not in a way that biases one axis over another for slicing. One thing we have put into yt is the ability to respond to signals like SIGUSR1 ; so if instead of "kill [pid]" you do "kill -SIGUSR1 [pid]" (where [pid] is the process id) it should -- the next time the event loop hits -- output where in the python code it is. But, if it's really hung, this probably won't do anything. Not responding to Ctrl-C indicates it's probably inside C code somewhere; a likely candidate for this is in the IO. Another thing to try is this exact same script, but after you put these lines into ~/.yt/config [yt] loglevel: 1 this will increase the level of logging, which will tell us a lot more. Other scripts that use different patterns for data access may also be illuminating: pf = load( ... ) dd = pf.h.all_data() print dd["Density"].min(), dd["Density"].max() for instance.
I installed yt using the installation script from the website, I don't think I changed any of the settings, or anything after the installation. The only thing I did before installing was "export CC=icc" to get HDF5 to install properly.
I'm hesitant to say this is a problem, but it may be. This would mean that the entire stack has been built with icc, but possibly only for the C code, not the C++ code. I've not seen a case in the past where HDF5 wouldn't compile with GNU (i.e., gcc) and there may be a point where matplotlib (C++ code internally) may not be interoperating well. My gut feeling is that rebuilding from scratch with the default environment variables is the best bet, just for the purposes of reducing the number of possible issues, but I'm not sure. -Matt
Thank you very much!
Cheers, Caroline
On 04/17/2013 01:42 PM, Matthew Turk wrote:
Hi Caroline,
Thanks for writing, and sorry that it's not working. Don't worry too much about sending the data. I'm sorry to hear that it's hanging and not responding, which isn't behavior we have often seen. Here are a couple questions that will help us figure out how things might have gone wrong.
* Did you run this via a script that you wrote? If you, could you run the command:
yt pastebin that_script.py
where "that_script.py" is the filename? That will give a URL, which you can include in a reply so we can see it.
* What output do you see on screen up to the point where the execution hangs? * How did you install yt? * Is there one particular piece of sample data that we can run the script you paste'd (above) on to see the behavior? * Have you made any changes to your installation -- for instance, to your matplotlib installation? * When it's hung, if you press Ctrl-C so that execution terminates, what is output to the screen? It should look like a traceback, where various functions and routines are listed in order and at the bottom it will say something like "KeyboardInterrupt"
Thanks very much, and let's see if we can get this working for you. :)
-Matt
On Wed, Apr 17, 2013 at 5:51 AM, Caroline Van Borm <borm@astro.rug.nl> wrote:
Hi Nathan,
I used the Enzo code (version 2.2) and was just running some of the included test problems. There is some example data available at http://lca.ucsd.edu/software/enzo/data/cookbook/ (I believe this is from an earlier version of Enzo), the plotting of which also results in the described problem. This is the first time I'm using yt.
Thanks, Caroline
On 04/16/2013 11:03 PM, Nathan Goldbaum wrote:
Hi Caroline,
Sorry to hear you're having trouble.
Can you let us know what code generated the dataset you're trying to plot? Have you been able to visualize data produced by this code in the past?
If you feel comfortable sharing your data and if it is small enough to be hosted on the web somewhere, it would be great if you could upload your dataset and either reply with a link to the list or send it to me privately so that one of us could try to take a look and see what exactly is going wrong. I understand that datasets can sometimes be sensitive, however it can be slow and difficult to debug problems like this over e-mail.
Cheers,
Nathan
On Apr 16, 2013, at 6:43 AM, Caroline Van Borm<borm@astro.rug.nl> wrote:
Dear yt users,
I have a problem when trying to make a SlicePlot along the y-axis of any data, for any field. yt just hangs and no plot is created. For the x- and z-axes everything works fine, and a ProjectionPlot along the y-axis is also not a problem. I have tried updating yt and installing the current development version, but to no avail.
Any help is much appreciated!
Best regards, Caroline _______________________________________________ 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 Matt, When I tried to build yt with everything set to default values, it was not possible to install HDF5. I had someone look at it for me and I don't know exactly what they did, but after rebuilding now everything is working properly. So I guess it really was a build problem. Thank you for your help! Cheers, Caroline On 04/18/2013 01:17 PM, Matthew Turk wrote:
Hi Caroline,
Hi Matthew,
I tried both running it from a script and interactively (with iyt). I really only used a minimum of code:
from yt.mods import * pf = EnzoStaticOutput("RD0007/RedshiftOutput0007") #I also tried: pf = load("RD0007/RedshiftOutput0007") SlicePlot(pf, 'y', 'Density').save()
Sample data to run this on can be found on
http://lca.ucsd.edu/software/enzo/data/cookbook/
Just download and unpack any of the RD000* folders, for instance RD0007 for the example code above.
On the screen, after the SlicePlot command it says
yt : [INFO ] 2013-04-18 12:16:59,830 Getting the binary hierarchy yt : [INFO ] 2013-04-18 12:16:59,838 Finished with binary hierarchy reading
and there it hangs. Pressing Ctrl-C doesn't do anything, I have to kill the process manually from another terminal. Interesting. I've never seen this behavior, and particularly not in a way that biases one axis over another for slicing. One thing we have
On Thu, Apr 18, 2013 at 6:29 AM, Caroline Van Borm<borm@astro.rug.nl> wrote: put into yt is the ability to respond to signals like SIGUSR1 ; so if instead of "kill [pid]" you do "kill -SIGUSR1 [pid]" (where [pid] is the process id) it should -- the next time the event loop hits -- output where in the python code it is. But, if it's really hung, this probably won't do anything.
Not responding to Ctrl-C indicates it's probably inside C code somewhere; a likely candidate for this is in the IO. Another thing to try is this exact same script, but after you put these lines into ~/.yt/config
[yt] loglevel: 1
this will increase the level of logging, which will tell us a lot more. Other scripts that use different patterns for data access may also be illuminating:
pf = load( ... ) dd = pf.h.all_data() print dd["Density"].min(), dd["Density"].max()
for instance.
I installed yt using the installation script from the website, I don't think I changed any of the settings, or anything after the installation. The only thing I did before installing was "export CC=icc" to get HDF5 to install properly. I'm hesitant to say this is a problem, but it may be. This would mean that the entire stack has been built with icc, but possibly only for the C code, not the C++ code. I've not seen a case in the past where HDF5 wouldn't compile with GNU (i.e., gcc) and there may be a point where matplotlib (C++ code internally) may not be interoperating well. My gut feeling is that rebuilding from scratch with the default environment variables is the best bet, just for the purposes of reducing the number of possible issues, but I'm not sure.
-Matt
Thank you very much!
Cheers, Caroline
On 04/17/2013 01:42 PM, Matthew Turk wrote:
Hi Caroline,
Thanks for writing, and sorry that it's not working. Don't worry too much about sending the data. I'm sorry to hear that it's hanging and not responding, which isn't behavior we have often seen. Here are a couple questions that will help us figure out how things might have gone wrong.
* Did you run this via a script that you wrote? If you, could you run the command:
yt pastebin that_script.py
where "that_script.py" is the filename? That will give a URL, which you can include in a reply so we can see it.
* What output do you see on screen up to the point where the execution hangs? * How did you install yt? * Is there one particular piece of sample data that we can run the script you paste'd (above) on to see the behavior? * Have you made any changes to your installation -- for instance, to your matplotlib installation? * When it's hung, if you press Ctrl-C so that execution terminates, what is output to the screen? It should look like a traceback, where various functions and routines are listed in order and at the bottom it will say something like "KeyboardInterrupt"
Thanks very much, and let's see if we can get this working for you. :)
-Matt
On Wed, Apr 17, 2013 at 5:51 AM, Caroline Van Borm<borm@astro.rug.nl> wrote:
Hi Nathan,
I used the Enzo code (version 2.2) and was just running some of the included test problems. There is some example data available at http://lca.ucsd.edu/software/enzo/data/cookbook/ (I believe this is from an earlier version of Enzo), the plotting of which also results in the described problem. This is the first time I'm using yt.
Thanks, Caroline
On 04/16/2013 11:03 PM, Nathan Goldbaum wrote:
Hi Caroline,
Sorry to hear you're having trouble.
Can you let us know what code generated the dataset you're trying to plot? Have you been able to visualize data produced by this code in the past?
If you feel comfortable sharing your data and if it is small enough to be hosted on the web somewhere, it would be great if you could upload your dataset and either reply with a link to the list or send it to me privately so that one of us could try to take a look and see what exactly is going wrong. I understand that datasets can sometimes be sensitive, however it can be slow and difficult to debug problems like this over e-mail.
Cheers,
Nathan
On Apr 16, 2013, at 6:43 AM, Caroline Van Borm<borm@astro.rug.nl> wrote:
Dear yt users,
I have a problem when trying to make a SlicePlot along the y-axis of any data, for any field. yt just hangs and no plot is created. For the x- and z-axes everything works fine, and a ProjectionPlot along the y-axis is also not a problem. I have tried updating yt and installing the current development version, but to no avail.
Any help is much appreciated!
Best regards, Caroline _______________________________________________ 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
participants (3)
-
Caroline Van Borm -
Matthew Turk -
Nathan Goldbaum