We have a workstation with 16 physical cores (32 threads with hyper threading) and we want to run DESeq2 faster using parallelisation. However, setting
parallel=TRUE often runs slower than without parallelisation, if it doesn't fail at some stage, such as fitting models and testing. Failing does not throw an error, but the process is stuck with no apparent CPU utilisation. Moreover, we can't control the number of cores used in parallelisation (even with
BPPARAMS=MulticoreParam(4)), it always uses all 32 cores. We tried it on RStudio and directly on R interpreter, still the same.
Is it a known issue with DESeq2, or do we have to fix something on our system?
The machine is running CentOS 7. R 3.6.3 was compiled from source with GCC 8.2.0 and we use OpenBLAS 0.3.5 for BLAS/LAPACK.
Any advice will be appreciated. Thanks a lot.