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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