[Rd] R 4.0.1-4.0.2 built with Intel Composer 19.0-19.1.1, error in "make check" on CentOS 7.7

Ryan Novosielski novo@|rj @end|ng |rom rutger@@edu
Fri Jun 26 19:03:03 CEST 2020

> On Jun 25, 2020, at 10:31 AM, Bjørn-Helge Mevik <b.h.mevik using usit.uio.no> wrote:
> Signed PGP part
> Ryan Novosielski <novosirj using rutgers.edu> writes:
>> Hi there,
>> I initially asked about this on r-help and was told this might be a better venue. I’m not really convinced from reading the posting guide, but I’ll give it a shot. It was also suggested that the R-Project doesn’t really care about building with “non-standard” compilers, but I can’t find any evidence of that on the website (indeed, there’s some mention of successful past builds, and the build itself is successful).
>> I built R 4.0.2 with the Intel Parallel Studio XE compiler suite, versions 19.0.x to 19.1.1. Build seems to go fine. I built it like this:
>> module purge
>> module load intel/19.1.1
>> module list
>> export CC=icc
>> export CXX=icpc
>> export F77=ifort
>> export FC=ifort
>> export AR=xiar
>> export LD=xild
>> export CFLAGS="-O3 -ipo -qopenmp -axAVX,CORE-AVX2,CORE-AVX512"
>> export F77FLAGS="-O3 -ipo -qopenmp -axAVX,CORE-AVX2,CORE-AVX512"
>> export FFLAGS="-O3 -ipo -qopenmp -axAVX,CORE-AVX2,CORE-AVX512"
>> export CXXFLAGS="-O3 -ipo -qopenmp -axAVX,CORE-AVX2,CORE-AVX512"
>> export MKL="-lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread"
>> VERSION=4.0.1
>> /scratch/novosirj/install-files/R-${VERSION}/configure --with-blas="$MKL" --with-lapack --prefix=/opt/sw/packages/intel-19_1/R-Project/${VERSION} && \
>>       make -j32 && make check && make -j32 install
> For what it is worth, we used to build R with the Intel compilers and
> MKL on our HPC cluster (on CentOS Linux), and we used the following
> setup.  Note the comments about -fp-model precise and -ipo.  It might no
> longer be a problem, but maybe worth checking.
> fast="-ip -O3 -qopt-mem-layout-trans=3 -xHost -mavx"
> ## Notes:
> ## -static and -ipo break compilation
> ## -no-prec-div breaks make check
> ## -fp-model precise is needed for make check
> ## -wd188 removes a lot of warnings (see R Inst. & Adm. manual)
> export CC="icc"
> export CFLAGS="$fast -wd188 -fp-model precise"
> export F77="ifort"
> export FFLAGS="$fast -fp-model precise"
> export CXX="icpc"
> export CXXFLAGS="$fast -fp-model precise"
> export FC="ifort"
> export FCFLAGS="$fast -fp-model precise"
> ## This works with intel 2011.10, at least:
> BLAS=--with-blas='-mkl=parallel'
> LAPACK=--with-lapack
> ## To make the linker find libraries in modules:
> export LDFLAGS=$(echo $LD_LIBRARY_PATH | sed 's/^/-L/; s/:/ -L/g')
> ./configure "$BLAS" "$LAPACK" --enable-BLAS-shlib --enable-R-shlib
> make -j 8
> make check
> make install

Thanks, Bjørn; -ipo no longer breaks compilation (I didn’t specify it, but I see that it was getting added automatically). I was really hoping that "-fp-model precise” (which also implies -prec-div which would seem to affect the other option mentioned) would have an impact on “make check” here, but apparently not. Also -wd188 is no longer required to hide warnings; this doesn’t seem to be happening anymore (but remember it myself from earlier on).

I guess it might make sense to check with Intel; we have support. I wish I could remember if this ever worked right, but I don’t think I thought/knew to run "make check" on our older builds.

|| \\UTGERS,  	 |---------------------------*O*---------------------------
||_// the State	 |         Ryan Novosielski - novosirj using rutgers.edu
|| \\ University | Sr. Technologist - 973/972.0922 (2x0922) ~*~ RBHS Campus
||  \\    of NJ	 | Office of Advanced Research Computing - MSB C630, Newark

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