I installed HDF5 1.8.7 using homebrew, and when I installed HDF5 I saw this
line in the output:
Found HDF5 headers at ``/usr/local/include``, library at
``/usr/local/lib``.
And it looks like everything in those paths is at 1.8.7, so I don't understand
why it would throw this error about mismatched versions.
Thanks,
-Ranjit
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 makes
>>>>> sense of it. Business sense. IT sense. Common sense.
>>>>> http://p.sf.net/sfu/splunk-d2d-oct
>>>>> _______________________________________________
>>>>> Pytables-users mailing list
>>>>> Pytables-users@lists.sourceforge.net
>>>>> 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_______________________________________________
>>>>> Pytables-users mailing list
>>>>> Pytables-users@lists.sourceforge.net
>>>>> 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
>>>> _______________________________________________
>>>> 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_______________________________________________
>>>> 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
>>> _______________________________________________
>>> 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_______________________________________________
>>> Pytables-users mailing list
>>> Pytables-users@lists.sourceforge.net
>>> 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
>> _______________________________________________
>> Pytables-users mailing list
>> Pytables-users@lists.sourceforge.net
>> 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_______________________________________________
>> 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
> _______________________________________________
> Pytables-users mailing list
> Pytables-users@lists.sourceforge.net
> 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_______________________________________________
> 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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