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

[Yang Ye]

On 11/9/2007 9:21 PM, David van der Spoel wrote:
> 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?
My Linux is ubuntu 32-bit on P4.
If mdrun is built without dmalloc, it will report realloc error from glibc.
Then I built mdrun with dmalloc, and it reports the line above ("realloc 
for g->edge[0]...,mshift.c. line 251...")
>>
>>>
>>>> Regards,
>>>> Yang Ye
>>>>
>>>>>
>>>>> Cheers,
>>>>>
>>>>> Bruce
>>>>>
>>>>
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>>>
>>
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