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 t=
ext,
=A0while the remaining parts are likely unreadable without MIME-aware too=
ls.
--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 dis=
covered
when trying to run an SEM. =A0The SEM is not bizarre; the covariance matr=
ix is
solve-able and the eigenvalues are greater than zero, and I do not believ=
e
the "sem" package per se to be the problem (as nlm keeps being the part t=
hat
fails, though I can't replicate this with other nlm tasks). =A0I apologiz=
e if
I have put too many much information in this message; I'm not a programme=
r
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, star=
t,
: =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, va=
r.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 ungracefull=
y,
and exits to the shell: iteration =3D 15 Step: =A0[1] =A01.253132e-02 =A01.183343e-02 -7.651342e-03 -2.490800e-03 =A02.2=
78938e-03
=A0[6] =A03.197431e-04 =A06.137849e-04 -2.496882e-03 -1.065829e-03 -2.118=
179e-03
[11] =A02.942936e-03 -1.335936e-03 -3.665618e-03 =A03.090566e-03 =A08.534=
956e-04
[16] -1.440421e-03 -5.230877e-04 -1.053686e-04 -9.771005e-04 -4.269216e-0=
4
[21] =A07.261694e-05 -1.039668e-03 -8.409151e-03 -3.497456e-03 =A02.21689=
9e-03
[26] -4.633520e-03 -4.052130e-03 -4.746537e-03 -1.589622e-03 -2.523766e-0=
4
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 -0.7046511=
6 =A00.85251098
[13] -0.18346956 =A00.66857787 =A00.57012481 =A00.39116561 =A00.91237990 =
=A00.63951482
[19] =A00.26601566 =A00.29240836 =A00.44710919 =A00.94734056 =A06.5203901=
5 =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 -4.283=
329e+00
=A0[6] -1.437250e+00 -6.558913e-01 =A01.358276e+00 =A07.930865e+05 -1.293=
853e+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+0=
7
[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 messa=
ge:
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 fai=
l
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 sta=
ge.
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/li= b/libptcblas.a /usr/local/lib/libatlas.a -lpthread" --with-lapack=3D"/usr/l= ocal/lib/liblapack.a /usr/local/lib/libptf77blas.a /usr/local/lib/libptcbla= s.a /usr/local/lib/libatlas.a -lpthread" --without-aqua CFLAGS=3D"-O3 -mtun= e=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" F77FLAG= S=3D"-O3 -mtune=3Dnocona -m32 -L/usr/lib/gcc/i686-apple-darwin9/4.2.1 -l gf= ortran" FCFLAGS=3D"-O3 -mtune=3Dnocona -m32 -L/usr/lib/gcc/i686-apple-darwi= n9/4.2.1 -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 'type2cha=
r'"
and "cannot coerce type 'weakref' to vector of type 'double'". =A0Running=
with
debug=3DTRUE also segfaults sometimes, even after achieving "Current iter=
ate
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_MON=
ETARY=3DC;LC_MESSAGES=3Den_US;LC_PAPER=3Den_US;LC_NAME=3DC;LC_ADDRESS=3DC;L= C_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=3D=
en_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, whethe=
r
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. 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--=20 Jeffrey Ryan jeffrey.ryan at insightalgo.com ia: insight algorithmics www.insightalgo.com