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

Dr. ABHIJIT BHATTACHARYYA b_abhijit2k at yahoo.co.in
Sun Aug 8 10:57:51 PDT 2010


Hi Jeff

I am grateful to you for your kind advice. I downloaded the rc file and typed
 setenv HDF5_DISABLE_VERSION_CHECK 2

which runs iyt. However, without the setenv I see that iyt is not starting. Now, 
after the usual ipython prompt, I tried to use import which gives me the 
following:

 $>iyt

Welcome to yt!


In [1]: from yt.mods.import *
------------------------------------------------------------
   File "<ipython console>", line 1
     from yt.mods.import *
                       ^
SyntaxError: invalid syntax


In [2]: 


Regs
Abhijit


________________________________
From: j s oishi <jsoishi at gmail.com>
To: Discussion of the yt analysis package <yt-users at lists.spacepope.org>
Sent: Sun, 8 August, 2010 11:05:06 PM
Subject: Re: [yt-users] IYT gives problem after updation of system

Hi Abhijit,

oops. I forgot that matplotlib doesn't install a matplotlibrc file by
default. You can download this sample:

http://matplotlib.sourceforge.net/users/customizing.html#matplotlibrc-sample

and modify it as I previously mentioned. Did yt work without a GUI?

jeff

On Sun, Aug 8, 2010 at 10:21 AM, Dr. ABHIJIT BHATTACHARYYA
<b_abhijit2k at yahoo.co.in> wrote:
> 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 at gmail.com>
> To: Discussion of the yt analysis package <yt-users at 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 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
>>
>>
>
>
>
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> _______________________________________________
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