Re: [scipion-users] make externally compiled HDF5 available for xmipp compile

[Hoover, D. (NIH/C. [E] <hoo...@hp...>]

Was it compiled with 1.8.x API compatibility macros?  I am seeing errors unless I compile HDF5 with --with-default-api-version=v18 option.

https://support.hdfgroup.org/HDF5/doc/RM/APICompatMacros.html

David

On 2/19/2021 9:43 AM, Pablo Conesa wrote:
> Mine is linked to :
> 
>      libhdf5_serial.so.103 => /usr/lib/x86_64-linux-gnu/libhdf5_serial.so.103 (0x00007f354a368000)
>      libhdf5_cpp.so.103 => /usr/lib/x86_64-linux-gnu/libhdf5_cpp.so.103 (0x00007f354a2eb000)
> 
> I think is 1.10.4
> 
> On 19/2/21 14:31, Hoover, David (NIH/CIT) [E] via scipion-users wrote:
>> One more question: what version of HDF5 does xmipp require?
>>
>> David
>>
>> On 2/19/2021 2:26 AM, Pablo Conesa wrote:
>>> Thanks Jason.
>>>
>>> There is a detailed "custom xmipp installation" page <https://github.com/I2PC/xmipp/wiki/Xmipp-configuration-(version-20.07)> where you can adapt xmipp to your system, providing default installation does not work.
>>>
>>>
>>> On 19/2/21 1:13, Jason Key wrote:
>>>> Hi David,
>>>>
>>>> On Thu, Feb 18, 2021 at 12:42 PM Hoover, David (NIH/CIT) [E] via
>>>> scipion-users<sci...@li...> wrote:
>>>>> Is there any way of making HDF5 headers and libraries available for compiling xmipp?
>>>>> That is, must I install HDF5 with yum or apt-get into /usr/lib and /usr/include, or is there an environment variable or configuration setting that can be set to force the compile to look elsewhere for the header and library files?
>>>> I was able to do this by adding INCDIRFLAGS and LIBDIRFLAGS variables
>>>> to the xmipp.conf file in "software/em/xmippSrc-v3.20.07".
>>>>
>>>> Best,
>>>> Jason
>>>>
>>> -- 
>>> Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*
>>>
>>>
>>> _______________________________________________
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>>>
>>
> -- 
> Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*
> 
> 
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-- 
David Hoover, Ph.D.
Computational Biologist
High Performance Computing Services,
Center for Information Technology,
National Institutes of Health
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Bethesda, MD 20892, USA
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Email: hoo...@hp...