rhdf5 build error undefined symbol: ompi_mpi_cxx_op_intercept
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fizwit • 0
@fizwit-15391
Last seen 3 months ago
Fred Hutch Cancer Research Center

Build Error  with rhdf5

Ubuntu 14.04

GCC 5.4  

OpenMPI/1.10.3-GCC-5.4.0-2.26

R 3.4.3

installing to /app/easybuild/software/R/3.4.3-foss-2016b-fh2/lib/R/library/rhdf5/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Error: package or namespace load failed for ‘rhdf5’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/app/easybuild/software/R/3.4.3-foss-2016b-fh2/lib/R/library/rhdf5/libs/rhdf5.so':
  /app/easybuild/software/R/3.4.3-foss-2016b-fh2/lib/R/library/rhdf5/libs/rhdf5.so: undefined symbol: ompi_mpi_cxx_op_intercept
Error: loading failed

We have a patch for the CXX_SEEK for installing HDF5.  rhdf5 installes a local copy of HDF5 which we already have.  It would be nice if rhdf5 could just link agaist out install.    Could someone please add an option to check the environement for hdf5 and not install it yet another copy of rhdf5?

thanks

 

rhdf5 ompi • 766 views
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