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

[Thu N. <t.n...@un...>]

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 3rd 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