[yt-users] IYT gives problem after updation of system

Dr. ABHIJIT BHATTACHARYYA b_abhijit2k at yahoo.co.in
Sun Aug 8 00:57:18 PDT 2010


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
>
>

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