[Rd] Bug in nlm, found using sem; failure in several flavors (PR#13883)

Sat Aug 8 00:35:14 CEST 2009

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  while the remaining parts are likely unreadable without MIME-aware tools.

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Hi Jeff,

 =09As mentioned in my message, I *did* replicate on another platform.=20
One platform was running linux in a VM, the other running MacOSX, on two
different physical machines.  The problem did not replicate on a PowerPC
box, so if it is a bug with intel chips, I think it's also appropriate to
report here given that the problem seems to cross the OS boundary.  I do no=
t
have access to a Windows machine.

 =09Also, I have spent a decent amount of time running memory testers on
the first machine's memory, to ensure that physical memory is not a
problem...the classic "memcheck" program finds no trouble.

 =09The CSV and .ram files both came through as base-64-encoded
attachments, which you actually quoted back to me in your response,
below...but in case your mail client can't read those and/or you are
interested in this bug, I have pasted them at the end of this message (sinc=
e
they're quite small).

 =09And thanks for the shout-out for bacon. I bought this domain name in
undergrad many years ago, and I must say, I've never regretted it!

--Adam

On Fri, 7 Aug 2009, Jeff Ryan wrote:

> Adam,
>
> It seems that your attachment didn't make it through.
>
> That aside, my experience with strange errors like those (random type
> not implemented ones) has been that you may be looking at a memory
> problem on you machine. Given that you can't replicate on another
> platform (and the .csv file didn't come through), I would think it
> wise to start there.
>
> My 2c.  And I love bacon too :)
>
> Jeff
>
> On Fri, Aug 7, 2009 at 1:10 PM, <adik at ilovebacon.org> wrote:
>> =A0This message is in MIME format. =A0The first part should be readable =
text,
>> =A0while the remaining parts are likely unreadable without MIME-aware to=
ols.
>>
>> --1660387551-1458482416-1249639718=3D:2997
>> Content-Type: TEXT/PLAIN; CHARSET=3DUS-ASCII; FORMAT=3Dflowed
>> Content-ID: <Pine.LNX.4.64.0908071039211.2997 at parser.ilovebacon.org>
>>
>> Hello,
>>
>> =A0 =A0 =A0 =A0There appears to be a bug in the nlm function, which I di=
scovered
>> when trying to run an SEM. =A0The SEM is not bizarre; the covariance mat=
rix is
>> solve-able and the eigenvalues are greater than zero, and I do not belie=
ve
>> the "sem" package per se to be the problem (as nlm keeps being the part =
that
>> fails, though I can't replicate this with other nlm tasks). =A0I apologi=
ze if
>> I have put too many much information in this message; I'm not a programm=
er
>> by trade so I don't really know what's going on here, which hampers my
>> ability to write consise bug reports.
>>
>> Here is the code I use:
>>
>> library(sem)
>> ice.S <- read.csv("iceS.csv") # attached
>> rownames(ice.S) <- ice.S[,1]
>> ice.S[,1] <- NULL
>> ice.S <- as.matrix(ice.S)
>> ice.ram <- specify.model("ice.ram") # attached
>> ice.N <- 342
>> ice.sem <- sem(ram=3Dice.ram, S=3Dice.S, N=3Dice.N)
>>
>> ...at this point, any number of problems could occur. I have seen the
>> following.
>>
>> 1) Simple lack of convergence. (might be my model's fault.)
>> 2) Error in nlm(if (analytic.gradient) objective.2 else objective.1, sta=
rt,
>> :
>> =A0 type 31 is unimplemented in 'type2char'
>> 3) =A0*** caught segfault ***
>> address 0xc019c87b, cause 'memory not mapped'
>>
>> Traceback:
>> =A01: nlm(if (analytic.gradient) objective.2 else objective.1, start,
>> hessian =3D TRUE, iterlim =3D maxiter, print.level =3D if (debug) 2 else=
 0,
>> typsize =3D typsize, ...)
>> =A02: sem.default(ram =3D ram, S =3D S, N =3D N, param.names =3D pars, v=
ar.names =3D
>> vars, =A0 =A0 fixed.x =3D fixed.x, debug =3D debug, ...)
>> =A03: sem(ram =3D ram, S =3D S, N =3D N, param.names =3D pars, var.names=
 =3D vars,
>> fixed.x =3D fixed.x, debug =3D debug, ...)
>> =A04: sem.mod(ram =3D ice.ram, S =3D ice.S, N =3D ice.N)
>> =A05: sem(ram =3D ice.ram, S =3D ice.S, N =3D ice.N)
>>
>> 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: 1
>> aborting ...
>> Segmentation fault
>> swiss:data$
>>
>> (no core was dumped).
>>
>> Trying with debug mode provides other interesting errors:
>>
>>> ice.sem <- sem(ram=3Dice.ram, S=3Dice.S, N=3Dice.N, debug=3DTRUE)
>>
>> ...gets up to some iteration (not always 15), and then R dies ungraceful=
ly,
>> and exits to the shell:
>>
>> iteration =3D 15
>> Step:
>> =A0[1] =A01.253132e-02 =A01.183343e-02 -7.651342e-03 -2.490800e-03 =A02.=
278938e-03
>> =A0[6] =A03.197431e-04 =A06.137849e-04 -2.496882e-03 -1.065829e-03 -2.11=
8179e-03
>> [11] =A02.942936e-03 -1.335936e-03 -3.665618e-03 =A03.090566e-03 =A08.53=
4956e-04
>> [16] -1.440421e-03 -5.230877e-04 -1.053686e-04 -9.771005e-04 -4.269216e-=
04
>> [21] =A07.261694e-05 -1.039668e-03 -8.409151e-03 -3.497456e-03 =A02.2168=
99e-03
>> [26] -4.633520e-03 -4.052130e-03 -4.746537e-03 -1.589622e-03 -2.523766e-=
04
>> Parameter:
>> =A0[1] -0.76604614 -1.19639662 =A00.83456888 =A00.72540413 =A00.08482452=
 =A00.56180393
>> =A0[7] =A00.50615814 =A00.55728015 =A00.83796696 =A00.88371335 -0.704651=
16 =A00.85251098
>> [13] -0.18346956 =A00.66857787 =A00.57012481 =A00.39116561 =A00.91237990=
 =A00.63951482
>> [19] =A00.26601566 =A00.29240836 =A00.44710919 =A00.94734056 =A06.520390=
15 =A00.02524762
>> [25] -0.01614603 =A02.88198219 =A00.03442452 =A03.52272237 =A01.44698423=
 -0.72964745
>> Function Value
>> [1] -15175.94
>> Gradient:
>> =A0[1] -2.085412e+07 -3.819717e+07 =A03.883989e+07 =A01.352594e+00 -4.28=
3329e+00
>> =A0[6] -1.437250e+00 -6.558913e-01 =A01.358276e+00 =A07.930865e+05 -1.29=
3853e+06
>> [11] -5.816627e+03 =A05.908197e+05 -2.705742e+08 -1.194400e+07 -4.007083=
e+07
>> [16] -4.143068e+07 -6.159782e-01 =A01.044274e-01 -8.591048e+00 -2.083471=
e+00
>> [21] -7.548753e-01 -5.418994e-01 -2.799228e+02 -1.321739e+07 -3.517728e+=
07
>> [26] -7.106654e+02 -7.335293e+06 -7.335285e+05 =A03.117764e-01 -2.234989=
e+04
>>
>> Abort trap
>> swiss:data$
>>
>> ...I have also seen convergence reached, and nlm then die with this mess=
age:
>>
>> Error in nlm(if (analytic.gradient) objective.2 else objective.1, start,
>> :
>> =A0 type 27 is unimplemented in 'type2char'
>>
>> (similar to above, but now referring to type 27)
>>
>> I have shown this effect (or something similar...never know how it'll fa=
il
>> next) on the following platforms:
>>
>>> version
>> =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0_
>> platform =A0 =A0 =A0 i386-apple-darwin9.7.0
>> arch =A0 =A0 =A0 =A0 =A0 i386
>> os =A0 =A0 =A0 =A0 =A0 =A0 darwin9.7.0
>> system =A0 =A0 =A0 =A0 i386, darwin9.7.0
>> status
>> major =A0 =A0 =A0 =A0 =A02
>> minor =A0 =A0 =A0 =A0 =A09.1
>> year =A0 =A0 =A0 =A0 =A0 2009
>> month =A0 =A0 =A0 =A0 =A006
>> day =A0 =A0 =A0 =A0 =A0 =A026
>> svn rev =A0 =A0 =A0 =A048839
>> language =A0 =A0 =A0 R
>> version.string R version 2.9.1 (2009-06-26)
>>
>>> sessionInfo()
>> R version 2.9.1 (2009-06-26)
>> i386-apple-darwin9.8.0
>>
>> locale:
>> en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>>
>> attached base packages:
>> [1] stats =A0 =A0 graphics =A0grDevices utils =A0 =A0 datasets =A0method=
s =A0 base
>>
>> other attached packages:
>> [1] sem_0.9-17
>>
>> loaded via a namespace (and not attached):
>> [1] tcltk_2.9.1 tools_2.9.1
>>
>> (I admit to having compiled this version of R myself (to link to a
>> hand-compiled ATLAS), though no errors were thrown in the compilation st=
age.
>> I compiled using this config string, at first...
>>
>> ./configure --prefix=3D/usr/local --with-x --disable-R-framework --enabl=
e-threads=3Dposix --with-blas=3D"/usr/local/lib/libptf77blas.a /usr/local/l=
ib/libptcblas.a /usr/local/lib/libatlas.a -lpthread" --with-lapack=3D"/usr/=
local/lib/liblapack.a /usr/local/lib/libptf77blas.a /usr/local/lib/libptcbl=
as.a /usr/local/lib/libatlas.a -lpthread" --without-aqua CFLAGS=3D"-O3 -mtu=
ne=3Dnocona -m32" CXXFLAGS=3D"-O3 -mtune=3Dnocona -m32" FFLAGS=3D"-O3 -mtun=
e=3Dnocona -m32 -L/usr/lib/gcc/i686-apple-darwin9/4.2.1 -l gfortran" F77FLA=
GS=3D"-O3 -mtune=3Dnocona -m32 -L/usr/lib/gcc/i686-apple-darwin9/4.2.1 -l g=
fortran" FCFLAGS=3D"-O3 -mtune=3Dnocona -m32 -L/usr/lib/gcc/i686-apple-darw=
in9/4.2.1 -l gfortran" LDFLAGS=3D"-m32 -L/sw/lib" CPPFLAGS=3D"-I/sw/include=
" CC=3Dgcc-4.2 F77=3Dgfortran-4.2 FC=3Dgfortran-4.2 CXX=3Dg++-4.2 OBJC=3Dgc=
c-4.2
>>
>> ...though I have also recompiled using simply this:
>>
>> ./configure --prefix=3D/usr/local --with-x --disable-R-framework
>>
>> ...and then re-installed SEM, and I got a few other, different error
>> messages and core dumps, "including type 11 is unimplemented in 'type2ch=
ar'"
>> and "cannot coerce type 'weakref' to vector of type 'double'". =A0Runnin=
g with
>> debug=3DTRUE also segfaults sometimes, even after achieving "Current ite=
rate
>> is probably solution" status.)
>>
>>> version
>> =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0_
>> platform =A0 =A0 =A0 x86_64-unknown-linux-gnu
>> arch =A0 =A0 =A0 =A0 =A0 x86_64
>> os =A0 =A0 =A0 =A0 =A0 =A0 linux-gnu
>> system =A0 =A0 =A0 =A0 x86_64, linux-gnu
>> status
>> major =A0 =A0 =A0 =A0 =A02
>> minor =A0 =A0 =A0 =A0 =A09.1
>> year =A0 =A0 =A0 =A0 =A0 2009
>> month =A0 =A0 =A0 =A0 =A006
>> day =A0 =A0 =A0 =A0 =A0 =A026
>> svn rev =A0 =A0 =A0 =A048839
>> language =A0 =A0 =A0 R
>> version.string R version 2.9.1 (2009-06-26)
>>
>>> sessionInfo()
>> R version 2.9.1 (2009-06-26)
>> x86_64-unknown-linux-gnu
>>
>> locale:
>> LC_CTYPE=3Den_US;LC_NUMERIC=3DC;LC_TIME=3Den_US;LC_COLLATE=3Den_US;LC_MO=
NETARY=3DC;LC_MESSAGES=3Den_US;LC_PAPER=3Den_US;LC_NAME=3DC;LC_ADDRESS=3DC;=
LC_TELEPHONE=3DC;LC_MEASUREMENT=3Den_US;LC_IDENTIFICATION=3DC
>>
>> attached base packages:
>> [1] stats =A0 =A0 graphics =A0grDevices utils =A0 =A0 datasets =A0method=
s =A0 base
>>
>> other attached packages:
>> [1] sem_0.9-17
>>
>> ...however, THIS platform does NOT show the bug:
>>
>>> version
>> =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0_
>> platform =A0 =A0 =A0 powerpc-unknown-linux-gnu
>> arch =A0 =A0 =A0 =A0 =A0 powerpc
>> os =A0 =A0 =A0 =A0 =A0 =A0 linux-gnu
>> system =A0 =A0 =A0 =A0 powerpc, linux-gnu
>> status
>> major =A0 =A0 =A0 =A0 =A02
>> minor =A0 =A0 =A0 =A0 =A09.1
>> year =A0 =A0 =A0 =A0 =A0 2009
>> month =A0 =A0 =A0 =A0 =A006
>> day =A0 =A0 =A0 =A0 =A0 =A026
>> svn rev =A0 =A0 =A0 =A048839
>> language =A0 =A0 =A0 R
>> version.string R version 2.9.1 (2009-06-26)
>>> sessionInfo()
>> R version 2.9.1 (2009-06-26)
>> powerpc-unknown-linux-gnu
>>
>> locale:
>> LC_CTYPE=3Den_US.UTF-8;LC_NUMERIC=3DC;LC_TIME=3Den_US.UTF-8;LC_COLLATE=
=3Den_US.UTF-8;LC_MONETARY=3DC;LC_MESSAGES=3Den_US.UTF-8;LC_PAPER=3Den_US.U=
TF-8;LC_NAME=3DC;LC_ADDRESS=3DC;LC_TELEPHONE=3DC;LC_MEASUREMENT=3Den_US.UTF=
-8;LC_IDENTIFICATION=3DC
>>
>> attached base packages:
>> [1] stats =A0 =A0 graphics =A0grDevices utils =A0 =A0 datasets =A0method=
s =A0 base
>>
>> other attached packages:
>> [1] sem_0.9-17
>>>
>>
>> ...for this system, the model simply repeatedly fails to converge, wheth=
er
>> debug is set or not.
>>
>> I have also tried altering my model. This has resulted in the same bugs,=
 but
>> instead of "every so often simply not converging," it actually converges=
 and
>> appears to be the model I asked R to solve...but this is rare.
>>
>> Please let me know if I can provide any other info.
>>
>> Cordially,
>> Adam D. I. Kramer
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>> MzkxMjQ1NTE2Mjk1NTksMC4yNTgwMzIzMjI4MjQ1OTksMC4xNjU1MzMyMDg3
>> NDM1NDcsMC4yNTYyNzQxOTU5ODMwMDQsLTAuMjIxOTE3MjIyOTMwMTksMC45
>> Mzc2MDc1MzMxODY1NzYsMC4zMTI2NjQxOTk2MzE2MjANCiJkZXNpcmVkIiwt
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>> MTY0LC0wLjIzOTEyNjk3MTQ4MDYyNSwwLjE0Nzg4NDM1MjU4ODQ5OSwtMC4y
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>> MDQzMzUsMC4xOTE0MjExMzQxODk2ODIsMC4zNDY0NDE0MTExMTYxNDcsLTAu
>> MjMxMDMyMDE0OTI3Mzk3LDAuMzEyNjY0MTk5NjMxNjIwLDAuOTYzMTMxNjM5
>> NTYwMTA4DQo=3D
>>
>> --1660387551-1458482416-1249639718=3D:2997--
>>
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>
>
>
> --=20
> Jeffrey Ryan
> jeffrey.ryan at insightalgo.com
>
> ia: insight algorithmics
> www.insightalgo.com
>

CSV:

"","wasrightchoice","tellgood","tellbest","important","complex","difficult"=
,"onlyself","manydimensions","howmuchinfo","equalinfo","couldavoid","posout=
come","negoutcome","control","desired"
"wasrightchoice",0.96369773178963,0.292736321229647,0.289852808489117,0.385=
266965362761,0.197644824696320,0.183041324062298,-0.146626347219879,0.14635=
4027797101,-0.132887596902506,-0.173965069111025,-0.268459162930567,-0.0678=
095375076222,0.180549925024377,-0.0420844364037874,-0.0730577896902967
"tellgood",0.292736321229647,0.955494246210856,0.757544193339566,0.19124118=
3203129,0.000174630417564688,0.00340887118071287,0.00963050474358034,0.0283=
894373316684,0.0188027539463299,-0.0157026381515985,-0.145795006741884,0.14=
2034396906879,0.00981538398434851,0.0705868756539732,0.108000449328313
"tellbest",0.289852808489117,0.757544193339566,0.948593590912408,0.23059895=
8597528,0.0302692106135439,0.0155447055783122,0.0321693281988669,0.06463123=
26187096,0.0102945085651246,-0.0196759997923009,-0.178765563354828,0.151343=
567761859,-0.0336559063307835,0.0929062279334898,0.159735618423335
"important",0.385266965362761,0.191241183203129,0.230598958597528,0.9644978=
8034361,0.647657141488375,0.514175974554114,-0.197506705917123,0.4747233324=
69875,-0.129091329816201,-0.189229123705341,-0.462195839265035,0.1241583395=
27322,0.160661307486559,-0.0864573727466265,-0.0683674842498801
"complex",0.197644824696320,0.000174630417564688,0.0302692106135439,0.64765=
7141488375,0.976321655762968,0.754978777309553,-0.262340425824052,0.6567175=
33361176,-0.160427139673018,-0.236210856083902,-0.385452100046623,0.0238775=
728277157,0.324525653164508,-0.240634804887055,-0.233696554189164
"difficult",0.183041324062298,0.00340887118071287,0.0155447055783122,0.5141=
75974554114,0.754978777309553,0.957324341661972,-0.183005587551624,0.523183=
993897632,-0.197833354430907,-0.228434713061776,-0.263587746021174,-0.04539=
71377700845,0.330075666526761,-0.234707517677586,-0.239126971480625
"onlyself",-0.146626347219879,0.00963050474358034,0.0321693281988669,-0.197=
506705917123,-0.262340425824052,-0.183005587551624,0.947852415443663,-0.268=
333979295612,0.0787191879215654,0.0800554430938036,0.163595277498758,-0.005=
07268608417704,-0.160137545871448,0.211257252287979,0.147884352588499
"manydimensions",0.146354027797101,0.0283894373316684,0.0646312326187096,0.=
474723332469875,0.656717533361176,0.523183993897632,-0.268333979295612,0.94=
991766261616,-0.113295667408177,-0.181576473170784,-0.279298417177261,0.044=
2481235082528,0.258349702460663,-0.196993346337214,-0.222533952633482
"howmuchinfo",-0.132887596902506,0.0188027539463299,0.0102945085651246,-0.1=
29091329816201,-0.160427139673018,-0.197833354430907,0.0787191879215654,-0.=
113295667408177,0.946722746137415,0.706976015582218,0.0923192704439934,0.21=
3032242473315,-0.209882431765110,0.239124551629559,0.219078352890657
"equalinfo",-0.173965069111025,-0.0157026381515985,-0.0196759997923009,-0.1=
89229123705341,-0.236210856083902,-0.228434713061776,0.0800554430938036,-0.=
181576473170784,0.706976015582218,0.964517562778328,0.180517325752387,0.163=
844640495983,-0.213804550043239,0.258032322824599,0.191820447404335
"couldavoid",-0.268459162930567,-0.145795006741884,-0.178765563354828,-0.46=
2195839265035,-0.385452100046623,-0.263587746021174,0.163595277498758,-0.27=
9298417177261,0.0923192704439934,0.180517325752387,0.963237309730726,-0.120=
130196392406,-0.0689659657057091,0.165533208743547,0.191421134189682
"posoutcome",-0.0678095375076222,0.142034396906879,0.151343567761859,0.1241=
58339527322,0.0238775728277157,-0.0453971377700845,-0.00507268608417704,0.0=
442481235082528,0.213032242473315,0.163844640495983,-0.120130196392406,0.93=
9107717186385,-0.291262391827671,0.256274195983004,0.346441411116147
"negoutcome",0.180549925024377,0.00981538398434851,-0.0336559063307835,0.16=
0661307486559,0.324525653164508,0.330075666526761,-0.160137545871448,0.2583=
49702460663,-0.209882431765110,-0.213804550043239,-0.0689659657057091,-0.29=
1262391827671,0.952552965796421,-0.22191722293019,-0.231032014927397
"control",-0.0420844364037874,0.0705868756539732,0.0929062279334898,-0.0864=
573727466265,-0.240634804887055,-0.234707517677586,0.211257252287979,-0.196=
993346337214,0.239124551629559,0.258032322824599,0.165533208743547,0.256274=
195983004,-0.22191722293019,0.937607533186576,0.312664199631620
"desired",-0.0730577896902967,0.108000449328313,0.159735618423335,-0.068367=
4842498801,-0.233696554189164,-0.239126971480625,0.147884352588499,-0.22253=
3952633482,0.219078352890657,0.191820447404335,0.191421134189682,0.34644141=
1116147,-0.231032014927397,0.312664199631620,0.963131639560108

RAM:

important <-- challenge, NA, 1
complex  <-- challenge, c.complex, NA
difficult <-- challenge, c.difficult, NA
manydimensions <-- challenge, c.manydimensions, NA
couldavoid <-- challenge, c.couldavoid, NA
onlyself <-- challenge, c.onlyself, NA

wasrightchoice <-- eval, NA, 1
tellgood <-- eval, e.tellgood, NA
tellbest <-- eval, e.tellbest, NA
negoutcome <-- eval, e.negoutcome, NA

equalinfo <-- informed, NA, 1
control <-- informed, i.control, NA
desired <-- informed, i.desired, NA
howmuchinfo <-- informed, i.howmuchinfo, NA
posoutcome <-- informed, i.posoutcome, NA

wasrightchoice <-> wasrightchoice, wasrightchoiceV, NA
tellgood <-> tellgood, tellgoodV, NA
tellbest <-> tellbest, tellbestV, NA
negoutcome <-> negoutcome, negoutcomeV, NA

onlyself <-> onlyself, onlyselfV, NA
important <-> important, importantV, NA
complex <-> complex, complexV, NA
difficult <-> difficult, difficultV, NA
manydimensions <-> manydimensions, manydimensionsV, NA
couldavoid <-> couldavoid, couldavoidV, NA

equalinfo <-> equalinfo, equalinfoV, NA
control <-> control, controlV, NA
desired <-> desired, desiredV, NA
howmuchinfo <-> howmuchinfo, howmuchinfoV, NA
posoutcome <-> posoutcome, posoutcomeV, NA

eval <-> eval, evalV, NA
challenge <-> challenge, challengeV, NA
informed <-> informed, informedV, NA
--1660387551-150661043-1249684349=:2997--