[R] inconsistency in mclapply.....
@k@h@y_e4 @end|ng |rom hotm@||@com
Sat Jun 10 16:44:12 CEST 2023
A million thanks for your precious time....
From: Ivan Krylov <krylov.r00t using gmail.com>
Sent: Saturday, June 10, 2023 7:50 PM
To: akshay kulkarni <akshay_e4 using hotmail.com>
Cc: R help Mailing list <r-help using r-project.org>
Subject: Re: [R] inconsistency in mclapply.....
On Sat, 10 Jun 2023 13:46:12 +0000
akshay kulkarni <akshay_e4 using hotmail.com> wrote:
> What if I switch to Ubuntu?
> I had a similar ( but not exactly the same) problem way back in 2018
> and switching to Ubuntu solved it.
You shouldn't have to switch distros for problems like this one.
What you need to switch is your OpenBLAS build: instead of using
OpenBLAS built with OpenMP support (which isn't even the default
when compiling OpenBLAS), use OpenBLAS built with pthreads support. It's
also likely, but not 100% guaranteed, that setting OMP_NUM_THREADS=1
will avoid the issue by never starting any additional threads for
OpenBLAS purposes. At least some documentation says that
OPENBLAS_NUM_THREADS is ignored on OpenMP builds of OpenBLAS, you
actually have to set OMP_NUM_THREADS=1 for it to take any effect.
I know very little about RHEL, but it seems that you already have a
pthreads build of OpenBLAS installed in
/usr/lib64/libopenblasp-r0.3.15.so; you just need to adjust the path to
the BLAS implementation used by R. If not, install the openblas-threads
Can you use flexiblas
switch the BLAS implementation to OPENBLAS-THREADS? This should be
possible by using the flexiblas R package or by setting environment
That said, I know for sure that on Debian and Ubuntu you get a choice
between libopenblas0-openmp / libopenblas0-pthread /
libopenblas0-serial, and installing any one of these packages except
libopenblas0-openmp should avoid the problem. (And the thread limit
should be set to 1 if you're running your tasks in parallel by other
[[alternative HTML version deleted]]
More information about the R-help