R devel - Aug 2009 - Bug in nlm, found using sem; failure in several flavors (PR#13882)

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
tools.
>
> --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
discovered
> when trying to run an SEM. =A0The SEM is not bizarre; the covariance matrix
is
> solve-able and the eigenvalues are greater than zero, and I do not believe
> 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
apologize if
> I have put too many much information in this message; I'm not a
programmer
> 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, start,
> :
> =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,
var.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 ungracefully,
> 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
-2.118179e-03
> [11] =A02.942936e-03 -1.335936e-03 -3.665618e-03 =A03.090566e-03
=A08.534956e-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
=A02.216899e-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 -0.70465116
=A00.85251098
> [13] -0.18346956 =A00.66857787 =A00.57012481 =A00.39116561 =A00.91237990
=A00.63951482
> [19] =A00.26601566 =A00.29240836 =A00.44710919 =A00.94734056 =A06.52039015
=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
-4.283329e+00
> =A0[6] -1.437250e+00 -6.558913e-01 =A01.358276e+00 =A07.930865e+05
-1.293853e+06
> [11] -5.816627e+03 =A05.908197e+05 -2.705742e+08 -1.194400e+07
-4.007083e+07
> [16] -4.143068e+07 -6.159782e-01 =A01.044274e-01 -8.591048e+00
-2.083471e+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
-2.234989e+04
>
> Abort trap
> swiss:data$
>
> ...I have also seen convergence reached, and nlm then die with this
message:
>
> 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
fail
> 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 =A0methods
=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
stage.
> I compiled using this config string, at first...
>
> ./configure --prefix=3D/usr/local --with-x --disable-R-framework
--enable-threads=3Dposix --with-blas=3D"/usr/local/lib/libptf77blas.a
/usr/local/lib/libptcblas.a /usr/local/lib/libatlas.a -lpthread"
--with-lapack=3D"/usr/local/lib/liblapack.a /usr/local/lib/libptf77blas.a
/usr/local/lib/libptcblas.a /usr/local/lib/libatlas.a -lpthread"
--without-aqua CFLAGS=3D"-O3 -mtune=3Dnocona -m32"
CXXFLAGS=3D"-O3 -mtune=3Dnocona -m32" FFLAGS=3D"-O3
-mtune=3Dnocona -m32 -L/usr/lib/gcc/i686-apple-darwin9/4.2.1 -l gfortran"
F77FLAGS=3D"-O3 -mtune=3Dnocona -m32
-L/usr/lib/gcc/i686-apple-darwin9/4.2.1 -l gfortran" FCFLAGS=3D"-O3
-mtune=3Dnocona -m32 -L/usr/lib/gcc/i686-apple-darwin9/4.2.1 -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=3Dgcc-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
'type2char'"
> and "cannot coerce type 'weakref' to vector of type
'double'". =A0Running with
> debug=3DTRUE also segfaults sometimes, even after achieving "Current
iterate
> 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_MONETARY=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 =A0methods
=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.UTF-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 =A0methods
=A0 base
>
> other attached packages:
> [1] sem_0.9-17
>>
>
> ...for this system, the model simply repeatedly fails to converge, whether
> 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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>
> --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