VMD-L Mailing List

From: Alexander A. Vakhrushev (makaveli.lcf_at_gmail.com)
Date: Tue Oct 07 2008 - 12:08:35 CDT

Thank you John for your explanations! Now it's clear for me.

2008/10/7 John Stone <johns_at_ks.uiuc.edu>:
>
> Alexander,
> VMD 1.8.5 didn't support files larger than 2/4GB on Windows, that's why
> the behavior has changed. The code I included in my reply is new and was
> required in order to support the large files. The old version of the dcdplugin
> can be made to work with the new version of VMD, but it won't support
> big trajectory files.
>
> Cheers,
> John
>
> On Tue, Oct 07, 2008 at 10:03:16PM +0500, Alexander A. Vakhrushev wrote:
>> John,
>>
>> It seems to me, that there were no such problems in v1.8.5, so I'll
>> recheck to find possible solution.
>>
>> 2008/10/7 John Stone <johns_at_ks.uiuc.edu>:
>> >
>> > Alexander,
>> >
>> > On Sat, Oct 04, 2008 at 08:55:52AM +0500, Alexander A. Vakhrushev wrote:
>> > [...]
>> >> I have the following question: Windows version of VMD does not allow
>> >> to load DCD trajectory file while it is being downloaded from remote
>> >> host (in other words when file is of incomplete size). When I stop
>> >> download even it was not finished everything goes OK. Linux version
>> >> does not has such behaviour. Would you suggest any solutions?
>> >
>> > The Windows version of the DCD plugin uses the Win32 binary file I/O
>> > APIs, which have different limitations and semantics than the
>> > read/write/seek calls on Unix. I believe the likely source of problems
>> > is the code we're forced to use on Windows to determine the size of
>> > large files (files larger than 4GB) since the Windows implementation of
>> > the normal libc calls is not capable of dealing with such large files:
>> >
>> > #if defined(_MSC_VER) && defined(FASTIO_NATIVEWIN32)
>> > /* the stat() call is not 64-bit savvy on Windows */
>> > /* so we have to use the fastio fseek/ftell routines for this */
>> > /* until we add a portable filesize routine for this purpose */
>> > fio_fseek(dcd->fd, 0, FIO_SEEK_END); /* seek to end of file */
>> > filesize = fio_ftell(dcd->fd);
>> > fio_fseek(dcd->fd, curpos, FIO_SEEK_SET); /* return to end of header */
>> > #else
>> > filesize = stbuf.st_size; /* this works ok on Unix machines */
>> > #endif
>> >
>> > You could try writing another piece of code to query the file size
>> > that behaves better with files that are in the process of being
>> > appended to, but it's really somewhat of a questionable scenario to
>> > attempt to load files that are in the process of being updated since
>> > OSes handle these things a bit differently.
>> >
>> > Cheers,
>> > John Stone
>> > vmd_at_ks.uiuc.edu
>> >
>> > --
>> > NIH Resource for Macromolecular Modeling and Bioinformatics
>> > Beckman Institute for Advanced Science and Technology
>> > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
>> > Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
>> > WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
>> >
>>
>>
>>
>> --
>> Best regards,
>>
>> Dr. Alexander Vakhrushev
>> Institute of Applied Mechanics
>> Dep. of Mech. and Phys.-Chem.
>> of heterogeneous media
>> UB of Russian Academy of Sciences
>> 34 T. Baramzinoy St.
>> Izhevsk, Russia 426067
>> ----------------------------------
>> ? ?????????,
>> ???????? ????????? ?????????????
>>
>> ?.?.-?.?., ?.?.?.
>> ???????? ?????????? ????????
>> ?????????? ?????????
>> ?????????? ???????? ????
>> 426067, ?. ??????
>> ??. ?. ?????????? 34
>> +7(3412)21-45-83
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
> 

-- 
Best regards,
Dr. Alexander Vakhrushev
Institute of Applied Mechanics
Dep. of Mech. and Phys.-Chem.
of heterogeneous media
UB of Russian Academy of Sciences
34 T. Baramzinoy St.
Izhevsk, Russia 426067
----------------------------------
С уважением,
    Вахрушев Александр Александрович
к.ф.-м.н., с.н.с.
Институт прикладной механики
Уральского Отделения
Российской Академии Наук
426067, г. Ижевск
ул. Т. Барамзиной 34
+7(3412)21-45-83