Read the Posting Guide ... this is definitely off-topic here. I think this is
an r-devel question, though I really don't know whether you will find interest
in discussing compilation of R with a non-standard tool chain. There are a lot
of "moving parts" in R and it can be challenging just to keep up with upgrades
in the standard tool chain without getting caught up in yet another one.
On June 17, 2020 3:04:30 PM PDT, Ryan Novosielski <novos...@rutgers.edu> wrote:
>Same story with R-devel 2020-06-16-r78702, everything else the same.
>Should I be reporting this someplace else?
>
>--
>____
>|| \\UTGERS,
>|---------------------------*O*---------------------------
>||_// the State | Ryan Novosielski - novos...@rutgers.edu
>|| \\ University | Sr. Technologist - 973/972.0922 (2x0922) ~*~ RBHS
>Campus
>|| \\ of NJ | Office of Advanced Research Computing - MSB C630,
>Newark
> `'
>
>> On Jun 13, 2020, at 10:16 PM, Ryan Novosielski <novos...@rutgers.edu>
>wrote:
>>
>> Signed PGP part
>> Hi there,
>>
>> Built R 4.0.1 with the Intel Composer 19.1.1. Build seems to go fine.
>I built it like this:
>>
>> module purge
>> module load intel/19.1.1
>> module list
>>
>> export CC=icc
>> export CXX=icpc
>> export F77=ifort
>> export FC=ifort
>> export AR=xiar
>> export LD=xild
>>
>> export CFLAGS="-O3 -ipo -qopenmp -axAVX,CORE-AVX2,CORE-AVX512"
>> export F77FLAGS="-O3 -ipo -qopenmp -axAVX,CORE-AVX2,CORE-AVX512"
>> export FFLAGS="-O3 -ipo -qopenmp -axAVX,CORE-AVX2,CORE-AVX512"
>> export CXXFLAGS="-O3 -ipo -qopenmp -axAVX,CORE-AVX2,CORE-AVX512"
>> export MKL="-lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5
>-lpthread"
>>
>> VERSION=4.0.1
>>
>> /scratch/novosirj/install-files/R-${VERSION}/configure
>--with-blas="$MKL" --with-lapack
>--prefix=/opt/sw/packages/intel-19_1/R-Project/${VERSION} && \
>> make -j32 && make check && make -j32 install
>>
>> However, the “make check" phase fails at this part:
>>
>> Testing examples for package ‘parallel’
>> make[2]: Leaving directory
>`/mnt/scratch/novosirj/R-4.0.1-intel-19.1-build/tests/Examples'
>> make[1]: Leaving directory
>`/mnt/scratch/novosirj/R-4.0.1-intel-19.1-build/tests'
>> make[1]: Entering directory
>`/mnt/scratch/novosirj/R-4.0.1-intel-19.1-build/tests'
>> running strict specific tests
>> make[2]: Entering directory
>`/mnt/scratch/novosirj/R-4.0.1-intel-19.1-build/tests'
>> running code in
>'/scratch/novosirj/install-files/R-4.0.1/tests/eval-etc.R' ... OK
>> comparing 'eval-etc.Rout' to
>'/scratch/novosirj/install-files/R-4.0.1/tests/eval-etc.Rout.save' ...
>OK
>> running code in
>'/scratch/novosirj/install-files/R-4.0.1/tests/simple-true.R' ... OK
>> comparing 'simple-true.Rout' to
>'/scratch/novosirj/install-files/R-4.0.1/tests/simple-true.Rout.save'
>... OK
>> running code in
>'/scratch/novosirj/install-files/R-4.0.1/tests/arith-true.R' ... OK
>> comparing 'arith-true.Rout' to
>'/scratch/novosirj/install-files/R-4.0.1/tests/arith-true.Rout.save'
>... OK
>> running code in
>'/scratch/novosirj/install-files/R-4.0.1/tests/arith.R' ... OK
>> comparing 'arith.Rout' to
>'/scratch/novosirj/install-files/R-4.0.1/tests/arith.Rout.save' ... OK
>> running code in
>'/scratch/novosirj/install-files/R-4.0.1/tests/lm-tests.R' ... OK
>> comparing 'lm-tests.Rout' to
>'/scratch/novosirj/install-files/R-4.0.1/tests/lm-tests.Rout.save' ...
>OK
>> /bin/sh: line 1: 62064 Segmentation fault (core dumped)
>LANGUAGE=en LC_ALL=C
>SRCDIR=/scratch/novosirj/install-files/R-4.0.1/tests
>R_DEFAULT_PACKAGES= ../bin/R --vanilla <
>/scratch/novosirj/install-files/R-4.0.1/tests/ok-errors.R >
>ok-errors.Rout.fail 2>&1
>> running code in
>'/scratch/novosirj/install-files/R-4.0.1/tests/ok-errors.R' ...make[2]:
>*** [ok-errors.Rout] Error 1
>> make[2]: Leaving directory
>`/mnt/scratch/novosirj/R-4.0.1-intel-19.1-build/tests'
>> make[1]: *** [test-Specific] Error 2
>> make[1]: Leaving directory
>`/mnt/scratch/novosirj/R-4.0.1-intel-19.1-build/tests'
>> make: *** [test-all-basics] Error 1
>>
>> Is this something I should be concerned about, or something I can
>fix? Not seeing any real information about what’s going wrong here.
>Here’s what’s contained in ok-errors.Rout.fail:
>>
>> ---
>> R version 4.0.1 (2020-06-06) -- "See Things Now"
>> Copyright (C) 2020 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.
>>
>> 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.
>>
>>> #### STRICT test suite in the spirit of no-segfaults,
>>> #### but with explicit statements.
>>>
>>> options(error=expression(NULL))
>>> stop("test of `options(error=expression(NULL))'")
>> Error: test of `options(error=expression(NULL))'
>>>
>>> if(FALSE) {
>> + ## these ought to work on machines with enough memory
>> + ## These segfaulted in 1.3.x , give "could not allocate" errors
>now
>> + integer(2^30+1)
>> + double(2^30+1)
>> + complex(2^30+1)
>> + character(2^30+1)
>> + vector("list", 2^30+2)
>> + }
>>>
>>> ## bad infinite recursion / on.exit / ... interactions
>>> ## catch the error to permit different error messages emitted
>>> ## (handling of infinite recursion is different in the AST
>interpreter
>>> ## and the byte-code interpreter)
>>>
>>> bar <- function() 1+1
>>> foo <- function() { on.exit(bar()); foo() }
>>> tryCatch(foo(), error=function(x) TRUE) # now simple "infinite
>recursion"
>>
>> *** caught segfault ***
>> address 0x7fff4dc1b9f8, cause 'memory not mapped'
>>
>> Traceback:
>> 1: foo()
>> 2: foo()
>> 3: foo()
>> 4: foo()
>>
>> ...
>>
>> 2712: foo()
>> 2713: foo()
>> 2714: foo()
>> 2715: foo()
>> 2716: foo()
>> 2717: foo()
>> 2718: foo()
>> 2719: doTryCatch(return(expr), name, parentenv, handler)
>> 2720: tryCatchOne(expr, names, parentenv, handlers[[1L]])
>> 2721: tryCatchList(expr, classes, parentenv, handlers)
>> 2722: tryCatch(foo(), error = function(x) TRUE)
>> An irrecoverable exception occurred. R is aborting now ...
>> ---
>>
>> Thanks in advance.
>>
>> --
>> ____
>> || \\UTGERS,
>|---------------------------*O*---------------------------
>> ||_// the State | Ryan Novosielski - novos...@rutgers.edu
>> || \\ University | Sr. Technologist - 973/972.0922 (2x0922) ~*~ RBHS
>Campus
>> || \\ of NJ | Office of Advanced Research Computing - MSB C630,
>Newark
>> `'
>>
>>
>>
--
Sent from my phone. Please excuse my brevity.
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