>>>>> 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 Jun 2023, at 12:44, Martin Maechler <maech...@stat.math.ethz.ch>
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:
/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
>>
>>> 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 <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
>>
>>
>>> [[alternative HTML version deleted]]
>>
>>> ______________________________________________
>>> R-devel@r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-devel
> [[alternative HTML version deleted]]
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