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@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@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@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) -------------------
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@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@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@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@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@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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@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@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@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@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@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@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@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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@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@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@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@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@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@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@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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participants (2)
-
Agarwal, Shankar -
Matthew Turk