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

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

Hi again Thu,

Xmipp looks for libhdf5* and hdf5.h files. For Centos7 libhdf5* are 
in//usr/lib64/ /and hdf5.h is in//usr/include/.///Please verify that you 
have the files in those paths and add them to INCDIRFLAGS and 
LIBDIRFLAGS in xmipp.config as

LIBDIRFLAGS= ... -L/usr/lib64
INCDIRFLAGS= ... -I/usr/include

After that run *./xmipp compileAndInstall*

Thank you for your detailed report. (It seems that for Centos7 Xmipp is 
not able to find hdf5 by default)


On 14/3/22 23:59, Thu Nguyen wrote:
>
> Thanks to all that responded.
>
> Unfortunately I am not faring any better. I have tried different 
> versions of hdf5-devel (1.8.12, 1.10.0,1.10.4,1.10.6), correctly edit 
> xmipp.conf for INCDIRFLAGS and LIBDIRFLAGS each time (as shown in my 
> latest error post), and even tried the 20.07 release as some suggested.
>
> The error seemed to turn up at different stages each time.
>
> One thing I just notice, in all my hdf5-devel installs, I never seem 
> to get the “serial” folder as shown in some discussions.  What does 
> this folder have?
>
> *----------------------------------------------------------------------------------------------------------------*
>
> *Thu D. Nguyen*
>
> Bio21 Institute
>
> The University of Melbourne, Victoria 3010 Australia
>
> *From:*Alberto Garcia Mena <alb...@cn...>
> *Sent:* Monday, 14 March 2022 6:49 PM
> *To:* Thu Nguyen <t.n...@un...>
> *Subject:* Re: [scipion-users] [EXT] Re: Problem compiling xmipp in 
> Scipion3 on Centos 7 cluster
>
> *External email: *Please exercise caution
>
> ------------------------------------------------------------------------
>
> Hello thu Nguyen,
>
> To avoid issues related to hdf5 we recommend uninstalling all hdf5 
> version and install only the hdf5-devel version using/sudo yum install 
> hdf5-devel./We have a installation guide for Centos 
> <https://github.com/I2PC/xmipp/wiki/Installing-Xmipp-on-CentOS-7-9.2009>.
>
> After the installation of hdf5-devel, run ./xmipp config which should 
> find the hdf5 path (usr/include/hdf5/serial) and should add this path 
> on the INDIRFLAGS in the xmipp.config file, after checking this you 
> could run ./xmipp and install it.
>
-- 
- Alberto GM -