Hi Jeff Thanks for the reply. However, the .matplotlib directory does not contain any rc file as shown in the following : $> ls -tls ~/.matplotlib/ total 244 4 drwx--x--x 2 vega users 4096 2010-08-08 22:47 tex.cache/ 240 -rw------- 1 vega users 243287 2010-08-08 22:47 fontList.cache $> I downloaded yt by svn and installed manually which gave no error. Regs Abhijit ________________________________ From: j s oishi <jsoishi@gmail.com> To: Discussion of the yt analysis package <yt-users@lists.spacepope.org> Sent: Sun, 8 August, 2010 10:38:08 PM Subject: Re: [yt-users] IYT gives problem after updation of system 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@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@barc.gov.in Residence: 811 Akashdeep Anushakti Nagar
Mumbai- 400094 Phone: +91.22.2558.0930 Mobile: +91.98201.49770
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________________________________ From: Matthew Turk <matthewturk@gmail.com> To: Discussion of the yt analysis package <yt-users@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@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@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
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