Comments (4)
Thanks for the link! I'll close this issue. This probably deserves more comprehensive documentation for rocker rstudio images, but that does seem outside the scope of this repo.
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I am not sure it was meant for rocker/r-ver
. Adjust as needed. Debugging help welcome.
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It appears that rocker/r-ver:3.6.1 R was configured to use OpenBLAS:
$ docker run -it --rm rocker/r-ver:3.5.3 R CMD config --all | grep -i blas
BLAS_LIBS = -lblas
$ docker run -it --rm rocker/r-ver:3.6.1 R CMD config --all | grep -i blas
BLAS_LIBS = -lopenblas
Adding a couple extra update-alternatives --install
commands seems to handle this:
update-alternatives --install /usr/lib/x86_64-linux-gnu/libopenblas.so libopenblas.so-x86_64-linux-gnu /opt/intel/mkl/lib/intel64/libmkl_rt.so 150
update-alternatives --install /usr/lib/x86_64-linux-gnu/libopenblas.so.0 libopenblas.so.0-x86_64-linux-gnu /opt/intel/mkl/lib/intel64/libmkl_rt.so 150
> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 9 (stretch)
Matrix products: default
BLAS/LAPACK: /opt/intel/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64_lin/libmkl_rt.so
(tested with the latest mkl, intel-mkl-64bit-2019.5-075
)
Not sure if this is general-purpose enough to add to this repo's script.sh---perhaps they could be added commented-out?
Also, off-topic, but just in case this surprise (to me) isn't somewhere: since libopenblasp is multi-threaded courtesy of OpenMP, the benchmark n <- 1e3 ; X <- matrix(rnorm(n*n),n,n); system.time(svd(X))
causes R 3.6.x to spawn a number of threads equal to the number of CPUs on the host, as that's the default behavior of libgomp. On an HPC cluster where R jobs might have been allocated/constrained via cgroups to a small fraction of the CPUs on the node, this can cause severe performance degradation (e.g., our average node has 48 processor cores---and for an R job that reserves 2 processor cores, a 48-thread R process doesn't perform so well...) . In that case, it is advised to set the OMP_NUM_THREADS environment variable to the number of CPUs that have been allocated to the R job.
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I think we should just close it. Maybe you can add what you discovered to the wiki, or just post a gist. This was always an unofficial script to just see how things go.
And rocker/r-ver was, as I understand my Rocker colleague, meant for stability so doing on the fly BLAS replacement from a third-party repo is a little ... strange.
But yes, update-alternatives
, properly instrumented, should cover this. (Also see https://lists.debian.org/debian-science/2019/10/msg00038.html for the latest in a longish development to completely overhaul LAPACK/BLAS for Debian ...)
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Related Issues (18)
- The script should be part of a Debian package HOT 1
- benchmarkme fails HOT 16
- Can the MKL script be adapted for dnf based fedora systems? HOT 3
- when using "sudo", the linux script does not work HOT 2
- Bumping priority number to > 100 HOT 3
- Translating into duprkit recipe HOT 2
- installation failed behind proxy HOT 1
- MKL threading HOT 3
- Adding MKL support to bioconductor docker HOT 7
- Not working on Ubuntu 20.04 HOT 1
- intel-mkl 2020.0.166-1 no longer has /opt/intel HOT 8
- MKL inconsistent results HOT 1
- segmentation fault HOT 2
- apt install intel-mkl in a non-interactive session HOT 4
- Fixing problems with MKL when using `intel-mkl` HOT 1
- Repository and package are now named `oneapi-mkl` HOT 1
- using MKL with rocker/r-devel HOT 4
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