Re: [scipion-users] Scipion and Ubuntu 22.04?

[Alberto G. M. <alb...@cn...>]

Hi again,

I tried to install xmipp in Ubuntu 22.04 from scratch and I get an error 
like "undefined reference to 'std::...". By default Ubuntu installed 
gcc-11 ( sudo apt build-essential). I installed gcc/g++-10, updated the 
symbolic links and removed and reinstalled libopenmpi-dev. After that, I 
was able to install Xmipp successively.

I hope that could help.||

||
||

On 29/4/22 7:45, Alberto Garcia Mena wrote:
>
> Hi Matt,
>
> Sorry to hear about the problems with your installation. Could you 
> share with me the error message? To get more information; what version 
> of gcc/g++ are you running to install Xmipp?, or what is the default 
> used by your machine? (gcc --version; g++ --version)
>
> On 28/4/22 22:36, Matt Harrington via scipion-users wrote:
>>
>> I get strange linker errors when building xmipp via Scipion in Ubuntu 
>> 22.04.  The linker isn't finding portions of the C++ standard library 
>> for some reason.  I see documentation about some linker problems 
>> arising when using HDF libraries, but I wasn't able to get it working 
>> by following the guidance.  Unsure how HDF issues would affect 
>> finding the standard library.  Since we're in a hurry to get this 
>> system back into production, I'll revert to Ubuntu 20.04 for now.
>>
>> Matt
>>
>> On Thu, Apr 28, 2022 at 5:20 AM Alberto Garcia Mena 
>> <alb...@cn...> wrote:
>>
>>     Hi Matt,
>>
>>     Yes, Xmipp runs with gcc 11 and older. CUDA has a compiler
>>     limitations and Xmipp manage it (telling if you need a newer
>>     version of the compiler). You can also check these
>>     compatililitieshttps://gist.github.com/ax3l/9489132
>>
>>     Best regards
>>
>>     On 28/4/22 9:15, Pablo Conesa wrote:
>>>
>>>     Hi Matt, Scipion3 is being recently installed in laptops here
>>>     with ubuntu 22.04. So it is possible.
>>>
>>>     The actual dependency for gcc is to compile Xmipp.
>>>
>>>     I've looked at the detailed Xmipp configuration page
>>>     <https://github.com/I2PC/xmipp/wiki/Xmipp-configuration-(version-20.07)#c-configuration>
>>>     and it doesn't explicitly mention the version although you are
>>>     right that in the past is being specified to be c++ 8.
>>>
>>>     I'm sure someone from Xmipp will pop up to clarify how to
>>>     install Xmipp in ubuntu 22.04 LTS.
>>>
>>>     All the best, Pablo.
>>>
>>>     On 27/4/22 19:14, Matt Harrington via scipion-users wrote:
>>>>
>>>>     Has Scipion been tested on Ubuntu 22.04?  It's the new LTS
>>>>     release of Ubuntu which came out last week.
>>>>
>>>>     I ask because GCC 8 does not appear to ship with 22.04, and the
>>>>     Scipion installation docs seem to hint that GCC 8 is required. 
>>>>     Here's an excerpt from the docs:
>>>>
>>>>         For Ubuntu:
>>>>
>>>>         sudo apt-get install gcc-8 g++-8 libopenmpi-dev make
>>>>
>>>>
>>>>     Matt
>>>>
>>>>
>>>>
>>>>     _______________________________________________
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>>>     -- 
>>>     Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*
>>>
>>>
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>>     -- 
>>     - Alberto GM -
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> -- 
> - Alberto GM -
>
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