Thanks, that helped some but it's still broken. now tables.test() outputs the
following error which is caused by a library mismatch. Any ideas about how to
debug this? I can't even find HDF5 1.8.5 installation it might be using:
In [1]: import tables
In [2]: tables.test()
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
PyTables version: 2.3
HDF5 version: 1.8.5-patch1
NumPy version: 2.0.0.dev-073bc39
Numexpr version: 1.4.2 (not using Intel's VML/MKL)
Zlib version: 1.2.3 (in Python interpreter)
LZO version: 2.05 (Apr 23 2011)
BZIP2 version: 1.0.5 (10-Dec-2007)
Blosc version: 1.1.2 (2010-11-04)
Cython version: 0.13
Python version: 2.6.6 |EPD 6.3-2 (64-bit)| (r266:84292, Sep 23 2010,
12:16:29)
[GCC 4.0.1 (Apple Inc. build 5488)]
Platform: darwin-i386
Byte-ordering: little
Detected cores: 2
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
Performing only a light (yet comprehensive) subset of the test suite.
If you want a more complete test, try passing the --heavy flag to this script
(or set the 'heavy' parameter in case you are using tables.test() call).
The whole suite will take more than 4 hours to complete on a relatively
modern CPU and around 512 MB of main memory.
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
/Library/Frameworks/EPD64.framework/Versions/6.3/lib/python2.6/site-packages/tables-2.3-py2.6-macosx-10.5-x86_64.egg/tables/tests/test_tables.py:1252:
DeprecationWarning: Setting NumPy dtype names is deprecated, the dtype will
become immutable in a future version
record.names = 'var1,var2,var3,var4,var5,var6,var7,var8,var9,var10'.split(',')
/Library/Frameworks/EPD64.framework/Versions/6.3/lib/python2.6/site-packages/tables-2.3-py2.6-macosx-10.5-x86_64.egg/tables/tests/test_tablesMD.py:461:
DeprecationWarning: Setting NumPy dtype names is deprecated, the dtype will
become immutable in a future version
record.names = 'var0,var1,var1_,var2,var3,var4,var5,var6,var7'.split(',')
Warning! ***HDF5 library version mismatched error***
The HDF5 header files used to compile this application do not match
the version used by the HDF5 library to which this application is linked.
Data corruption or segmentation faults may occur if the application continues.
This can happen when an application was compiled by one version of HDF5 but
linked with a different version of static or shared HDF5 library.
You should recompile the application or check your shared library related
settings such as 'LD_LIBRARY_PATH'.
You can, at your own risk, disable this warning by setting the environment
variable 'HDF5_DISABLE_VERSION_CHECK' to a value of '1'.
Setting it to 2 or higher will suppress the warning messages totally.
Headers are 1.8.5, library is 1.8.7
SUMMARY OF THE HDF5 CONFIGURATION
=================================
General Information:
-------------------
HDF5 Version: 1.8.7
Configured on: Wed Oct 12 15:20:32 PDT 2011
Configured by: rjchacko@Almaden.local
Configure mode: production
Host system: i386-apple-darwin10.8.0
Uname information: Darwin Almaden.local 10.8.0 Darwin Kernel
Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386
i386
Byte sex: little-endian
Libraries:
Installation point: /usr/local/Cellar/hdf5/1.8.7
Compiling Options:
------------------
Compilation Mode: production
C Compiler: /usr/bin/cc
CFLAGS: -O3 -march=core2 -msse4.1 -w -pipe
H5_CFLAGS: -std=c99 -pedantic -Wall -Wextra -Wundef
-Wshadow -Wpointer-arith -Wbad-function-cast -Wcast-qual -Wcast-align
-Wwrite-strings -Wconversion -Waggregate-return -Wstrict-prototypes
-Wmissing-prototypes -Wmissing-declarations -Wredundant-decls -Wnested-externs
-Winline -Wno-long-long -Wfloat-equal -Wmissing-format-attribute
-Wmissing-noreturn -Wpacked -Wdisabled-optimization -Wformat=2
-Wunreachable-code -Wendif-labels -Wdeclaration-after-statement
-Wold-style-definition -Winvalid-pch -Wvariadic-macros -Wnonnull -Winit-self
-Wmissing-include-dirs -Wswitch-default -Wswitch-enum -Wunused-macros
-Wunsafe-loop-optimizations -Wc++-compat -Wvolatile-register-var
-Wstrict-overflow -O3 -fomit-frame-pointer -finline-functions
AM_CFLAGS:
CPPFLAGS:
H5_CPPFLAGS: -DNDEBUG -UH5_DEBUG_API
AM_CPPFLAGS:
Shared C Library: yes
Static C Library: yes
Statically Linked Executables: no
LDFLAGS:
H5_LDFLAGS:
AM_LDFLAGS:
Extra libraries: -lsz -lz -lm
Archiver: ar
Ranlib: ranlib
Debugged Packages:
API Tracing: no
Languages:
----------
Fortran: no
C++: yes
C++ Compiler: /usr/bin/c++
C++ Flags: -O3 -march=core2 -msse4.1 -w -pipe
H5 C++ Flags:
AM C++ Flags:
Shared C++ Library: yes
Static C++ Library: yes
Features:
---------
Parallel HDF5: no
High Level library: yes
Threadsafety: no
Default API Mapping: v18
With Deprecated Public Symbols: yes
I/O filters (external): deflate(zlib),szip(encoder)
I/O filters (internal): shuffle,fletcher32,nbit,scaleoffset
MPE: no
Direct VFD: no
dmalloc: no
Clear file buffers before write: yes
Using memory checker: no
Function Stack Tracing: no
GPFS: no
Strict File Format Checks: no
Optimization Instrumentation: no
Large File Support (LFS): no
H5dump Packed Bits: yes
Bye...
Abort trap
On Oct 13, 2011, at 10/13/11 11:26 AM, Anthony Scopatz wrote:
> Ooops I forgot! numexpr also might use mkl....
>
> Could you run the following code and report back the output?
>
> import numexpr
> print numexpr.use_vml
> print numexpr.get_vml_version()
>
> I bet numexpr was compiled expecting MKL, but since you don't have it, it
> fails. Thanks!
>
> On Thu, Oct 13, 2011 at 1:55 PM, Ranjit Chacko <rjcha...@gmail.com> wrote:
> I don't remember how I installed it now actually. Is there a way for me to
> check whether numpy is linked against MKL? I'm not sure how it could be
> though, since I don't have the MKL framework on my computer at all.
>
> On Oct 13, 2011, at 10/13/11 10:28 AM, Anthony Scopatz wrote:
>
>> Hmmm, is this also how how are you getting numpy?
>>
>> It may be the case that if your numpy is linked against MKL, that then
>> PyTables also needs to be linled against MKL.
>>
>> On Thu, Oct 13, 2011 at 12:00 PM, Ranjit Chacko <rjcha...@gmail.com> wrote:
>> I'm running Snow Leopard. I've tried installing pytables using both
>> easy_install, and by downloading the source and compiling. I get the same
>> errors either way.
>>
>> On Oct 13, 2011, at 10/13/11 7:55 AM, Anthony Scopatz wrote:
>>
>>> Hmm... How did you install pytables? What platform are you on?
>>>
>>> On Thu, Oct 13, 2011 at 10:33 AM, Ranjit Chacko <rjcha...@gmail.com> wrote:
>>> NumPy is working fine, and it passes all of its tests. I'm not sure why
>>> there's a reference to MKL in the PyTables error though because I don't
>>> have that installed on my machine. Also I can't find where the HDF5 1.8.5
>>> headers might be. The only HDF5 libraries I can see on my machine are 1.8.7.
>>>
>>> Thanks,
>>>
>>> -Ranjit
>>>
>>> On Oct 12, 2011, at 10/12/11 9:15 PM, Anthony Scopatz wrote:
>>>
>>>> Hello Ranjit,
>>>>
>>>> Does NumPy Work? To the best of my knowledge, numpy is the only thing in
>>>> that stack that might link against the MKL. How are you getting numpy?
>>>>
>>>> Be Well
>>>> Anthony
>>>>
>>>> On Wed, Oct 12, 2011 at 7:51 PM, Ranjit Chacko <rjcha...@gmail.com> wrote:
>>>> I just tried to install pytables, and when I run tables.test() I get the
>>>> following error:
>>>>
>>>> -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
>>>> PyTables version: 2.3
>>>> HDF5 version: 1.8.5-patch1
>>>> NumPy version: 2.0.0.dev-073bc39
>>>>
>>>>
>>>> *** libmkl_mc.dylib *** failed with error : dlopen(libmkl_mc.dylib, 1):
>>>> image not found
>>>> *** libmkl_mc.dylib *** failed with error : dlopen(libmkl_mc.dylib, 1):
>>>> image not found
>>>> MKL FATAL ERROR: Cannot load neither libmkl_mc.dylib nor libmkl_mc.dylib
>>>>
>>>>
>>>> Also when I try to open a new file I get a warning about the library
>>>> version being mismatched, and that "Headers are 1.8.5, library is 1.8.7".
>>>>
>>>> How do I fix this?
>>>>
>>>> Thanks,
>>>>
>>>> -Ranjit
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> All the data continuously generated in your IT infrastructure contains a
>>>> definitive record of customers, application performance, security
>>>> threats, fraudulent activity and more. Splunk takes this data and makes
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>>>>
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>>>> definitive record of customers, application performance, security
>>>> threats, fraudulent activity and more. Splunk takes this data and makes
>>>> sense of it. Business sense. IT sense. Common sense.
>>>> http://p.sf.net/sfu/splunk-d2d-oct_______________________________________________
>>>> Pytables-users mailing list
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>>>> https://lists.sourceforge.net/lists/listinfo/pytables-users
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> All the data continuously generated in your IT infrastructure contains a
>>> definitive record of customers, application performance, security
>>> threats, fraudulent activity and more. Splunk takes this data and makes
>>> sense of it. Business sense. IT sense. Common sense.
>>> http://p.sf.net/sfu/splunk-d2d-oct
>>> _______________________________________________
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>>> https://lists.sourceforge.net/lists/listinfo/pytables-users
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>>>
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>>> All the data continuously generated in your IT infrastructure contains a
>>> definitive record of customers, application performance, security
>>> threats, fraudulent activity and more. Splunk takes this data and makes
>>> sense of it. Business sense. IT sense. Common sense.
>>> http://p.sf.net/sfu/splunk-d2d-oct_______________________________________________
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>>
>>
>> ------------------------------------------------------------------------------
>> All the data continuously generated in your IT infrastructure contains a
>> definitive record of customers, application performance, security
>> threats, fraudulent activity and more. Splunk takes this data and makes
>> sense of it. Business sense. IT sense. Common sense.
>> http://p.sf.net/sfu/splunk-d2d-oct
>> _______________________________________________
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>>
>>
>> ------------------------------------------------------------------------------
>> All the data continuously generated in your IT infrastructure contains a
>> definitive record of customers, application performance, security
>> threats, fraudulent activity and more. Splunk takes this data and makes
>> sense of it. Business sense. IT sense. Common sense.
>> http://p.sf.net/sfu/splunk-d2d-oct_______________________________________________
>> Pytables-users mailing list
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>> https://lists.sourceforge.net/lists/listinfo/pytables-users
>
>
> ------------------------------------------------------------------------------
> All the data continuously generated in your IT infrastructure contains a
> definitive record of customers, application performance, security
> threats, fraudulent activity and more. Splunk takes this data and makes
> sense of it. Business sense. IT sense. Common sense.
> http://p.sf.net/sfu/splunk-d2d-oct
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> https://lists.sourceforge.net/lists/listinfo/pytables-users
>
>
> ------------------------------------------------------------------------------
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> definitive record of customers, application performance, security
> threats, fraudulent activity and more. Splunk takes this data and makes
> sense of it. Business sense. IT sense. Common sense.
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------------------------------------------------------------------------------
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definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2d-oct
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