[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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