[Rd] Installation of R-4.3.1 with intel 2022
Giuseppe Calò
g|u@eppe@c@|o @end|ng |rom cmcc@|t
Fri Jul 21 07:32:47 CEST 2023
Thanks Prof. Brian,
Currently I’m using oneapi 2022.1.0 in particular ifort 2021.6.0 20220226
(not ifx).
Thanks for the clarification.
Regards,
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
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email: giuseppe.calo using cmcc.it
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Il giorno mar 18 lug 2023 alle ore 11:18 Prof Brian Ripley <
ripley using stats.ox.ac.uk> ha scritto:
> 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
> >>
> >> Le informazioni contenute in questo messaggio di posta elettronica e
> >> negli allegati se presenti sono riservate e confidenziali: ne è
> >> vietata la diffusione in qualsiasi modo o forma (GDPR 2016/679).
> >> Qualora lei non fosse il destinatario del messaggio, la invito a non
> >> diffonderlo e ad eliminarlo dandone gentilmente comunicazione al
> >> mittente.
> >>
> >> The information included in this e-mail and any attachments are
> >> confidential and may also be privileged (GDPR 2016/679).
> >> If you are not the correct recipient, you are kindly requested to
> >> notify the sender immediately, to cancel it and not disclose the
> >> contents to any other person.
> >>
> >>
> >>
> >>
> >>
> >> [[alternative HTML version deleted]]
> >>
> >> ______________________________________________
> >> R-devel using r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/r-devel
> >
> > ______________________________________________
> > R-devel using r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
>
> --
> Brian D. Ripley, ripley using stats.ox.ac.uk
> Emeritus Professor of Applied Statistics, University of Oxford
>
>
--
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Giuseppe Calò
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presso Complesso Ecotekne - Università del Salento
Prov.le Lecce - Monteroni - 73100 Lecce IT
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