46981 2004-04-06 10:58 0000 media-gfx/gnuplot-3.8j segfaults when trying to do a fit 2005-01-09 07:48:48 0000 1 1 1 Unclassified Gentoo Linux Applications unspecified All Linux RESOLVED FIXED P2 normal --- 1 armin@despammed.com g2boojum@gentoo.org armin@despammed.com 2004-04-06 10:58:34 0000 gnuplot segfaults after attempting to do a linear fit. The crash occurs while the final results are printed. Reproducible: Always Steps to Reproduce: 1. start gnuplot 2. try to do fit [range] expression "filename" via parameters 3. Actual Results: The fit is successful; the program crashes when displaying the results as seen below: After 5 iterations the fit converged. final sum of squares of residuals : 0.00181103 rel. change during last iteration : -9.97883e-07 degrees of freedom (ndf) : 10 rms of residuals (stdfit) = sqrt(WSSR/ndf) : 0.0134575 variance of residuals (reduced chisquare) = WSSR/ndf : 0.000181103 Final set of parameters Asymptotic Standard Error ======================= ========================== a = -14.6228 +/- 0.673 (4.602%) Segmentation fault Expected Results: successful display of the fitting parameters. repeating with "strace gnuplot" produces the following famous last words: --- SIGSEGV (Segmentation fault) @ 0 (0) --- +++ killed by SIGSEGV +++ the flags used when merging are: CFLAGS="-pipe -O2 -finline -freorder-functions -freorder-blocks -ffast-math -fomit-frame-pointer" g2boojum@gentoo.org 2004-04-06 14:57:30 0000 Could you provide specific data and fitting commands so that I can try it out here using exactly the same input? armin@despammed.com 2004-04-06 15:11:29 0000 Created an attachment (id=28809) sample data attached is a sample data file (sample.dat) steps: gnuplot fit [0.1:0.12] a*x+b "sample.dat" using (1/($1)):(($3)**2) via a,b at this point, the fit converges after 5 iterations and the gnuplot segfaults after displaying the first line of the result: [...] Final set of parameters Asymptotic Standard Error ======================= ========================== a = -12.3508 +/- 0.4276 (3.462%) Segmentation fault g2boojum@gentoo.org 2004-04-07 18:25:27 0000 Thank you very much for the data and example, I really appreciate it. (Incidentally, I've been using gnuplot for ten years or so, and I had no idea that it did fits. Cool!) My guess is that it's your CFLAGS, but I can't reproduce it. Even w/ your CFLAGS gnuplot seems to work on my machine, so it might be a dependency. Nonetheless, would you mind remerging w/ CFLAGS="-O2 -mcpu=i686 -fomit-frame-pointer" and seeing if that works? If that fails, the next step is to ask you to either strace gnuplot or run it from gdb, either one of which should let us know where it's segfaulting. Thanks! > gnuplot G N U P L O T Version 3.8j patchlevel 0 last modified Wed Nov 27 20:49:08 GMT 2002 System: Linux 2.6.3-gentoo-r1 Copyright(C) 1986 - 1993, 1999 - 2002 Thomas Williams, Colin Kelley and many others This is a pre-version of gnuplot 4.0. Please refer to the documentation for command syntax changes. The old syntax will be accepted throughout the 4.0 series, but all save files use the new syntax. Type `help` to access the on-line reference manual The gnuplot FAQ is available from http://www.gnuplot.info/faq/ Send comments and requests for help to <info-gnuplot-beta@dartmouth.edu> Send bugs, suggestions and mods to <info-gnuplot-beta@dartmouth.edu> Terminal type set to 'x11' gnuplot> fit [0.1:0.12] a*x+b "sample.dat" u (1/($1)):(($3)**2) via a,b Iteration 0 WSSR : 14.761 delta(WSSR)/WSSR : 0 delta(WSSR) : 0 limit for stopping : 1e-05 lambda : 0.711307 initial set of free parameter values a = 1 b = 1 / Iteration 1 WSSR : 0.114571 delta(WSSR)/WSSR : -127.837 delta(WSSR) : -14.6464 limit for stopping : 1e-05 lambda : 0.0711307 resultant parameter values a = 0.887916 b = 0.110179 / Iteration 2 WSSR : 0.0831861 delta(WSSR)/WSSR : -0.377286 delta(WSSR) : -0.0313849 limit for stopping : 1e-05 lambda : 0.00711307 resultant parameter values a = -0.454838 b = 0.230027 / Iteration 3 WSSR : 0.00212404 delta(WSSR)/WSSR : -38.1641 delta(WSSR) : -0.0810621 limit for stopping : 1e-05 lambda : 0.000711307 resultant parameter values a = -11.3808 b = 1.42104 / Iteration 4 WSSR : 0.00158143 delta(WSSR)/WSSR : -0.343113 delta(WSSR) : -0.00054261 limit for stopping : 1e-05 lambda : 7.11307e-05 resultant parameter values a = -12.3499 b = 1.52669 / Iteration 5 WSSR : 0.00158143 delta(WSSR)/WSSR : -2.69974e-07 delta(WSSR) : -4.26945e-10 limit for stopping : 1e-05 lambda : 7.11307e-06 resultant parameter values a = -12.3508 b = 1.52679 After 5 iterations the fit converged. final sum of squares of residuals : 0.00158143 rel. change during last iteration : -2.69974e-07 degrees of freedom (ndf) : 15 rms of residuals (stdfit) = sqrt(WSSR/ndf) : 0.0102678 variance of residuals (reduced chisquare) = WSSR/ndf : 0.000105429 Final set of parameters Asymptotic Standard Error ======================= ========================== a = -12.3508 +/- 0.4276 (3.462%) b = 1.52679 +/- 0.04668 (3.057%) correlation matrix of the fit parameters: a b a 1.000 b -0.999 1.000 armin@despammed.com 2004-04-07 20:42:19 0000 Can't remerge with -mcpu=i686 on amd64, sorry (the toolchain is 64bit only by default and I don't have enough time to get a cross-compiler up and running). Besides, using the same gnuplot version on 32bit x86 does not crash (at least, it hasn't for me for anything). The point is, it's marked as 'stable' on amd64. If this is indeed a 64bit issue, is it possible to verify whether anything similar appears on ia64? (as that is also marked stable). a backtrace from gdb shows the following: Program received signal SIGSEGV, Segmentation fault. 0x0000002a9663b936 in strnlen () from /lib/libc.so.6 (gdb) bt #0 0x0000002a9663b936 in strnlen () from /lib/libc.so.6 #1 0x0000002a9661030f in vfprintf () from /lib/libc.so.6 #2 0x00000000004146c8 in init_color () #3 0x00000000004126d9 in init_color () #4 0x0000000000414566 in init_color () #5 0x000000000040ac6e in init_color () #6 0x000000000040a85f in init_color () #7 0x000000000040a74a in init_color () #8 0x0000000000435fff in matherr () #9 0x0000002a965e08b1 in __libc_start_main () from /lib/libc.so.6 #10 0x00000000004049aa in ?? () g2boojum@gentoo.org 2004-04-08 05:15:41 0000 Oh! I'm sorry, I didn't realize you were using amd64. (In fact, reading back through your bug report I don't see this information anywhere, although I could have missed it.) I can't test it here, so I'm going to reassign this bug to the amd64 folks and I'll cc the ia64 team as well. Thanks. kugelfang@gentoo.org 2004-04-08 06:57:42 0000 I can confirm this bug on my amd64 box. Following the output of nonstripped backtrace (same command and sample data as Armin provided): *cut off* After 5 iterations the fit converged. final sum of squares of residuals : 0.00158143 rel. change during last iteration : -2.69974e-07 degrees of freedom (ndf) : 15 rms of residuals (stdfit) = sqrt(WSSR/ndf) : 0.0102678 variance of residuals (reduced chisquare) = WSSR/ndf : 0.000105429 Final set of parameters Asymptotic Standard Error ======================= ========================== a = -12.3508 +/- 0.4276 (3.462%) Program received signal SIGSEGV, Segmentation fault. 0x0000002a9662bcb6 in strnlen () from /lib/libc.so.6 (gdb) bt #0 0x0000002a9662bcb6 in strnlen () from /lib/libc.so.6 #1 0x0000002a966004aa in vfprintf () from /lib/libc.so.6 #2 0x0000000000414e4a in Dblfn () #3 0x0000000000412ba4 in regress () #4 0x00000000004145fb in fit_command () #5 0x000000000040af45 in command () #6 0x000000000040ab2c in do_line () #7 0x000000000040aa5d in com_line () #8 0x0000000000436e45 in main () (gdb) I'll have a look on that later... armin@despammed.com 2004-04-08 09:37:05 0000 compiled the last available build on sf.net: G N U P L O T Version 3.8k patchlevel 3 last modified Mon Mar 29 15:17:53 CEST 2004 crashes in the same place. Here's a backtrace on the debug build: (gdb) bt #0 0x0000002a9663b936 in strnlen () from /lib/libc.so.6 #1 0x0000002a9661030f in vfprintf () from /lib/libc.so.6 #2 0x00000000004198f9 in Dblfn (fmt=0x4d3268 "%-15.15s = %-15g %-3.3s %-12.4g (%.4g%%)\n") at fit.c:1688 #3 0x00000000004173d8 in regress (a=0x648490) at fit.c:777 #4 0x0000000000419773 in fit_command () at fit.c:1638 #5 0x000000000040c7ec in command () at command.c:511 #6 0x000000000040c3ae in do_line () at command.c:368 #7 0x000000000040c28d in com_line () at command.c:327 #8 0x000000000044fcb7 in main (argc=1, argv=0x7fbffff398) at plot.c:626 It happens as it tries to write the last output line (a= [...] ) to the log file. Could this actually be a libc bug (as vprintf fails to print to a file a line that successfully printed to stdout)? agriffis@gentoo.org 2004-04-08 11:04:44 0000 Nice backtrace.. :-) How about working on a patch? kugelfang@gentoo.org 2004-04-08 11:45:41 0000 Ok, uncommenting vfprintf(log_f, fmt, args); in src/fit.c:Dlbfn() solves the segfault. Probably a sizeof() problem with log_f on 64bit Archs ? kugelfang@gentoo.org 2004-04-08 18:28:30 0000 Works for me now. The problem was less using vfprintf on a file but more calling it without re-initializing "args" via VA_START. Made a patch against it + a patch to the ebuild. kugelfang@gentoo.org 2004-04-08 18:30:27 0000 Created an attachment (id=28922) Patch for media-gfx/gnuplot-3.8j kugelfang@gentoo.org 2004-04-08 18:31:39 0000 Created an attachment (id=28923) Patch for media-gfx/gnuplot-3.8j ebuild armin@despammed.com 2004-04-08 19:47:12 0000 It does not seem necessary to remove printing to the log. Indeed, doing va_end(args); VA_START(args, fmt); between the two vprintf() calls seems to take care of it. armin@despammed.com 2004-04-08 20:12:50 0000 after looking at the c99 standard, this seems to be a gnuplot bug rather than an amd64 one. specifically, 7.15 par. 3 says that the va_list argument (args) is supposed to be in an invalid state after the first vfprintf() call. So maybe make the patch required for all archs until a fix is available upstream? also posted as a bug on the gnuplot sf.net bugtracker here: http://sourceforge.net/tracker/index.php?func=detail&aid=932162&group_id=2055&atid=102055 lv@gentoo.org 2004-04-08 21:03:31 0000 I've committed an amd64-specific ebuild for this to CVS. if this fix needs to exist on all archs, then I'll leave that decision up to somebody other than myself. I'm re-assigning this bug to the maintainer for this package, but it should be fixed on amd64 now. give it a bit to reach rsync. g2boojum@gentoo.org 2005-01-09 07:48:11 0000 Closing, since there's been no recent input. g2boojum@gentoo.org 2005-01-09 07:48:48 0000 Really closing this time. 28809 2004-04-06 15:11 0000 sample data sample.dat text/plain CjEyCTAuNDM4NTgxCS0wLjY0NzI1NwkwLjk5OTgzNAkwLjc3ODEzNQktMy40MTEwMQoxMS45CTAu NDM5ODY5CS0wLjY0MjAxOAkwLjk5OTkxNAkwLjc4MjA5MwktMy40MTUyNwoxMS44CTAuNDM4Mzc2 CS0wLjYzMDUzNwkwLjk5OTg4OQkwLjc2OTQ3NAktMy40MjkyCjExLjcJMC40MzkwMDIJLTAuNjI1 NTg4CTAuOTk5ODMxCTAuNzcxOTY0CS0zLjQ0MjE3CjExLjYJMC40MzkyMjkJLTAuNjI0NTc0CTAu OTk5OTU1CTAuNzcxMzMyCS0zLjQ1NzM4CjExLjUJMC40Mzc5ODgJLTAuNjIwMTkyCTEuMDAwMDMJ MC43NjUxODEJLTMuNDYxNzkKMTEuNAkwLjQzODI3NQktMC42MjI0NjEJMS4wMDAyCTAuNzY1MTM0 CS0zLjQ4NTI4CjExLjMJMC40MzczMDYJLTAuNjEzMDkyCTEuMDAwMDQJMC43NjIyNwktMy40OTkw NgoxMS4yCTAuNDM2OTM3CS0wLjYwNTc1OQkxLjAwMDA4CTAuNzYwOTA3CS0zLjUwMTcyCjExLjEJ 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