[gmx-users] gmx 3.3.2 explodes with libc.so.6

David van der Spoel spoel at xray.bmc.uu.se
Fri Nov 9 14:09:04 CET 2007

Yang Ye wrote:
> On 11/9/2007 6:47 PM, Bruce Milne wrote:
>> Dear Li Qiang,
>>>> it seems another guy get the same error(cannot pass gmxtest with
>>>> rb1/acetonitrilRF) as me. and it sounds like the compatible problem
>>>> between GROMACS 3.3.2 and and UBUNTU 7.10. Both are rather new.
>>>> Herein I just suggest and hope others may help to install 3.3.2 on new
>>>> ubuntu 7.10 to confirm the problem. 
>> I have just installed 3.3.2 on my (64-bit) Ubuntu 7.10 machine 
>> (dual-core Athlon64 4000+, 2GB RAM) and run the serial tests. All the 
>> single and double precision tests passed with and without assembly 
>> loop optimizations so I guess it's not simply Ubuntu 7.10 that is to 
>> blame (unless what you are seeing is a 32-bit distribution-specific 
>> problem?).
> Quite likely a 32-bit specific problem.
> Could anyone install dmalloc and configure gromacs to build with dmalloc 
> and run the test with the new mdrun?
> I did mine and found that it was due to one line in mshift.c 
> "srenew(g->edge[0],n); "
> mdrun output:
> realloc for g->edge[0] (24 bytes, file mshift.c, line 251, 
> g->edge[0]=0x0x       1)

So is this in the rb1 test? I compiled the code with dmalloc on my Mac 
and it passed all tests (except dec+water due to very small energy 

> Regards,
> Yang Ye
>> Cheers,
>> Bruce
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David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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