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

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

Hi Scipion experts !

I administer a cluster built with Centos 7.  The cluster has scipion2 and users want to have scipion3 installed, mainly to use the topography plugins.

I followed the instructions and have Scipion3 core installed fine, but when it comes to building xmipp, I always have this error:

         libXmipp.so: undefined reference to `non-virtual thunk to H5::H5File::throwException ...

I guess it relates to hdf5.  I do have hdf5 and hdf5-devel install via yum, and make sure than 'conda list' does not have any hdf5 installed, but it makes no differences.

As centos 7 has them up to version 1.8.12 only, I wonder if this is the cause of the problem.  I seem to have read somewhere that xmipp requires at least hdf5 1.10.4 but could not confirm it.

I hope anyone has a solution for this.  Being a cluster, I do not have the freedom as stand-alone servers: whatever changes has to be implemented on all the nodes.

FYI, I have tried gcc 7.2.0 and 8.5.0, cuda 10,11 , they made no differences

Thank you all in advance


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Thu D. Nguyen

Bio21 Institute
The University of Melbourne, Victoria 3010 Australia