adik at ilovebacon.org
2009-Aug-07 18:10 UTC
[Rd] Bug in nlm, found using sem; failure in several flavors (PR#13881)
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Hello,
There appears to be a bug in the nlm function, which I discovered
when trying to run an SEM. The 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). I 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=ice.ram, S=ice.S, N=ice.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,
:
type 31 is unimplemented in 'type2char'
3) *** caught segfault ***
address 0xc019c87b, cause 'memory not mapped'
Traceback:
1: nlm(if (analytic.gradient) objective.2 else objective.1, start,
hessian = TRUE, iterlim = maxiter, print.level = if (debug) 2 else 0,
typsize = typsize, ...)
2: sem.default(ram = ram, S = S, N = N, param.names = pars, var.names vars,
fixed.x = fixed.x, debug = debug, ...)
3: sem(ram = ram, S = S, N = N, param.names = pars, var.names = vars,
fixed.x = fixed.x, debug = debug, ...)
4: sem.mod(ram = ice.ram, S = ice.S, N = ice.N)
5: sem(ram = ice.ram, S = ice.S, N = 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=ice.ram, S=ice.S, N=ice.N, debug=TRUE)
...gets up to some iteration (not always 15), and then R dies ungracefully,
and exits to the shell:
iteration = 15
Step:
[1] 1.253132e-02 1.183343e-02 -7.651342e-03 -2.490800e-03 2.278938e-03
[6] 3.197431e-04 6.137849e-04 -2.496882e-03 -1.065829e-03 -2.118179e-03
[11] 2.942936e-03 -1.335936e-03 -3.665618e-03 3.090566e-03 8.534956e-04
[16] -1.440421e-03 -5.230877e-04 -1.053686e-04 -9.771005e-04 -4.269216e-04
[21] 7.261694e-05 -1.039668e-03 -8.409151e-03 -3.497456e-03 2.216899e-03
[26] -4.633520e-03 -4.052130e-03 -4.746537e-03 -1.589622e-03 -2.523766e-04
Parameter:
[1] -0.76604614 -1.19639662 0.83456888 0.72540413 0.08482452 0.56180393
[7] 0.50615814 0.55728015 0.83796696 0.88371335 -0.70465116 0.85251098
[13] -0.18346956 0.66857787 0.57012481 0.39116561 0.91237990 0.63951482
[19] 0.26601566 0.29240836 0.44710919 0.94734056 6.52039015 0.02524762
[25] -0.01614603 2.88198219 0.03442452 3.52272237 1.44698423 -0.72964745
Function Value
[1] -15175.94
Gradient:
[1] -2.085412e+07 -3.819717e+07 3.883989e+07 1.352594e+00 -4.283329e+00
[6] -1.437250e+00 -6.558913e-01 1.358276e+00 7.930865e+05 -1.293853e+06
[11] -5.816627e+03 5.908197e+05 -2.705742e+08 -1.194400e+07 -4.007083e+07
[16] -4.143068e+07 -6.159782e-01 1.044274e-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 3.117764e-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,
:
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
_
platform i386-apple-darwin9.7.0
arch i386
os darwin9.7.0
system i386, darwin9.7.0
status
major 2
minor 9.1
year 2009
month 06
day 26
svn rev 48839
language 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 graphics grDevices utils datasets methods 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=/usr/local --with-x --disable-R-framework
--enable-threads=posix --with-blas="/usr/local/lib/libptf77blas.a
/usr/local/lib/libptcblas.a /usr/local/lib/libatlas.a -lpthread"
--with-lapack="/usr/local/lib/liblapack.a /usr/local/lib/libptf77blas.a
/usr/local/lib/libptcblas.a /usr/local/lib/libatlas.a -lpthread"
--without-aqua CFLAGS="-O3 -mtune=nocona -m32" CXXFLAGS="-O3
-mtune=nocona -m32" FFLAGS="-O3 -mtune=nocona -m32
-L/usr/lib/gcc/i686-apple-darwin9/4.2.1 -l gfortran" F77FLAGS="-O3
-mtune=nocona -m32 -L/usr/lib/gcc/i686-apple-darwin9/4.2.1 -l gfortran"
FCFLAGS="-O3 -mtune=nocona -m32 -L/usr/lib/gcc/i686-apple-darwin9/4.2.1 -l
gfortran" LDFLAGS="-m32 -L/sw/lib"
CPPFLAGS="-I/sw/include" CC=gcc-4.2 F77=gfortran-4.2 FC=gfortran-4.2
CXX=g++-4.2 OBJC=gcc-4.2
...though I have also recompiled using simply this:
./configure --prefix=/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'". Running with
debug=TRUE also segfaults sometimes, even after achieving "Current iterate
is probably solution" status.)
> version
_
platform x86_64-unknown-linux-gnu
arch x86_64
os linux-gnu
system x86_64, linux-gnu
status
major 2
minor 9.1
year 2009
month 06
day 26
svn rev 48839
language 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=en_US;LC_NUMERIC=C;LC_TIME=en_US;LC_COLLATE=en_US;LC_MONETARY=C;LC_MESSAGES=en_US;LC_PAPER=en_US;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US;LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] sem_0.9-17
...however, THIS platform does NOT show the bug:
> version
_
platform powerpc-unknown-linux-gnu
arch powerpc
os linux-gnu
system powerpc, linux-gnu
status
major 2
minor 9.1
year 2009
month 06
day 26
svn rev 48839
language 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=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods 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=:2997--
Jeff Ryan
2009-Aug-07 19:35 UTC
[Rd] Bug in nlm, found using sem; failure in several flavors (PR#13881)
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:> ?This message is in MIME format. ?The first part should be readable text, > ?while the remaining parts are likely unreadable without MIME-aware tools. > > --1660387551-1458482416-1249639718=:2997 > Content-Type: TEXT/PLAIN; CHARSET=US-ASCII; FORMAT=flowed > Content-ID: <Pine.LNX.4.64.0908071039211.2997 at parser.ilovebacon.org> > > Hello, > > ? ? ? ?There appears to be a bug in the nlm function, which I discovered > when trying to run an SEM. ?The 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). ?I 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=ice.ram, S=ice.S, N=ice.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, > : > ? type 31 is unimplemented in 'type2char' > 3) ?*** caught segfault *** > address 0xc019c87b, cause 'memory not mapped' > > Traceback: > ?1: nlm(if (analytic.gradient) objective.2 else objective.1, start, > hessian = TRUE, iterlim = maxiter, print.level = if (debug) 2 else 0, > typsize = typsize, ...) > ?2: sem.default(ram = ram, S = S, N = N, param.names = pars, var.names > vars, ? ? fixed.x = fixed.x, debug = debug, ...) > ?3: sem(ram = ram, S = S, N = N, param.names = pars, var.names = vars, > fixed.x = fixed.x, debug = debug, ...) > ?4: sem.mod(ram = ice.ram, S = ice.S, N = ice.N) > ?5: sem(ram = ice.ram, S = ice.S, N = 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=ice.ram, S=ice.S, N=ice.N, debug=TRUE) > > ...gets up to some iteration (not always 15), and then R dies ungracefully, > and exits to the shell: > > iteration = 15 > Step: > ?[1] ?1.253132e-02 ?1.183343e-02 -7.651342e-03 -2.490800e-03 ?2.278938e-03 > ?[6] ?3.197431e-04 ?6.137849e-04 -2.496882e-03 -1.065829e-03 -2.118179e-03 > [11] ?2.942936e-03 -1.335936e-03 -3.665618e-03 ?3.090566e-03 ?8.534956e-04 > [16] -1.440421e-03 -5.230877e-04 -1.053686e-04 -9.771005e-04 -4.269216e-04 > [21] ?7.261694e-05 -1.039668e-03 -8.409151e-03 -3.497456e-03 ?2.216899e-03 > [26] -4.633520e-03 -4.052130e-03 -4.746537e-03 -1.589622e-03 -2.523766e-04 > Parameter: > ?[1] -0.76604614 -1.19639662 ?0.83456888 ?0.72540413 ?0.08482452 ?0.56180393 > ?[7] ?0.50615814 ?0.55728015 ?0.83796696 ?0.88371335 -0.70465116 ?0.85251098 > [13] -0.18346956 ?0.66857787 ?0.57012481 ?0.39116561 ?0.91237990 ?0.63951482 > [19] ?0.26601566 ?0.29240836 ?0.44710919 ?0.94734056 ?6.52039015 ?0.02524762 > [25] -0.01614603 ?2.88198219 ?0.03442452 ?3.52272237 ?1.44698423 -0.72964745 > Function Value > [1] -15175.94 > Gradient: > ?[1] -2.085412e+07 -3.819717e+07 ?3.883989e+07 ?1.352594e+00 -4.283329e+00 > ?[6] -1.437250e+00 -6.558913e-01 ?1.358276e+00 ?7.930865e+05 -1.293853e+06 > [11] -5.816627e+03 ?5.908197e+05 -2.705742e+08 -1.194400e+07 -4.007083e+07 > [16] -4.143068e+07 -6.159782e-01 ?1.044274e-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 ?3.117764e-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, > : > ? 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 > ? ? ? ? ? ? ? ?_ > platform ? ? ? i386-apple-darwin9.7.0 > arch ? ? ? ? ? i386 > os ? ? ? ? ? ? darwin9.7.0 > system ? ? ? ? i386, darwin9.7.0 > status > major ? ? ? ? ?2 > minor ? ? ? ? ?9.1 > year ? ? ? ? ? 2009 > month ? ? ? ? ?06 > day ? ? ? ? ? ?26 > svn rev ? ? ? ?48839 > language ? ? ? 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 ? ? graphics ?grDevices utils ? ? datasets ?methods ? 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=/usr/local --with-x --disable-R-framework --enable-threads=posix --with-blas="/usr/local/lib/libptf77blas.a /usr/local/lib/libptcblas.a /usr/local/lib/libatlas.a -lpthread" --with-lapack="/usr/local/lib/liblapack.a /usr/local/lib/libptf77blas.a /usr/local/lib/libptcblas.a /usr/local/lib/libatlas.a -lpthread" --without-aqua CFLAGS="-O3 -mtune=nocona -m32" CXXFLAGS="-O3 -mtune=nocona -m32" FFLAGS="-O3 -mtune=nocona -m32 -L/usr/lib/gcc/i686-apple-darwin9/4.2.1 -l gfortran" F77FLAGS="-O3 -mtune=nocona -m32 -L/usr/lib/gcc/i686-apple-darwin9/4.2.1 -l gfortran" FCFLAGS="-O3 -mtune=nocona -m32 -L/usr/lib/gcc/i686-apple-darwin9/4.2.1 -l gfortran" LDFLAGS="-m32 -L/sw/lib" CPPFLAGS="-I/sw/include" CC=gcc-4.2 F77=gfortran-4.2 FC=gfortran-4.2 CXX=g++-4.2 OBJC=gcc-4.2 > > ...though I have also recompiled using simply this: > > ./configure --prefix=/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'". ?Running with > debug=TRUE also segfaults sometimes, even after achieving "Current iterate > is probably solution" status.) > >> version > ? ? ? ? ? ? ? ?_ > platform ? ? ? x86_64-unknown-linux-gnu > arch ? ? ? ? ? x86_64 > os ? ? ? ? ? ? linux-gnu > system ? ? ? ? x86_64, linux-gnu > status > major ? ? ? ? ?2 > minor ? ? ? ? ?9.1 > year ? ? ? ? ? 2009 > month ? ? ? ? ?06 > day ? ? ? ? ? ?26 > svn rev ? ? ? ?48839 > language ? ? ? 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=en_US;LC_NUMERIC=C;LC_TIME=en_US;LC_COLLATE=en_US;LC_MONETARY=C;LC_MESSAGES=en_US;LC_PAPER=en_US;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US;LC_IDENTIFICATION=C > > attached base packages: > [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base > > other attached packages: > [1] sem_0.9-17 > > ...however, THIS platform does NOT show the bug: > >> version > ? ? ? ? ? ? ? ?_ > platform ? ? ? powerpc-unknown-linux-gnu > arch ? ? ? ? ? powerpc > os ? ? ? ? ? ? linux-gnu > system ? ? ? ? powerpc, linux-gnu > status > major ? ? ? ? ?2 > minor ? ? ? ? ?9.1 > year ? ? ? ? ? 2009 > month ? ? ? ? ?06 > day ? ? ? ? ? ?26 > svn rev ? ? ? ?48839 > language ? ? ? 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=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C > > attached base packages: > [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? 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. 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