[yt-users] ENZO and YT on NCSA-Cobalt
Agarwal, Shankar
sagarwal at ku.edu
Thu Jun 25 12:58:06 PDT 2009
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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