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

[Teemu Murtola]

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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