[gmx-users] g_principal: memory corruption

[David van der Spoel]

On 2010-07-03 02.40, kulleperuma.kulleperuma at utoronto.ca wrote:
> Hi all,
>
> I am using Gromacs-4.0.5 g_principal for a system with a protein of 132
> resiudes, ~450 octane molecules and ~9000 water molecules, as below,
>
> g_principal -f pos_Rep.xtc -s em.tpr -n index.ndx (Protein was the
> selected group ).
> I get the follwing message soon after I selected Protein
>
> Reading frame 0 time 0.000 *** glibc detected *** g_principal: malloc():
> memory corruption: 0x000000000646c250 ***
> ======= Backtrace: =========
> /lib64/libc.so.6[0x2b4788cd24ac]
> /lib64/libc.so.6(__libc_calloc+0xc0)[0x2b4788cd3ce0]
> g_principal[0x41071c]
> g_principal[0x471aff]
> g_principal[0x472237]
> g_principal[0x410539]
> g_principal[0x40251f]
> g_principal[0x402139]
> /lib64/libc.so.6(__libc_start_main+0xf4)[0x2b4788c7d974]
> g_principal[0x402079]
> ======= Memory map: ========
>
> .................
>
> This error didn't occur and ran smoothly when .gro file was selected for
> -f flag, but failed even for a shorter trajectory file.
>
> What is the way around for this problem
> Thank you in advance!
>
>
>
>
>
>
Please submit a bugzilla with a short trajectory (since it crashes at 
time 0 one frame is enough).

-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se