[yt-users] ENZO and YT on NCSA-Cobalt
Matthew Turk
matthewturk at gmail.com
Thu Jun 25 14:16:01 PDT 2009
Hi Shankar,
All of those can be ignored. :) I'm glad to hear things are now
working for you!
-Matt
On Thu, Jun 25, 2009 at 2:14 PM, Agarwal, Shankar<sagarwal at ku.edu> wrote:
> Awesome! Awesome! Awesome!
>
> Barring the following, I am now able to access data files using yt.
>
>
> -----------------------------------
> $ /u/ac/sagarwal/enzov1.5/src/yt/doc/yt-ia64/bin/python2.6 setup.py develop
>
> /u/ac/sagarwal/enzov1.5/src/yt/doc/yt-ia64/lib/python2.6/distutils/dist.py:266: UserWarning: Unknown distribution option: 'app'
> warnings.warn(msg)
>
> /u/ac/sagarwal/enzov1.5/src/yt/doc/yt-ia64/lib/python2.6/site-packages/numpy/distutils/misc_util.py:1343: DeprecationWarning: os.popen4 is deprecated. Use the subprocess module.
> sin, sout = os.popen4('svnversion')
>
> running develop
> running build_scripts
> copying and adjusting scripts/fimport -> build/scripts.linux-ia64-2.6
> .
> .
> .
> blah blah
>
>
> And...
>
> [sagarwal at co-login jj]$ iyt
> yt.lagos INFO 2009-06-25 15:38:31,887 No HDF4 support
> /u/ac/sagarwal/enzov1.5/src/yt/doc/yt-ia64/lib/python2.6/site-packages/IPython/Magic.py:38: DeprecationWarning: the sets module is deprecated
> from sets import Set
>
> Welcome to yt!
>
>
> In [1]:
>
> -------------------------------------
>
>
>
> Thanks Matt.
>
>
> regards
> shankar
> KU Cosmology
>
>
>
>
> -----Original Message-----
> From: yt-users-bounces at lists.spacepope.org on behalf of Matthew Turk
> Sent: Thu 6/25/2009 3:14 PM
> To: Discussion of the yt analysis package
> Subject: Re: [yt-users] ENZO and YT on NCSA-Cobalt
>
> 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)
>>
>>
>> -------------------
>> _______________________________________________
>> yt-users mailing list
>> yt-users at lists.spacepope.org
>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>
> _______________________________________________
> yt-users mailing list
> yt-users at lists.spacepope.org
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>
>
> _______________________________________________
> yt-users mailing list
> yt-users at lists.spacepope.org
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>
>
More information about the yt-users
mailing list