[Rd] Installation of R-4.3.1 with intel 2022
Giuseppe Calò
g|u@eppe@c@|o @end|ng |rom cmcc@|t
Wed Jun 21 13:26:23 CEST 2023
Ok, I’ll reinstall in /juno/opt/sources/R/R-4.3.1-intel21/
Other outputs:
************
[root using 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"
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> 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 <maechler using 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.calo using 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.kalibera using 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.calo using 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]]
>>>>
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>>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>
>
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