What happens if you _don't_ use the "natural language" syntax and use the
rather cryptic, old Amber one instead?
On Fri, Jan 27, 2012 at 8:51 AM, Jan-Philip Gehrcke <jgehrcke.googlemail.com
> wrote:
> Huhu!
>
> We're using Amber 11 (including all bugfixes up to last week) and observed
> a compiler-dependent error while parsing a DISANG file in sander. For ICC
> 12.1, things work properly, while for GCC 4.6.2, sander crashes. Details
> below.
>
> We've assembled a small test case. It is performing a minimization of some
> system with sander, using this input (min2.in):
>
> &cntrl
>> imin = 1,
>> maxcyc = 6000,
>> ncyc = 3000,
>> ntb = 1,
>> ntr = 0,
>> cut = 8,
>> nmropt = 1,
>> &end
>> &wt
>> type ='END',
>> &end
>> LISTOUT=POUT
>> DISANG=../rest
>>
>
>
> The `rest` file is attached.
>
> I'm running the minimization using the following command:
>
> sander -O -i ../min2.in -o min2.out -p ../top.top -c ../min1.crd -r
>> min2.rst
>>
>
>
>
> Result on Amber 11 compiled with GCC 4.6.2 on CentOS 5.7
> ==============================**==========================
> Sander crashes "immediately".. presumably while parsing the `rest` file.
> min2.out:
>
> > [...]
>
>> Here is the input file:
>> [...]
>> ------------------------------**------------------------------**
>> --------------------
>> 1. RESOURCE USE:
>> ------------------------------**------------------------------**
>> --------------------
>>
>> | Flags:
>> getting new box info from bottom of inpcrd
>> | INFO: Old style inpcrd file read
>>
>> | peek_ewald_inpcrd: Box info found
>> |Largest sphere to fit in unit cell has radius = 21.977
>> Error: Invalid atom or grouping specified in restraint.
>> restraint = "torsion [:70.C1, :70.O5, :70.C5, :70.C4]"
>>
>
>
> Result on Amber 11 compiled with ICC 12.1 on Ubuntu 10.04
> ==============================**===========================
> The minimization works.
>
>
> Final remarks
> =============
> I've compiled both of these Amber environments and also performed the
> automatic tests in $AMBERHOME/test. As far as I remember, this problem has
> not been catched by an Amber test case.
>
> I have to add that although I cannot provide a repro, our group observed
> this problem already with Amber 10 and other (older) compilers. There, I
> have been told that the occurrence of the error depended on
> - the operating system or
> - the hardware
> but definitely not on the executable, because it was always the same.
>
> However, with Amber 11, the sander binary created with ICC 12.1 seems to
> work fine on each system I could test it on, while the sander binary
> created with GCC 4.6.2 seems to fail on all of these systems.
>
>
> I hope that this problem can be easily tracked down. If I can be of any
> further help, please let me know what I can do.
>
>
> Thanks,
>
> Jan-Philip
>
>
>
>
>
>
>
>
>
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>
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Jan 27 2012 - 07:30:03 PST
