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

[David van der Spoel]

Yang Ye wrote:
> On 11/9/2007 9:09 PM, David van der Spoel wrote:
>> 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 
>> differences).
> Yes.
> Try 32-bit? 64-bit on my Opteron is alright too (with and without dmalloc).
This is a 32 bit OS AFAIK (Mac OS X 10.5) with gcc 4.0.1
Anyway how did you obtain the above result?
What command line?
> 
>>
>>> Regards,
>>> Yang Ye
>>>
>>>>
>>>> Cheers,
>>>>
>>>> Bruce
>>>>
>>>
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>>
>>
> 
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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