[R] Spare some CPU cycles for testing lme?
Douglas Bates
bates at stat.wisc.edu
Mon Sep 13 17:03:24 CEST 2004
Marc Schwartz wrote:
> On Mon, 2004-09-13 at 07:40, Frank Samuelson wrote:
>
>>If anyone has a few extra CPU cycles to spare,
>>I'd appreciate it if you could verify a problem that I
>>have encountered. Run the code
>>below and tell me if it crashes your R before
>>completion.
>>
>>library(lme4)
>>data(bdf)
>>dump<-sapply( 1:50000, function(i) {
>> fm <- lme(langPOST ~ IQ.ver.cen + avg.IQ.ver.cen, data = bdf,
>> random = ~ IQ.ver.cen | schoolNR);
>> cat(" ",i,"\r")
>> 0
>>})
>>
>>The above code simply reruns the example from the
>>lme help page a large number of times and returns a bunch
>>of 0's, so you'll need to have the lme4 and Matrix
>>packages installed. It might take a while to complete,
>>but you can always nice it and let it run.
>>
>>I'm attempting to bootstrap lme() from the lme4 package,
>>but it causes a
>>segfault after a couple hundred iterations. This happens on
>>my Linux x86 RedHat 7.3, 8.0, 9.0, FC1 systems w/ 1.9.1
>>and devel 2.0.0 (not all possible combinations actually
>>tested.)
>>I've communicated w/ Douglas Bates about this and he
>>doesn't appear to have the problem.
>>
>>Thanks for any help.
>>
>>-Frank
>>
>
>
> Replicated here on FC 2 running:
>
> Version 1.9.1 Patched (2004-09-07)
>
> The backtrace from gdb follows. It would probably make sense to move
> this thread to r-devel. As you can see, it got through 10,546 runs
> before segfaulting.
>
> cc: to Doug.
>
> HTH,
>
> Marc Schwartz
>
>
>
>>dump<-sapply( 1:50000, function(i) {
>
> + fm <- lme(langPOST ~ IQ.ver.cen + avg.IQ.ver.cen, data = bdf,
> + random = ~ IQ.ver.cen | schoolNR);
> + cat(" ",i,"\r")
> + 0
> + })
> 10546
> Program received signal SIGSEGV, Segmentation fault.
> 0x00982242 in _int_free () from /lib/tls/libc.so.6
> (gdb) bt
> #0 0x00982242 in _int_free () from /lib/tls/libc.so.6
> #1 0x0098373b in free () from /lib/tls/libc.so.6
> #2 0x080c4003 in ReleaseLargeFreeVectors () at memory.c:695
> #3 0x080c5999 in RunGenCollect (size_needed=1144) at memory.c:1282
> #4 0x080c7084 in R_gc_internal (size_needed=1144) at memory.c:1933
> #5 0x080c6b67 in Rf_allocVector (type=16, length=2287) at memory.c:1788
> #6 0x0809b6b1 in Rf_duplicate (s=0xbed5d40) at duplicate.c:150
> #7 0x0809b335 in Rf_duplicate (s=0xb64a3bc) at duplicate.c:100
> #8 0x0809b517 in Rf_duplicate (s=0xbed15a8) at duplicate.c:142
> #9 0x0809b777 in Rf_duplicate (s=0xb3f6048) at duplicate.c:137
> #10 0x080a796d in EnsureLocal (symbol=0x9719f38, rho=0xb64c2b8) at
> eval.c:765
> #11 0x080a8691 in evalseq (expr=0x9719f38, rho=0xb64c2b8, forcelocal=1,
> tmploc=0xb64a340) at eval.c:1135
> #12 0x080a8847 in applydefine (call=0x97f9818, op=0x9705264,
> args=0x97f9834, rho=0xb64c2b8) at eval.c:1199
> #13 0x080a7055 in Rf_eval (e=0x97f9818, rho=0xb64c2b8) at eval.c:375
> #14 0x080a8436 in do_begin (call=0x97f97fc, op=0x9705168,
> args=0x97f97e0, rho=0xb64c2b8) at eval.c:1046
> #15 0x080a7055 in Rf_eval (e=0x97f97fc, rho=0xb64c2b8) at eval.c:375
> #16 0x080a7055 in Rf_eval (e=0x97f9bdc, rho=0xb64c2b8) at eval.c:375
> #17 0x080a8436 in do_begin (call=0x97f4ac8, op=0x9705168,
> args=0x97f9bc0, rho=0xb64c2b8) at eval.c:1046
> #18 0x080a7055 in Rf_eval (e=0x97f4ac8, rho=0xb64c2b8) at eval.c:375
> #19 0x080a7301 in Rf_applyClosure (call=0xb64c130, op=0x97f9a8c,
> arglist=0xb64c050, rho=0xb65989c,
> suppliedenv=0xb64c0f8) at eval.c:566
> #20 0x080cd2fb in applyMethod (call=0xb64c130, op=0x97f9a8c,
> args=0xb64c050, rho=0xb65989c, newrho=0xb64c0f8)
> at objects.c:119
> #21 0x080cd985 in Rf_usemethod (generic=0x81a1f2b "[", obj=0xb3ebbc0,
> call=0x9a668f0, args=0xb64c050,
> rho=0xb65989c, callrho=0xb65989c, defrho=0x96f6338, ans=0xfef58728)
> at objects.c:326
> #22 0x080a994d in Rf_DispatchOrEval (call=0x9a668f0, op=0x9705050,
> generic=0x81a1f2b "[", args=0xb64bffc,
> rho=0xb65989c, ans=0xfef58728, dropmissing=0, argsevald=1) at
> eval.c:1719
> #23 0x0811d5aa in do_subset (call=0x9a668f0, op=0x9705050,
> args=0x9a66944, rho=0xb65989c) at subset.c:504
> #24 0x080a7055 in Rf_eval (e=0x9a668f0, rho=0xb65989c) at eval.c:375
> #25 0x080a8bc3 in do_set (call=0x9a66880, op=0x9705264, args=0x9a668b8,
> rho=0xb65989c) at eval.c:1271
> #26 0x080a7055 in Rf_eval (e=0x9a66880, rho=0xb65989c) at eval.c:375
> ---Type <return> to continue, or q <return> to quit---
> #27 0x080a8436 in do_begin (call=0x9a67184, op=0x9705168,
> args=0x9a66864, rho=0xb65989c) at eval.c:1046
> #28 0x080a7055 in Rf_eval (e=0x9a67184, rho=0xb65989c) at eval.c:375
> #29 0x080a7055 in Rf_eval (e=0x9a66c44, rho=0xb65989c) at eval.c:375
> #30 0x080a8436 in do_begin (call=0x9a66b10, op=0x9705168,
> args=0x9a66c28, rho=0xb65989c) at eval.c:1046
> #31 0x080a7055 in Rf_eval (e=0x9a66b10, rho=0xb65989c) at eval.c:375
> #32 0x080a7301 in Rf_applyClosure (call=0xb659730, op=0x9a67900,
> arglist=0xb65a558, rho=0xb65966c,
> suppliedenv=0xb6596f8) at eval.c:566
> #33 0x080cd2fb in applyMethod (call=0xb659730, op=0x9a67900,
> args=0xb65a558, rho=0xb65966c, newrho=0xb6596f8)
> at objects.c:119
> #34 0x080cd985 in Rf_usemethod (generic=0x9b1f300 "model.matrix",
> obj=0xb415a64, call=0x9a6783c,
> args=0x96f6338, rho=0xb65966c, callrho=0xb415bb4, defrho=0xa038100,
> ans=0xfef59288) at objects.c:326
> #35 0x080cdd45 in do_usemethod (call=0x9a6783c, op=0x9713ca8,
> args=0x9a67874, env=0xb65966c) at objects.c:389
> #36 0x080a7055 in Rf_eval (e=0x9a6783c, rho=0xb65966c) at eval.c:375
> #37 0x080a7301 in Rf_applyClosure (call=0xa9e8b04, op=0x9a677cc,
> arglist=0xb65a558, rho=0xb415bb4,
> suppliedenv=0x96f6338) at eval.c:566
> #38 0x080a6e60 in Rf_eval (e=0xa9e8b04, rho=0xb415bb4) at eval.c:410
> #39 0x080a6d8b in Rf_eval (e=0xb65a328, rho=0xb65a408) at eval.c:354
> #40 0x080a6d8b in Rf_eval (e=0xb65a4b0, rho=0xb65a408) at eval.c:354
> #41 0x0806c791 in do_bind (call=0x9733fb8, op=0x9707e44, args=0xb65a4cc,
> env=0xb65a408) at bind.c:877
> #42 0x080cd029 in do_internal (call=0xa20, op=0x9706418, args=0x9733fd4,
> env=0xb65a408) at names.c:1057
> #43 0x080a7055 in Rf_eval (e=0x9733f2c, rho=0xb65a408) at eval.c:375
> #44 0x080a8436 in do_begin (call=0x9734060, op=0x9705168,
> args=0x9733f10, rho=0xb65a408) at eval.c:1046
> #45 0x080a7055 in Rf_eval (e=0x9734060, rho=0xb65a408) at eval.c:375
> #46 0x080a7301 in Rf_applyClosure (call=0xa9e8acc, op=0x9733e30,
> arglist=0xb65a344, rho=0xb415bb4,
> suppliedenv=0x96f6338) at eval.c:566
> #47 0x080a6e60 in Rf_eval (e=0xa9e8acc, rho=0xb415bb4) at eval.c:410
> #48 0x080a8d8a in Rf_evalList (el=0xa9e8ab0, rho=0xb415bb4) at
> eval.c:1360
> #49 0x080a6f7d in Rf_eval (e=0xa9e8a94, rho=0xb415bb4) at eval.c:396
> #50 0x080a8d8a in Rf_evalList (el=0xa9e8a78, rho=0xb415bb4) at
> eval.c:1360
> #51 0x080a97c0 in Rf_DispatchOrEval (call=0xa9e9868, op=0x9706788,
> generic=0x8181b21 "c", args=0xa9e9884,
> rho=0xb415bb4, ans=0xfef5a278, dropmissing=1, argsevald=0) at
> eval.c:1735
> ---Type <return> to continue, or q <return> to quit---
> #52 0x0806be69 in do_c (call=0xa9e9868, op=0x9706788, args=0xa9e9884,
> env=0xb415bb4) at bind.c:562
> #53 0x080a7055 in Rf_eval (e=0xa9e9868, rho=0xb415bb4) at eval.c:375
> #54 0x080a8bc3 in do_set (call=0xa9e9814, op=0x9705264, args=0xa9e9830,
> rho=0xb415bb4) at eval.c:1271
> #55 0x080a7055 in Rf_eval (e=0xa9e9814, rho=0xb415bb4) at eval.c:375
> #56 0x080a8436 in do_begin (call=0xa9e9d28, op=0x9705168,
> args=0xa9e97f8, rho=0xb415bb4) at eval.c:1046
> #57 0x080a7055 in Rf_eval (e=0xa9e9d28, rho=0xb415bb4) at eval.c:375
> #58 0x080a755d in R_execClosure (call=0xb4167f0, op=0xae393ac,
> arglist=0xb4162a4, rho=0xb631a38,
> newrho=0xb415bb4) at eval.c:651
> #59 0x080a7813 in R_execMethod (op=0xae393ac, rho=0xb41649c) at
> eval.c:753
> #60 0x00f86763 in R_standardGeneric (fname=0xacd6c40, ev=0xb41649c,
> fdef=0xb41657c)
> at methods_list_dispatch.c:610
> #61 0x080cf6dc in do_standardGeneric (call=0xacd89d8, op=0x9713c00,
> args=0xb41657c, env=0xb41649c)
> at objects.c:982
> #62 0x080a6fe3 in Rf_eval (e=0xacd89d8, rho=0xb41649c) at eval.c:398
> #63 0x080a7301 in Rf_applyClosure (call=0xb4167f0, op=0xaca9a34,
> arglist=0xb4162a4, rho=0xb631a38,
> suppliedenv=0x96f6338) at eval.c:566
> #64 0x080a6e60 in Rf_eval (e=0xb4167f0, rho=0xb631a38) at eval.c:410
> #65 0x080a948c in do_eval (call=0x98a581c, op=0x97100c8, args=0xb416138,
> rho=0xb4160e4) at eval.c:1541
> #66 0x080cd029 in do_internal (call=0x2f00, op=0x9706418,
> args=0xb416138, env=0xb4160e4) at names.c:1057
> #67 0x080a7055 in Rf_eval (e=0x98a5790, rho=0xb4160e4) at eval.c:375
> #68 0x080a7301 in Rf_applyClosure (call=0xa9ecfd8, op=0x98a6644,
> arglist=0xb41603c, rho=0xb4179c0,
> suppliedenv=0x96f6338) at eval.c:566
> #69 0x080a6e60 in Rf_eval (e=0xa9ecfd8, rho=0xb4179c0) at eval.c:410
> #70 0x080a8d8a in Rf_evalList (el=0xa9ecfbc, rho=0xb4179c0) at
> eval.c:1360
> #71 0x080a6f7d in Rf_eval (e=0xa9ecf84, rho=0xb4179c0) at eval.c:396
> #72 0x080a8436 in do_begin (call=0xa9ecd54, op=0x9705168,
> args=0xa9ecf68, rho=0xb4179c0) at eval.c:1046
> #73 0x080a7055 in Rf_eval (e=0xa9ecd54, rho=0xb4179c0) at eval.c:375
> #74 0x080a755d in R_execClosure (call=0xb41889c, op=0xae39770,
> arglist=0xb418094, rho=0xb631a38,
> newrho=0xb4179c0) at eval.c:651
> #75 0x080a7813 in R_execMethod (op=0xae39770, rho=0xb41828c) at
> eval.c:753
> #76 0x00f86763 in R_standardGeneric (fname=0xacd6c40, ev=0xb41828c,
> fdef=0xb418388)
> ---Type <return> to continue, or q <return> to quit---
> at methods_list_dispatch.c:610
> #77 0x080cf6dc in do_standardGeneric (call=0xacd89d8, op=0x9713c00,
> args=0xb418388, env=0xb41828c)
> at objects.c:982
> #78 0x080a6fe3 in Rf_eval (e=0xacd89d8, rho=0xb41828c) at eval.c:398
> #79 0x080a7301 in Rf_applyClosure (call=0xb41889c, op=0xaca9a34,
> arglist=0xb418094, rho=0xb631a38,
> suppliedenv=0x96f6338) at eval.c:566
> #80 0x080a6e60 in Rf_eval (e=0xb41889c, rho=0xb631a38) at eval.c:410
> #81 0x080a948c in do_eval (call=0x98a581c, op=0x97100c8, args=0xb417f28,
> rho=0xb418e68) at eval.c:1541
> #82 0x080cd029 in do_internal (call=0x2f00, op=0x9706418,
> args=0xb417f28, env=0xb418e68) at names.c:1057
> #83 0x080a7055 in Rf_eval (e=0x98a5790, rho=0xb418e68) at eval.c:375
> #84 0x080a7301 in Rf_applyClosure (call=0xa9dd984, op=0x98a6644,
> arglist=0xb418dc0, rho=0xb631498,
> suppliedenv=0x96f6338) at eval.c:566
> #85 0x080a6e60 in Rf_eval (e=0xa9dd984, rho=0xb631498) at eval.c:410
> #86 0x080a8d8a in Rf_evalList (el=0xa9dd968, rho=0xb631498) at
> eval.c:1360
> #87 0x080a6f7d in Rf_eval (e=0xa9dd930, rho=0xb631498) at eval.c:396
> #88 0x080a8436 in do_begin (call=0xa9de368, op=0x9705168,
> args=0xa9dd914, rho=0xb631498) at eval.c:1046
> #89 0x080a7055 in Rf_eval (e=0xa9de368, rho=0xb631498) at eval.c:375
> #90 0x080a755d in R_execClosure (call=0xafc54a0, op=0xae3994c,
> arglist=0xb631a8c, rho=0xb631a38,
> newrho=0xb631498) at eval.c:651
> #91 0x080a7813 in R_execMethod (op=0xae3994c, rho=0xb631c84) at
> eval.c:753
> #92 0x00f86763 in R_standardGeneric (fname=0xacd6c40, ev=0xb631c84,
> fdef=0xb630dd0)
> at methods_list_dispatch.c:610
> #93 0x080cf6dc in do_standardGeneric (call=0xacd89d8, op=0x9713c00,
> args=0xb630dd0, env=0xb631c84)
> at objects.c:982
> #94 0x080a6fe3 in Rf_eval (e=0xacd89d8, rho=0xb631c84) at eval.c:398
> #95 0x080a7301 in Rf_applyClosure (call=0xafc54a0, op=0xaca9a34,
> arglist=0xb631a8c, rho=0xb631a38,
> suppliedenv=0x96f6338) at eval.c:566
> #96 0x080a6e60 in Rf_eval (e=0xafc54a0, rho=0xb631a38) at eval.c:410
> #97 0x080a8bc3 in do_set (call=0xafc54f4, op=0x9705264, args=0xafc54d8,
> rho=0xb631a38) at eval.c:1271
> #98 0x080a7055 in Rf_eval (e=0xafc54f4, rho=0xb631a38) at eval.c:375
> #99 0x080a8436 in do_begin (call=0xafc5510, op=0x9705168,
> args=0xafc552c, rho=0xb631a38) at eval.c:1046
> ---Type <return> to continue, or q <return> to quit---
> #100 0x080a7055 in Rf_eval (e=0xafc5510, rho=0xb631a38) at eval.c:375
> #101 0x080a7301 in Rf_applyClosure (call=0xafc5280, op=0xafc5a50,
> arglist=0xb631a00, rho=0xafc4c28,
> suppliedenv=0x96f6338) at eval.c:566
> #102 0x080a6e60 in Rf_eval (e=0xafc5280, rho=0xafc4c28) at eval.c:410
> #103 0x0805f297 in do_lapply (call=0x990c12c, op=0x9711180, args=0x2933,
> rho=0xafc4c28) at apply.c:60
> #104 0x080cd029 in do_internal (call=0x3480, op=0x9706418,
> args=0x990c19c, env=0xafc4c28) at names.c:1057
> #105 0x080a7055 in Rf_eval (e=0x990c0a0, rho=0xafc4c28) at eval.c:375
> #106 0x080a8bc3 in do_set (call=0x990c04c, op=0x9705264, args=0x990c068,
> rho=0xafc4c28) at eval.c:1271
> #107 0x080a7055 in Rf_eval (e=0x990c04c, rho=0xafc4c28) at eval.c:375
> #108 0x080a8436 in do_begin (call=0x990c43c, op=0x9705168,
> args=0x990c030, rho=0xafc4c28) at eval.c:1046
> #109 0x080a7055 in Rf_eval (e=0x990c43c, rho=0xafc4c28) at eval.c:375
> #110 0x080a7301 in Rf_applyClosure (call=0x99f649c, op=0x990ccb4,
> arglist=0xafc4b80, rho=0xafc591c,
> suppliedenv=0x96f6338) at eval.c:566
> #111 0x080a6e60 in Rf_eval (e=0x99f649c, rho=0xafc591c) at eval.c:410
> #112 0x080a8bc3 in do_set (call=0x99f6448, op=0x9705264, args=0x99f6464,
> rho=0xafc591c) at eval.c:1271
> #113 0x080a7055 in Rf_eval (e=0x99f6448, rho=0xafc591c) at eval.c:375
> #114 0x080a8436 in do_begin (call=0x99f56e4, op=0x9705168,
> args=0x99f642c, rho=0xafc591c) at eval.c:1046
> #115 0x080a7055 in Rf_eval (e=0x99f56e4, rho=0xafc591c) at eval.c:375
> #116 0x080a7301 in Rf_applyClosure (call=0xafc5778, op=0x99f6e1c,
> arglist=0xafc583c, rho=0x9716e0c,
> suppliedenv=0x96f6338) at eval.c:566
> #117 0x080a6e60 in Rf_eval (e=0xafc5778, rho=0x9716e0c) at eval.c:410
> #118 0x080a8bc3 in do_set (call=0xafc57cc, op=0x9705264, args=0xafc57b0,
> rho=0x9716e0c) at eval.c:1271
> #119 0x080a7055 in Rf_eval (e=0xafc57cc, rho=0x9716e0c) at eval.c:375
> #120 0x080c1ba7 in Rf_ReplIteration (rho=0x9716e0c,
> savestack=-1070969512, browselevel=0, state=0xfef5dd40)
> at main.c:250
> #121 0x080c1d4f in R_ReplConsole (rho=0x9716e0c, savestack=0,
> browselevel=0) at main.c:298
> #122 0x080c25d3 in run_Rmainloop () at main.c:656
> #123 0x0812478c in main (ac=1, av=0xfef5e254) at system.c:99
>
> end of backtrace.
>
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As Frank said, I have been unable to get this example to segfault on a
Debian system. It definitely looks like memory problems so I would
suggest running it with gctorture set. However, you should use a
machine that you won't need for several days :-)
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