adik at ilovebacon.org
2009-Aug-07 22:35 UTC
[Rd] Bug in nlm, found using sem; failure in several flavors (PR#13883)
This message is in MIME format. The first part should be readable text, while the remaining parts are likely unreadable without MIME-aware tools. --1660387551-150661043-1249684349=:2997 Content-Type: TEXT/PLAIN; charset=iso-8859-1; format=flowed Content-Transfer-Encoding: QUOTED-PRINTABLE 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 not 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 (since 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 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. 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"wasrightchoice",0.96369773178963,0.292736321229647,0.289852808489117,0.385266965362761,0.197644824696320,0.183041324062298,-0.146626347219879,0.146354027797101,-0.132887596902506,-0.173965069111025,-0.268459162930567,-0.0678095375076222,0.180549925024377,-0.0420844364037874,-0.0730577896902967 "tellgood",0.292736321229647,0.955494246210856,0.757544193339566,0.191241183203129,0.000174630417564688,0.00340887118071287,0.00963050474358034,0.0283894373316684,0.0188027539463299,-0.0157026381515985,-0.145795006741884,0.142034396906879,0.00981538398434851,0.0705868756539732,0.108000449328313 "tellbest",0.289852808489117,0.757544193339566,0.948593590912408,0.230598958597528,0.0302692106135439,0.0155447055783122,0.0321693281988669,0.0646312326187096,0.0102945085651246,-0.0196759997923009,-0.178765563354828,0.151343567761859,-0.0336559063307835,0.0929062279334898,0.159735618423335 "important",0.385266965362761,0.191241183203129,0.230598958597528,0.96449788034361,0.647657141488375,0.514175974554114,-0.197506705917123,0.474723332469875,-0.129091329816201,-0.189229123705341,-0.462195839265035,0.124158339527322,0.160661307486559,-0.0864573727466265,-0.0683674842498801 "complex",0.197644824696320,0.000174630417564688,0.0302692106135439,0.647657141488375,0.976321655762968,0.754978777309553,-0.262340425824052,0.656717533361176,-0.160427139673018,-0.236210856083902,-0.385452100046623,0.0238775728277157,0.324525653164508,-0.240634804887055,-0.233696554189164 "difficult",0.183041324062298,0.00340887118071287,0.0155447055783122,0.514175974554114,0.754978777309553,0.957324341661972,-0.183005587551624,0.523183993897632,-0.197833354430907,-0.228434713061776,-0.263587746021174,-0.0453971377700845,0.330075666526761,-0.234707517677586,-0.239126971480625 "onlyself",-0.146626347219879,0.00963050474358034,0.0321693281988669,-0.197506705917123,-0.262340425824052,-0.183005587551624,0.947852415443663,-0.268333979295612,0.0787191879215654,0.0800554430938036,0.163595277498758,-0.00507268608417704,-0.160137545871448,0.211257252287979,0.147884352588499 "manydimensions",0.146354027797101,0.0283894373316684,0.0646312326187096,0.474723332469875,0.656717533361176,0.523183993897632,-0.268333979295612,0.94991766261616,-0.113295667408177,-0.181576473170784,-0.279298417177261,0.0442481235082528,0.258349702460663,-0.196993346337214,-0.222533952633482 "howmuchinfo",-0.132887596902506,0.0188027539463299,0.0102945085651246,-0.129091329816201,-0.160427139673018,-0.197833354430907,0.0787191879215654,-0.113295667408177,0.946722746137415,0.706976015582218,0.0923192704439934,0.213032242473315,-0.209882431765110,0.239124551629559,0.219078352890657 "equalinfo",-0.173965069111025,-0.0157026381515985,-0.0196759997923009,-0.189229123705341,-0.236210856083902,-0.228434713061776,0.0800554430938036,-0.181576473170784,0.706976015582218,0.964517562778328,0.180517325752387,0.163844640495983,-0.213804550043239,0.258032322824599,0.191820447404335 "couldavoid",-0.268459162930567,-0.145795006741884,-0.178765563354828,-0.462195839265035,-0.385452100046623,-0.263587746021174,0.163595277498758,-0.279298417177261,0.0923192704439934,0.180517325752387,0.963237309730726,-0.120130196392406,-0.0689659657057091,0.165533208743547,0.191421134189682 "posoutcome",-0.0678095375076222,0.142034396906879,0.151343567761859,0.124158339527322,0.0238775728277157,-0.0453971377700845,-0.00507268608417704,0.0442481235082528,0.213032242473315,0.163844640495983,-0.120130196392406,0.939107717186385,-0.291262391827671,0.256274195983004,0.346441411116147 "negoutcome",0.180549925024377,0.00981538398434851,-0.0336559063307835,0.160661307486559,0.324525653164508,0.330075666526761,-0.160137545871448,0.258349702460663,-0.209882431765110,-0.213804550043239,-0.0689659657057091,-0.291262391827671,0.952552965796421,-0.22191722293019,-0.231032014927397 "control",-0.0420844364037874,0.0705868756539732,0.0929062279334898,-0.0864573727466265,-0.240634804887055,-0.234707517677586,0.211257252287979,-0.196993346337214,0.239124551629559,0.258032322824599,0.165533208743547,0.256274195983004,-0.22191722293019,0.937607533186576,0.312664199631620 "desired",-0.0730577896902967,0.108000449328313,0.159735618423335,-0.0683674842498801,-0.233696554189164,-0.239126971480625,0.147884352588499,-0.222533952633482,0.219078352890657,0.191820447404335,0.191421134189682,0.346441411116147,-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--
Ben Bolker
2009-Aug-10 19:52 UTC
[Rd] Bug in nlm, found using sem; failure in several flavors (PR#13883)
A wild guess, based on some recent "non-deterministic" behavior in lme4: could this be driven by a bug in optimized linear algebra libraries (BLAS/LAPACK)? (Unfortunately, I'm not clear on how to check the versions of BLAS/LAPACK being used and whether they are subject to bugs, but perhaps someone else can comment ...) Ben Bolker Adam D. I. Kramer-2 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. > > --1660387551-150661043-1249684349=:2997 > Content-Type: TEXT/PLAIN; charset=iso-8859-1; format=flowed > Content-Transfer-Encoding: QUOTED-PRINTABLE > > 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. 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"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-- > > ______________________________________________ > R-devel at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > >-- View this message in context: http://www.nabble.com/Re%3A-Bug-in-nlm%2C-found-using-sem--failure-in-several-flavors-%28PR-13883%29-tp24875708p24906063.html Sent from the R devel mailing list archive at Nabble.com.
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