On Mon, Mar 23, 2015 at 10:06 AM, Vijay Achari <glycoamber.gmail.com> wrote:
> I found out that there are 27 empty white spaces between the columns of the
> data file. So I reduced the only one empty white space.
>
> Now this works for me.
Good. The next version of cpptraj will implement dynamic resizing of
the internal buffer to avoid this issue altogether. Thanks for the
report,
-Dan
>
> I used command awk.
>
> *awk '{$1=$1}1' file*
>
>
> Thanks.
> Vijay
>
>
> On Mon, Mar 23, 2015 at 10:32 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
>> Hi,
>>
>> On Mon, Mar 23, 2015 at 12:32 AM, Vijay Achari <glycoamber.gmail.com>
>> wrote:
>> > Internal Error: Input line size > internal buffer size (16384)
>> > Internal Error: Increase the size of BufferedLine::DEFAULT_BUFFERSIZE
>> and recompile
>>
>> This error occurs when you have very long lines in your input data
>> file (greater than 16k characters). If you have lines longer than this
>> in your input data file, unfortunately the only workaround is to do as
>> the error message suggests. I'll have to consider implementing a
>> better fix in the future.
>>
>> > Can I get any help to resolve this error? If I run with smaller number of
>> > frames (1000), I don't have problem.
>>
>> Since you don't get the error when you run with fewer frames, this
>> makes me think that maybe the formatting in the file
>> 'onlyData-hbLifeTime-maltoLyo12per-solulte-solute-O11.dat' gets messed
>> up at some point. Do you expect the lines to be longer than 16k
>> characters? If not it's possible you're missing a newline (or several)
>> somewhere in the file.
>>
>> -Dan
>>
>> >
>> > I am running this calculation in Centos 6.3 with 96 GB memory.
>> >
>> > Regards
>> > Vijay
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
>> --
>> -------------------------
>> Daniel R. Roe, PhD
>> Department of Medicinal Chemistry
>> University of Utah
>> 30 South 2000 East, Room 307
>> Salt Lake City, UT 84112-5820
>> http://home.chpc.utah.edu/~cheatham/
>> (801) 587-9652
>> (801) 585-6208 (Fax)
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Mon Mar 23 2015 - 13:00:02 PDT
