AMBER Archive (2009)

Subject: Re: [AMBER] ambertools and Snow Leopard 64 bits kernel

From: Tom Joseph (ttjoseph_at_gmail.com)
Date: Tue Sep 22 2009 - 19:18:17 CDT

I was able to reproduce these failures.

In the nab testcase, strange object code that nukes pointers returned
from functions is generated, causing the segfault. I suspect it has
something to do with 32 vs 64 bit linking, but I don't know enough
about Apple's linker to know what's going on here. For the antechamber
failure...not sure what's going on there; perhaps some antechamber
expert can comment?

For the time being perhaps it's best to use nab and antechamber on
another platform.

--Tom

2009/9/22 Alan <alanwilter_at_gmail.com>:
> Thanks Tom, it did help.
>
> However, nab still fails and from antechamber the last test failed with:
> ==============================================================
> cd antechamber/chemokine && ./Run.1b2t
> make: *** [test.antechamber] Error 1
>
> [DETAILED]
>
> ../../../exe/antechamber -fi pdb -fo ac -i 1b2t.pdb -o 1b2t.ac -at amber \
>>    -s 2 -pf yes
>
> The atom number exceeds the MAXATOM, reallocate memory
> Info: the bond number exceeds MAXBOND, reallocate memory automatically
> Running: /Users/alan/Programmes/amber10/bin/bondtype -j full -i
> ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
>
> Info: the atom number exceeds the MAXATOM, reallocate memory automatically
> ---Judge bond type for Residue 1 with ID of 0 and Name of MET ---
>
> [snip]
>
> ---Judge bond type for Residue 15 with ID of 14 and Name of LYS ---
>
> The frozen atom type can only be 1, 2, 3, 7 (aromatic single), 8
> (aromatic double)Error: cannot run
> "/Users/alan/Programmes/amber10/bin/bondtype -j full -i
> ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac" in
> judgebondtype() of antechamber.c properly, exit
>
> Many thanks,
>
> Alan
>
> On Tue, Sep 22, 2009 at 19:12, Tom Joseph <ttjoseph_at_gmail.com> wrote:
>> When you compiled antechamber, did you get warnings such as the following?
>>
>> alc.c:155: warning: call to __builtin___strcpy_chk will always
>> overflow destination buffer
>>
>> If so, this is a bug in antechamber - there are several instances
>> where a string is copied into a char array that is too small. Please
>> try the attached patch.
>>
>> --Tom
>>
>> 2009/9/22 Alan <alanwilter_at_gmail.com>:
>>> Hi there,
>>>
>>> I would like to know if there's other already using (or trying to use)
>>> AmberTools with Snow Leopard in 64 bits kernel.
>>>
>>> I did a try and although I had a nice compilation (gcc/gfortran with
>>> -m64), running tests failed for:
>>>
>>> nab, antechamber (some cases)
>>>
>>> For example:
>>>
>>> make -f Makefile_at test.nab
>>> ( cd nab; make test )
>>> =====================================================
>>> Running test to make dna duplex:
>>>
>>> /bin/sh: line 1: 21844 Segmentation fault      ./duplex < duplex.in
>>> make[1]: *** [duplex_test] Error 139
>>> make: *** [test.nab] Error 2
>>>
>>> make -f Makefile_at test.antechamber
>>> cd antechamber/top2mol2 && ./Run.top2mol2
>>> diffing sustiva.mol2.save with sustiva.mol2
>>> PASSED
>>> ==============================================================
>>> [snip]
>>> ==============================================================
>>> diffing fluorescein_f2.mol2.save with fluorescein_f2.mol2
>>> possible FAILURE:  check fluorescein_f2.mol2.dif
>>> ==============================================================
>>> cd antechamber/c60 && ./Run.c60
>>> Abort
>>>  ./Run.c60:  Program error
>>> make: *** [test.antechamber] Error 1
>>>
>>> Many thanks in advance,
>>>
>>> Alan
>>>
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>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
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