Re: [Rd] help for memory problem with 64-bit machines

From: Hin-Tak Leung <hin-tak.leung_at_cimr.cam.ac.uk>
Date: Fri 05 Jan 2007 - 16:50:37 GMT

I got the same error with 64-bit R 2.4.1 on FC6 x86_64, and 32-bit R 2.4.1 on the same machine is okay. There is definitely something wrong with your code.

I would suggest fixing all the compier warnings - there are piles of them about uninitialized variables, and about doing comparison between signed and unsigned expressions, etc first. Put -Wall in CFLAGS CXXFLAGS and FFLAGS and you'll see.

good luck.

Hin-Tak Leung

Jorge Cadima wrote:
> Hello,
>
> I would appreciate *any* ideas on this problem. I'm the maintainer of a
> package ("subselect"), which on CRAN's Daily Package Checks is OK on all
> flavours of R, except r-devel Linux x86_64, where there is a "memory not
> mapped" segfault with the very first example that is tried out (output below).
> Additionally, a user with an AMD64 machine has just reported a similar
> problem, and kindly ran a couple of tests identifying the culprit (output
> below):a Fortran routine. Unfortunately, I don't have 64-bit machines
> available and the segfault has not occured with other machines, so I am having
> trouble trying to spot the problem.
>
> I suspect the problem lies in one of two things:
>
> 1) The Fortran subroutine where the crash occurs has variable-length arrays.
> Could there be a problem with this (the user who spotted the problem is
> running the gfortran gcc compiler - I presume r-devel Linux x86_64 does too)?
> 3) the guilty routine ("randsk1") calls a second routine ("randint") which, in
> turn, calls R's Random Number Generator. Can the problem arise in the
> Fortran/R interface?
>
> As I said, any idea of what the problem may be, or where I can look for help,
> would be much appreciated.
>
> In despair, but with best regards,
> Jorge Cadima
>
> -------------------------------------------------------------------------------
> ---
> --- Cran Daily Package check output -------------------------------------------
> ---
> -------------------------------------------------------------------------------
> ---
>
> * using R version 2.5.0 Under development (unstable) (2007-01-03 r40349)
> * checking for file 'subselect/DESCRIPTION' ... OK
> * this is package 'subselect' version '0.9-999'
> * checking package dependencies ... OK
> (...)
> * creating subselect-Ex.R ... OK
> * checking examples ... ERROR
> Running examples in 'subselect-Ex.R' failed.
> The error most likely occurred in:
>
> > ### * anneal
> >
> > flush(stderr()); flush(stdout())
> >
> > ### Name: anneal
> > ### Title: Simulated Annealing Search for an optimal k-variable subset
> > ### Aliases: anneal
> > ### Keywords: manip
> >
> > ### ** Examples
> >
> >
> > ## --------------------------------------------------------------------
> >
> > ##
> > ## (1) For illustration of use, a small data set with very few
> iterations
> > ## of the algorithm, using the RM criterion.
> > ##
> >
> > data(swiss)
> > anneal(cor(swiss),2,3,nsol=4,niter=10,criterion="RM")
>
> *** caught segfault ***
> address 0x47cd37c, cause 'memory not mapped'
>
> Traceback:
> 1: .Fortran("anneal", as.integer(criterio), as.integer(p),
> as.double(as.vector(mat)), as.integer(kmin), as.integer(kmax),
> as.double(valores), as.integer(vars), as.double(bestval), as.integer(bestvar),
> as.integer(nexclude), as.integer(exc), as.integer(ninclude), as.integer(inc),
> as.integer(nsol), as.integer(niter), as.logical(improvement),
> as.double(cooling), as.double(temp), as.integer(coolfreq),
> as.integer(length(pcindices)), as.integer(pcindices), as.logical(esp),
> as.logical(silog), as.integer(as.vector(initialsol)), as.double(valp),
> as.double(as.vector(vecp)), as.double(as.vector(H)), as.integer(r), PACKAGE =
> "subselect")
> 2: anneal(cor(swiss), 2, 3, nsol = 4, niter = 10, criterion = "RM")
> aborting ...
>
> -------------------------------------------------------------------------------
> -----
> ------- user's tests output ---------------------------------------------------
> --
> -------------------------------------------------------------------------------
> --
>
> The install
> ===========
>
> work:/home/jimmy/R # R CMD INSTALL subselect_0.9-999.tar.gz
> * Installing *source* package 'subselect' ...
> ** libs
> gfortran -fpic -c anneal.f -o anneal.o
> gfortran -fpic -c auxiliar.f -o auxiliar.o
> g++ -I/usr/lib64/R/include -I/usr/lib64/R/include -I/usr/local/include
> -fpic -g -O2 -c CCRcrt.cpp -o CCRcrt.o
>
> (...)
>
> g++ -I/usr/lib64/R/include -I/usr/lib64/R/include -I/usr/local/include
> -fpic -g -O2 -c Wrkf1.cpp -o Wrkf1.o
> g++ -shared -L/usr/local/lib64 -o subselect.so anneal.o auxiliar.o CCRcrt.o
> GCDcrt.o genetic.o Gstatma.o improve.o MStcrt.o NewtonRp.o Qforms.o RMcrt.o
> Rnk3CCRcrt.o RVcrt.o SpecialArrays.o SR_datatrnsf.o SR_intf.o SRI_sscma.o
> Sscma.o Subsets.o Varsmbo.o VSQforms.o wrap.o Wrkf1.o -L/usr/lib64/R/lib
> -lRlapack -lgfortran -lm -lgcc_s -lgfortran -lm -lgcc_s -L/usr/lib64/R/lib -lR
> ** R
> ** inst
> ** preparing package for lazy loading
> ** help
> >>> Building/Updating help pages for package 'subselect'
> Formats: text html latex example
> anneal text html latex example
>
> (...)
>
> zeta2 text html latex example
> ** building package indices ...
> * DONE (subselect)
> work:/home/jimmy/R #
>
>
>
> The library is put into:
> /usr/lib64/R/library/subselect/libs/subselect.so
>
> and nm -s give me (in part):
>
> work:/home/jimmy/R # nm -s /usr/lib64/R/library/subselect/libs/subselect.so
> 0000000000012a4c T anneal_
> ....
> 0000000000014580 T randint_
> 000000000001446a T randsk1_
> U Rf_error
> 000000000003470f T rndend_
> 0000000000034704 T rndstart_
> U Rprintf
> ....
> etc
>
> So randsk1 is there.
>
>
> Running the subselect example from the manual:
>
> jimmy@work:~> R
>
> R : Copyright 2006, The R Foundation for Statistical Computing
> Version 2.3.1 (2006-06-01)
> ISBN 3-900051-07-0
>
> 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.
>

>> library(subselect)
>> data(swiss)
>> anneal(cor(swiss),2,3,nsol=4,niter=10,criterion="RM")

>
> *** caught segfault ***
> address 0xffffffffb03f38dc, cause 'memory not mapped'
>
> Traceback:
> 1: .Fortran("anneal", as.integer(criterio), as.integer(p),
> as.double(as.vector(mat)), as.integer(kmin), as.integer(kmax),
> as.double(valores), as.integer(vars), as.double(bestval),
> as.integer(bestvar), as.integer(nexclude), as.integer(exc),
> as.integer(ninclude), as.integer(inc), as.integer(nsol),
> as.integer(niter), as.logical(improvement), as.double(cooling),
> as.double(temp), as.integer(coolfreq), as.integer(length(pcindices)),
> as.integer(pcindices), as.logical(esp), as.logical(silog),
> as.integer(as.vector(initialsol)), as.double(valp),
> as.double(as.vector(vecp)), as.double(as.vector(H)), as.integer(r),
> PACKAGE = "subselect")
> 2: anneal(cor(swiss), 2, 3, nsol = 4, niter = 10, criterion = "RM")
>
> Possible actions:
> 1: abort (with core dump)
> 2: normal R exit
> 3: exit R without saving workspace
> 4: exit R saving workspace
> Selection:
>
>
> Running R in the debugger with this input file:
>
> library(subselect)
> data(swiss)
> anneal(cor(swiss),2,3,nsol=4,niter=10,criterion="RM")
>
> (gdb) run
>
> Program received signal SIGSEGV, Segmentation fault.
> 0x00002b86c2ed9526 in randsk1_ () from /usr/lib64/R/library/subselect/libs/subs
> elect.so
> (gdb)
>
>
>
>
>
> ------------------------------------------------------------------------
>
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> https://stat.ethz.ch/mailman/listinfo/r-devel


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