Dear Arnau,
On 07/07/2020 16:14, Arnau wrote:
Hi all,
I'm trying to build latest R (4.0.2) using EasyBuild 4.2.1 and foss/2020a:
ml list
Currently Loaded Modules:
1) GCCcore/9.3.0 4) GCC/9.3.0 7)
libxml2/2.9.10-GCCcore-9.3.0 10) UCX/1.8.0-GCCcore-9.3.0 13)
gompi/2020a 16) foss/2020a
2) zlib/1.2.11-GCCcore-9.3.0 5) numactl/2.0.13-GCCcore-9.3.0 8)
libpciaccess/0.16-GCCcore-9.3.0 11) OpenMPI/4.0.3-GCC-9.3.0 14)
FFTW/3.3.8-gompi-2020a
3) binutils/2.34-GCCcore-9.3.0 6) XZ/5.2.5-GCCcore-9.3.0 9)
hwloc/2.2.0-GCCcore-9.3.0 12) OpenBLAS/0.3.9-GCC-9.3.0 15)
ScaLAPACK/2.1.0-gompi-2020a
Are you loading these modules yourself before installing R?
If so, that's not recommended (and EasyBuild should be telling you that).
During the build I see a warning message:
"WARNING: R is configured to be built without BLAS/LAPACK, which
will result in (very) poor performance"
Checking the logs I see:
External libraries: pcre2, readline, BLAS(OpenBLAS), curl
so for some reason LAPACK from OpenBLAS is not found.
in the logs I see:
== 2020-07-07 15:34:57,378 environment.py:97 INFO Environment
variable BLAS_LIBS set to -lopenblas -lgfortran (previously undefined)
[...]
./configure
--prefix=/home/bria/easybuildinstall/software/R/4.0.2-foss-2020a
--build=x86_64-pc-linux-gnu --host=x86_64-pc-linux-gnu
--enable-threads --enable-BLAS-shlib --enable-R-shlib
--enable-R-profiling --enable-memory-profiling --with-pic
--enable-prebuilt-html --with-recommended-packages=no --with-libtiff
--with-readline --with-libpng --with-jpeglib --with-tcltk
--with-tcl-config=$EBROOTTCL/lib/tclConfig.sh
--with-tk-config=$EBROOTTK/lib/tkConfig.sh --with-cairo
--enable-java --with-x=yes *--with-blas --with-lapack*
--with-tcl-config=/apps/prod/easybuild/sl7.x86_64/software/Tcl/8.6.10-GCCcore-9.3.0/lib/tclConfig.sh
--with-tk-config=/apps/prod/easybuild/sl7.x86_64/software/Tk/8.6.10-GCCcore-9.3.0/lib/tkConfig.sh
--with-cairo --with-jpeglib --with-libpng --with-libtiff
so with-blas and with-lapack are present.
What 's happening? in previous build (with older toolcahins like 2017b)
LACPAK from OpenBLAS is found:
External libraries: readline, BLAS(OpenBLAS), *LAPACK(in
blas)*, curl
Anyone could give a hand on this one?
I'm not seeing the problem you are describing with R 4.0.0 built with
foss/2020a...
Can you maybe share your EasyBuild log file, and the easyconfig file
you're using for this?
You'll need to try and pinpoint why R thinks there's no LAPACK support
in the OpenBLAS installation (because there is).
regards,
Kenneth
TIA,
Arnau
