[yt-users] ENZO and YT on NCSA-Cobalt

Matthew Turk matthewturk at gmail.com
Thu Jun 25 13:14:23 PDT 2009


Hi Shankar,

Looks like you're using a very old version of yt from last year before
the 'load' function had been included, and so it's picking up the
matplotlib load.  The enzo repository switched over to the current
stable version sometime over a month ago and the installation
instructions should not lead to installation of this particular
version.  I believe you ran a freshly checked out installation script,
so all the dependencies should be in place.  What we will do is
instead delete the old installation of yt (but not the dependencies)
and then replace it with a new one.

We deleted the installed yt with:

$ rm -rf /u/ac/sagarwal/enzov1.5/src/yt/doc/yt-ia64/lib/python2.6/site-packages/yt*

Then to update the enzo svn (whcih points to the current stable branch
of yt) we do this:

$ cd /u/ac/sagarwal/enzov1.5/src/
$ svn up

At this point, it should update your yt installation.  You can verify
that you have the newest one available by checking that in yt/setup.py
VERSION is set to "1.5dev".  If it is not, then you have a broken enzo
checkout and, in *a different directory* you should run a fresh copy
of the install script that I sent you on the enzo mailing list
yesterday.  If it *is* set to 1.5dev, then execute this to update the
yt installation:

$ cd yt
$ /u/ac/sagarwal/enzov1.5/src/yt/doc/yt-ia64/bin/python2.6 setup.py develop

That should update the yt installation to 1.5.  Please let us know if
this does not work for you!

Best wishes,

Matt

On Thu, Jun 25, 2009 at 12:58 PM, Agarwal, Shankar<sagarwal at ku.edu> wrote:
> Hi, I am running ENZO on NCSA,Cobalt.
>
> I have Enzo cosmology simulation output (RD0002 directory with a bunch of RedshiftOutput0002.cpu**** files)
> When I do 'iyt' I get ...
>
>
> [sagarwal at co-login jj]$ iyt
> yt.lagos   WARNING    2009-06-25 14:47:03,269 No HDF4 support
> yt.lagos   WARNING    2009-06-25 14:47:03,284 No PyTables. Data serialization will fail.
> /u/ac/sagarwal/enzov1.5/src/yt/yt/lagos/__init__.py:55: DeprecationWarning: the sets module is deprecated
>  import sets
>
> Welcome to yt!
>
>
> In [1]: from yt.mods import *
> In [2]: pf=load('RedshiftOutput0002')
> ERROR: An unexpected error occurred while tokenizing input
> The following traceback may be corrupted or invalid
> The error message is: ('EOF in multi-line statement', (389, 0))
>
> ---------------------------------------------------------------------------
> ValueError                                Traceback (most recent call last)
>
> /u/ac/sagarwal/enzov1.5/src/yt/scripts/iyt in <module>()
> ----> 1
>      2
>      3
>      4
>      5
>
> /u/ac/sagarwal/enzov1.5/src/yt/doc/yt-ia64/lib/python2.6/site-packages/matplotlib/mlab.pyc in load(fname, comments, delimiter, converters, skiprows, usecols, unpack, dtype)
>   1457         else:
>   1458             row = [converterseq[j](val)
> -> 1459                       for j,val in enumerate(splitfunc(line))]
>   1460         thisLen = len(row)
>   1461         X.append(row)
>
> ValueError: invalid literal for float(): InitialCycleNumber
>
> In [3]:
>
>
>
>
> I thought ENZO and YT are customized for NCSA,Cobalt.
> Feedback is highly appreciated.
>
> Shankar
> KU Cosmology
>
>
> I recently (today) got the latest ENZO version through svn. I built ENZO, INITS, RING and YT following the instructions on enzo webpage. I have following issues...
>
> INITS and RING went fine.
>
> ENZO compiled and installed fine (I could get enzo.exe) but gave me this on "make install"...
>
> [sagarwal at co-login enzo]$ make install
> if [ ! -e ../../bin ]; then mkdir ../../bin; fi
> cp: cannot stat `gridtests.exe': No such file or directory
> make: [install] Error 1 (ignored)
> cp: cannot stat `ealfloattests.exe': No such file or directory
> make: [install] Error 1 (ignored)
> cp: cannot stat `ealinttests.exe': No such file or directory
> make: [install] Error 1 (ignored)
> cp: cannot stat `readgridtests.exe': No such file or directory
> make: [install] Error 1 (ignored)
> cp: cannot stat `analysisbaseclasstests.exe': No such file or directory
> make: [install] Error 1 (ignored)
> make -s show-flags   >& ../../bin/enzo.show-flags
> make -s show-config  >& ../../bin/enzo.show-config
> make -s show-version >& ../../bin/enzo.show-version
> make -s show-diff    >& ../../bin/enzo.show-diff
> [sagarwal at co-login enzo]$
>
>
>
>
>
> While building YT...i got the following warnings/errors...
>
> H5E.c: in function `H5Eprint':
> H5E.c:467: warning: trace info was not inserted
>
> H5FD.c(3670): warning #810: conversion from "void *" to "herr_t={int}" may lose significant bits
>        HGOTO_ERROR(H5E_VFL, H5E_UNSUPPORTED, NULL, "file driver has no `get_vfd_handle' method");
>
>
> H5FDmulti.c(208): warning #266: function "strlen" declared implicitly
>      if (NULL==(x=malloc(strlen(s)+1))) return NULL;
>
> h5diff_dset.c(259): warning #186: pointless comparison of unsigned integer with zero
>      if (storage_size1<0 || storage_size2<0)
>
> running build
> running build_ext
> INFO: Can't locate Tcl/Tk libs and/or headers
> building '_struct' extension
>
>
> Failed to find the necessary bits to build these modules:
> _hashlib           _sqlite3           _ssl
> _tkinter           bsddb185           dl
> imageop            sunaudiodev
> To find the necessary bits, look in setup.py in detect_modules() for the module's name.
>
>
>
> Running from numpy source directory.
> /u/ac/sagarwal/enzov1.5/src/yt/doc/yt-ia64/src/numpy-1.2.1/numpy/distutils/misc_util.py:1343: DeprecationWarning: os.popen4 is deprecated.  Use the subprocess module.
>  sin, sout = os.popen4('svnversion')
> non-existing path in 'numpy/distutils': 'site.cfg'
> F2PY Version 2_5972
> blas_opt_info:
> blas_mkl_info:
>  libraries mkl,vml,guide not found in /u/ac/sagarwal/enzov1.5/src/yt/doc/yt-ia64/lib
>  libraries mkl,vml,guide not found in /usr/local/lib
>  libraries mkl,vml,guide not found in /usr/lib
>  NOT AVAILABLE
>
>
>
> compile options: '-Inumpy/core/src -Inumpy/core/include -I/u/ac/sagarwal/enzov1.5/src/yt/doc/yt-ia64/include/python2.6 -c'
> gcc: _configtest.c
> gcc -pthread _configtest.o -o _configtest
> _configtest
> failure.
> removing: _configtest.c _configtest.o _configtest
>
>
>
> Running from numpy source directory.
> /u/ac/sagarwal/enzov1.5/src/yt/doc/yt-ia64/src/numpy-1.2.1/numpy/distutils/misc_util.py:1343: DeprecationWarning: os.popen4 is deprecated.  Use the subprocess module.
>  sin, sout = os.popen4('svnversion')
> non-existing path in 'numpy/distutils': 'site.cfg'
> F2PY Version 2_5972
> blas_opt_info:
> blas_mkl_info:
>  libraries mkl,vml,guide not found in /u/ac/sagarwal/enzov1.5/src/yt/doc/yt-ia64/lib
>  libraries mkl,vml,guide not found in /usr/local/lib
>  libraries mkl,vml,guide not found in /usr/lib
>  NOT AVAILABLE
>
>
>
> atlas_info:
>  libraries f77blas,cblas,atlas not found in /u/ac/sagarwal/enzov1.5/src/yt/doc/yt-ia64/lib
>  libraries lapack_atlas not found in /u/ac/sagarwal/enzov1.5/src/yt/doc/yt-ia64/lib
>  libraries f77blas,cblas,atlas not found in /usr/local/lib
>  libraries lapack_atlas not found in /usr/local/lib
>  libraries f77blas,cblas,atlas not found in /usr/lib
>  libraries lapack_atlas not found in /usr/lib
> numpy.distutils.system_info.atlas_info
>  NOT AVAILABLE
>
>
>
> BUILDING MATPLOTLIB
>            matplotlib: 0.98.5.2
>                python: 2.6.1 (r261:67515, Jun 24 2009, 18:14:59)  [GCC
>                        4.1.2 20070115 (prerelease) (SUSE Linux)]
>              platform: linux2
>
> REQUIRED DEPENDENCIES
>                 numpy: 1.2.1
>             freetype2: 9.8.3
>
> OPTIONAL BACKEND DEPENDENCIES
>                libpng: 1.2.8
>               Tkinter: no
>                        * TKAgg requires Tkinter
>              wxPython: no
>                        * wxPython not found
>                  Gtk+: no
>                        * Building for Gtk+ requires pygtk; you must be able
>                        * to "import gtk" in your build/install environment
>       Mac OS X native: no
>                    Qt: no
>                   Qt4: no
>                 Cairo: no
>
> OPTIONAL DATE/TIMEZONE DEPENDENCIES
>              datetime: present, version unknown
>              dateutil: matplotlib will provide
>                  pytz: matplotlib will provide
> adding pytz
>
> OPTIONAL USETEX DEPENDENCIES
>                dvipng: no
>           ghostscript: 8.15.3
>                 latex: no
>
> [Edit setup.cfg to suppress the above messages]
>
>
>
>
>
> BUILDING IPYTHON
>                python: 2.6.1 (r261:67515, Jun 24 2009, 18:14:59)  [GCC
>                        4.1.2 20070115 (prerelease) (SUSE Linux)]
>              platform: linux2
>
> OPTIONAL DEPENDENCIES
>        zope.Interface: Not found (required for parallel computing
>                        capabilities)
>               Twisted: Not found (required for parallel computing
>                        capabilities)
>              Foolscap: Not found (required for parallel computing
>                        capabilities)
>               OpenSSL: Not found (required if you want security in the
>                        parallel computing capabilities)
>                sphinx: Not found (required for building documentation)
>              pygments: Not found (required for syntax highlighting
>                        documentation)
>                  nose: Not found (required for running the test suite)
>               pexpect: no (required for running standalone doctests)
>
>
> -------------------
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