[yt-users] IYT gives problem after updation of system
j s oishi
jsoishi at gmail.com
Sun Aug 8 10:08:08 PDT 2010
Hi Abhijit,
Since you said that your OpenSUSE upgrade excluded /usr/local, I'm
assuming that you build this matplotlib either from the yt install
script or manually. It looks like the tkagg backend was excluded
during the matplotlib process, possibly because the pacakges it relies
on aren't installed by default in your new OpenSUSE distribution.
First, try changing the backend in your .matplotlibrc file, which you
can find in
~/.matplotlib/matplotlibrc
If you're using GNOME, try GTKAgg; if you're using KDE, try Qt4Agg.
TkAgg has very few requirements, but you may not have the tk-devel
package (or its OpenSUSE equivalent; I don't use that distribution, so
I don't know exactly what it's called).
Finally, you can verify that matplotlib works without a GUI backend by
writing a very simple yt script that plots and saves a file, something
like
from yt.mods import *
pf =load("DD0010/data0010")
pc = PlotCollection(pf)
for i in range(3):
pc.add_slice("Density",i)
pc.save('test')
and then do
$ python the_above_script.py -dAgg
and it will attempt to run that script using the Agg matplotlib
backend, which requires no GUI.
Hope this is helpful,
Jeff
On Sun, Aug 8, 2010 at 12:57 AM, Dr. ABHIJIT BHATTACHARYYA
<b_abhijit2k at yahoo.co.in> wrote:
> Hi
> I did, but result is -ve. I feel that may be, matplotlib or other python
> related routine has error. I am using Python 2.6.5 (r265:79063, Jul 5 2010,
> 11:46:13) and IPython 0.10. After unsuccessful attempt I tried to re-install
> yt manually using svn which did not give any error. However, still iyt is
> not working.
> regs
> Abhi
>
> $> iyt
> Traceback (most recent call last):
> File "/usr/local/bin/iyt", line 5, in <module>
> pkg_resources.run_script('yt==1.7', 'iyt')
> File
> "/usr/local/lib64/python2.6/site-packages/distribute-0.6.10-py2.6.egg/pkg_resources.py",
> line 461, in run_script
> self.require(requires)[0].run_script(script_name, ns)
> File
> "/usr/local/lib64/python2.6/site-packages/distribute-0.6.10-py2.6.egg/pkg_resources.py",
> line 1194, in run_script
> execfile(script_filename, namespace, namespace)
> File
> "/usr/local/lib64/python2.6/site-packages/yt-1.7-py2.6-linux-x86_64.egg/EGG-INFO/scripts/iyt",
> line 32, in <module>
> ip_shell = IPython.Shell.IPShellMatplotlib(user_ns=namespace)
> File "/usr/local/lib/python2.6/site-packages/IPython/Shell.py", line 1106,
> in __init__
> shell_class=MatplotlibShell)
> File "/usr/local/lib/python2.6/site-packages/IPython/Shell.py", line 73,
> in __init__
> debug=debug,shell_class=shell_class)
> File "/usr/local/lib/python2.6/site-packages/IPython/ipmaker.py", line
> 100, in make_IPython
> embedded=embedded,**kw)
> File "/usr/local/lib/python2.6/site-packages/IPython/Shell.py", line 627,
> in __init__
> user_ns,user_global_ns,b2 =
> self._matplotlib_config(name,user_ns,user_global_ns)
> File "/usr/local/lib/python2.6/site-packages/IPython/Shell.py", line 556,
> in _matplotlib_config
> import matplotlib.pylab as pylab
> File "/usr/lib64/python2.6/site-packages/matplotlib/pylab.py", line 259,
> in <module>
> from matplotlib.pyplot import *
> File "/usr/lib64/python2.6/site-packages/matplotlib/pyplot.py", line 95,
> in <module>
> new_figure_manager, draw_if_interactive, show = pylab_setup()
> File "/usr/lib64/python2.6/site-packages/matplotlib/backends/__init__.py",
> line 25, in pylab_setup
> globals(),locals(),[backend_name])
> ImportError: No module named backend_tkagg
> $>
> $> setenv HDF5_DISABLE_VERSION_CHECK 2
> $> iyt
> Traceback (most recent call last):
> File "/usr/local/bin/iyt", line 5, in <module>
> pkg_resources.run_script('yt==1.7', 'iyt')
> File
> "/usr/local/lib64/python2.6/site-packages/distribute-0.6.10-py2.6.egg/pkg_resources.py",
> line 461, in run_script
> self.require(requires)[0].run_script(script_name, ns)
> File
> "/usr/local/lib64/python2.6/site-packages/distribute-0.6.10-py2.6.egg/pkg_resources.py",
> line 1194, in run_script
> execfile(script_filename, namespace, namespace)
> File
> "/usr/local/lib64/python2.6/site-packages/yt-1.7-py2.6-linux-x86_64.egg/EGG-INFO/scripts/iyt",
> line 32, in <module>
> ip_shell = IPython.Shell.IPShellMatplotlib(user_ns=namespace)
> File "/usr/local/lib/python2.6/site-packages/IPython/Shell.py", line 1106,
> in __init__
> shell_class=MatplotlibShell)
> File "/usr/local/lib/python2.6/site-packages/IPython/Shell.py", line 73,
> in __init__
> debug=debug,shell_class=shell_class)
> File "/usr/local/lib/python2.6/site-packages/IPython/ipmaker.py", line
> 100, in make_IPython
> embedded=embedded,**kw)
> File "/usr/local/lib/python2.6/site-packages/IPython/Shell.py", line 627,
> in __init__
> user_ns,user_global_ns,b2 =
> self._matplotlib_config(name,user_ns,user_global_ns)
> File "/usr/local/lib/python2.6/site-packages/IPython/Shell.py", line 556,
> in _matplotlib_config
> import matplotlib.pylab as pylab
> File "/usr/lib64/python2.6/site-packages/matplotlib/pylab.py", line 259,
> in <module>
> from matplotlib.pyplot import *
> File "/usr/lib64/python2.6/site-packages/matplotlib/pyplot.py", line 95,
> in <module>
> new_figure_manager, draw_if_interactive, show = pylab_setup()
> File "/usr/lib64/python2.6/site-packages/matplotlib/backends/__init__.py",
> line 25, in pylab_setup
> globals(),locals(),[backend_name])
> ImportError: No module named backend_tkagg
> $>
>
> Dr. Abhijit Bhattacharyya [Scientific Officer]
> Control Instrumentation Division (CnID)
> Electronics and Instrumentation Group (E&I Group)
> Reactor Control Division Building (RCnD Building)
> Bhabha Atomic Research Center (BARC)
> Trombay, Mumbai - 400 085
> Phone: +91.22.2559.5493
> Email: vega at barc.gov.in
> Residence:
> 811 Akashdeep
> Anushakti Nagar
>
> Mumbai- 400094
> Phone: +91.22.2558.0930
> Mobile: +91.98201.49770
>
> GPS: 19 deg 01 min 54.52 secs North;
>
> 72 deg 55 min 46.30 secs East
>
> ________________________________
> From: Matthew Turk <matthewturk at gmail.com>
> To: Discussion of the yt analysis package <yt-users at lists.spacepope.org>
> Sent: Sun, 8 August, 2010 3:13:14 AM
> Subject: Re: [yt-users] IYT gives problem after updation of system
>
> Hi Abhijit,
>
> Setting HDF5_DISABLE_VERSION_CHECK to 2 should be okay in this case. Let us
> know if it acts up, though!
>
> -Matt
>
> On Aug 7, 2010 2:22 PM, "Dr. ABHIJIT BHATTACHARYYA"
> <b_abhijit2k at yahoo.co.in> wrote:
>
> Hi
>
> I upgraded my system to OpenSUSE 11.3. I kept 'iyt' and 'enzo' in
> '/usr/local' while I only upgraded '/' while '/' and '/usr/local' are two
> different partitions. Now Enzo is working while iyt gives following error.
>
> $> iyt
> Warning! ***HDF5 library version mismatched error***
> The HDF5 header files used to compile this application do not match
> the version used by the HDF5 library to which this application is linked.
> Data corruption or segmentation faults may occur if the application
> continues.
> This can happen when an application was compiled by one version of HDF5 but
> linked with a different version of static or shared HDF5 library.
> You should recompile the application or check your shared library related
> settings such as 'LD_LIBRARY_PATH'.
> You can, at your own risk, disable this warning by setting the environment
> variable 'HDF5_DISABLE_VERSION_CHECK' to a value of '1'.
> Setting it to 2 or higher will suppress the warning messages totally.
> Headers are 1.8.5, library is 1.8.4
> SUMMARY OF THE HDF5 CONFIGURATION
> =================================
>
> General Information:
> -------------------
> HDF5 Version: 1.8.4-patch1
> Configured on: Sat May 29 02:41:00 IST 2010
> Configured by: root at Pakudidi
> Configure mode: production
> Host system: x86_64-unknown-linux-gnu
> Uname information: Linux Pakudidi 2.6.31-rc9-7-default #1 SMP
> 2009-09-08 18:49:15 +0200 x86_64 x86_64 x86_64 GNU/Linux
> Byte sex: little-endian
> Libraries:
> Installation point: /usr/local
>
> Compiling Options:
> ------------------
> Compilation Mode: production
> C Compiler: /usr/bin/gcc (gcc-4.4.1)
> CFLAGS:
> H5_CFLAGS: -std=c99 -pedantic -Wall -Wextra -Wundef
> -Wshadow -Wpointer-arith -Wbad-function-cast -Wcast-qual -Wcast-align
> -Wwrite-strings -Wconversion -Waggregate-return -Wstrict-prototypes
> -Wmissing-prototypes -Wmissing-declarations -Wredundant-decls
> -Wnested-externs -Winline -Wno-long-long -Wfloat-equal
> -Wmissing-format-attribute -Wmissing-noreturn -Wpacked
> -Wdisabled-optimization -Wformat=2 -Wunreachable-code -Wendif-labels
> -Wdeclaration-after-statement -Wold-style-definition -Winvalid-pch
> -Wvariadic-macros -Wnonnull -Winit-self -Wmissing-include-dirs
> -Wswitch-default -Wswitch-enum -Wunused-macros -Wunsafe-loop-optimizations
> -Wc++-compat -Wstrict-overflow -Wlogical-op -Wlarger-than=2048 -Wvla
> -Wsync-nand -Wframe-larger-than=16384 -Wpacked-bitfield-compat -O0
> -fomit-frame-pointer -finline-functions
> AM_CFLAGS:
> CPPFLAGS:
> H5_CPPFLAGS: -D_POSIX_SOURCE -DNDEBUG -UH5_DEBUG_API
> AM_CPPFLAGS: -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE
> -D_FILE_OFFSET_BITS=64 -D_BSD_SOURCE
> Shared Libraries: yes
> Static Libraries: yes
> Statically Linked Executables: no
> LDFLAGS:
> AM_LDFLAGS:
> Extra libraries: -lz -lm
> Archiver: ar
> Ranlib: ranlib
> Debugged Packages:
> API Tracing: no
>
> Languages:
> ----------
> Fortran: yes
> Fortran Compiler: ifort
> Fortran Flags:
> H5 Fortran Flags: -O3
> AM Fortran Flags: -fPIC
> C++: yes
> C++ Compiler: g++
> C++ Flags:
> H5 C++ Flags:
> AM C++ Flags:
>
> Features:
> ---------
> Parallel HDF5: no
> High Level library: yes
> Threadsafety: no
> Default API Mapping: v18
> With Deprecated Public Symbols: yes
> I/O filters (external): deflate(zlib)
> I/O filters (internal): shuffle,fletcher32,nbit,scaleoffset
> MPE: no
> Direct VFD: no
> dmalloc: no
> Clear file buffers before write: yes
> Using memory checker: no
> Function Stack Tracing: no
> GPFS: no
> Strict File Format Checks: no
> Optimization Instrumentation: no
> Linux Large File Support (LFS): yes
> Bye...
> Abort
> $>
>
> Can you help me how to proceed?
> Thanks and Regs
> Abhijit
>
>
> _______________________________________________
> yt-users mailing list
> yt-users at lists.spacepope.org
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>
>
>
> _______________________________________________
> yt-users mailing list
> yt-users at lists.spacepope.org
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>
>
--
----------------
i am dot org: www.jsoishi.org
More information about the yt-users
mailing list