<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:arial,helvetica,sans-serif;font-size:10pt">Hi Jeff<br><br>I am grateful to you for your kind advice. I downloaded the rc file and typed<br> setenv HDF5_DISABLE_VERSION_CHECK 2<br><br>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:<br><br> $>iyt<br><br>Welcome to yt!<br><br><br>In [1]: from yt.mods.import *<br>------------------------------------------------------------<br> File "<ipython console>", line 1<br> from yt.mods.import *<br> ^<br>SyntaxError: invalid syntax<br><br><br>In [2]: <br><br><div style="font-family: arial,helvetica,sans-serif;
font-size: 10pt;">Regs<br>Abhijit<br><div style="font-family: tahoma,new york,times,serif; font-size: 10pt;"><font face="Tahoma" size="2"><hr size="1"><b><span style="font-weight: bold;">From:</span></b> j s oishi <jsoishi@gmail.com><br><b><span style="font-weight: bold;">To:</span></b> Discussion of the yt analysis package <yt-users@lists.spacepope.org><br><b><span style="font-weight: bold;">Sent:</span></b> Sun, 8 August, 2010 11:05:06 PM<br><b><span style="font-weight: bold;">Subject:</span></b> Re: [yt-users] IYT gives problem after updation of system<br></font><br>Hi Abhijit,<br><br>oops. I forgot that matplotlib doesn't install a matplotlibrc file by<br>default. You can download this sample:<br><br><a href="http://matplotlib.sourceforge.net/users/customizing.html#matplotlibrc-sample" target="_blank">http://matplotlib.sourceforge.net/users/customizing.html#matplotlibrc-sample</a><br><br>and modify it as I previously mentioned. Did yt
work without a GUI?<br><br>jeff<br><br>On Sun, Aug 8, 2010 at 10:21 AM, Dr. ABHIJIT BHATTACHARYYA<br><<a ymailto="mailto:b_abhijit2k@yahoo.co.in" href="mailto:b_abhijit2k@yahoo.co.in">b_abhijit2k@yahoo.co.in</a>> wrote:<br>> Hi Jeff<br>> Thanks for the reply. However, the .matplotlib directory does not contain<br>> any rc file as shown in the following :<br>><br>> $> ls -tls ~/.matplotlib/<br>> total 244<br>> 4 drwx--x--x 2 vega users 4096 2010-08-08 22:47 tex.cache/<br>> 240 -rw------- 1 vega users 243287 2010-08-08 22:47 fontList.cache<br>> $><br>><br>> I downloaded yt by svn and installed manually which gave no error.<br>> Regs<br>> Abhijit<br>><br>><br>><br>><br>> ________________________________<br>> From: j s oishi <<a ymailto="mailto:jsoishi@gmail.com" href="mailto:jsoishi@gmail.com">jsoishi@gmail.com</a>><br>> To: Discussion of the yt analysis
package <<a ymailto="mailto:yt-users@lists.spacepope.org" href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a>><br>> Sent: Sun, 8 August, 2010 10:38:08 PM<br>> Subject: Re: [yt-users] IYT gives problem after updation of system<br>><br>> Hi Abhijit,<br>><br>> Since you said that your OpenSUSE upgrade excluded /usr/local, I'm<br>> assuming that you build this matplotlib either from the yt install<br>> script or manually. It looks like the tkagg backend was excluded<br>> during the matplotlib process, possibly because the pacakges it relies<br>> on aren't installed by default in your new OpenSUSE distribution.<br>> First, try changing the backend in your .matplotlibrc file, which you<br>> can find in<br>><br>> ~/.matplotlib/matplotlibrc<br>><br>> If you're using GNOME, try GTKAgg; if you're using KDE, try Qt4Agg.<br>><br>> TkAgg has very few requirements, but you may not
have the tk-devel<br>> package (or its OpenSUSE equivalent; I don't use that distribution, so<br>> I don't know exactly what it's called).<br>><br>> Finally, you can verify that matplotlib works without a GUI backend by<br>> writing a very simple yt script that plots and saves a file, something<br>> like<br>><br>> from yt.mods import *<br>><br>> pf =load("DD0010/data0010")<br>> pc = PlotCollection(pf)<br>><br>> for i in range(3):<br>> pc.add_slice("Density",i)<br>><br>> pc.save('test')<br>><br>><br>> and then do<br>><br>> $ python the_above_script.py -dAgg<br>><br>> and it will attempt to run that script using the Agg matplotlib<br>> backend, which requires no GUI.<br>><br>> Hope this is helpful,<br>><br>> Jeff<br>><br>> On Sun, Aug 8, 2010 at 12:57 AM, Dr. ABHIJIT BHATTACHARYYA<br>> <<a ymailto="mailto:b_abhijit2k@yahoo.co.in"
href="mailto:b_abhijit2k@yahoo.co.in">b_abhijit2k@yahoo.co.in</a>> wrote:<br>>> Hi<br>>> I did, but result is -ve. I feel that may be, matplotlib or other python<br>>> related routine has error. I am using Python 2.6.5 (r265:79063, Jul 5<br>>> 2010,<br>>> 11:46:13) and IPython 0.10. After unsuccessful attempt I tried to<br>>> re-install<br>>> yt manually using svn which did not give any error. However, still iyt is<br>>> not working.<br>>> regs<br>>> Abhi<br>>><br>>> $> iyt<br>>> Traceback (most recent call last):<br>>> File "/usr/local/bin/iyt", line 5, in <module><br>>> pkg_resources.run_script('yt==1.7', 'iyt')<br>>> File<br>>><br>>> "/usr/local/lib64/python2.6/site-packages/distribute-0.6.10-py2.6.egg/pkg_resources.py",<br>>> line 461, in run_script<br>>>
self.require(requires)[0].run_script(script_name, ns)<br>>> File<br>>><br>>> "/usr/local/lib64/python2.6/site-packages/distribute-0.6.10-py2.6.egg/pkg_resources.py",<br>>> line 1194, in run_script<br>>> execfile(script_filename, namespace, namespace)<br>>> File<br>>><br>>> "/usr/local/lib64/python2.6/site-packages/yt-1.7-py2.6-linux-x86_64.egg/EGG-INFO/scripts/iyt",<br>>> line 32, in <module><br>>> ip_shell = IPython.Shell.IPShellMatplotlib(user_ns=namespace)<br>>> File "/usr/local/lib/python2.6/site-packages/IPython/Shell.py", line<br>>> 1106,<br>>> in __init__<br>>> shell_class=MatplotlibShell)<br>>> File "/usr/local/lib/python2.6/site-packages/IPython/Shell.py", line 73,<br>>> in __init__<br>>> debug=debug,shell_class=shell_class)<br>>>
File "/usr/local/lib/python2.6/site-packages/IPython/ipmaker.py", line<br>>> 100, in make_IPython<br>>> embedded=embedded,**kw)<br>>> File "/usr/local/lib/python2.6/site-packages/IPython/Shell.py", line<br>>> 627,<br>>> in __init__<br>>> user_ns,user_global_ns,b2 =<br>>> self._matplotlib_config(name,user_ns,user_global_ns)<br>>> File "/usr/local/lib/python2.6/site-packages/IPython/Shell.py", line<br>>> 556,<br>>> in _matplotlib_config<br>>> import matplotlib.pylab as pylab<br>>> File "/usr/lib64/python2.6/site-packages/matplotlib/pylab.py", line 259,<br>>> in <module><br>>> from matplotlib.pyplot import *<br>>> File "/usr/lib64/python2.6/site-packages/matplotlib/pyplot.py", line 95,<br>>> in <module><br>>>
new_figure_manager, draw_if_interactive, show = pylab_setup()<br>>> File<br>>> "/usr/lib64/python2.6/site-packages/matplotlib/backends/__init__.py",<br>>> line 25, in pylab_setup<br>>> globals(),locals(),[backend_name])<br>>> ImportError: No module named backend_tkagg<br>>> $><br>>> $> setenv HDF5_DISABLE_VERSION_CHECK 2<br>>> $> iyt<br>>> Traceback (most recent call last):<br>>> File "/usr/local/bin/iyt", line 5, in <module><br>>> pkg_resources.run_script('yt==1.7', 'iyt')<br>>> File<br>>><br>>> "/usr/local/lib64/python2.6/site-packages/distribute-0.6.10-py2.6.egg/pkg_resources.py",<br>>> line 461, in run_script<br>>> self.require(requires)[0].run_script(script_name, ns)<br>>> File<br>>><br>>>
"/usr/local/lib64/python2.6/site-packages/distribute-0.6.10-py2.6.egg/pkg_resources.py",<br>>> line 1194, in run_script<br>>> execfile(script_filename, namespace, namespace)<br>>> File<br>>><br>>> "/usr/local/lib64/python2.6/site-packages/yt-1.7-py2.6-linux-x86_64.egg/EGG-INFO/scripts/iyt",<br>>> line 32, in <module><br>>> ip_shell = IPython.Shell.IPShellMatplotlib(user_ns=namespace)<br>>> File "/usr/local/lib/python2.6/site-packages/IPython/Shell.py", line<br>>> 1106,<br>>> in __init__<br>>> shell_class=MatplotlibShell)<br>>> File "/usr/local/lib/python2.6/site-packages/IPython/Shell.py", line 73,<br>>> in __init__<br>>> debug=debug,shell_class=shell_class)<br>>> File "/usr/local/lib/python2.6/site-packages/IPython/ipmaker.py", line<br>>> 100, in
make_IPython<br>>> embedded=embedded,**kw)<br>>> File "/usr/local/lib/python2.6/site-packages/IPython/Shell.py", line<br>>> 627,<br>>> in __init__<br>>> user_ns,user_global_ns,b2 =<br>>> self._matplotlib_config(name,user_ns,user_global_ns)<br>>> File "/usr/local/lib/python2.6/site-packages/IPython/Shell.py", line<br>>> 556,<br>>> in _matplotlib_config<br>>> import matplotlib.pylab as pylab<br>>> File "/usr/lib64/python2.6/site-packages/matplotlib/pylab.py", line 259,<br>>> in <module><br>>> from matplotlib.pyplot import *<br>>> File "/usr/lib64/python2.6/site-packages/matplotlib/pyplot.py", line 95,<br>>> in <module><br>>> new_figure_manager, draw_if_interactive, show = pylab_setup()<br>>> File<br>>>
"/usr/lib64/python2.6/site-packages/matplotlib/backends/__init__.py",<br>>> line 25, in pylab_setup<br>>> globals(),locals(),[backend_name])<br>>> ImportError: No module named backend_tkagg<br>>> $><br>>><br>>> Dr. Abhijit Bhattacharyya [Scientific Officer]<br>>> Control Instrumentation Division (CnID)<br>>> Electronics and Instrumentation Group (E&I Group)<br>>> Reactor Control Division Building (RCnD Building)<br>>> Bhabha Atomic Research Center (BARC)<br>>> Trombay, Mumbai - 400 085<br>>> Phone: +91.22.2559.5493<br>>> Email: <a ymailto="mailto:vega@barc.gov.in" href="mailto:vega@barc.gov.in">vega@barc.gov.in</a><br>>> Residence:<br>>> 811 Akashdeep<br>>> Anushakti Nagar<br>>><br>>> Mumbai- 400094<br>>> Phone: +91.22.2558.0930<br>>> Mobile: +91.98201.49770<br>>><br>>> GPS: 19 deg 01 min 54.52
secs North;<br>>><br>>> 72 deg 55 min 46.30 secs East<br>>><br>>> ________________________________<br>>> From: Matthew Turk <<a ymailto="mailto:matthewturk@gmail.com" href="mailto:matthewturk@gmail.com">matthewturk@gmail.com</a>><br>>> To: Discussion of the yt analysis package <<a ymailto="mailto:yt-users@lists.spacepope.org" href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a>><br>>> Sent: Sun, 8 August, 2010 3:13:14 AM<br>>> Subject: Re: [yt-users] IYT gives problem after updation of system<br>>><br>>> Hi Abhijit,<br>>><br>>> Setting HDF5_DISABLE_VERSION_CHECK to 2 should be okay in this case. Let<br>>> us<br>>> know if it acts up, though!<br>>><br>>> -Matt<br>>><br>>> On Aug 7, 2010 2:22 PM, "Dr. ABHIJIT BHATTACHARYYA"<br>>> <<a
ymailto="mailto:b_abhijit2k@yahoo.co.in" href="mailto:b_abhijit2k@yahoo.co.in">b_abhijit2k@yahoo.co.in</a>> wrote:<br>>><br>>> Hi<br>>><br>>> I upgraded my system to OpenSUSE 11.3. I kept 'iyt' and 'enzo' in<br>>> '/usr/local' while I only upgraded '/' while '/' and '/usr/local' are two<br>>> different partitions. Now Enzo is working while iyt gives following error.<br>>><br>>> $> iyt<br>>> Warning! ***HDF5 library version mismatched error***<br>>> The HDF5 header files used to compile this application do not match<br>>> the version used by the HDF5 library to which this application is linked.<br>>> Data corruption or segmentation faults may occur if the application<br>>> continues.<br>>> This can happen when an application was compiled by one version of HDF5<br>>> but<br>>> linked with a different version of static or shared HDF5 library.<br>>>
You should recompile the application or check your shared library related<br>>> settings such as 'LD_LIBRARY_PATH'.<br>>> You can, at your own risk, disable this warning by setting the environment<br>>> variable 'HDF5_DISABLE_VERSION_CHECK' to a value of '1'.<br>>> Setting it to 2 or higher will suppress the warning messages totally.<br>>> Headers are 1.8.5, library is 1.8.4<br>>> SUMMARY OF THE HDF5 CONFIGURATION<br>>> =================================<br>>><br>>> General Information:<br>>> -------------------<br>>> HDF5 Version: 1.8.4-patch1<br>>>
Configured on: Sat May 29 02:41:00 IST 2010<br>>> Configured by: root@Pakudidi<br>>> Configure mode: production<br>>> Host system: x86_64-unknown-linux-gnu<br>>> Uname information: Linux Pakudidi 2.6.31-rc9-7-default #1<br>>> SMP<br>>> 2009-09-08 18:49:15 +0200 x86_64 x86_64 x86_64 GNU/Linux<br>>>
Byte sex: little-endian<br>>> Libraries:<br>>> Installation point: /usr/local<br>>><br>>> Compiling Options:<br>>> ------------------<br>>> Compilation Mode: production<br>>> C Compiler: /usr/bin/gcc (gcc-4.4.1)<br>>>
CFLAGS:<br>>> H5_CFLAGS: -std=c99 -pedantic -Wall -Wextra -Wundef<br>>> -Wshadow -Wpointer-arith -Wbad-function-cast -Wcast-qual -Wcast-align<br>>> -Wwrite-strings -Wconversion -Waggregate-return -Wstrict-prototypes<br>>> -Wmissing-prototypes -Wmissing-declarations -Wredundant-decls<br>>> -Wnested-externs -Winline -Wno-long-long -Wfloat-equal<br>>> -Wmissing-format-attribute -Wmissing-noreturn -Wpacked<br>>> -Wdisabled-optimization -Wformat=2 -Wunreachable-code -Wendif-labels<br>>> -Wdeclaration-after-statement -Wold-style-definition -Winvalid-pch<br>>> -Wvariadic-macros -Wnonnull -Winit-self -Wmissing-include-dirs<br>>> -Wswitch-default -Wswitch-enum -Wunused-macros -Wunsafe-loop-optimizations<br>>> -Wc++-compat -Wstrict-overflow -Wlogical-op -Wlarger-than=2048
-Wvla<br>>> -Wsync-nand -Wframe-larger-than=16384 -Wpacked-bitfield-compat -O0<br>>> -fomit-frame-pointer -finline-functions<br>>> AM_CFLAGS:<br>>> CPPFLAGS:<br>>> H5_CPPFLAGS: -D_POSIX_SOURCE -DNDEBUG -UH5_DEBUG_API<br>>> AM_CPPFLAGS: -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE<br>>> -D_FILE_OFFSET_BITS=64 -D_BSD_SOURCE<br>>>
Shared Libraries: yes<br>>> Static Libraries: yes<br>>> Statically Linked Executables: no<br>>> LDFLAGS:<br>>> AM_LDFLAGS:<br>>> Extra libraries: -lz -lm<br>>> Archiver: ar<br>>> Ranlib:
ranlib<br>>> Debugged Packages:<br>>> API Tracing: no<br>>><br>>> Languages:<br>>> ----------<br>>> Fortran: yes<br>>> Fortran Compiler: ifort<br>>> Fortran Flags:<br>>> H5 Fortran Flags: -O3<br>>> AM Fortran
Flags: -fPIC<br>>> C++: yes<br>>> C++ Compiler: g++<br>>> C++ Flags:<br>>> H5 C++ Flags:<br>>> AM C++ Flags:<br>>><br>>> Features:<br>>> ---------<br>>> Parallel HDF5:
no<br>>> High Level library: yes<br>>> Threadsafety: no<br>>> Default API Mapping: v18<br>>> With Deprecated Public Symbols: yes<br>>> I/O filters (external): deflate(zlib)<br>>> I/O filters (internal): shuffle,fletcher32,nbit,scaleoffset<br>>> MPE: no<br>>> Direct VFD:
no<br>>> dmalloc: no<br>>> Clear file buffers before write: yes<br>>> Using memory checker: no<br>>> Function Stack Tracing: no<br>>> GPFS: no<br>>> Strict File Format Checks: no<br>>> Optimization Instrumentation: no<br>>> Linux Large File Support (LFS): yes<br>>> Bye...<br>>> Abort<br>>> $><br>>><br>>> Can you help me how to proceed?<br>>> Thanks and Regs<br>>> Abhijit<br>>><br>>><br>>>
_______________________________________________<br>>> yt-users mailing list<br>>> <a ymailto="mailto:yt-users@lists.spacepope.org" href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a><br>>> <a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org" target="_blank">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br>>><br>>><br>>><br>>> _______________________________________________<br>>> yt-users mailing list<br>>> <a ymailto="mailto:yt-users@lists.spacepope.org" href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a><br>>> <a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org" target="_blank">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br>>><br>>><br>><br>><br>><br>> --<br>> ----------------<br><span>> i am dot org: <a target="_blank"
href="http://www.jsoishi.org">www.jsoishi.org</a></span><br>> _______________________________________________<br>> yt-users mailing list<br>> <a ymailto="mailto:yt-users@lists.spacepope.org" href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a><br>> <a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org" target="_blank">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br>><br>><br>> _______________________________________________<br>> yt-users mailing list<br>> <a ymailto="mailto:yt-users@lists.spacepope.org" href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a><br>> <a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org" target="_blank">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br>><br>><br><br><br><br>-- <br>----------------<br><span>i am dot org: <a target="_blank"
href="http://www.jsoishi.org">www.jsoishi.org</a></span><br>_______________________________________________<br>yt-users mailing list<br><a ymailto="mailto:yt-users@lists.spacepope.org" href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a><br><a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org" target="_blank">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br></div></div>
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