[Rd] Installation of R-4.3.1 with intel 2022

[Tomas Kalibera]

On 6/20/23 18:47, Giuseppe Calò wrote:
> Hi all,
> I have the issue:
>
> icc -std=c99 -std=gnu11 -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O3 -wd188 -ip -mp  -c eval.c -o eval.o
> arithmetic.c(66): warning #274: declaration is not visible outside of function
>    int matherr(struct exception *exc)
>                       ^
>
> arithmetic.c(68): error: pointer to incomplete class type is not allowed
>        switch (exc->type) {
>                ^
>
> arithmetic.c(69): error: identifier "DOMAIN" is undefined
>        case DOMAIN:
>             ^
>
> arithmetic.c(70): error: identifier "SING" is undefined
>        case SING:
>             ^
>
> arithmetic.c(73): error: identifier "OVERFLOW" is undefined
>        case OVERFLOW:
>             ^
>
> arithmetic.c(76): error: identifier "UNDERFLOW" is undefined
>        case UNDERFLOW:
>             ^
>
> arithmetic.c(77): error: pointer to incomplete class type is not allowed
>    	exc->retval = 0.0;
>
> icc -std=c99 -std=gnu11 -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O3 -wd188 -ip -mp  -c flexiblas.c -o flexiblas.o
> icc: command line remark #10148: option '-mp' not supported
> compilation aborted for arithmetic.c (code 2)
> make[3]: *** [../../Makeconf:129: arithmetic.o] Error 2
> make[3]: *** Waiting for unfinished jobs....
> icc: command line remark #10148: option '-mp' not supported
> make[3]: Leaving directory '/opt/sources/R/R-4.3.1-intel21/src/main'
> make[2]: *** [Makefile:140: R] Error 2
> make[2]: Leaving directory '/opt/sources/R/R-4.3.1-intel21/src/main'
> make[1]: *** [Makefile:28: R] Error 1
> make[1]: Leaving directory '/opt/sources/R/R-4.3.1-intel21/src'
> make: *** [Makefile:62: R] Error 1
>
> with oneapi-2022.1.0/compiler-rt/2022.1.0; oneapi-2022.1.0/mkl/2022.1.0 while building R-4.3.1 on redhat 8.4 glibc2.28-189
>
> I followed a workaround proposed:
> https://community.intel.com/t5/Intel-C-Compiler/Error-when-compiling-R-from-source-code-ubuntu-18-04/m-p/1176401/thread-id/36575 <https://community.intel.com/t5/Intel-C-Compiler/Error-when-compiling-R-from-source-code-ubuntu-18-04/m-p/1176401/thread-id/36575>
>
> Deactivate  HAVE_MATHERR macro in src/include/config.h

Hi Giuseppe,

thanks for the report. Undefining HAVE_MATHERR seems a valid work-around 
to me, based on reading the thread above and the sources.

We could improve this in R, if keeping this code, at least improve the 
configure check so that it also tests for the presence of the macros.

> Using this workaroud I get R with:
>
> BLAS/LAPACK: /opt/intel/oneapi_2022.2.0/mkl/2022.1.0/lib/intel64/libmkl_intel_lp64.so.2;  LAPACK version 3.9.0
>
> is correct?
>
> Is these a way to avoid arithmetic issue?
>
> My configure is:
>
> module load intel-2021.6.0/2021.6.0 oneapi-2022.1.0/mkl
> MKL="-L${MKLROOT}/lib/intel64 -lmkl_gf_lp64 -lmkl_core -lmkl_gnu_thread -dl -fopenmp"
> export CC="icc -std=c99"
> export CFLAGS="-g -O3 -wd188 -ip -mp"
> export FC=ifort
> export FLAGS="-g -O3 -mp"
> export CXX=icpc
> export CXXFLAGS="-g -O3 -mp"
> SHLIB_CXXLD=icpc
> export MKL_INTERFACE_LAYER=GNU,LP64
> export MKL_THREADING_LAYER=GNU
> ./configure --prefix=/opt/intel-2021.6.0/R/4.3.1 --with-blas="$MKL" --with-lapack  --enable-memory-profiling --enable-BLAS-shlib --enable-R-shlib --enable-R-static-lib --with-pcre2

AFAIK, neither icc nor MKL is regularly tested with R/CRAN packages, so 
the risk of running into some issues is somewhat higher than for say GCC 
and the reference BLAS/LAPACK.

Some hints on using icc and MKL can be found in the R Admin manual, 
https://cran.r-project.org/doc/manuals/r-release/R-admin.html. Unless 
you have done that already, you might want to check your configuration 
against those, I didn't spot any obvious issue. If you find any other 
problem, please report, so that it could be fixed or the hints updated.

Thanks,
Tomas

>
> Thanks a lot,
> Giuseppe.
>
> ———————————————————————————————————————
> Giuseppe Calò
>
> Fondazione CMCC
> Centro Euro-Mediterraneo sui Cambiamenti Climatici presso Complesso Ecotekne
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> http://www.cmcc.it <http://www.cmcc.it/>
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>
> mobile: (+39) 3208190020
> email: giuseppe.calo using cmcc.it
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