Installation of R-4.3.1 with intel 2022

Wed, Jun 21, 2023 4:26 AM

Ok, I?ll reinstall in /juno/opt/sources/R/R-4.3.1-intel21/

Other outputs:

************
[root at juno-n001][/root]>  tail -n 20 /juno/opt/sources/R/R-4.3.1-intel21/tests/d-p-q-r-tst-2.Rout.fail 

 0  1  2  3  4  5  6 
13 22 30 22 10  1  2

0  1  2  3  4  5 
10 35 28 18  4  5

+     for(pr in c(1e-8, 1e-9, 1e-10)) {
+         nDup <- !duplicated( pb <- pbinom(k, n, pr) )
+         qb <- qbinom(pb[nDup], n, pr)
+         pn1 <- pb[nDup] < if(b64) 1 else 1 - 3*.Machine$double.eps
+         stopifnot(k[nDup][pn1] == qb[pn1]) ##^^^^^ fudge needed (Linux 32-b)
+     }
+ }
Error: k[nDup][pn1] == qb[pn1] are not all TRUE
Execution halted


************
/juno/opt/intel-2021.6.0/R/4.3.1/bin/R

R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

List of 29
 $ double.eps               : num 2.22e-16
 $ double.neg.eps           : num 1.11e-16
 $ double.xmin              : num 2.23e-308
 $ double.xmax              : num 1.8e+308
 $ double.base              : int 2
 $ double.digits            : int 53
 $ double.rounding          : int 5
 $ double.guard             : int 0
 $ double.ulp.digits        : int -52
 $ double.neg.ulp.digits    : int -53
 $ double.exponent          : int 11
 $ double.min.exp           : int -1022
 $ double.max.exp           : int 1024
 $ integer.max              : int 2147483647
 $ sizeof.long              : int 8
 $ sizeof.longlong          : int 8
 $ sizeof.longdouble        : int 16
 $ sizeof.pointer           : int 8
 $ sizeof.time_t            : int 8
 $ longdouble.eps           : num 1.08e-19
 $ longdouble.neg.eps       : num 5.42e-20
 $ longdouble.digits        : int 64
 $ longdouble.rounding      : int 5
 $ longdouble.guard         : int 0
 $ longdouble.ulp.digits    : int -63
 $ longdouble.neg.ulp.digits: int -64
 $ longdouble.exponent      : int 15
 $ longdouble.min.exp       : int -16382
 $ longdouble.max.exp       : int 16384

Thanks

On 21 Jun 2023, at 12:44, Martin Maechler <maechler at stat.math.ethz.ch> wrote:

Giuseppe Cal? 
   on Wed, 21 Jun 2023 09:17:14 +0200 writes:

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?

Only if you tell us more about the resulting

 d-p-q-r-tst-2.Rout.fail
                   ^^^^^   file

e.g. giving us the last 20 lines or so, e.g. from
 tail -n 20 /juno/opt/sources/R/R-4.3.1-intel21/tests/d-p-q-r-tst-2.Rout.fail 

Also, in addition to the output of sessionInfo(),  the  output of

      str(.Machine)

maybe interesting.  Once I'd see these, I might have to ask further questions
(possibly off-mailinglist), so it'd be good if you keep the
R "installation" in  '/juno/opt/sources/R/R-4.3.1-intel21/  for
minor "experiments".

Best regards,
Martin

Martin Maechler
ETH Zurich  and  R Core team

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 Cal?

Fondazione CMCC
Centro Euro-Mediterraneo sui Cambiamenti Climatici presso Complesso Ecotekne 
Universit? 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 at cmcc.it

Le informazioni contenute in questo messaggio di posta elettronica e negli allegati se presenti sono riservate e confidenziali: ne ? 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.

On 21 Jun 2023, at 09:10, Tomas Kalibera <tomas.kalibera at gmail.com> wrote:


On 6/20/23 18:47, Giuseppe Cal? 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 Cal?

Fondazione CMCC
Centro Euro-Mediterraneo sui Cambiamenti Climatici presso Complesso Ecotekne
Universit? 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 at cmcc.it

Le informazioni contenute in questo messaggio di posta elettronica e negli allegati se presenti sono riservate e confidenziali: ne ? 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 at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel

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

Installation of R-4.3.1 with intel 2022

Thread (10 messages)