[yt-users] yt install script on NICS Kraken

Matthew Turk matthewturk at gmail.com
Mon May 11 16:04:44 PDT 2009


Hi David,

So what it's trying to do is import the WX GUI toolkit; I think this
is probably not going to work on Kraken, even if you set the
appropriate variable in the install script to 1.  (On many other
systems, however, it will work.)  What this will mean is that for the
most part, interactive display of plots may not work -- I will run
some tests to see if WX can be installed on Kraken, which would fix
this and allow for windows to pop up, etc etc.

What I've done for now is commit a new version of the iyt script that
will fall back on a basic matplotlib shell if wx can't be found.  I've
committed this in r1301 ( http://yt.enzotools.org/changeset/1301 )
which you can get either by svn upping in the src/yt-svn-trunk
directory or simply re-running the install script (it will not
overwrite existing installations.)

Please let me know if this doesn't work!

-Matt

On Mon, May 11, 2009 at 3:52 PM, David A. Ventimiglia <ventimig at msu.edu> wrote:
> Hi Matt,
>
> Ok, I'm getting slap-happy.  The previous error message I posted was due
> to me screwing up my PATH variable.  Now, I get:
>
> ventimig at kraken-pwd4(XT5):~> iyt
> yt.lagos   WARNING    2009-05-11 18:50:56,844 No HDF4 support
> /nics/b/home/ventimig/scratch/yt-x86_64/lib/python2.6/site-packages/IPython/Magic.py:38: DeprecationWarning: the sets module is deprecated
>  from sets import Set
> ---------------------------------------------------------------------------
> ImportError                               Traceback (most recent call last)
>
> /nics/b/home/ventimig/scratch/yt-x86_64/src/yt-trunk-svn/scripts/iyt in <module>()
>      5 del require
>      6 __file__ = '/nics/b/home/ventimig/scratch/yt-x86_64/src/yt-trunk-svn/scripts/iyt'
> ----> 7 execfile(__file__)
>      8
>      9
>
> /nics/b/home/ventimig/scratch/yt-x86_64/src/yt-trunk-svn/scripts/iyt in <module>()
>     19     sys.exit()
>     20
> ---> 21 ip_shell = IPython.Shell.IPShellMatplotlibWX(user_ns=namespace)
>     22
>     23 # The rest is a modified version of the IPython default profile code
>
>
> /nics/b/home/ventimig/scratch/yt-x86_64/lib/python2.6/site-packages/IPython/Shell.pyc in __init__(self, argv, user_ns, user_global_ns, debug)
>   1116     def __init__(self,argv=None,user_ns=None,user_global_ns=None,debug=1):
>   1117         IPShellWX.__init__(self,argv,user_ns,user_global_ns,debug,
> -> 1118                            shell_class=MatplotlibMTShell)
>   1119         _load_pylab(self.IP.user_ns)
>   1120
>
> /nics/b/home/ventimig/scratch/yt-x86_64/lib/python2.6/site-packages/IPython/Shell.pyc in __init__(self, argv, user_ns, user_global_ns, debug, shell_class)
>    876                                                                wantedwxversion)
>    877
> --> 878         import wx
>    879
>    880         threading.Thread.__init__(self)
>
> ImportError: No module named wx
>
>
>
> On Mon, 2009-05-11 at 15:40 -0700, David A. Ventimiglia wrote:
>> Hi Matt,
>>
>> Thanks for the quick and detailed reply.  After swapping the PrgEnv-pgi
>> environment in favor of the PrgEnv-gnu env, and running the yt
>> install_script.sh file from the development trunk, I get a different
>> error on Kraken:
>>
>> ========================================================================
>> ventimig at kraken-pwd3(XT5):~/scratch> iyt
>> yt.lagos   WARNING    2009-05-11 18:32:13,681 No HDF4 support
>> /nics/b/home/ventimig/scratch/yt-x86_64/lib/python2.6/site-packages/IPython/Magic.py:38: DeprecationWarning: the sets module is deprecated
>>   from sets import Set
>> Traceback (most recent call last):
>>   File "/nics/b/home/ventimig/scratch/yt-x86_64/bin/iyt", line 7, in <module>
>>     execfile(__file__)
>>   File "/nics/b/home/ventimig/scratch/yt-x86_64/src/yt-trunk-svn/scripts/iyt", line 3, in <module>
>>     from yt.mods import *
>>   File "/nics/b/home/ventimig/scratch/yt-x86_64/src/yt-trunk-svn/yt/mods.py", line 33, in <module>
>>     import yt.raven as raven
>>   File "/nics/b/home/ventimig/scratch/yt-x86_64/src/yt-trunk-svn/yt/raven/__init__.py", line 44, in <module>
>>     import matplotlib.image
>>   File "/nics/b/home/ventimig/scratch/yt-x86_64/lib/python2.6/site-packages/matplotlib/image.py", line 13, in <module>
>>     from matplotlib import artist as martist
>>   File "/nics/b/home/ventimig/scratch/yt-x86_64/lib/python2.6/site-packages/matplotlib/artist.py", line 5, in <module>
>>     from transforms import Bbox, IdentityTransform, TransformedBbox, TransformedPath
>>   File "/nics/b/home/ventimig/scratch/yt-x86_64/lib/python2.6/site-packages/matplotlib/transforms.py", line 34, in <module>
>>     from matplotlib._path import affine_transform
>> ImportError: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by /nics/b/home/ventimig/scratch/yt-x86_64/lib/python2.6/site-packages/matplotlib/_path.so)
>>
>> Any ideas?  Thanks in advance!
>> Best,
>> David
>>
>>
>>
>> On Mon, 2009-05-11 at 12:37 -0700, Matthew Turk wrote:
>> > Hi David,
>> >
>> > Unfortunately, compiling with the PGI compilers on Kraken (unless you
>> > are doing a static-linking, which Stephen Skory has documented here:
>> > http://yt.enzotools.org/wiki/CrayXT5Installation ) is a bit of a pain.
>> >  I would recommend that you use gcc.  I'm afraid I don't know how to
>> > get the PGI compilers to work properly -- but you might be able to do
>> > some modification of the LD_LIBRARY_PATH to make them work.
>> >
>> > I'd recommend that you run the install script, unmodified, after
>> > module swapping the PGI for GNU environments:
>> >
>> > $ module swap PrgEnv-pgi PrgEnv-gnu
>> > $ bash install_script.sh
>> >
>> > In a fresh environment, this works for me.  If you already have run
>> > the install script, you may have to remove your existing yt
>> > installation directory and run it again.  I apologize that this is a
>> > bit of a time-consuming task, but I believe it should work.
>> >
>> > Good luck, and please let us know if this works!
>> >
>> > -Matt
>> >
>> > On Mon, May 11, 2009 at 12:34 PM, David A. Ventimiglia <ventimig at msu.edu> wrote:
>> > > Hello,
>> > >
>> > > I'm new to yt, so I apologize if I'm doing something dumb.  But, I'm
>> > > trying to install yt on Kraken and am having a little trouble.
>> > > install_script.sh appeared to run fine, but when I run iyt I get these
>> > > errors:
>> > >
>> > > yt.lagos   WARNING    2009-05-11 15:09:47,175 No HDF4 support
>> > > yt.lagos   WARNING    2009-05-11 15:09:47,185 No h5py. Data serialization will fail.
>> > > Traceback (most recent call last):
>> > >  File "/nics/b/home/ventimig/scratch/yt-x86_64/bin/iyt", line 7, in <module>
>> > >    execfile(__file__)
>> > >  File "/nics/b/home/ventimig/scratch/yt-x86_64/src/yt-trunk-svn/scripts/iyt", line 3, in <module>
>> > >    from yt.mods import *
>> > >  File "/nics/b/home/ventimig/scratch/yt-x86_64/src/yt-trunk-svn/yt/mods.py", line 32, in <module>
>> > >    import yt.lagos as lagos
>> > >  File "/nics/b/home/ventimig/scratch/yt-x86_64/src/yt-trunk-svn/yt/lagos/__init__.py", line 74, in <module>
>> > >    import HDF5LightReader
>> > > ImportError: libpgc.so: cannot open shared object file: No such file or directory
>> > >
>> > > Evidently it can't find one of the Portland Group libraries, but I
>> > > thought all that'd be taken care of by having the PrgEnv-pgi module
>> > > loaded.  What am I doing wrong?  Thanks!
>> > >
>> > > Best,
>> > > David Ventimiglia
>> > > ventimig at msu.edu
>> > >
>> > >
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