Closed ck37 closed 5 years ago
Confirmed on another cluster as well (XSEDE bridges), this time with a more recent MKL and slightly different .so files displayed. Looks like libmkl_core.so might be the best one to look for, or just "libmkl".
[ck37@br005 3-analysis]$ lsof -p 17013 | grep libmkl
R 17013 ck37 mem REG 0,42 28137653 54600213 /opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64_lin/libmkl_core.so (br001.opa.bridges.psc.edu:/nfs/opt/intel)
R 17013 ck37 mem REG 0,42 28634975 54600196 /opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64_lin/libmkl_intel_thread.so (br001.opa.bridges.psc.edu:/nfs/opt/intel)
R 17013 ck37 mem REG 0,42 9734508 54600205 /opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64_lin/libmkl_intel_lp64.so (br001.opa.bridges.psc.edu:/nfs/opt/intel)
Thanks for the report. So in the above code, what should be returned for blas & lapack?
Thanks
I think "mkl" would be reasonable - that is what R shows in ./configure when building from source.
Do you mkl
for both blas & lapack?
I just noticed, but does the lp
in libmkl_intel_lp64.so
stand for lapack?
Yep it's used for both blas & lapack. Not sure about intel_lp64 but that makes sense.
On Tue, Sep 26, 2017 at 9:26 AM, Colin Gillespie notifications@github.com wrote:
Do you mkl for both blas & lapack?
I just noticed, but does the lp in libmkl_intel_lp64.so stand for lapack?
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Trying it on another system it looks like there is a different lapack path, so that current proposed grep search would need to be modified a bit:
/global/software/sl-6.x86_64/modules/langs/intel/2015.6.233/mkl/lib/intel64/libmkl_gf_lp64.so
Thanks. I've updated the blas detection in the latest GitHub version. It should pick up your configuration. Would you check when you have a minute?
Using sessionInfo should return the correct lib
Hello,
It looks like get_linear_algebra() does not detect Intel MKL blas/lapack when R is compiled to use that - it just returns character(0) for $blas and $lapack.
Looks like it should be an easy fix to detect one of the MKL libraries though:
This is using R 3.4.2-beta, Intel MKL 2015.6.233, and gcc 4.8.5.
(Here are the instructions I used to compile R with MKL on my cluster: https://github.com/ck37/savio-xsede-notes/blob/master/compile-R.md)
Cheers, Chris