[yt-users] yt install script on NICS Kraken

David A. Ventimiglia ventimig at msu.edu
Mon May 11 15:52:47 PDT 2009 

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
> > >
> > >
> > > _______________________________________________
> > > yt-users mailing list
> > > yt-users at lists.spacepope.org
> > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> > >
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> > yt-users mailing list
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> > 
> 
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