repeatable segfault - on Mac
On Sep 8, 2011, at 10:01 , Martin Maechler wrote:
David Winsemius <dwinsemius at comcast.net> on Tue, 6 Sep 2011 00:38:13 -0400 writes:
I can reproduce: eigen(crossprod(matrix(1:2000, 50)) + (0+0i), T, T)
*** caught segfault *** address 0x102d0e028, cause 'memory not mapped'
Traceback:
1: .Call("La_rs_cmplx", x, only.values, PACKAGE = "base")
2: eigen(crossprod(matrix(1:2000, 50)) + (0 + (0+0i)), T, T)
##---- after restart
sessionInfo()
R version 2.13.1 (2011-07-08) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
attached base packages: [1] stats graphics grDevices utils datasets methods base
With OSX 10.5.8
Also happens with 32 bit R [R.app GUI 1.41 (5874) i386-apple-darwin9.8.0]
It does not happen on Linux (different versions) nor Windows (2.13.1 patched, early August). As this is calling LAPACK code, I guess that this is yet another case where the Mac version of optimized BLAS / LAPACK is playing wrongly.
Hmm, it does happen too on OSX (64bit) with a recent R-devel, vanilla compiled with LAPACK_LIBS='-L$(R_HOME)/lib$(R_ARCH) -lRlapack' I tried recompiling with -O0, still happening: Program received signal EXC_BAD_ACCESS, Could not access memory. Reason: KERN_INVALID_ADDRESS at address: 0x0000000102ddc128 0x000000010046805e in zher2k (uplo=@0x7fff5fbf9b0e, trans=@0x1039fc54b, n=@0x7fff5fbf98cc, k=@0x7fff5fbf98e0, alpha=@0x1039fc528, a=0x102198228, lda=@0x7fff5fbf9b08, b=0x1023abca8, ldb=@0x7fff5fbf98f4, beta=@0x1039fc660, c=0x10219d228, ldc=@0x7fff5fbf9b08, _uplo=1, _trans=12) at ../../../../R/src/extra/blas/cmplxblas.f:1566 1566 TEMP1 = ALPHA*DCONJG( B( J, L ) ) (gdb) where #0 0x000000010046805e in zher2k (uplo=@0x7fff5fbf9b0e, trans=@0x1039fc54b, n=@0x7fff5fbf98cc, k=@0x7fff5fbf98e0, alpha=@0x1039fc528, a=0x102198228, lda=@0x7fff5fbf9b08, b=0x1023abca8, ldb=@0x7fff5fbf98f4, beta=@0x1039fc660, c=0x10219d228, ldc=@0x7fff5fbf9b08, _uplo=1, _trans=12) at ../../../../R/src/extra/blas/cmplxblas.f:1566 #1 0x00000001039939aa in zhetrd (uplo=@0x7fff5fbf9b0e, n=@0x7fff5fbf9b08, a=0x102198028, lda=@0x7fff5fbf9b08, d=0x100597f28, e=0x102e02d58, tau=0x1023ab828, work=0x1023abaa8, lwork=@0x7fff5fbf9a30, info=@0x7fff5fbf9a44, _uplo=1) at ../../../../R/src/modules/lapack/cmplx.f:8841 #2 0x000000010399209e in zheev (jobz=@0x7fff5fbf9b0f, uplo=@0x7fff5fbf9b0e, n=@0x7fff5fbf9b08, a=0x102198028, lda=@0x7fff5fbf9b08, w=0x100597f28, work=0x1023ab828, lwork=@0x7fff5fbf9b04, rwork=0x102e02d58, info=@0x7fff5fbf9b00, _jobz=10096376, _uplo=36013056) at ../../../../R/src/modules/lapack/cmplx.f:8275 #3 0x00000001007f102e in modLa_rs_cmplx (xin=0x102258400, only_values=0x1009a0ef8) at ../../../../R/src/modules/lapack/Lapack.c:776 #4 0x0000000100103baf in La_rs_cmplx (x=0x102258400, only_values=0x1009a0ef8) at ../../../R/src/main/lapack.c:113 #5 0x000000010007a82b in do_dotcall (call=0x1026c62e8, op=0x100864718, args=0x1026d9278, env=0x1026d4278) at ../../../R/src/main/dotcode.c:845 Segmentation fault (The segfault appears to be gdb itself tripping over) -pd
Martin Maechler
David Winsemius
On Sep 6, 2011, at 12:12 AM, robin hankin wrote:
Hi. macosx 10.6.8 With R-2.13.1 and also revision 56948 I get the following repeatable segfault: wt118:~% R --vanilla --quiet
R.Version()
$platform [1] "x86_64-apple-darwin9.8.0" $arch [1] "x86_64" $os [1] "darwin9.8.0" $system [1] "x86_64, darwin9.8.0" $status [1] "" $major [1] "2" $minor [1] "13.1" $year [1] "2011" $month [1] "07" $day [1] "08" $`svn rev` [1] "56322" $language [1] "R" $version.string [1] "R version 2.13.1 (2011-07-08)"
eigen(crossprod(matrix(1:2000, 50)) + (0+0i), T, T)
*** caught segfault ***
address 0x1038000a8, cause 'memory not mapped'
Traceback:
1: .Call("La_rs_cmplx", x, only.values, PACKAGE = "base")
2: eigen(crossprod(matrix(1:2000, 50)) + (0 + (0+0i)), T, T)
Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection: 2
wt118:~%
--
Robin Hankin
Uncertainty Analyst
hankin.robin at gmail.com
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David Winsemius, MD Heritage Laboratories West Hartford, CT
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______________________________________________ R-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Peter Dalgaard, Professor Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com