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

[Carlos O. S. <co...@cn...>]

Dear David,

this compilation issue really goes out of my expertise. Which are the 
compilation errors you see? If they are solved by using different 
functions from Xmipp, we may try to solve them. If you want, we could 
have a separate call to see these errors in detail.

Kind regards, Carlos Oscar

On 2/23/21 12:40 PM, Pablo Conesa wrote:
>
>
> -------- Forwarded Message --------
> Subject: 	Re: [scipion-users] make externally compiled HDF5 available 
> for xmipp compile
> Date: 	Fri, 19 Feb 2021 11:22:13 -0500
> From: 	Hoover, David (NIH/CIT) [E] via scipion-users 
> <sci...@li...>
> Reply-To: 	Mailing list for Scipion users 
> <sci...@li...>
> To: 	sci...@li...
> CC: 	Hoover, David (NIH/CIT) [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*
>>>>
>>>>
>>>> _______________________________________________
>>>> scipion-users mailing list
>>>> sci...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/scipion-users
>>>>
>>>
>> -- 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
> 12 South Dr., Rm 2N207
> Bethesda, MD 20892, USA
> TEL: (+1) 301-435-2986
> Email:hoo...@hp...
>
>
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