[gmx-developers] g_dielectric_d: corrupted double-linked list
Michael Brunsteiner
mbx0009 at yahoo.com
Wed Dec 21 15:33:36 CET 2011
hi,
i guess this belongs into the developers rather then the users list:
i simulate a simple box with apprx 3000 TIP3P waters at ambient conditions, then do:
g_dipoles_d -f my.trr -s my.tpr -corr total -o dip_sqr
followed by:
g_dielectric_d -f dipcorr.xvg
the second command gives me an error from glibc (some memory issue?)
included below. (this is on a PC with:
uname -a
Linux rcpetemp1 2.6.35-28-generic #49-Ubuntu SMP Tue Mar 1 14:39:03 UTC 2011 x86_64 GNU/Linux
)
BTW, the first command (g_dipoles puts the following line on stdout:
"Epsilon = 561.138"
is this the dielectrioc permittivity? if so, its quite far off the literature value (<100)
is my simulation time too short (200 ps) or what else could be the reason
for this discrepancy?
regards,
michael
the output of: g_dielectric_d -f dipcorr.xvg ...
Read data set containing 2 colums and 501 rows
Assuming (from data) that timestep is 0.2, nxtail = 501
Creating standard deviation numbers ...
nbegin = 25, x[nbegin] = 5, tbegin = 5
*** glibc detected *** g_dielectric_d: corrupted double-linked list: 0x0000000002075c60 ***
======= Backtrace: =========
/lib/libc.so.6(+0x774b6)[0x7f89fc7c84b6]
/lib/libc.so.6(+0x7bb5c)[0x7f89fc7ccb5c]
/lib/libc.so.6(__libc_calloc+0xc4)[0x7f89fc7cf254]
/usr/local/gromacs/lib/libgmx_d.so.6(save_calloc+0x6d)[0x7f89fd1af41d]
/usr/local/gromacs/lib/libgmxana_d.so.6(do_lmfit+0xbf8)[0x7f89fe1563b8]
/usr/local/gromacs/lib/libgmxana_d.so.6(gmx_dielectric+0xae3)[0x7f89fe1d0293]
g_dielectric_d(main+0x9)[0x400809]
/lib/libc.so.6(__libc_start_main+0xfe)[0x7f89fc76fd8e]
g_dielectric_d[0x400739]
======= Memory map: ========
00400000-00401000 r-xp 00000000 09:00 145518700 /usr/local/gromacs/bin/g_dielectric_d
00600000-00601000 r--p 00000000 09:00 145518700 /usr/local/gromacs/bin/g_dielectric_d
00601000-00602000 rw-p 00001000 09:00 145518700 /usr/local/gromacs/bin/g_dielectric_d
02075000-02096000 rw-p 00000000 00:00 0 [heap]
7f89f8000000-7f89f8021000 rw-p 00000000 00:00 0
7f89f8021000-7f89fc000000 ---p 00000000 00:00 0
7f89fc323000-7f89fc338000 r-xp 00000000 09:00 273023036 /lib/libgcc_s.so.1
7f89fc338000-7f89fc537000 ---p 00015000 09:00 273023036 /lib/libgcc_s.so.1
7f89fc537000-7f89fc538000 r--p 00014000 09:00 273023036 /lib/libgcc_s.so.1
7f89fc538000-7f89fc539000 rw-p 00015000 09:00 273023036 /lib/libgcc_s.so.1
7f89fc539000-7f89fc54f000 r-xp 00000000 09:00 273023219 /lib/libz.so.1.2.3.4
7f89fc54f000-7f89fc74f000 ---p 00016000 09:00 273023219 /lib/libz.so.1.2.3.4
7f89fc74f000-7f89fc750000 r--p 00016000 09:00 273023219 /lib/libz.so.1.2.3.4
7f89fc750000-7f89fc751000 rw-p 00017000 09:00 273023219 /lib/libz.so.1.2.3.4
7f89fc751000-7f89fc8cb000 r-xp 00000000 09:00 273023283 /lib/libc-2.12.1.so
7f89fc8cb000-7f89fcaca000 ---p 0017a000 09:00 273023283 /lib/libc-2.12.1.so
7f89fcaca000-7f89fcace000 r--p 00179000 09:00 273023283 /lib/libc-2.12.1.so
7f89fcace000-7f89fcacf000 rw-p 0017d000 09:00 273023283 /lib/libc-2.12.1.so
7f89fcacf000-7f89fcad4000 rw-p 00000000 00:00 0
7f89fcad4000-7f89fcaec000 r-xp 00000000 09:00 273023286 /lib/libpthread-2.12.1.so
7f89fcaec000-7f89fcceb000 ---p 00018000 09:00 273023286 /lib/libpthread-2.12.1.so
7f89fcceb000-7f89fccec000 r--p 00017000 09:00 273023286 /lib/libpthread-2.12.1.so
7f89fccec000-7f89fcced000 rw-p 00018000 09:00 273023286 /lib/libpthread-2.12.1.so
7f89fcced000-7f89fccf1000 rw-p 00000000 00:00 0
7f89fccf1000-7f89fcd73000 r-xp 00000000 09:00 273023294 /lib/libm-2.12.1.so
7f89fcd73000-7f89fcf72000 ---p 00082000 09:00 273023294 /lib/libm-2.12.1.so
7f89fcf72000-7f89fcf73000 r--p 00081000 09:00 273023294 /lib/libm-2.12.1.so
7f89fcf73000-7f89fcf74000 rw-p 00082000 09:00 273023294 /lib/libm-2.12.1.so
7f89fcf74000-7f89fcf76000 r-xp 00000000 09:00 273023305 /lib/libdl-2.12.1.so
7f89fcf76000-7f89fd176000 ---p 00002000 09:00 273023305 /lib/libdl-2.12.1.so
7f89fd176000-7f89fd177000 r--p 00002000 09:00 273023305 /lib/libdl-2.12.1.so
7f89fd177000-7f89fd178000 rw-p 00003000 09:00 273023305 /lib/libdl-2.12.1.so
7f89fd178000-7f89fd55d000 r-xp 00000000 09:00 145518648 /usr/local/gromacs/lib/libgmx_d.so.6
7f89fd55d000-7f89fd75c000 ---p 003e5000 09:00 145518648 /usr/local/gromacs/lib/libgmx_d.so.6
7f89fd75c000-7f89fd762000 r--p 003e4000 09:00 145518648 /usr/local/gromacs/lib/libgmx_d.so.6
7f89fd762000-7f89fd76d000 rw-p 003ea000 09:00 145518648 /usr/local/gromacs/lib/libgmx_d.so.6
7f89fd76d000-7f89fd76e000 rw-p 00000000 00:00 0
7f89fd76e000-7f89fd8b2000 r-xp 00000000 09:00 116262699 /usr/lib/libxml2.so.2.7.7
7f89fd8b2000-7f89fdab1000 ---p 00144000 09:00 116262699 /usr/lib/libxml2.so.2.7.7
7f89fdab1000-7f89fdab9000 r--p 00143000 09:00 116262699 /usr/lib/libxml2.so.2.7.7
7f89fdab9000-7f89fdabb000 rw-p 0014b000 09:00 116262699 /usr/lib/libxml2.so.2.7.7
7f89fdabb000-7f89fdabc000 rw-p 00000000 00:00 0
7f89fdabc000-7f89fdbb0000 r-xp 00000000 09:00 116266924 /usr/lib/libfftw3.so.3.2.4
7f89fdbb0000-7f89fddaf000 ---p 000f4000 09:00 116266924 /usr/lib/libfftw3.so.3.2.4
7f89fddaf000-7f89fddb6000 r--p 000f3000 09:00 116266924 /usr/lib/libfftw3.so.3.2.4
7f89fddb6000-7f89fddb7000 rw-p 000fa000 09:00 116266924 /usr/lib/libfftw3.so.3.2.4
7f89fddb7000-7f89fdf26000 r-xp 00000000 09:00 145518652 /usr/local/gromacs/lib/libmd_d.so.6
7f89fdf26000-7f89fe126000 ---p 0016f000 09:00 145518652 /usr/local/gromacs/lib/libmd_d.so.6
7f89fe126000-7f89fe127000 r--p 0016f000 09:00 145518652 /usr/local/gromacs/lib/libmd_d.so.6
7f89fe127000-7f89fe129000 rw-p 00170000 09:00 145518652 /usr/local/gromacs/lib/libmd_d.so.6
7f89fe129000-7f89fe365000 r-xp 00000000 09:00 145518668 /usr/local/gromacs/lib/libgmxana_d.so.6
7f89fe365000-7f89fe564000 ---p 0023c000 09:00 145518668 /usr/local/gromacs/lib/libgmxana_d.so.6
7f89fe564000-7f89fe569000 r--p 0023b000 09:00 145518668 /usr/local/gromacs/lib/libgmxana_d.so.6
7f89fe569000-7f89fe56e000 rw-p 00240000 09:00 145518668 /usr/local/gromacs/lib/libgmxana_d.so.6
7f89fe56e000-7f89fe56f000 rw-p 00000000 00:00 0
7f89fe56f000-7f89fe58f000 r-xp 00000000 09:00 273023295 /lib/ld-2.12.1.so
7f89fe764000-7f89fe76b000 rw-p 00000000 00:00 0
7f89fe78c000-7f89fe78f000 rw-p 00000000 00:00 0
7f89fe78f000-7f89fe790000 r--p 00020000 09:00 273023295 /lib/ld-2.12.1.so
7f89fe790000-7f89fe791000 rw-p 00021000 09:00 273023295 /lib/ld-2.12.1.so
7f89fe791000-7f89fe792000 rw-p 00000000 00:00 0
7fff65a01000-7fff65a20000 rwxp 00000000 00:00 0 [stack]
7fff65a20000-7fff65a22000 rw-p 00000000 00:00 0
7fff65add000-7fff65ade000 r-xp 00000000 00:00 0 [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]
Aborted
===============================Why be happy when you could be normal?
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