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
______________________________________________
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
