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

John Wise jwise at astro.princeton.edu
Sun Aug 8 16:44:52 PDT 2010


Hi Abhijit,

There shouldn't be a period between mods and import.  The correct
syntax would be

from yt.mods import *

Cheers,
John

On Sun, 08 Aug 2010 at 23:27 +0530, Dr. ABHIJIT BHATTACHARYYA wrote:
> 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
> >>
> >>
> >
> >
> >
> > --
> > ----------------
> > i am dot org: www.jsoishi.org
> > _______________________________________________
> > 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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