[R] R 4.0.1 built with Intel Composer 19.1.1, error in R CMD make check on CentOS 7.7

Ryan Novosielski novo@|rj @end|ng |rom rutger@@edu
Sun Jun 14 04:16:38 CEST 2020

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"


/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'

 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 - novosirj using rutgers.edu
|| \\ University | Sr. Technologist - 973/972.0922 (2x0922) ~*~ RBHS Campus
||  \\    of NJ	 | Office of Advanced Research Computing - MSB C630, Newark

-------------- next part --------------
A non-text attachment was scrubbed...
Name: signature.asc
Type: application/pgp-signature
Size: 195 bytes
Desc: Message signed with OpenPGP
URL: <https://stat.ethz.ch/pipermail/r-help/attachments/20200614/e62d9041/attachment.sig>

More information about the R-help mailing list