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bmcgough avatar bmcgough commented on June 17, 2024

openCyto (installing by hand with the R-bundle-Bioconductor/3.5-foss-2016b-fh1 module loaded) ultimately depends on ncdfFlow, which is installed in the bundle, but not loading:

> library('ncdfFlow') Loading required package: flowCore Loading required package: RcppArmadillo Loading required package: BH Error: package or namespace load failed for ‘ncdfFlow’ in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/app/easybuild/software/R-bundle-Bioconductor/3.5-foss-2016b-R-3.4.0-fh1/ncdfFlow/libs/ncdfFlow.so': /app/easybuild/software/R-bundle-Bioconductor/3.5-foss-2016b-R-3.4.0-fh1/ncdfFlow/libs/ncdfFlow.so: undefined symbol: ompi_mpi_cxx_op_intercept

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proychou avatar proychou commented on June 17, 2024

@mikejiang Any idea why this might be happening? I requested Sci Comp to install openCyto for use on the rhinos.

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mikejiang avatar mikejiang commented on June 17, 2024

Looks like the ncdfFlow is linked to hdf5 library that was compiled with mpi support, which is not necessary for ncdfFlow. Anyway, it is currently not able to find the open mpi symbol and is probably due to the runtime LD path setting. Try to add the mpi library path to LD_LIBRARY_PATH see if it helps.

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fizwit avatar fizwit commented on June 17, 2024

R-bundle-Bioconductor-3.5-foss-2016b-R-3.4.1-fh2.eb
('openCyto', '1.14.0', bioconductor_options),

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