[gmx-users] Analysis of old xtc file using gromacs-5 tools

[Venkat Reddy]

Hi,
Sorry for the confusion. Now I have generated a small xtc file and a very
big pdb file. I can able to access small xtc file but unable to read the
large pdb file (~10GB) (terminating with the same error as reported
earlier). Does it mean my installation has some problem?

On Mon, Oct 5, 2015 at 7:41 PM, Teemu Murtola <teemu.murtola at gmail.com>
wrote:

> Hi,
>
> That unfortunately doesn't tell us anything, since 1.5GB can still be read
> with 32-bit file operations. You didn't answer any of the questions: can
> you open very small xtc files, or very large (requiring 64-bit access)
> gro/pdb files, or not? We are still thinking that you should be able to
> open any files smaller than 2GB just fine, but you are making confusing
> claims that seem to contradict this, so this needs to be sorted out before
> we can really conclude anything.
>
> Best regards,
> Teemu
>
> On Mon, Oct 5, 2015, 08:32 Venkat Reddy <venkat4bt at gmail.com> wrote:
>
> > Hi,
> > Sorry for the delay in reply.
> > I am able to access pdb/gro files of size 1.5 GB with Gromacs-5.1
> version.
> > My Desktop is 32-bit whereas my xtc files were generated on our super
> > cluster, which runs on 64-bit O.S.
> >
> > On Fri, Oct 2, 2015 at 9:46 AM, Teemu Murtola <teemu.murtola at gmail.com>
> > wrote:
> >
> > > Hi,
> > >
> > > On Thu, Oct 1, 2015 at 6:30 PM Szilárd Páll <pall.szilard at gmail.com>
> > > wrote:
> > >
> > > > On Thu, Oct 1, 2015 at 8:01 AM, Venkat Reddy <venkat4bt at gmail.com>
> > > wrote:
> > > > > Gromacs-5.1 version can not read xtc files. However, it can access
> > > single
> > > > > frame gro/pdb files.
> > > > >
> > > >
> > > > That's a bold claim that IMO requires equally strong proof.
> > > >
> > >
> > > I agree with Szilard. Are you saying that you cannot even read a
> > > single-frame xtc file with just a few kB in size? How about other
> binary
> > > files (e.g., trr)? How about large (>2GB) gro files?
> > >
> > > In your other mail to the list you were talking about a 32-bit Ubuntu
> VM.
> > > > Are you sure you're not running into in incompatibility issue between
> > the
> > > > 32-bit binaries vs 64-bit xtc file(s) you're trying to read?
> > > >
> > >
> > > I would still suspect that the underlying reason is that for some
> reason,
> > > 5.1 gets compiled without large file support in your system, which
> makes
> > > even plain fopen() fail on large files. The build system should give an
> > > error if it cannot find 64-bit file support, but the check may be
> > > imperfect. Someone who can reproduce the issue (i.e., has access to a
> > > similar OS and other environment) should try what is actually required
> to
> > > get 64-bit file support working there. Based on the information you
> > posted
> > > in Redmine, the build system already checks that off_t is 64-bit
> without
> > > any extra defines on your system. The checks in the build system have
> not
> > > changed between 5.0 and 5.1, though.
> > >
> > > Teemu
> > > --
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> > >
> >
> >
> >
> > --
> > With Best Wishes
> > Venkat Reddy Chirasani
> > PhD student
> > Laboratory of Computational Biophysics
> > Department of Biotechnology
> > IIT Madras
> > Chennai
> > INDIA-600036
> > --
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-- 
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036