thr3ads.net - R devel - [Rd] seg.fault from nlme::gnls() {was "[R-sig-ME] GNLS Crash"} [Sep 2008]

If this information is useful, please help other people find it:
Share via:

Martin Maechler

2008-Sep-27 09:20 UTC

[Rd] seg.fault from nlme::gnls() {was "[R-sig-ME] GNLS Crash"}

>>>>> "VW" == Viechtbauer Wolfgang (STAT)
<Wolfgang.Viechtbauer at STAT.unimaas.nl>
>>>>>     on Fri, 26 Sep 2008 18:00:19 +0200 writes:
    VW> Hi all, I'm trying to fit a marginal (longitudinal)
    VW> model with an exponential serial correlation function to
    VW> the Orange tree data set. However, R crashes frequently
    VW> when using the gnls() function. With the following
    VW> simple example, I was able to reproduce the problem.


    VW> gnls.exp <- gnls(circumference ~ Asym/(1 + exp(-(age-xmid)/scal))
,
    VW> data = Orange, correlation = corExp(form = ~1 | Tree),
    VW> start = c(Asym=150, xmid=750, scal=300))

Yes, I can reproduce it (on a Linux (RHEL 5) 64bit server), using
R 2.8.0 alpha : Use this

for(i in 1:20)# for MM: ca. 8 to 10 times --> seg.fault
try(
gnls.exp <- gnls(circumference ~ Asym/(1 + exp(-(age-xmid)/scal)) ,
              data = Orange, correlation = corExp(form = ~1 | Tree),
              start = c(Asym=150, xmid=750, scal=300))
)

If I run it in the debugger and then do a backtrace
I see

Error in gnls(circumference ~ Asym/(1 + exp(-(age - xmid)/scal)), data = Orange,
:
  Step halving factor reduced below minimum in NLS step

[............................................................]
[...................the same about 6 times...................]
[............................................................]

Error in gnls(circumference ~ Asym/(1 + exp(-(age - xmid)/scal)), data = Orange,
:
  Step halving factor reduced below minimum in NLS step
Error in .makeMessage(..., domain = domain) : 
  incorrect number of arguments to "<-"
Error in .makeMessage(..., domain = domain) : 
  incorrect number of arguments to "<-"

Program received signal SIGABRT, Aborted.
0x0000003294e30155 in raise () from /lib64/libc.so.6
(gdb) bt
#0  0x0000003294e30155 in raise () from /lib64/libc.so.6
#1  0x0000003294e31bf0 in abort () from /lib64/libc.so.6
#2  0x00000000004184f5 in R_gc_internal (size_needed=0)
    at ../../../R/src/main/memory.c:761
#3  0x000000000041b121 in Rf_cons (car=0x1b2ec088, cdr=0x1a3436d8)
    at ../../../R/src/main/memory.c:1755
#4  0x0000000000578472 in applydefine (call=<value optimized out>, 
    op=0x1a3617a8, args=0x1ad47590, rho=0x1b2ea428)
    at ../../../R/src/include/Rinlinedfuns.h:153
#5  0x0000000000575a42 in Rf_eval (e=0x1ad47558, rho=0x1b2ea428)
    at ../../../R/src/main/eval.c:461
#6  0x0000000000576d50 in do_begin (call=0x1ad48450, op=0x1a362518, 
    args=0x1ad47520, rho=0x1b2ea428) at ../../../R/src/main/eval.c:1174
#7  0x0000000000575a42 in Rf_eval (e=0x1ad48450, rho=0x1b2ea428)
    at ../../../R/src/main/eval.c:461
#8  0x0000000000578f9c in Rf_applyClosure (call=0x1b2e9958, op=0x1ad48370, 
    arglist=0x1b2e9a70, rho=0x1b690298, suppliedenv=0x1b2e99c8)
    at ../../../R/src/main/eval.c:667
#9  0x00000000004285b9 in Rf_usemethod (generic=0x67e8d7 "[", 
    obj=<value optimized out>, call=<value optimized out>, 
    args=<value optimized out>, rho=0xffffffffffffffff,
callrho=0x1b690298,
    defrho=0x1a384f28, ans=0x7fffcaa8d5a8) at ../../../R/src/main/objects.c:311
#10 0x0000000000576a25 in Rf_DispatchOrEval (call=0x1a81d8d0, op=0x1a3622e8, 
    generic=0x67e8d7 "[", args=0x1a81d908, rho=0x1b690298,
ans=0x7fffcaa8d5a8,
    dropmissing=0, argsevald=0) at ../../../R/src/main/eval.c:1930
#11 0x00000000004afc40 in do_subset (call=0x7716, op=0x7716, 
    args=0xffffffffffffffff, rho=0x1b690298)
    at ../../../R/src/main/subset.c:577
#12 0x0000000000575a42 in Rf_eval (e=0x1a81d8d0, rho=0x1b690298)
    at ../../../R/src/main/eval.c:461
#13 0x00000000005780c7 in applydefine (call=0x1a81d748, op=0x1a3617a8, 
    args=0x6, rho=0xffffffffffffffff) at ../../../R/src/main/eval.c:1318
#14 0x0000000000575a42 in Rf_eval (e=0x1a81d748, rho=0x1b690298)
    at ../../../R/src/main/eval.c:461
#15 0x00000000005775de in do_for (call=0x1a81d668, op=0x1a360180, 
    args=0x1a81d6a0, rho=0x1b690298) at ../../../R/src/main/eval.c:1073

..... and more (downto #155 for R's main(...)

This is a bug,  probably in the C code of package nlme
which I guess corrupts memory somehere earlier, and we are
seeing the effect only later.
I'll leave this to the (memory-)debugging experts...

Martin

    VW> On my and one other computer, R usually crashes when calling the
gnls() function with this code three times in a row. I stumbled across this when
trying to fit this model with different starting values.

    VW> Version information:

    VW> platform       i386-pc-mingw32             
    ......
    VW> version.string R version 2.7.2 (2008-08-25)

    VW> Can anybody help figure out what causes this problem?

    VW> Best,

    VW> -- 
    VW> Wolfgang Viechtbauer 
    VW> ?Department of Methodology and Statistics 
    VW> ?University of Maastricht, The Netherlands 
    VW> ?http://www.wvbauer.com/ 

    VW> _______________________________________________
    VW> R-sig-mixed-models at r-project.org mailing list
    VW> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models

William Dunlap

2008-Sep-29 19:03 UTC

head link

[Rd] seg.fault from nlme::gnls() {was "[R-sig-ME] GNLS Crash"}

When I run this under valgrind with gctorture(TRUE) I see memory
misuse in mat_mult (matrix.c, line 82):
% R-2.8.0-dev --debugger=valgrind --debugger-args=--db-attach=yes
... copyright blah blah ...> data(Orange)
> gctorture(TRUE)
> gnls(circumference ~ Asym/(1 + exp(-(age-xmid)/scal)) ,+ data = Orange, correlation = corExp(form = ~1 | Tree),
+ start = c(Asym=150, xmid=750, scal=300))
r==5894== Invalid read of size 4
==5894==    at 0x580268F: mult_mat (matrix.c:82)
==5894==    by 0x57FF1B0: corStruct_recalc (corStruct.c:70)
==5894==    by 0x5801F89: gnls_objective (gnls.c:100)
==5894==    by 0x58020FE: fit_gnls (gnls.c:152)
==5894==    by 0x81439A2: do_dotCode (dotcode.c:1758)
==5894==    by 0x8161C56: Rf_eval (eval.c:487)
==5894==    by 0x81637D5: do_set (eval.c:1422)
==5894==    by 0x8161B3B: Rf_eval (eval.c:461)
==5894==    by 0x816384B: do_begin (eval.c:1174)
==5894==    by 0x8161B3B: Rf_eval (eval.c:461)
==5894==    by 0x816397B: do_repeat (eval.c:1137)
==5894==    by 0x8161B3B: Rf_eval (eval.c:461)
==5894==  Address 0x4E4A8CC is 12 bytes inside a block of size 864 free'd
==5894==    at 0x40052A3: free (vg_replace_malloc.c:233)
==5894==    by 0x805ACFD: R_gc_internal (memory.c:767)
==5894==    by 0x805B933: Rf_cons (memory.c:1755)
==5894==    by 0x805B98E: Rf_allocList (memory.c:2094)
==5894==    by 0x815AB4C: replaceCall (Rinlinedfuns.h:84)
==5894==    by 0x8163476: applydefine (eval.c:919)
==5894==    by 0x8161B3B: Rf_eval (eval.c:461)
==5894==    by 0x816384B: do_begin (eval.c:1174)
==5894==    by 0x8161B3B: Rf_eval (eval.c:461)
==5894==    by 0x8161B3B: Rf_eval (eval.c:461)
==5894==    by 0x816384B: do_begin (eval.c:1174)
==5894==    by 0x8161B3B: Rf_eval (eval.c:461)

My copy of valgrind doesn't get along with my copy of gdb,
so when it pops into gdb the debugger doesn't get any
information from *.so files.  I don't have the time now
to put printf statements into mat_mult.

Bill Dunlap
wdunlap tibco.com 

-----Original Message-----
From: r-devel-bounces at r-project.org [mailto:r-devel-bounces at r-project.org]
On Behalf Of Martin Maechler
Sent: Saturday, September 27, 2008 2:20 AM
To: Viechtbauer Wolfgang (STAT)
Cc: r-sig-mixed-models at r-project.org; R-devel at stat.math.ethz.ch
Subject: [Rd] seg.fault from nlme::gnls() {was "[R-sig-ME] GNLS
Crash"}
>>>>> "VW" == Viechtbauer Wolfgang (STAT)
<Wolfgang.Viechtbauer at STAT.unimaas.nl>
>>>>>     on Fri, 26 Sep 2008 18:00:19 +0200 writes:
    VW> Hi all, I'm trying to fit a marginal (longitudinal)
    VW> model with an exponential serial correlation function to
    VW> the Orange tree data set. However, R crashes frequently
    VW> when using the gnls() function. With the following
    VW> simple example, I was able to reproduce the problem.


    VW> gnls.exp <- gnls(circumference ~ Asym/(1 + exp(-(age-xmid)/scal))
,
    VW> data = Orange, correlation = corExp(form = ~1 | Tree),
    VW> start = c(Asym=150, xmid=750, scal=300))

Yes, I can reproduce it (on a Linux (RHEL 5) 64bit server), using R 2.8.0 alpha
: Use this

for(i in 1:20)# for MM: ca. 8 to 10 times --> seg.fault try( gnls.exp <-
gnls(circumference ~ Asym/(1 + exp(-(age-xmid)/scal)) ,
              data = Orange, correlation = corExp(form = ~1 | Tree),
              start = c(Asym=150, xmid=750, scal=300))
)

If I run it in the debugger and then do a backtrace I see

Error in gnls(circumference ~ Asym/(1 + exp(-(age - xmid)/scal)), data = Orange,
:
  Step halving factor reduced below minimum in NLS step

[............................................................]
[...................the same about 6 times...................]
[............................................................]

Error in gnls(circumference ~ Asym/(1 + exp(-(age - xmid)/scal)), data = Orange,
:
  Step halving factor reduced below minimum in NLS step Error in
.makeMessage(..., domain = domain) :
  incorrect number of arguments to "<-"
Error in .makeMessage(..., domain = domain) : 
  incorrect number of arguments to "<-"

Program received signal SIGABRT, Aborted.
0x0000003294e30155 in raise () from /lib64/libc.so.6
(gdb) bt
#0  0x0000003294e30155 in raise () from /lib64/libc.so.6
#1  0x0000003294e31bf0 in abort () from /lib64/libc.so.6
#2  0x00000000004184f5 in R_gc_internal (size_needed=0)
    at ../../../R/src/main/memory.c:761
#3  0x000000000041b121 in Rf_cons (car=0x1b2ec088, cdr=0x1a3436d8)
    at ../../../R/src/main/memory.c:1755
#4  0x0000000000578472 in applydefine (call=<value optimized out>, 
    op=0x1a3617a8, args=0x1ad47590, rho=0x1b2ea428)
    at ../../../R/src/include/Rinlinedfuns.h:153
#5  0x0000000000575a42 in Rf_eval (e=0x1ad47558, rho=0x1b2ea428)
    at ../../../R/src/main/eval.c:461
#6  0x0000000000576d50 in do_begin (call=0x1ad48450, op=0x1a362518, 
    args=0x1ad47520, rho=0x1b2ea428) at ../../../R/src/main/eval.c:1174
#7  0x0000000000575a42 in Rf_eval (e=0x1ad48450, rho=0x1b2ea428)
    at ../../../R/src/main/eval.c:461
#8  0x0000000000578f9c in Rf_applyClosure (call=0x1b2e9958, op=0x1ad48370, 
    arglist=0x1b2e9a70, rho=0x1b690298, suppliedenv=0x1b2e99c8)
    at ../../../R/src/main/eval.c:667
#9  0x00000000004285b9 in Rf_usemethod (generic=0x67e8d7 "[", 
    obj=<value optimized out>, call=<value optimized out>, 
    args=<value optimized out>, rho=0xffffffffffffffff,
callrho=0x1b690298,
    defrho=0x1a384f28, ans=0x7fffcaa8d5a8) at ../../../R/src/main/objects.c:311
#10 0x0000000000576a25 in Rf_DispatchOrEval (call=0x1a81d8d0, op=0x1a3622e8,
    generic=0x67e8d7 "[", args=0x1a81d908, rho=0x1b690298,
ans=0x7fffcaa8d5a8,
    dropmissing=0, argsevald=0) at ../../../R/src/main/eval.c:1930
#11 0x00000000004afc40 in do_subset (call=0x7716, op=0x7716, 
    args=0xffffffffffffffff, rho=0x1b690298)
    at ../../../R/src/main/subset.c:577
#12 0x0000000000575a42 in Rf_eval (e=0x1a81d8d0, rho=0x1b690298)
    at ../../../R/src/main/eval.c:461
#13 0x00000000005780c7 in applydefine (call=0x1a81d748, op=0x1a3617a8, 
    args=0x6, rho=0xffffffffffffffff) at ../../../R/src/main/eval.c:1318
#14 0x0000000000575a42 in Rf_eval (e=0x1a81d748, rho=0x1b690298)
    at ../../../R/src/main/eval.c:461
#15 0x00000000005775de in do_for (call=0x1a81d668, op=0x1a360180, 
    args=0x1a81d6a0, rho=0x1b690298) at ../../../R/src/main/eval.c:1073

..... and more (downto #155 for R's main(...)

This is a bug,  probably in the C code of package nlme which I guess corrupts
memory somehere earlier, and we are seeing the effect only later.
I'll leave this to the (memory-)debugging experts...

Martin

    VW> On my and one other computer, R usually crashes when calling the
gnls() function with this code three times in a row. I stumbled across this when
trying to fit this model with different starting values.

    VW> Version information:

    VW> platform       i386-pc-mingw32             
    ......
    VW> version.string R version 2.7.2 (2008-08-25)

    VW> Can anybody help figure out what causes this problem?

    VW> Best,

    VW> -- 
    VW> Wolfgang Viechtbauer 
    VW> ?Department of Methodology and Statistics 
    VW> ?University of Maastricht, The Netherlands 
    VW> ?http://www.wvbauer.com/ 

    VW> _______________________________________________
    VW> R-sig-mixed-models at r-project.org mailing list
    VW> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models

______________________________________________
R-devel at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel

Reasonably Related Threads

Search for more reasonably related threads

R devel - Sep 2008 - seg.fault from nlme::gnls() {was "[R-sig-ME] GNLS Crash"}

[Rd] seg.fault from nlme::gnls() {was "[R-sig-ME] GNLS Crash"}

[Rd] seg.fault from nlme::gnls() {was "[R-sig-ME] GNLS Crash"}

Reasonably Related Threads