Jason,
as I am still quite new to Amber, I am not sure what you mean. Could you
give an example? You say this old syntax is cryptic, so I would say that
translating the natural language to the cryptic language is not a good
general solution to this problem.
I assume that trying this translation is important for debugging
purposes -- so, how should we start there?
Cheers
On 01/27/2012 04:28 PM, Jason Swails wrote:
> 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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>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>
>
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Received on Fri Jan 27 2012 - 08:30:02 PST
