[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 07:27:45 CEST 2023
Thanks Prof. Brian,
Current 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
http://www.cmcc.it
https://goo.gl/maps/wtahPDbNVen
mobile: (+39) 3208190020
email: giuseppe.calo using cmcc.it
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> On 18 Jul 2023, at 11:18, Prof Brian Ripley <ripley using stats.ox.ac.uk> wrote:
>
> 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.
>>>
>>>
>>>
>>>
>>>
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>>>
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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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