Thanks Tomas,
With my configure (I follower Admin manual for intel) and deleting
HAVE_MATHERR in config I’m able to perform, configure, make and make install,
only make check has this issue:
running code in 'array-subset.R' ... OK
running code in 'reg-tests-1a.R' ... OK
running code in 'reg-tests-1b.R' ... OK
running code in 'reg-tests-1c.R' ... OK
running code in 'reg-tests-1d.R' ... OK
running code in 'reg-tests-1e.R' ... OK
running code in 'reg-tests-2.R' ... OK
comparing 'reg-tests-2.Rout' to './reg-tests-2.Rout.save' ... OK
running code in 'reg-examples1.R' ... OK
running code in 'reg-examples2.R' ... OK
running code in 'reg-packages.R' ... OK
running code in 'p-qbeta-strict-tst.R' ... OK
running code in 'd-p-q-r-tst-2.R' ...make[3]: *** [Makefile.common:117:
d-p-q-r-tst-2.Rout] Error 1
make[3]: Leaving directory '/juno/opt/sources/R/R-4.3.1-intel21/tests'
make[2]: *** [Makefile.common:320: test-Reg] Error 2
make[2]: Leaving directory '/juno/opt/sources/R/R-4.3.1-intel21/tests'
make[1]: *** [Makefile.common:190: test-all-basics] Error 1
make[1]: Leaving directory '/juno/opt/sources/R/R-4.3.1-intel21/tests'
make: *** [Makefile:307: check] Error 2
Do you have some suggestion about this error?
Checking MKL on installing R it is:
Matrix products: default
BLAS/LAPACK:
/juno/opt/intel/oneapi_2022.2.0/mkl/2022.1.0/lib/intel64/libmkl_intel_lp64.so.2;
LAPACK version 3.9.0
And
ldd /juno/opt/intel-2021.6.0/R/4.3.1/lib64/R/lib/libRblas.so| grep mkl
libmkl_intel_lp64.so.2 =>
/juno/opt/intel/oneapi_2022.2.0/mkl/2022.1.0/lib/intel64/libmkl_intel_lp64.so.2
(0x00007f01ba508000)
libmkl_intel_thread.so.2 =>
/juno/opt/intel/oneapi_2022.2.0/mkl/2022.1.0/lib/intel64/libmkl_intel_thread.so.2
(0x00007f01b6d94000)
libmkl_core.so.2 =>
/juno/opt/intel/oneapi_2022.2.0/mkl/2022.1.0/lib/intel64/libmkl_core.so.2
(0x00007f01b29be000)
About you, is R using right mkl? (Oneapi mkl)
Thanks,
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.c...@cmcc.it
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> On 21 Jun 2023, at 09:10, Tomas Kalibera <tomas.kalib...@gmail.com> 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.c...@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@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
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