[Rd] Installation of R-4.3.1 with intel 2022
Prof Brian Ripley
r|p|ey @end|ng |rom @t@t@@ox@@c@uk
Tue Jul 18 11:18:20 CEST 2023
Note that 'intel 2022' is a bit vague. The current version is 2023.1.0,
and that has both the 'classic' (icc/icpc/ifort which it seems you used)
and new (icx/ixpx/ifx) compilers -- the former are said to be going to
be discontinued later this year. R did not know about ifx so did not
build with the new set.
The parts of the manual Tomas referred to were about the old compilers:
the manual has now been re-written in R-devel and R-patched to major on
the newer ones. We have patched the code to work with both old and new
compilers, pending a more thorough investigation of matherr.
In our experiments Intel Fortran only worked in conjunction with oneAPI
MKL -- see the manual. It seems ifx is still under development, so it
should pay to use only the latest versions.
This is the first report on Intel compilers since 2015, so they are
rather low priority for the R developers.
On 21/06/2023 08:10, Tomas Kalibera wrote:
>
> 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
>> Università del Salento - Strada Prov.le Lecce - Monteroni 73100 Lecce IT
>> http://www.cmcc.it <http://www.cmcc.it/>
>> https://goo.gl/maps/wtahPDbNVen
>>
>> mobile: (+39) 3208190020
>> email: giuseppe.calo using cmcc.it
>>
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--
Brian D. Ripley, ripley using stats.ox.ac.uk
Emeritus Professor of Applied Statistics, University of Oxford
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