[yt-users] yt install script on NICS Kraken

David A. Ventimiglia ventimig at msu.edu
Mon May 11 16:40:28 PDT 2009 

Hi Matt,

That worked like a charm.  Thanks!

Best,
David

On Mon, 2009-05-11 at 16:04 -0700, Matthew Turk wrote:
> 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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