[gmx-users] Buffer Overflow Problem on Ubuntu Linux

[Venky Krishnamani]

Hi,

I installed gromacs 3.3.3 on Ubuntu Linux 9.10 running on a Intel(R) Core(TM)2 Quad CPU @ 2.40GHz w/ 4 GB RAM. I am getting the following errors for any of the gromacs commands, even when I am using the -h option to list the options available for that command. I removed the installation and installed a fresh copy of the 3.3.3 version. Then the commands work for a couple of times and again generates the same error of "buffer overflow" for all the subsequent tries once it starts throwing that error.

Then I tried to run the same simulation setup on another computer running AMD Phenom II running @ 3.00 GHz w/ 4 GB RAM and Gromacs 3.3.3. Everything runs without a hitch. 

Below is a part of the error generated.
------------------------------

NNODES=4, MYRANK=0, HOSTNAME=xion
NNODES=4, MYRANK=1, HOSTNAME=xion
NNODES=4, MYRANK=3, HOSTNAME=xion
NNODES=4, MYRANK=2, HOSTNAME=xion
NODEID=1 argc=4
NODEID=0 argc=4
NODEID=3 argc=4
NODEID=2 argc=4
                         :-)  G  R  O  M  A  C  S  (-:

*** buffer overflow detected ***: mdrun_mpi terminated
======= Backtrace: =========
/lib/libc.so.6(__fortify_fail+0x37)[0x7f6bc65185f7]
/lib/libc.so.6[0x7f6bc65175a0]
/lib/libc.so.6[0x7f6bc6516457]
mdrun_mpi[0x4f7ea3]
mdrun_mpi[0x4f80da]
mdrun_mpi[0x4f8145]
mdrun_mpi[0x4e984a]
mdrun_mpi[0x4ea126]
mdrun_mpi[0x425d6c]
/lib/libc.so.6(__libc_start_main+0xfd)[0x7f6bc643fabd]
mdrun_mpi[0x403449]
======= Memory map: ========
00400000-0067f000 r-xp 00000000 08:01 2546                               /usr/local/gromac
s/bin/mdrun_mpi
0087e000-0087f000 r-xp 0027e000 08:01 2546                               /usr/local/gromac
s/bin/mdrun_mpi
0087f000-00887000 rwxp 0027f000 08:01 2546                               /usr/local/gromac
s/bin/mdrun_mpi
00887000-0088d000 rwxp 00000000 00:00 0 
01b06000-01b2f000 rwxp 00000000 00:00 0                                  [heap]
7f6bc4bc8000-7f6bc4bde000 r-xp 00000000 08:01 7915                       /lib/libgcc_s.so.
1

--------------------------------

Do you think there is some hardware issue?

Thanks any help regarding this is appreciated.

Venky

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Venky Krishnamani
Dr.Janos K. Lanyi Lab,
D320, Medical Sciences I
University of California, Irvine
Irvine, CA 92697
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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