Re: [scipion-users] [EXT] Re: Problem compiling xmipp in Scipion3 on Centos 7 cluster

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

Glad to hear it.

I'm sure hdf5 creates some problems, also the compiler version.

Thanks for your patience and for your installation report. I have 
updated the wiki page 
<https://github.com/I2PC/xmipp/wiki/Installing-Xmipp-on-CentOS-7-9.2009> 
for installing Xmipp on Centos7, reporting the problems with hdf5.

Thanks again for your patience and I hope you enjoy Scipion&Xmipp.

If you have any other problems related to Scipion / xmipp, please write 
to us.


BR



On 17/3/22 11:18, Thu Nguyen wrote:
> Dear All,
>
>> Thanks to All that have responded and helped.  For a whole week, I 
>> have tried without success with countless combinations of gcc, cuda 
>> and hdf5. Now I can report that I have "sort-of" solved my own 
>> problem.  I hope this will help someone who might have the same issue.
>>
>>   * Asumming the centos 7 hdf5-devel installed with yum (1.8.12) was
>>     not doing its job, I uninstalled it.  No trace of hdf5* in
>>     /usr/include of /usr/lib64.
>>   * I used gcc 8.5.0 to compile and install hdf 1.10.3 from source,
>>     installed at /usr/local/hdf5. Please note, I have used this
>>     version before, but as rpms from a 3^rd  party (Springdale
>>     Computational, Princeton); this time I built my own.
>>   * I ran ./xmipp cleanAll.  This erase averything including contents
>>     of the src folder I think.
>>   * then ./xmipp config.  This time the config said it could not find
>>     hdf5 and asked me to put it in, so I was able to specify the
>>     include and lib paths to the new hdf5 (usr/local/hdf5/include and
>>     lib)
>>   * ./xmipp all will redownload everything, compile and install
>>
>> I am so glad to finally see the line that said xmipp installed 
>> sucessfully.
>            In the process I learned to clean up after a failed build; 
> how to rebuild the xmipp.config file and do other things with the 
> ./xmipp. Also when trying with gcc5.3, I got a message complaining 
> about "inline variables", which on my search I read that it is a C++17 
> feature that gcc only fully supports in their version 8's.  That 
> confirms the need for gcc8; I am not sure if my previous use of gcc 
> 7.2.0 contributed to the failure or not (would not have the energy to 
> go back and try !)
>
> In saying I sort-of solve the problem, the cluster needs packages to 
> be in rpm form to be auto-deployed to compute nodes, so I will have to 
> find a way to get my hdf5 to them, but this is outside the focus of 
> this forum
>
> Again thank for all your help, specially those who have email me 
> personally with plenty of hints.
>
>
>
> ___________________________________________________
>
> Thu D. Nguyen
>
> Bio21 Institute
>
> The University of Melbourne
>
>
>
>
-- 
- Alberto GM -