Test cases:
Run.comprehensive passed all tests
Run.rms passed all tests
Run.matrix failed with an error
ptraj: analyze fluctuation matrices
*** glibc detected *** ../../exe/ptraj: free(): invalid next size (fast):
0x00000000029c9a90 ***
======= Backtrace: =========
/lib/libc.so.6[0x7f2149961cb8]
/lib/libc.so.6(cfree+0x76)[0x7f2149964276]
../../exe/ptraj[0x41f1bd]
../../exe/ptraj[0x4999e4]
../../exe/ptraj[0x43e32f]
../../exe/ptraj[0x438ac4]
../../exe/ptraj[0x405be8]
/lib/libc.so.6(__libc_start_main+0xe6)[0x7f21499085a6]
../../exe/ptraj[0x405889]
======= Memory map: ========
00400000-0085c000 r-xp 00000000 08:21 126168
/home/swails/newamber/10.04.09/amber11/bin/ptraj
00a5c000-00a67000 rwxp 0045c000 08:21 126168
/home/swails/newamber/10.04.09/amber11/bin/ptraj
00a67000-00a84000 rwxp 00a67000 00:00 0
02932000-02a38000 rwxp 02932000 00:00 0
[heap]
7f2140000000-7f2140021000 rwxp 7f2140000000 00:00 0
7f2140021000-7f2144000000 ---p 7f2140021000 00:00 0
7f21442fc000-7f21496e6000 rwxp 7f21442fc000 00:00 0
7f21496e6000-7f21496e8000 r-xp 00000000 08:21 8830977
/lib/libdl-2.9.so
7f21496e8000-7f21498e8000 ---p 00002000 08:21 8830977
/lib/libdl-2.9.so
7f21498e8000-7f21498e9000 r-xp 00002000 08:21 8830977
/lib/libdl-2.9.so
7f21498e9000-7f21498ea000 rwxp 00003000 08:21 8830977
/lib/libdl-2.9.so
7f21498ea000-7f2149a52000 r-xp 00000000 08:21 6995970
/lib/libc-2.9.so
7f2149a52000-7f2149c52000 ---p 00168000 08:21 6995970
/lib/libc-2.9.so
7f2149c52000-7f2149c56000 r-xp 00168000 08:21 6995970
/lib/libc-2.9.so
7f2149c56000-7f2149c57000 rwxp 0016c000 08:21 6995970
/lib/libc-2.9.so
7f2149c57000-7f2149c5c000 rwxp 7f2149c57000 00:00 0
7f2149c5c000-7f2149c72000 r-xp 00000000 08:21 12501054
/lib/libgcc_s.so.1
7f2149c72000-7f2149e72000 ---p 00016000 08:21 12501054
/lib/libgcc_s.so.1
7f2149e72000-7f2149e73000 r-xp 00016000 08:21 12501054
/lib/libgcc_s.so.1
7f2149e73000-7f2149e74000 rwxp 00017000 08:21 12501054
/lib/libgcc_s.so.1
7f2149e74000-7f2149ef8000 r-xp 00000000 08:21 8830978
/lib/libm-2.9.so
7f2149ef8000-7f214a0f7000 ---p 00084000 08:21 8830978
/lib/libm-2.9.so
7f214a0f7000-7f214a0f8000 r-xp 00083000 08:21 8830978
/lib/libm-2.9.so
7f214a0f8000-7f214a0f9000 rwxp 00084000 08:21 8830978
/lib/libm-2.9.so
7f214a0f9000-7f214a110000 r-xp 00000000 08:21 8830988
/lib/libpthread-2.9.so
7f214a110000-7f214a30f000 ---p 00017000 08:21 8830988
/lib/libpthread-2.9.so
7f214a30f000-7f214a310000 r-xp 00016000 08:21 8830988
/lib/libpthread-2.9.so
7f214a310000-7f214a311000 rwxp 00017000 08:21 8830988
/lib/libpthread-2.9.so
7f214a311000-7f214a315000 rwxp 7f214a311000 00:00 0
7f214a315000-7f214a335000 r-xp 00000000 08:21 6750215
/lib/ld-2.9.so
7f214a498000-7f214a514000 rwxp 7f214a498000 00:00 0
7f214a52f000-7f214a534000 rwxp 7f214a52f000 00:00 0
7f214a534000-7f214a535000 r-xp 0001f000 08:21 6750215
/lib/ld-2.9.so
7f214a535000-7f214a536000 rwxp 00020000 08:21 6750215
/lib/ld-2.9.so
7fff5251f000-7fff52535000 rwxp 7ffffffe9000 00:00 0
[stack]
7fff525fd000-7fff525fe000 r-xp 7fff525fd000 00:00 0
[vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0
[vsyscall]
Aborted
./Run.matrix: Program error
I'm using the intel compilers version icc (ICC) 11.0 20090318 (same version
number for ifort). I'm also using the MKL version 10.1. I'm running on
GNU/Linux (ubuntu). I have an older compilation of amber11 checked out a
couple months ago using the same setup and it passes all tests and does not
throw the exception.
Thanks,
Jason Swails
uname -a returns:
Linux Batman 2.6.28-15-generic #49-Ubuntu SMP Tue Aug 18 19:25:34 UTC 2009
x86_64 GNU/Linux
On Sun, Oct 4, 2009 at 9:59 PM, case <case.biomaps.rutgers.edu> wrote:
> On Sun, Oct 04, 2009, Jason Swails wrote:
>
> > Trajectory files are now created, but I'm still getting the same floating
> > point exception that I was getting before. Sometimes it prevents the
> > creation of the output, and other times it doesn't (though I don't know
> the
> > exact conditions of either case, the floating point exception always
> > appears). I've put the three files (mdcrd, prmtop, and ptraj input) that
> > caused this error in http://qtp.ufl.edu/~swails/ptraj_files/ (since I
> don't
> > know how appropriate it is to attach files to emails sent to the
> listserv).
>
> Just to get up to date:
>
> 1. Do the test cases work for you?
>
> 2. What compiler, OS, etc. are you using?
>
> ...thx...dac
>
>
> _______________________________________________
> AMBER-Developers mailing list
> AMBER-Developers.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber-developers
>
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Received on Sun Oct 04 2009 - 20:00:02 PDT
