Dear Prof. Ripley,
Am Montag, den 21.02.2011, 11:40 +0000 schrieb Prof Brian Ripley:
> So there is very likely a bug in your system software or compiler.
> There is no such problem on other x86_64 systems (including
> Fedora 14 and 12, FreeBSD, Solaris and Windows).
>
> You can debug segfaults for yourself (see 'Writing R Extensions') or
> ask your vendor for support.
I still suffer from the same problem, but now with R version 2.12.2.
> On Mon, 21 Feb 2011, Juergen Rose wrote:
>
> > Am Montag, den 21.02.2011, 11:11 +0100 schrieb Juergen Rose:
> >> Hi,
..
> >> With large(?) matrices eigen produces on several of my systems
> >> segfaults:
> >>
> >>> data(iris)
> >>> D <- dist(iris[,-5])
..
> >>> eigen(D)
> >>
> >> *** caught segfault ***
> >> address (nil), cause 'unknown'
> >>
> >> Traceback:
> >> 1: .Call("La_rs", x, only.values, PACKAGE = "base")
> >> 2: eigen(D)
The problem happens only if blas-atlas and lapack-atlas are the current
libraries, it not happens with blas-reference and lapack-reference.
I tried also to follow 'Writing R Extensions', but I not really
understand, what I should do in my case. Have I to compile the libraries
and R with debugging information?
I tried without debugging information in R:
> data(iris)
> D <- dist(iris[,-5])
> debug(eigen)
> eigen(D)
debugging in: eigen(D)
debug: {
x <- as.matrix(x)
if (!is.null(dimnames(x)))
dimnames(x) <- list(NULL, NULL)
n <- nrow(x)
if (!n)
stop("0 x 0 matrix")
if (n != ncol(x))
stop("non-square matrix in 'eigen'")
complex.x <- is.complex(x)
if (!complex.x && !is.double(x))
storage.mode(x) <- "double"
if (!all(is.finite(x)))
stop("infinite or missing values in 'x'")
if (missing(symmetric))
symmetric <- isSymmetric.matrix(x)
if (!EISPACK) {
if (symmetric) {
z <- if (!complex.x)
.Call("La_rs", x, only.values, PACKAGE = "base")
else .Call("La_rs_cmplx", x, only.values, PACKAGE = "base")
ord <- rev(seq_along(z$values))
}
else {
z <- if (!complex.x)
.Call("La_rg", x, only.values, PACKAGE = "base")
else .Call("La_rg_cmplx", x, only.values, PACKAGE = "base")
ord <- sort.list(Mod(z$values), decreasing = TRUE)
}
return(list(values = z$values[ord], vectors = if (!only.values)
z$vectors[,
ord, drop = FALSE]))
}
dbl.n <- double(n)
if (symmetric) {
if (complex.x) {
xr <- Re(x)
xi <- Im(x)
z <- .Fortran("ch", n, n, xr, xi, values = dbl.n,
!only.values, vectors = xr, ivectors = xi, dbl.n,
dbl.n, double(2 * n), ierr = integer(1L), PACKAGE =
"base")
if (z$ierr)
stop(gettextf("'ch' returned code %d in 'eigen'",
z$ierr), domain = NA)
if (!only.values)
z$vectors <- matrix(complex(real = z$vectors,
imaginary = z$ivectors), ncol = n)
}
else {
z <- .Fortran("rs", n, n, x, values = dbl.n, !only.values,
vectors = x, dbl.n, dbl.n, ierr = integer(1L),
PACKAGE = "base")
if (z$ierr)
stop(gettextf("'rs' returned code %d in 'eigen'",
z$ierr), domain = NA)
}
ord <- sort.list(z$values, decreasing = TRUE)
}
else {
if (complex.x) {
xr <- Re(x)
xi <- Im(x)
z <- .Fortran("cg", n, n, xr, xi, values = dbl.n,
ivalues = dbl.n, !only.values, vectors = xr,
ivectors = xi, dbl.n, dbl.n, dbl.n, ierr = integer(1L),
PACKAGE = "base")
if (z$ierr)
stop(gettextf("'cg' returned code %d in 'eigen'",
z$ierr), domain = NA)
z$values <- complex(real = z$values, imaginary = z$ivalues)
if (!only.values)
z$vectors <- matrix(complex(real = z$vectors,
imaginary = z$ivectors), ncol = n)
}
else {
z <- .Fortran("rg", n, n, x, values = dbl.n, ivalues =
dbl.n,
!only.values, vectors = x, integer(n), dbl.n,
ierr = integer(1L), PACKAGE = "base")
if (z$ierr)
stop(gettextf("'rg' returned code %d in 'eigen'",
z$ierr), domain = NA)
ind <- z$ivalues > 0L
if (any(ind)) {
ind <- seq.int(n)[ind]
z$values <- complex(real = z$values, imaginary = z
$ivalues)
if (!only.values) {
z$vectors[, ind] <- complex(real = z$vectors[,
ind], imaginary = z$vectors[, ind + 1])
z$vectors[, ind + 1] <- Conj(z$vectors[, ind])
}
}
}
ord <- sort.list(Mod(z$values), decreasing = TRUE)
}
list(values = z$values[ord], vectors = if (!only.values) z
$vectors[,
ord, drop = FALSE])
}
Browse[2]> start
function (x, ...)
UseMethod("start")
<environment: namespace:stats>
Browse[2]>
valgrind
How to proceed? I also tried to use valgrind:
rose@moose:/home/rose(7)$ R -d valgrind --vanilla
==15631== Memcheck, a memory error detector
==15631== Copyright (C) 2002-2010, and GNU GPL'd, by Julian Seward et
al.
==15631== Using Valgrind-3.6.1 and LibVEX; rerun with -h for copyright
info
==15631== Command: /usr/lib64/R/bin/exec/R --vanilla
==15631==
valgrind: Fatal error at startup: a function redirection
valgrind: which is mandatory for this platform-tool combination
valgrind: cannot be set up. Details of the redirection are:
valgrind:
valgrind: A must-be-redirected function
valgrind: whose name matches the pattern: strlen
valgrind: in an object with soname matching: ld-linux-x86-64.so.2
valgrind: was not found whilst processing
valgrind: symbols from the object with soname: ld-linux-x86-64.so.2
valgrind:
valgrind: Possible fixes: (1, short term): install glibc's debuginfo
valgrind: package on this machine. (2, longer term): ask the packagers
valgrind: for your Linux distribution to please in future ship a non-
valgrind: stripped ld.so (or whatever the dynamic linker .so is called)
valgrind: that exports the above-named function using the standard
valgrind: calling conventions for this platform. The package you need
valgrind: to install for fix (1) is called
valgrind:
valgrind: On Debian, Ubuntu: libc6-dbg
valgrind: On SuSE, openSuSE, Fedora, RHEL: glibc-debuginfo
valgrind:
valgrind: Cannot continue -- exiting now. Sorry.
That means for me with GENTOO, that I have to compile glibc with
debuginfo. Is it correct?
Regards
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