wrong numpy version

Hi all guys,

I am using RHEL6 and I am ploting figures throughout my project, so I wanted some workaroung blocking show() function call. I have found few solutions that use multiprocessing, so finally i finished with this:

pool.map(plot_graph, c)

and

def plot_graph(*args):
plt.figure(args[0][2])
plt.bar(args[0][1][:-1], args[0][0], width=1)
plt.show()

But when I have more than one figure the following error occures:

/usr/lib64/python2.6/site-packages/matplotlib/backends/backend_gtk.py:621: DeprecationWarning: Use the new widget gtk.Tooltip
self.tooltips = gtk.Tooltips()
/usr/lib64/python2.6/site-packages/matplotlib/backends/backend_gtk.py:621: DeprecationWarning: Use the new widget gtk.Tooltip

self.tooltips = gtk.Tooltips()
[xcb] Unknown sequence number while processing queue
[xcb] Most likely this is a multi-threaded client and XInitThreads has not been called
[xcb] Aborting, sorry about that.
python: xcb_io.c:273: poll_for_event: Assertion `!xcb_xlib_threads_sequence_lost’ failed.

runner.py: Fatal IO error 0 (Success) on X server :0.0.

Since my version of matplolib doesnt support blocking = false solution, I wanted to install new version. For that I installed new version of numpy but when i run python setup.py build in matplolib foldet i get following:

Edit setup.cfg to change the build options

BUILDING MATPLOTLIB
matplotlib: yes [1.3.1]
python: yes [2.6.6 (r266:84292, May 27 2013, 05:35:12) [GCC
4.4.7 20120313 (Red Hat 4.4.7-3)]]

          platform: yes [linux2]

REQUIRED DEPENDENCIES AND EXTENSIONS
numpy: yes [version 1.8.0]
dateutil: yes [using dateutil version 1.4.1]
tornado: yes [tornado was not found. It is required for the

                    WebAgg backend. pip/easy_install may attempt to
                    install it after matplotlib.]
         pyparsing: yes [pyparsing was not found. It is required for
                    mathtext support. pip/easy_install may attempt to

                    install it after matplotlib.]
             pycxx: yes [Couldn't import.  Using local copy.]
            libagg: yes [pkg-config information for 'libagg' could not
                    be found. Using local copy.]

          freetype: yes [version 9.22.3]
               png: yes [version 1.2.49]

OPTIONAL SUBPACKAGES
sample_data: yes [installing]
toolkits: yes [installing]
tests: yes [nose 0.11.1 or later is required to run the

                    matplotlib test suite]

OPTIONAL BACKEND EXTENSIONS
macosx: no [Mac OS-X only]
qt4agg: yes [installing, Qt: 4.6.2, PyQt4: 4.6.2]
gtk3agg: no [Requires pygobject to be installed.]

         gtk3cairo: no  [Requires pygobject to be installed.]
            gtkagg: yes [installing, Gtk: 2.18.9 pygtk: 2.16.0]
             tkagg: yes [installing, version 73770]
             wxagg: yes [installing, version 2.8.12.0]

               gtk: yes [installing, Gtk: 2.18.9 pygtk: 2.16.0]
               agg: yes [installing]
             cairo: yes [installing, version 1.8.6]
         windowing: no  [Microsoft Windows only]

OPTIONAL LATEX DEPENDENCIES
dvipng: yes [version 1.14]
ghostscript: yes [version 8.70]
latex: yes [version 3.1415926]
pdftops: no

Traceback (most recent call last):

File “setup.py”, line 268, in
**extra_args
File “/usr/lib64/python2.6/distutils/core.py”, line 113, in setup
_setup_distribution = dist = klass(attrs)
File “build/bdist.linux-x86_64/egg/setuptools/dist.py”, line 221, in init

File “build/bdist.linux-x86_64/egg/setuptools/dist.py”, line 245, in fetch_build_eggs
File “build/bdist.linux-x86_64/egg/pkg_resources.py”, line 592, in resolve
plugin_projects.sort() # scan project names in alphabetic order

pkg_resources.VersionConflict: (numpy 1.4.1 (/usr/lib64/python2.6/site-packages), Requirement.parse(‘numpy>=1.5’))

When I run python and check numpy version it is indeed 1.8.0, but matplotlib buils script somehow founded older one.

I would be really happy if somebody can help me overcome problem with many figures.

Best and cheers

···


Nemanja Savić

The issue is rather complex, and it is a very difficult one to solve on our
end. What is happening is that in order to build matplotlib from source,
you need to compile against the numpy headers at build-time. Unfortunately,
python packaging being what it is, there is difficulty in making sure that
the version of numpy that will be installed is the version used for the
build. You seem to have numpy installed both at the system level and
possibly at the user level. If possible, I would try removing numpy from
your system level (and that likely means removing any other installed
package that depends on it, and reinstalling via source).

Ben Root

···

On Tue, Nov 12, 2013 at 7:37 AM, Nemanja Savic <vlasinac@...287...> wrote:

Hi all guys,

I am using RHEL6 and I am ploting figures throughout my project, so I
wanted some workaroung blocking show() function call. I have found few
solutions that use multiprocessing, so finally i finished with this:

pool.map(plot_graph, c)

and

def plot_graph(*args):
    plt.figure(args[0][2])
    plt.bar(args[0][1][:-1], args[0][0], width=1)
    plt.show()

But when I have more than one figure the following error occures:

/usr/lib64/python2.6/site-packages/matplotlib/backends/backend_gtk.py:621:
DeprecationWarning: Use the new widget gtk.Tooltip
  self.tooltips = gtk.Tooltips()
/usr/lib64/python2.6/site-packages/matplotlib/backends/backend_gtk.py:621:
DeprecationWarning: Use the new widget gtk.Tooltip
  self.tooltips = gtk.Tooltips()
[xcb] Unknown sequence number while processing queue
[xcb] Most likely this is a multi-threaded client and XInitThreads has not
been called
[xcb] Aborting, sorry about that.
python: xcb_io.c:273: poll_for_event: Assertion
`!xcb_xlib_threads_sequence_lost' failed.
runner.py: Fatal IO error 0 (Success) on X server :0.0.

Since my version of matplolib doesnt support blocking = false solution, I
wanted to install new version. For that I installed new version of numpy
but when i run python setup.py build in matplolib foldet i get following:

Edit setup.cfg to change the build options

BUILDING MATPLOTLIB
            matplotlib: yes [1.3.1]
                python: yes [2.6.6 (r266:84292, May 27 2013, 05:35:12)
[GCC
                        4.4.7 20120313 (Red Hat 4.4.7-3)]]
              platform: yes [linux2]

REQUIRED DEPENDENCIES AND EXTENSIONS
                 numpy: yes [version 1.8.0]
              dateutil: yes [using dateutil version 1.4.1]
               tornado: yes [tornado was not found. It is required for the
                        WebAgg backend. pip/easy_install may attempt to
                        install it after matplotlib.]
             pyparsing: yes [pyparsing was not found. It is required for
                        mathtext support. pip/easy_install may attempt to
                        install it after matplotlib.]
                 pycxx: yes [Couldn't import. Using local copy.]
                libagg: yes [pkg-config information for 'libagg' could not
                        be found. Using local copy.]
              freetype: yes [version 9.22.3]
                   png: yes [version 1.2.49]

OPTIONAL SUBPACKAGES
           sample_data: yes [installing]
              toolkits: yes [installing]
                 tests: yes [nose 0.11.1 or later is required to run the
                        matplotlib test suite]

OPTIONAL BACKEND EXTENSIONS
                macosx: no [Mac OS-X only]
                qt4agg: yes [installing, Qt: 4.6.2, PyQt4: 4.6.2]
               gtk3agg: no [Requires pygobject to be installed.]
             gtk3cairo: no [Requires pygobject to be installed.]
                gtkagg: yes [installing, Gtk: 2.18.9 pygtk: 2.16.0]
                 tkagg: yes [installing, version 73770]
                 wxagg: yes [installing, version 2.8.12.0]
                   gtk: yes [installing, Gtk: 2.18.9 pygtk: 2.16.0]
                   agg: yes [installing]
                 cairo: yes [installing, version 1.8.6]
             windowing: no [Microsoft Windows only]

OPTIONAL LATEX DEPENDENCIES
                dvipng: yes [version 1.14]
           ghostscript: yes [version 8.70]
                 latex: yes [version 3.1415926]
               pdftops: no

Traceback (most recent call last):
  File "setup.py", line 268, in <module>
    **extra_args
  File "/usr/lib64/python2.6/distutils/core.py", line 113, in setup
    _setup_distribution = dist = klass(attrs)
  File "build/bdist.linux-x86_64/egg/setuptools/dist.py", line 221, in
__init__
  File "build/bdist.linux-x86_64/egg/setuptools/dist.py", line 245, in
fetch_build_eggs
  File "build/bdist.linux-x86_64/egg/pkg_resources.py", line 592, in
resolve
    plugin_projects.sort() # scan project names in alphabetic order
pkg_resources.VersionConflict: (numpy 1.4.1
(/usr/lib64/python2.6/site-packages), Requirement.parse('numpy>=1.5'))

When I run python and check numpy version it is indeed 1.8.0, but
matplotlib buils script somehow founded older one.

I would be really happy if somebody can help me overcome problem with many
figures.

Best and cheers

I see. But is there any other way to cope with this x server problem and multiple figures plotting?

···

On Tue, Nov 12, 2013 at 3:21 PM, Benjamin Root <ben.root@…1304…> wrote:


Nemanja Savić

On Tue, Nov 12, 2013 at 7:37 AM, Nemanja Savic <vlasinac@…287…> wrote:

Hi all guys,

I am using RHEL6 and I am ploting figures throughout my project, so I wanted some workaroung blocking show() function call. I have found few solutions that use multiprocessing, so finally i finished with this:

pool.map(plot_graph, c)

and

def plot_graph(*args):
plt.figure(args[0][2])
plt.bar(args[0][1][:-1], args[0][0], width=1)
plt.show()

But when I have more than one figure the following error occures:

/usr/lib64/python2.6/site-packages/matplotlib/backends/backend_gtk.py:621: DeprecationWarning: Use the new widget gtk.Tooltip
self.tooltips = gtk.Tooltips()
/usr/lib64/python2.6/site-packages/matplotlib/backends/backend_gtk.py:621: DeprecationWarning: Use the new widget gtk.Tooltip

self.tooltips = gtk.Tooltips()
[xcb] Unknown sequence number while processing queue
[xcb] Most likely this is a multi-threaded client and XInitThreads has not been called
[xcb] Aborting, sorry about that.
python: xcb_io.c:273: poll_for_event: Assertion `!xcb_xlib_threads_sequence_lost’ failed.

runner.py: Fatal IO error 0 (Success) on X server :0.0.

Since my version of matplolib doesnt support blocking = false solution, I wanted to install new version. For that I installed new version of numpy but when i run python setup.py build in matplolib foldet i get following:

Edit setup.cfg to change the build options

BUILDING MATPLOTLIB
matplotlib: yes [1.3.1]
python: yes [2.6.6 (r266:84292, May 27 2013, 05:35:12) [GCC
4.4.7 20120313 (Red Hat 4.4.7-3)]]

          platform: yes [linux2]

REQUIRED DEPENDENCIES AND EXTENSIONS
numpy: yes [version 1.8.0]
dateutil: yes [using dateutil version 1.4.1]
tornado: yes [tornado was not found. It is required for the

                    WebAgg backend. pip/easy_install may attempt to
                    install it after matplotlib.]
         pyparsing: yes [pyparsing was not found. It is required for
                    mathtext support. pip/easy_install may attempt to




                    install it after matplotlib.]
             pycxx: yes [Couldn't import.  Using local copy.]
            libagg: yes [pkg-config information for 'libagg' could not
                    be found. Using local copy.]




          freetype: yes [version 9.22.3]
               png: yes [version 1.2.49]

OPTIONAL SUBPACKAGES
sample_data: yes [installing]
toolkits: yes [installing]
tests: yes [nose 0.11.1 or later is required to run the

                    matplotlib test suite]

OPTIONAL BACKEND EXTENSIONS
macosx: no [Mac OS-X only]
qt4agg: yes [installing, Qt: 4.6.2, PyQt4: 4.6.2]
gtk3agg: no [Requires pygobject to be installed.]

         gtk3cairo: no  [Requires pygobject to be installed.]
            gtkagg: yes [installing, Gtk: 2.18.9 pygtk: 2.16.0]
             tkagg: yes [installing, version 73770]
             wxagg: yes [installing, version 2.8.12.0]




               gtk: yes [installing, Gtk: 2.18.9 pygtk: 2.16.0]
               agg: yes [installing]
             cairo: yes [installing, version 1.8.6]
         windowing: no  [Microsoft Windows only]

OPTIONAL LATEX DEPENDENCIES
dvipng: yes [version 1.14]
ghostscript: yes [version 8.70]
latex: yes [version 3.1415926]
pdftops: no

Traceback (most recent call last):

File “setup.py”, line 268, in
**extra_args
File “/usr/lib64/python2.6/distutils/core.py”, line 113, in setup
_setup_distribution = dist = klass(attrs)
File “build/bdist.linux-x86_64/egg/setuptools/dist.py”, line 221, in init

File “build/bdist.linux-x86_64/egg/setuptools/dist.py”, line 245, in fetch_build_eggs
File “build/bdist.linux-x86_64/egg/pkg_resources.py”, line 592, in resolve
plugin_projects.sort() # scan project names in alphabetic order

pkg_resources.VersionConflict: (numpy 1.4.1 (/usr/lib64/python2.6/site-packages), Requirement.parse(‘numpy>=1.5’))

When I run python and check numpy version it is indeed 1.8.0, but matplotlib buils script somehow founded older one.

I would be really happy if somebody can help me overcome problem with many figures.

Best and cheers

The issue is rather complex, and it is a very difficult one to solve on our end. What is happening is that in order to build matplotlib from source, you need to compile against the numpy headers at build-time. Unfortunately, python packaging being what it is, there is difficulty in making sure that the version of numpy that will be installed is the version used for the build. You seem to have numpy installed both at the system level and possibly at the user level. If possible, I would try removing numpy from your system level (and that likely means removing any other installed package that depends on it, and reinstalling via source).

Ben Root

Hi all guys, I am back to the same issue again. At the moment I am not able to reazlize where does matplotlib configure script find that my version of numpy is 1.4.1?

···

On Tue, Nov 12, 2013 at 4:20 PM, Nemanja Savic <vlasinac@…287…> wrote:

I see. But is there any other way to cope with this x server problem and multiple figures plotting?


Nemanja Savić

On Tue, Nov 12, 2013 at 3:21 PM, Benjamin Root <ben.root@…1304…> wrote:


Nemanja Savić

On Tue, Nov 12, 2013 at 7:37 AM, Nemanja Savic <vlasinac@…287…> wrote:

Hi all guys,

I am using RHEL6 and I am ploting figures throughout my project, so I wanted some workaroung blocking show() function call. I have found few solutions that use multiprocessing, so finally i finished with this:

pool.map(plot_graph, c)

and

def plot_graph(*args):
plt.figure(args[0][2])
plt.bar(args[0][1][:-1], args[0][0], width=1)
plt.show()

But when I have more than one figure the following error occures:

/usr/lib64/python2.6/site-packages/matplotlib/backends/backend_gtk.py:621: DeprecationWarning: Use the new widget gtk.Tooltip
self.tooltips = gtk.Tooltips()
/usr/lib64/python2.6/site-packages/matplotlib/backends/backend_gtk.py:621: DeprecationWarning: Use the new widget gtk.Tooltip

self.tooltips = gtk.Tooltips()
[xcb] Unknown sequence number while processing queue
[xcb] Most likely this is a multi-threaded client and XInitThreads has not been called
[xcb] Aborting, sorry about that.
python: xcb_io.c:273: poll_for_event: Assertion `!xcb_xlib_threads_sequence_lost’ failed.

runner.py: Fatal IO error 0 (Success) on X server :0.0.

Since my version of matplolib doesnt support blocking = false solution, I wanted to install new version. For that I installed new version of numpy but when i run python setup.py build in matplolib foldet i get following:

Edit setup.cfg to change the build options

BUILDING MATPLOTLIB
matplotlib: yes [1.3.1]
python: yes [2.6.6 (r266:84292, May 27 2013, 05:35:12) [GCC
4.4.7 20120313 (Red Hat 4.4.7-3)]]

          platform: yes [linux2]

REQUIRED DEPENDENCIES AND EXTENSIONS
numpy: yes [version 1.8.0]
dateutil: yes [using dateutil version 1.4.1]
tornado: yes [tornado was not found. It is required for the

                    WebAgg backend. pip/easy_install may attempt to
                    install it after matplotlib.]
         pyparsing: yes [pyparsing was not found. It is required for
                    mathtext support. pip/easy_install may attempt to





                    install it after matplotlib.]
             pycxx: yes [Couldn't import.  Using local copy.]
            libagg: yes [pkg-config information for 'libagg' could not
                    be found. Using local copy.]





          freetype: yes [version 9.22.3]
               png: yes [version 1.2.49]

OPTIONAL SUBPACKAGES
sample_data: yes [installing]
toolkits: yes [installing]
tests: yes [nose 0.11.1 or later is required to run the

                    matplotlib test suite]

OPTIONAL BACKEND EXTENSIONS
macosx: no [Mac OS-X only]
qt4agg: yes [installing, Qt: 4.6.2, PyQt4: 4.6.2]
gtk3agg: no [Requires pygobject to be installed.]

         gtk3cairo: no  [Requires pygobject to be installed.]
            gtkagg: yes [installing, Gtk: 2.18.9 pygtk: 2.16.0]
             tkagg: yes [installing, version 73770]
             wxagg: yes [installing, version 2.8.12.0]





               gtk: yes [installing, Gtk: 2.18.9 pygtk: 2.16.0]
               agg: yes [installing]
             cairo: yes [installing, version 1.8.6]
         windowing: no  [Microsoft Windows only]

OPTIONAL LATEX DEPENDENCIES
dvipng: yes [version 1.14]
ghostscript: yes [version 8.70]
latex: yes [version 3.1415926]
pdftops: no

Traceback (most recent call last):

File “setup.py”, line 268, in
**extra_args
File “/usr/lib64/python2.6/distutils/core.py”, line 113, in setup
_setup_distribution = dist = klass(attrs)
File “build/bdist.linux-x86_64/egg/setuptools/dist.py”, line 221, in init

File “build/bdist.linux-x86_64/egg/setuptools/dist.py”, line 245, in fetch_build_eggs
File “build/bdist.linux-x86_64/egg/pkg_resources.py”, line 592, in resolve
plugin_projects.sort() # scan project names in alphabetic order

pkg_resources.VersionConflict: (numpy 1.4.1 (/usr/lib64/python2.6/site-packages), Requirement.parse(‘numpy>=1.5’))

When I run python and check numpy version it is indeed 1.8.0, but matplotlib buils script somehow founded older one.

I would be really happy if somebody can help me overcome problem with many figures.

Best and cheers

The issue is rather complex, and it is a very difficult one to solve on our end. What is happening is that in order to build matplotlib from source, you need to compile against the numpy headers at build-time. Unfortunately, python packaging being what it is, there is difficulty in making sure that the version of numpy that will be installed is the version used for the build. You seem to have numpy installed both at the system level and possibly at the user level. If possible, I would try removing numpy from your system level (and that likely means removing any other installed package that depends on it, and reinstalling via source).

Ben Root

The solution is following:

uninstall numpy using yum.

build numpy from source and install it.

Build matplotlib from source!

Best

···

On Mon, Feb 3, 2014 at 3:29 PM, Nemanja Savic <vlasinac@…287…> wrote:

Hi all guys, I am back to the same issue again. At the moment I am not able to reazlize where does matplotlib configure script find that my version of numpy is 1.4.1?


Nemanja Savić

On Tue, Nov 12, 2013 at 4:20 PM, Nemanja Savic <vlasinac@…287…> wrote:

I see. But is there any other way to cope with this x server problem and multiple figures plotting?


Nemanja Savić

On Tue, Nov 12, 2013 at 3:21 PM, Benjamin Root <ben.root@…1304…> wrote:


Nemanja Savić

On Tue, Nov 12, 2013 at 7:37 AM, Nemanja Savic <vlasinac@…287…> wrote:

Hi all guys,

I am using RHEL6 and I am ploting figures throughout my project, so I wanted some workaroung blocking show() function call. I have found few solutions that use multiprocessing, so finally i finished with this:

pool.map(plot_graph, c)

and

def plot_graph(*args):
plt.figure(args[0][2])
plt.bar(args[0][1][:-1], args[0][0], width=1)
plt.show()

But when I have more than one figure the following error occures:

/usr/lib64/python2.6/site-packages/matplotlib/backends/backend_gtk.py:621: DeprecationWarning: Use the new widget gtk.Tooltip
self.tooltips = gtk.Tooltips()
/usr/lib64/python2.6/site-packages/matplotlib/backends/backend_gtk.py:621: DeprecationWarning: Use the new widget gtk.Tooltip

self.tooltips = gtk.Tooltips()
[xcb] Unknown sequence number while processing queue
[xcb] Most likely this is a multi-threaded client and XInitThreads has not been called
[xcb] Aborting, sorry about that.
python: xcb_io.c:273: poll_for_event: Assertion `!xcb_xlib_threads_sequence_lost’ failed.

runner.py: Fatal IO error 0 (Success) on X server :0.0.

Since my version of matplolib doesnt support blocking = false solution, I wanted to install new version. For that I installed new version of numpy but when i run python setup.py build in matplolib foldet i get following:

Edit setup.cfg to change the build options

BUILDING MATPLOTLIB
matplotlib: yes [1.3.1]
python: yes [2.6.6 (r266:84292, May 27 2013, 05:35:12) [GCC
4.4.7 20120313 (Red Hat 4.4.7-3)]]

          platform: yes [linux2]

REQUIRED DEPENDENCIES AND EXTENSIONS
numpy: yes [version 1.8.0]
dateutil: yes [using dateutil version 1.4.1]
tornado: yes [tornado was not found. It is required for the

                    WebAgg backend. pip/easy_install may attempt to
                    install it after matplotlib.]
         pyparsing: yes [pyparsing was not found. It is required for
                    mathtext support. pip/easy_install may attempt to






                    install it after matplotlib.]
             pycxx: yes [Couldn't import.  Using local copy.]
            libagg: yes [pkg-config information for 'libagg' could not
                    be found. Using local copy.]






          freetype: yes [version 9.22.3]
               png: yes [version 1.2.49]

OPTIONAL SUBPACKAGES
sample_data: yes [installing]
toolkits: yes [installing]
tests: yes [nose 0.11.1 or later is required to run the

                    matplotlib test suite]

OPTIONAL BACKEND EXTENSIONS
macosx: no [Mac OS-X only]
qt4agg: yes [installing, Qt: 4.6.2, PyQt4: 4.6.2]
gtk3agg: no [Requires pygobject to be installed.]

         gtk3cairo: no  [Requires pygobject to be installed.]
            gtkagg: yes [installing, Gtk: 2.18.9 pygtk: 2.16.0]
             tkagg: yes [installing, version 73770]
             wxagg: yes [installing, version 2.8.12.0]






               gtk: yes [installing, Gtk: 2.18.9 pygtk: 2.16.0]
               agg: yes [installing]
             cairo: yes [installing, version 1.8.6]
         windowing: no  [Microsoft Windows only]

OPTIONAL LATEX DEPENDENCIES
dvipng: yes [version 1.14]
ghostscript: yes [version 8.70]
latex: yes [version 3.1415926]
pdftops: no

Traceback (most recent call last):

File “setup.py”, line 268, in
**extra_args
File “/usr/lib64/python2.6/distutils/core.py”, line 113, in setup
_setup_distribution = dist = klass(attrs)
File “build/bdist.linux-x86_64/egg/setuptools/dist.py”, line 221, in init

File “build/bdist.linux-x86_64/egg/setuptools/dist.py”, line 245, in fetch_build_eggs
File “build/bdist.linux-x86_64/egg/pkg_resources.py”, line 592, in resolve
plugin_projects.sort() # scan project names in alphabetic order

pkg_resources.VersionConflict: (numpy 1.4.1 (/usr/lib64/python2.6/site-packages), Requirement.parse(‘numpy>=1.5’))

When I run python and check numpy version it is indeed 1.8.0, but matplotlib buils script somehow founded older one.

I would be really happy if somebody can help me overcome problem with many figures.

Best and cheers

The issue is rather complex, and it is a very difficult one to solve on our end. What is happening is that in order to build matplotlib from source, you need to compile against the numpy headers at build-time. Unfortunately, python packaging being what it is, there is difficulty in making sure that the version of numpy that will be installed is the version used for the build. You seem to have numpy installed both at the system level and possibly at the user level. If possible, I would try removing numpy from your system level (and that likely means removing any other installed package that depends on it, and reinstalling via source).

Ben Root