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

Teemu Murtola teemu.murtola at gmail.com
Fri Oct 2 06:17:03 CEST 2015


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.


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