Re: [Rd] Installation of R-4.3.1 with intel 2022

[Giuseppe Calò]

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
http://www.cmcc.it
https://goo.gl/maps/wtahPDbNVen

mobile: (+39) 3208190020
email: giuseppe.c...@cmcc.it


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Il giorno mar 18 lug 2023 alle ore 11:18 Prof Brian Ripley <
rip...@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 

Re: [Rd] Installation of R-4.3.1 with intel 2022

[Giuseppe Calò]

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.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.




> On 18 Jul 2023, at 11:18, Prof Brian Ripley  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
>>>  
>>> 
>>> 
>>> 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 

Re: [Rd] Installation of R-4.3.1 with intel 2022

[Prof Brian Ripley]

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
 


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 

Re: [Rd] Installation of R-4.3.1 with intel 2022

[Martin Maechler]

> Giuseppe Calò 
> on Thu, 22 Jun 2023 16:30:03 +0200 writes:

> yes I think it is caused by the absence of matther in glibc. To compile R 
with icc I disabled matther (with gcc matherr is self disabled). Is it safe to 
keep it disabled matherr?

Others, e.g., Tomas, is much more expert than me about such
error signalling,
but *no*, I do not think that a disabled  matherr  is a problem,
notably as you mention gcc doing it anyway, and gcc does not
show a problem AFAIK.

Martin

> ———
> Giuseppe Calò

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Re: [Rd] Installation of R-4.3.1 with intel 2022

[Giuseppe Calò]

yes I think it is caused by the absence of matther in glibc. To compile R with 
icc I disabled matther (with gcc matherr is self disabled). Is it safe to keep 
it disabled matherr?

———
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

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.




> On 22 Jun 2023, at 16:23, Martin Maechler  wrote:
> 
> Thank you, Giuseppe,
> 
> so indeed using the same restriction has we had on 32-bit
> platforms seems sufficient here.
> 
> Your .Machine() is 100% the same as mine (Linux Fedora 36; using
> GCC, R's BLAS and OS-provided Lapack), so that cannot help to
> detect that your R is set up differently than mainline versions
> of R.
> 
> My guess would be that this difference is not because of the use
> if icc, but only because of the libmath-part (not the
> BLAS/Lapack part) of MKL ... but of course that's only a guess. 
> 
> Would anyone know how to reliably detect from within R that R is
> linked against an MKL math library?
> .. if not generally, may be in the subset of cases where
> 
>   .Platform$OS.type == "unix" &&
>Sys.info ()[["sysname"]] == "Linux"
> 
> ??
> 
> 
> Of course, we could fudge our checks and look for 'mkl' in
> 
>extSoftVersion()["BLAS"]
> 
> and/or
> 
>La_library()
> 
> but I said above that it's much more probable that the
> "libmath"-part of MKL is at stake here, not the BLAS or Lapack
> one.


[[alternative HTML version deleted]]

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Re: [Rd] Installation of R-4.3.1 with intel 2022

[Martin Maechler]

> Giuseppe Calò 
> on Thu, 22 Jun 2023 14:52:00 +0200 writes:

 > Hello Martin, this is output


> 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)

[.]

>> ## qbinom() tests:
>> M <- .Machine$integer.max
>> k <- 0:32
>> pqBinom <- function(epsF = 0, details=FALSE, pr = c(e_8=1e-8,e_9=1e-9, 
e10=1e-10)) {
> +lapply(c(M.2 = (M+1)/2, M=M, `2M`=2*M, `10M`=10*M), # 'n'
> +   function(n)
> +   lapply(pr, function(pr) {
> +   nDup <- !duplicated( pb <- pbinom(k, n, pr) )
> +   qb <- qbinom(pb[nDup], n, pr)
> +   pn1 <- pb[nDup] < 1 - epsF * .Machine$double.eps
> +   ok <- k[nDup][pn1] == qb[pn1]
> +   if(details)
> +   list(pb=pb, qb=qb, nDup=nDup, ok=ok, epsF=epsF)
> +   else ok
> +   })
> +   )
> + }
>> 
>> Dpqb0<- pqBinom(details=TRUE)
>> Dpqb.3e  <- pqBinom(3, details=TRUE)
>> 
>> saveRDS(list(M=M, k=k, Dpqb0=Dpqb0, Dpqb.3e=Dpqb.3e),
> +file = "pqBinom_res.rds")
>> pqb0   <- pqBinom()
>> pqb.3e <- pqBinom(3)
>> table(unlist(pqb0))
> FALSE  TRUE
> 2   292
>> table(unlist(pqb.3e))
> TRUE
> 288

>> sessionInfo()
> R version 4.3.1 (2023-06-16)
> Platform: x86_64-pc-linux-gnu (64-bit)
> Running under: Red Hat Enterprise Linux 8.4 (Ootpa)
> 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
> locale:
> [1] LC_CTYPE=en_US.UTF-8   LC_NUMERIC=C
> [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
> [5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8
> [7] LC_PAPER=en_US.UTF-8   LC_NAME=C
> [9] LC_ADDRESS=C   LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
> time zone: Europe/Rome
> tzcode source: system (glibc)
> attached base packages:
> [1] stats graphics  grDevices utils datasets  methods   base

> loaded via a namespace (and not attached):
> [1] compiler_4.3.1
>> quit()

> File attached
> Thanks,
> Giuseppe.

Thank you, Giuseppe,

so indeed using the same restriction has we had on 32-bit
platforms seems sufficient here.

Your .Machine() is 100% the same as mine (Linux Fedora 36; using
GCC, R's BLAS and OS-provided Lapack), so that cannot help to
detect that your R is set up differently than mainline versions
of R.

My guess would be that this difference is not because of the use
if icc, but only because of the libmath-part (not the
BLAS/Lapack part) of MKL ... but of course that's only a guess. 

Would anyone know how to reliably detect from within R that R is
linked against an MKL math library?
.. if not generally, may be in the subset of cases where

   .Platform$OS.type == "unix" &&
Sys.info()[["sysname"]] == "Linux"

??


Of course, we could fudge our checks and look for 'mkl' in

extSoftVersion()["BLAS"]

and/or

La_library()

but I said above that it's much more probable that the
"libmath"-part of MKL is at stake here, not the BLAS or Lapack
one.


> -
> 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

> [.]
> [.]
> [.]

> x[DELETED ATTACHMENT external: pqBinom_res_GuisepC.rds, Untyped binary 
data]

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Re: [Rd] Installation of R-4.3.1 with intel 2022

[Giuseppe Calò]

Hello Martin, this is output

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.

> ## qbinom() tests:
> M <- .Machine$integer.max
> k <- 0:32
> pqBinom <- function(epsF = 0, details=FALSE, pr = c(e_8=1e-8, e_9=1e-9, 
> e10=1e-10)) {
+lapply(c(M.2 = (M+1)/2, M=M, `2M`=2*M, `10M`=10*M), # 'n'
+   function(n)
+   lapply(pr, function(pr) {
+   nDup <- !duplicated( pb <- pbinom(k, n, pr) )
+   qb <- qbinom(pb[nDup], n, pr)
+   pn1 <- pb[nDup] < 1 - epsF * .Machine$double.eps
+   ok <- k[nDup][pn1] == qb[pn1]
+   if(details)
+   list(pb=pb, qb=qb, nDup=nDup, ok=ok, epsF=epsF)
+   else ok
+   })
+   )
+ }
> 
> Dpqb0<- pqBinom(details=TRUE)
> Dpqb.3e  <- pqBinom(3, details=TRUE)
> 
> saveRDS(list(M=M, k=k, Dpqb0=Dpqb0, Dpqb.3e=Dpqb.3e),
+file = "pqBinom_res.rds")
> pqb0   <- pqBinom()
> pqb.3e <- pqBinom(3)
> table(unlist(pqb0))

FALSE  TRUE 
2   292 
> table(unlist(pqb.3e))

TRUE 
 288 
> sessionInfo()
R version 4.3.1 (2023-06-16)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux 8.4 (Ootpa)

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

locale:
 [1] LC_CTYPE=en_US.UTF-8   LC_NUMERIC=C  
 [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8   LC_NAME=C 
 [9] LC_ADDRESS=C   LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C   

time zone: Europe/Rome
tzcode source: system (glibc)

attached base packages:
[1] stats graphics  grDevices utils datasets  methods   base 

loaded via a namespace (and not attached):
[1] compiler_4.3.1
> quit()

File attached 

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

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.




> On 22 Jun 2023, at 14:34, Martin Maechler  wrote:
> 
>> Giuseppe Calò 
>>on Wed, 21 Jun 2023 13:26:23 +0200 writes:
> 
>> Ok, I’ll reinstall in /juno/opt/sources/R/R-4.3.1-intel21/
>> Other outputs:
> 
>> 
>> [root@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 
>>> (t2 <- table(rbinom(100, 10*M, pr = 1e-10)) )
> 
>> 0  1  2  3  4  5 
>> 10 35 28 18  4  5 
>>> stopifnot(0:6 %in% names(tt), sum(tt) == 100, sum(t2) == 100) ## no NaN 
>>> there
>>> ## related qbinom() tests:
>>> k <- 0:32
>>> for(n in c((M+1)/2, M, 2*M, 10*M)) {
>> + 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
> 
> Ok, thank you, Giuseppe!
> 
> From your .Machine below, indeed b64 is TRUE above
> 
> Now, I'd like to get the details: can you please send me (or
> make available for  download) the binary file
> "pqBinom_res.rds"
> 
> which will result from this:
> 
> -
> 
> ## qbinom() tests:
> M <- 

Re: [Rd] Installation of R-4.3.1 with intel 2022

[Martin Maechler]

> Giuseppe Calò 
> on Wed, 21 Jun 2023 13:26:23 +0200 writes:

> Ok, I’ll reinstall in /juno/opt/sources/R/R-4.3.1-intel21/
> Other outputs:

> 
> [root@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 
>> (t2 <- table(rbinom(100, 10*M, pr = 1e-10)) )

> 0  1  2  3  4  5 
> 10 35 28 18  4  5 
>> stopifnot(0:6 %in% names(tt), sum(tt) == 100, sum(t2) == 100) ## no NaN 
there
>> ## related qbinom() tests:
>> k <- 0:32
>> for(n in c((M+1)/2, M, 2*M, 10*M)) {
> + 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

Ok, thank you, Giuseppe!

>From your .Machine below, indeed b64 is TRUE above

Now, I'd like to get the details: can you please send me (or
make available for  download) the binary file
 "pqBinom_res.rds"

which will result from this:

-

## qbinom() tests:
M <- .Machine$integer.max
k <- 0:32
pqBinom <- function(epsF = 0, details=FALSE, pr = c(e_8=1e-8, e_9=1e-9, 
e10=1e-10)) {
lapply(c(M.2 = (M+1)/2, M=M, `2M`=2*M, `10M`=10*M), # 'n'
   function(n)
   lapply(pr, function(pr) {
   nDup <- !duplicated( pb <- pbinom(k, n, pr) )
   qb <- qbinom(pb[nDup], n, pr)
   pn1 <- pb[nDup] < 1 - epsF * .Machine$double.eps
   ok <- k[nDup][pn1] == qb[pn1]
   if(details)
   list(pb=pb, qb=qb, nDup=nDup, ok=ok, epsF=epsF)
   else ok
   })
   )
}

Dpqb0<- pqBinom(details=TRUE)
Dpqb.3e  <- pqBinom(3, details=TRUE)

saveRDS(list(M=M, k=k, Dpqb0=Dpqb0, Dpqb.3e=Dpqb.3e),
file = "pqBinom_res.rds")

-

You may can also reply in public, posting the summary output
you'll get from

pqb0   <- pqBinom()
pqb.3e <- pqBinom(3)
table(unlist(pqb0))
table(unlist(pqb.3e))

In case the 2nd table would show all TRUE also on your platform,
*AND* if you also send the results of  sessionInfo()
{I've also asked you about in the last e-mail !}
we'd already know enough to adapt the test, but I'd be
interested to learn a bit more (via the above *.rds file).   

Thank you for helping to find more about the internal accuracy
achievement on a not-so-common (yet?) platform.

Best,
Martin


> 
> /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.

>> str(.Machine)
> 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 

Re: [Rd] Installation of R-4.3.1 with intel 2022

[Giuseppe Calò]

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

Other outputs:


[root@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 
> (t2 <- table(rbinom(100, 10*M, pr = 1e-10)) )

 0  1  2  3  4  5 
10 35 28 18  4  5 
> stopifnot(0:6 %in% names(tt), sum(tt) == 100, sum(t2) == 100) ## no NaN there
> ## related qbinom() tests:
> k <- 0:32
> for(n in c((M+1)/2, M, 2*M, 10*M)) {
+ 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.

>  str(.Machine)
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  wrote:
> 
>> Giuseppe Calò 
>>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: 
>> 

Re: [Rd] Installation of R-4.3.1 with intel 2022

[Martin Maechler]

> Giuseppe Calò 
> 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 
(0x7f01ba508000)
> libmkl_intel_thread.so.2 => 
/juno/opt/intel/oneapi_2022.2.0/mkl/2022.1.0/lib/intel64/libmkl_intel_thread.so.2
 (0x7f01b6d94000)
> libmkl_core.so.2 => 
/juno/opt/intel/oneapi_2022.2.0/mkl/2022.1.0/lib/intel64/libmkl_core.so.2 
(0x7f01b29be000)

> 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

> 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.




>> On 21 Jun 2023, at 09:10, 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:
>>> ^
>>> 
   

Re: [Rd] Installation of R-4.3.1 with intel 2022

[Giuseppe Calò]

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 
(0x7f01ba508000)
libmkl_intel_thread.so.2 => 
/juno/opt/intel/oneapi_2022.2.0/mkl/2022.1.0/lib/intel64/libmkl_intel_thread.so.2
 (0x7f01b6d94000)
libmkl_core.so.2 => 
/juno/opt/intel/oneapi_2022.2.0/mkl/2022.1.0/lib/intel64/libmkl_core.so.2 
(0x7f01b29be000)

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  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 

Re: [Rd] Installation of R-4.3.1 with intel 2022

[Tomas Kalibera]

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
 


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 
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.

[Rd] Installation of R-4.3.1 with intel 2022

[Giuseppe Calò]

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
 


Deactivate  HAVE_MATHERR macro in src/include/config.h

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

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 
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.





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