No problem, Ranjit!
I wish we could really fix the header mismatch issue. Luckily, I know that
the HDF5 API didn't change between 1.8.5 -> 1.8.7, so using out of date
headers in this case is OK. For larger version jumps (1.6 -> 1.8) this
little trick wouldn't work ~_~.
Let us know if you have any other issues...
Be Well
Anthony
On Thu, Oct 13, 2011 at 4:13 PM, Ranjit Chacko <rjcha...@gmail.com> wrote:
> Setting 'HDF5_DISABLE_VERSION_CHECK' to 1 seems to work. The tests ran and
> passed except for one error message saying something about unsupported
> byteorder.
>
> Thanks again for your help!
>
> On Oct 13, 2011, at 10/13/11 12:05 PM, Anthony Scopatz wrote:
>
> [snip]
>
>
>> 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
>>
>
> This will disable the errors and warnings. Alternatively, you could find
> the 1.8.5 headers and replace them with the 1.8.7 ones, or you could install
> hdf5 1.8.7. I don't have any experience with mac development, so I
> couldn't tell you how or where to reinstall this stuff.
>
> Maybe Josh or Antonio or someone else will pop up with better advice ;)
>
>
>> 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
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>>>>>> sense of it. Business sense. IT sense. Common sense.
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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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>>>>>
>>>>>
>>>>>
>>>>> ------------------------------------------------------------------------------
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>>>>> 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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>>>>>
>>>>
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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.
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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.
>>>
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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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>>
>> ------------------------------------------------------------------------------
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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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>>
>
> ------------------------------------------------------------------------------
> 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.
>
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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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> 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.
http://p.sf.net/sfu/splunk-d2d-oct
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