X Window System error

Mic · October 2, 2012, 5:28am

Hi,

I have got the following error with the following code:
$ python mpl.py

Traceback (most recent call last):

File “/usr/lib64/python2.7/site-packages/matplotlib/backends/backend_gtk.py”, line 398, in expose_event

self._render_figure(self._pixmap, w, h)

File “/usr/lib64/python2.7/site-packages/matplotlib/backends/backend_gtkagg.py”, line 75, in _render_figure

FigureCanvasAgg.draw(self)

File “/usr/lib64/python2.7/site-packages/matplotlib/backends/backend_agg.py”, line 416, in draw

self.renderer = self.get_renderer()

File “/usr/lib64/python2.7/site-packages/matplotlib/backends/backend_agg.py”, line 435, in get_renderer

self.renderer = RendererAgg(w, h, self.figure.dpi)

File “/usr/lib64/python2.7/site-packages/matplotlib/backends/backend_agg.py”, line 72, in init

self._renderer = _RendererAgg(int(width), int(height), dpi, debug=False)

ValueError: width and height must each be below 32768

The program ‘mpl.py’ received an X Window System error.

This probably reflects a bug in the program.

The error was ‘BadAlloc (insufficient resources for operation)’.

(Details: serial 486 error_code 11 request_code 53 minor_code 0)

(Note to programmers: normally, X errors are reported asynchronously;

that is, you will receive the error a while after causing it.

To debug your program, run it with the --sync command line

option to change this behavior. You can then get a meaningful

backtrace from your debugger if you break on the gdk_x_error() function.)

With the following code:

*import random *

*import matplotlib.pyplot as plt *

···

**

_coverages = [random.randint(1,10)*2] * 4605 _

_contig_names = [‘AAB0008r’] * len(coverages) _

*# Set the figure size *

*#fig = plt.figure(1, [20, 2]) *

_fig = plt.figure(figsize=(int(len(coverages)*0.1), 4)) _

**

*ax = fig.add_subplot(111) *

**

*# Set the x-axis limit *

*#ax.set_xlim(-1,100) *

*ax.set_xlim(0,len(coverages)) *

*#ax.set_ylim(0,3) *

*ax.yaxis.grid(True, linestyle=’-’, which=‘major’, color=‘grey’, alpha=0.5) *

**

*ind = range(len(coverages)) *

*rects = ax.bar(ind, coverages, width=0.1, align=‘center’, color=‘thistle’) *

*ax.set_xticks(ind) *

#ax.set_xticklabels(contig_names)

#ax.tick_params(axis=‘both’, which=‘major’, labelsize=10)

#ax.tick_params(axis=‘both’, which=‘minor’, labelsize=8)

#function to auto-rotate the x axis labels

fig.autofmt_xdate()

plt.setp(ax.get_xticklabels(), fontsize=8, rotation=‘vertical’)

plt.show()

How is it possible to get big charts?

Thank you in advance.

Eric_Firing1 · October 2, 2012, 6:04am

Hi,

I have got the following error with the following code:
/$ python mpl.py/
/Traceback (most recent call last)
/ File
"/usr/lib64/python2.7/site-packages/matplotlib/backends/backend_gtk.py",
line 398, in expose_event/
/ self._render_figure(self._pixmap, w, h)/
/ File
"/usr/lib64/python2.7/site-packages/matplotlib/backends/backend_gtkagg.py",
line 75, in _render_figure/
/ FigureCanvasAgg.draw(self)/
/ File
"/usr/lib64/python2.7/site-packages/matplotlib/backends/backend_agg.py",
line 416, in draw/
/ self.renderer = self.get_renderer()/
/ File
"/usr/lib64/python2.7/site-packages/matplotlib/backends/backend_agg.py",
line 435, in get_renderer/
/ self.renderer = RendererAgg(w, h, self.figure.dpi)/
/ File
"/usr/lib64/python2.7/site-packages/matplotlib/backends/backend_agg.py",
line 72, in __init__/
/ self._renderer = _RendererAgg(int(width), int(height), dpi,
debug=False)/
/ValueError: width and height must each be below 32768/
/The program 'mpl.py' received an X Window System error./
/This probably reflects a bug in the program./
/The error was 'BadAlloc (insufficient resources for operation)'./
/ (Details: serial 486 error_code 11 request_code 53 minor_code 0)/
/ (Note to programmers: normally, X errors are reported asynchronously;/
/ that is, you will receive the error a while after causing it./
/ To debug your program, run it with the --sync command line/
/ option to change this behavior. You can then get a meaningful/
/ backtrace from your debugger if you break on the gdk_x_error()
function.)/

With the following code:
/import random /
/import matplotlib.pyplot as plt /
//
/coverages = [random.randint(1,10)*2] * 4605 /
/contig_names = ['AAB0008r'] * len(coverages) /
/# Set the figure size /
/#fig = plt.figure(1, [20, 2]) /
/fig = plt.figure(figsize=(int(len(coverages)*0.1), 4)) /
//
/ax = fig.add_subplot(111) /
//
/# Set the x-axis limit /
/#ax.set_xlim(-1,100) /
/ax.set_xlim(0,len(coverages)) /
/#ax.set_ylim(0,3) /
/ax.yaxis.grid(True, linestyle='-', which='major', color='grey',
alpha=0.5) /
//
/ind = range(len(coverages)) /
/rects = ax.bar(ind, coverages, width=0.1, align='center',
color='thistle') /
/ax.set_xticks(ind) /
/#ax.set_xticklabels(contig_names)/
/#ax.tick_params(axis='both', which='major', labelsize=10)/
/#ax.tick_params(axis='both', which='minor', labelsize=8)/
/
/#function to auto-rotate the x axis labels/
/fig.autofmt_xdate()/
/plt.setp(ax.get_xticklabels(), fontsize=8, rotation='vertical')/
/plt.show()/

How is it possible to get big charts?

It looks like you are trying to make a figure that is 460 inches by 4 inches. How do you expect to display or print it? I think displaying it is out of the question, so you would need to use a non-interactive backend. I don't know whether ps or pdf can handle those sorts of dimensions.

Eric

···

On 2012/10/01 7:28 PM, Mic wrote:

Thank you in advance.

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Mic · October 2, 2012, 2:12pm

Hi Eric,

I have a dataset which contains about 4600 values.

Is it possible to display 4600 values with a bar char and labels?

Thank you in advance.

···

On Tue, Oct 2, 2012 at 4:04 PM, Eric Firing <efiring@…202…> wrote:

On 2012/10/01 7:28 PM, Mic wrote:

Hi,

I have got the following error with the following code:

/$ python mpl.py/

/Traceback (most recent call last)

/ File

“/usr/lib64/python2.7/site-packages/matplotlib/backends/backend_gtk.py”,

line 398, in expose_event/

/ self._render_figure(self._pixmap, w, h)/

/ File

“/usr/lib64/python2.7/site-packages/matplotlib/backends/backend_gtkagg.py”,

line 75, in _render_figure/

/ FigureCanvasAgg.draw(self)/

/ File

“/usr/lib64/python2.7/site-packages/matplotlib/backends/backend_agg.py”,

line 416, in draw/

/ self.renderer = self.get_renderer()/

/ File

“/usr/lib64/python2.7/site-packages/matplotlib/backends/backend_agg.py”,

line 435, in get_renderer/

/ self.renderer = RendererAgg(w, h, self.figure.dpi)/

/ File

“/usr/lib64/python2.7/site-packages/matplotlib/backends/backend_agg.py”,

line 72, in init/

/ self._renderer = _RendererAgg(int(width), int(height), dpi,

debug=False)/

/ValueError: width and height must each be below 32768/

/The program ‘mpl.py’ received an X Window System error./

/This probably reflects a bug in the program./

/The error was ‘BadAlloc (insufficient resources for operation)’./

/ (Details: serial 486 error_code 11 request_code 53 minor_code 0)/

/ (Note to programmers: normally, X errors are reported asynchronously;/

/ that is, you will receive the error a while after causing it./

/ To debug your program, run it with the --sync command line/

/ option to change this behavior. You can then get a meaningful/

/ backtrace from your debugger if you break on the gdk_x_error()

function.)/

With the following code:

/import random /

/import matplotlib.pyplot as plt /

//

/coverages = [random.randint(1,10)*2] * 4605 /

/contig_names = [‘AAB0008r’] * len(coverages) /

/# Set the figure size /

/#fig = plt.figure(1, [20, 2]) /

/fig = plt.figure(figsize=(int(len(coverages)*0.1), 4)) /

//

/ax = fig.add_subplot(111) /

//

/# Set the x-axis limit /

/#ax.set_xlim(-1,100) /

/ax.set_xlim(0,len(coverages)) /

/#ax.set_ylim(0,3) /

/ax.yaxis.grid(True, linestyle=‘-’, which=‘major’, color=‘grey’,

alpha=0.5) /

//

/ind = range(len(coverages)) /

/rects = ax.bar(ind, coverages, width=0.1, align=‘center’,

color=‘thistle’) /

/ax.set_xticks(ind) /

/#ax.set_xticklabels(contig_names)/

/#ax.tick_params(axis=‘both’, which=‘major’, labelsize=10)/

/#ax.tick_params(axis=‘both’, which=‘minor’, labelsize=8)/

/

/

/

/

/#function to auto-rotate the x axis labels/

/fig.autofmt_xdate()/

/plt.setp(ax.get_xticklabels(), fontsize=8, rotation=‘vertical’)/

/plt.show()/

How is it possible to get big charts?

It looks like you are trying to make a figure that is 460 inches by 4

inches. How do you expect to display or print it? I think displaying

it is out of the question, so you would need to use a non-interactive

backend. I don’t know whether ps or pdf can handle those sorts of

dimensions.

Eric

Thank you in advance.

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Eric_Firing1 · October 2, 2012, 5:07pm

Hi Eric,
I have a dataset which contains about 4600 values.

Is it possible to display 4600 values with a bar char and labels?

Thank you in advance.

Mic,

I don't think so, as a practical matter. A screen doesn't even have that many pixels of width.

Eric

···

On 2012/10/02 4:12 AM, Mic wrote:

On Tue, Oct 2, 2012 at 4:04 PM, Eric Firing <efiring@...202... > <mailto:efiring@…202…>> wrote:

    On 2012/10/01 7:28 PM, Mic wrote:
     > Hi,
     >
     > I have got the following error with the following code:
     > /$ python mpl.py/ <http://mpl.py/>
     > /Traceback (most recent call last)
     > / File
     >
    "/usr/lib64/python2.7/site-packages/matplotlib/backends/backend_gtk.py",
     > line 398, in expose_event/
     > / self._render_figure(self._pixmap, w, h)/
     > / File
     >
    "/usr/lib64/python2.7/site-packages/matplotlib/backends/backend_gtkagg.py",
     > line 75, in _render_figure/
     > / FigureCanvasAgg.draw(self)/
     > / File
     >
    "/usr/lib64/python2.7/site-packages/matplotlib/backends/backend_agg.py",
     > line 416, in draw/
     > / self.renderer = self.get_renderer()/
     > / File
     >
    "/usr/lib64/python2.7/site-packages/matplotlib/backends/backend_agg.py",
     > line 435, in get_renderer/
     > / self.renderer = RendererAgg(w, h, self.figure.dpi)/
     > / File
     >
    "/usr/lib64/python2.7/site-packages/matplotlib/backends/backend_agg.py",
     > line 72, in __init__/
     > / self._renderer = _RendererAgg(int(width), int(height), dpi,
     > debug=False)/
     > /ValueError: width and height must each be below 32768/
     > /The program 'mpl.py' received an X Window System error./
     > /This probably reflects a bug in the program./
     > /The error was 'BadAlloc (insufficient resources for operation)'./
     > / (Details: serial 486 error_code 11 request_code 53 minor_code 0)/
     > / (Note to programmers: normally, X errors are reported
    asynchronously;/
     > / that is, you will receive the error a while after causing it./
     > / To debug your program, run it with the --sync command line/
     > / option to change this behavior. You can then get a meaningful/
     > / backtrace from your debugger if you break on the gdk_x_error()
     > function.)/
     >
     > With the following code:
     > /import random /
     > /import matplotlib.pyplot as plt /
     > //
     > /coverages = [random.randint(1,10)*2] * 4605 /
     > /contig_names = ['AAB0008r'] * len(coverages) /
     > /# Set the figure size /
     > /#fig = plt.figure(1, [20, 2]) /
     > /fig = plt.figure(figsize=(int(len(coverages)*0.1), 4)) /
     > //
     > /ax = fig.add_subplot(111) /
     > //
     > /# Set the x-axis limit /
     > /#ax.set_xlim(-1,100) /
     > /ax.set_xlim(0,len(coverages)) /
     > /#ax.set_ylim(0,3) /
     > /ax.yaxis.grid(True, linestyle='-', which='major', color='grey',
     > alpha=0.5) /
     > //
     > /ind = range(len(coverages)) /
     > /rects = ax.bar(ind, coverages, width=0.1, align='center',
     > color='thistle') /
     > /ax.set_xticks(ind) /
     > /#ax.set_xticklabels(contig_names)/
     > /#ax.tick_params(axis='both', which='major', labelsize=10)/
     > /#ax.tick_params(axis='both', which='minor', labelsize=8)/
     > /
     > /#function to auto-rotate the x axis labels/
     > /fig.autofmt_xdate()/
     > /plt.setp(ax.get_xticklabels(), fontsize=8, rotation='vertical')/
     > /plt.show()/
     >
     > How is it possible to get big charts?

    It looks like you are trying to make a figure that is 460 inches by 4
    inches. How do you expect to display or print it? I think displaying
    it is out of the question, so you would need to use a non-interactive
    backend. I don't know whether ps or pdf can handle those sorts of
    dimensions.

    Eric

     >
     > Thank you in advance.
     >
    ------------------------------------------------------------------------------
     > Don't let slow site performance ruin your business. Deploy New
    Relic APM
     > Deploy New Relic app performance management and know exactly
     > what is happening inside your Ruby, Python, PHP, Java, and .NET app
     > Try New Relic at no cost today and get our sweet Data Nerd shirt too!
     > http://p.sf.net/sfu/newrelic-dev2dev
     >
     > _______________________________________________
     > Matplotlib-users mailing list
     > Matplotlib-users@lists.sourceforge.net
    <mailto:Matplotlib-users@lists.sourceforge.net>
     > matplotlib-users List Signup and Options
     >

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    Deploy New Relic app performance management and know exactly
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    Try New Relic at no cost today and get our sweet Data Nerd shirt too!
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Damon_McDougall3 · October 2, 2012, 6:14pm

If you have that much data, a bar chart is probably not the way to go.
Maybe try taking the height of what would be each bar and using that
as a y-coordinate array then call plt.plot(y)? You'll get a line plot,
and the x axis may not make a huge amount of sense, but at least
you'll see all your data.

Or, perhaps even a histogram?

It's hard to advise without knowing your application, but that should
help at least a little. Good luck!

Best wishes,
Damon

···

On Tue, Oct 2, 2012 at 6:07 PM, Eric Firing <efiring@...202...> wrote:

On 2012/10/02 4:12 AM, Mic wrote:

Hi Eric,
I have a dataset which contains about 4600 values.

Is it possible to display 4600 values with a bar char and labels?

Thank you in advance.

Mic,

I don't think so, as a practical matter. A screen doesn't even have
that many pixels of width.

Eric

On Tue, Oct 2, 2012 at 4:04 PM, Eric Firing <efiring@...202... >> <mailto:efiring@…202…>> wrote:

    On 2012/10/01 7:28 PM, Mic wrote:
     > Hi,
     >
     > I have got the following error with the following code:
     > /$ python mpl.py/ <http://mpl.py/>
     > /Traceback (most recent call last)
     > / File
     >
    "/usr/lib64/python2.7/site-packages/matplotlib/backends/backend_gtk.py",
     > line 398, in expose_event/
     > / self._render_figure(self._pixmap, w, h)/
     > / File
     >
    "/usr/lib64/python2.7/site-packages/matplotlib/backends/backend_gtkagg.py",
     > line 75, in _render_figure/
     > / FigureCanvasAgg.draw(self)/
     > / File
     >
    "/usr/lib64/python2.7/site-packages/matplotlib/backends/backend_agg.py",
     > line 416, in draw/
     > / self.renderer = self.get_renderer()/
     > / File
     >
    "/usr/lib64/python2.7/site-packages/matplotlib/backends/backend_agg.py",
     > line 435, in get_renderer/
     > / self.renderer = RendererAgg(w, h, self.figure.dpi)/
     > / File
     >
    "/usr/lib64/python2.7/site-packages/matplotlib/backends/backend_agg.py",
     > line 72, in __init__/
     > / self._renderer = _RendererAgg(int(width), int(height), dpi,
     > debug=False)/
     > /ValueError: width and height must each be below 32768/
     > /The program 'mpl.py' received an X Window System error./
     > /This probably reflects a bug in the program./
     > /The error was 'BadAlloc (insufficient resources for operation)'./
     > / (Details: serial 486 error_code 11 request_code 53 minor_code 0)/
     > / (Note to programmers: normally, X errors are reported
    asynchronously;/
     > / that is, you will receive the error a while after causing it./
     > / To debug your program, run it with the --sync command line/
     > / option to change this behavior. You can then get a meaningful/
     > / backtrace from your debugger if you break on the gdk_x_error()
     > function.)/
     >
     > With the following code:
     > /import random /
     > /import matplotlib.pyplot as plt /
     > //
     > /coverages = [random.randint(1,10)*2] * 4605 /
     > /contig_names = ['AAB0008r'] * len(coverages) /
     > /# Set the figure size /
     > /#fig = plt.figure(1, [20, 2]) /
     > /fig = plt.figure(figsize=(int(len(coverages)*0.1), 4)) /
     > //
     > /ax = fig.add_subplot(111) /
     > //
     > /# Set the x-axis limit /
     > /#ax.set_xlim(-1,100) /
     > /ax.set_xlim(0,len(coverages)) /
     > /#ax.set_ylim(0,3) /
     > /ax.yaxis.grid(True, linestyle='-', which='major', color='grey',
     > alpha=0.5) /
     > //
     > /ind = range(len(coverages)) /
     > /rects = ax.bar(ind, coverages, width=0.1, align='center',
     > color='thistle') /
     > /ax.set_xticks(ind) /
     > /#ax.set_xticklabels(contig_names)/
     > /#ax.tick_params(axis='both', which='major', labelsize=10)/
     > /#ax.tick_params(axis='both', which='minor', labelsize=8)/
     > /
     > /
     > /
     > /
     > /#function to auto-rotate the x axis labels/
     > /fig.autofmt_xdate()/
     > /plt.setp(ax.get_xticklabels(), fontsize=8, rotation='vertical')/
     > /plt.show()/
     >
     > How is it possible to get big charts?

    It looks like you are trying to make a figure that is 460 inches by 4
    inches. How do you expect to display or print it? I think displaying
    it is out of the question, so you would need to use a non-interactive
    backend. I don't know whether ps or pdf can handle those sorts of
    dimensions.

    Eric

     >
     > Thank you in advance.

--
Damon McDougall
http://www.damon-is-a-geek.com
B2.39
Mathematics Institute
University of Warwick
Coventry
West Midlands
CV4 7AL
United Kingdom