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

[Teemu Murtola]

Thanks for the clarification. I updated the Redmine issue (
http://redmine.gromacs.org/issues/1834) with a summary and next steps. I
unfortunately do not have access to various systems to test the issue, but
I put some guesses on the possible reasons in the issue.

Best regards,
Teemu

On Tue, Oct 6, 2015, 07:37 Venkat Reddy <venkat4bt at gmail.com> wrote:

> 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
> > > > --
> > > > Gromacs Users mailing list
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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
> --
> Gromacs Users mailing list
>
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> posting!
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