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 <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
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