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

[Yang Ye]

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).

>
>> Regards,
>> Yang Ye
>>
>>>
>>> Cheers,
>>>
>>> Bruce
>>>
>>
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>