[gmx-users] curious 'File not found' error

[Luciane Vieira de Mello]

Hi

A while back I posted a message about a 2GB file size limit in Linux that
was causing problems with big trajectories.  Upgrading to 2.4.18 kernel
removed the general problem but another, less serious one, remains.
Visualization with ngmx just shows me around 2GB worth of trajectory - it
seems like there is a separate limitation in that program.  Has anyone
else seen this?  This does *not* apply to other gromacs programs that I
have tried.  For example tpbconv reads the entire trajectory with no
problems.

Part of the advice I got last time was to use .xtc instead of .trr.  This
would be nice to save space, but I always understood that I needed trr
rather than xtc to restart crashed trajectories.  Is this true?
Unfortunately the restarting is generally necessary.

Luciane

+-------------------------------------------------------------------------+
|                  Dra. Luciane Vieira de Mello Rigden                    |
| e-mail: mello at cenargen.embrapa.br                                       |
| Embrapa Recursos Geneticos e Biotecnologia                              |
| Parque Estacao Biologica           |  http://www.cenargen.embrapa.br    |
| PqEB - Final - Av. W3 Norte        |  Phone:  +55 (61)448-4741          |
| 70770-900, Brasilia-D.F.-BRAZIL    |  Fax:    +55 (61)340-3658          |
+-------------------------------------------------------------------------+



On 16 Jan 2003, David wrote:

> On Thu, 2003-01-16 at 18:52, Luciane Vieira de Mello wrote:
> > Dear David
> >
> > I've been trying to read a big file
> >
> > -rwxrwxrwx    1 mello    desenv   4327006208 Jan 16 13:44 traj.trr
> >
> > with kernel 2.4.18.
> >
> > It opens fine with ngmx which shows that Linux constraint has been removed
> > (no more 'file not found' error).  However, although it contains around
> > 3.8 ns
> >
> > [mello at coruja protein+2PG_new]$ tail md.lis
> > ....
> > step 3873410, will finish at Fri Jan 24 11:57:08 2003
> >
> > it only shows up to 1.8 ns
> >
> > Last frame        912 time 1824.000
> > WARNING: Incomplete frame: nr 913 time 1826
> >
> > Is there some limit in GROMACS too?  Maybe something that's been fixed in
> > a more recent version (we have 3.14)
> That is the most recent official version. You can turn on the large file
> support at the compilation stage, but configure does it by default if
> the OS supports it. I don't know about the rpms.
>
> It looks like a 2Gb problem still. Is this just ngmx, or also other
> programs? By the way, using .xtc will save you a factor of three in size
> for the trajectory.
>
> And please do send your questions to the gmx-users list....
> --
> Groeten, David.
> ________________________________________________________________________
> Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
> Husargatan 3, Box 596,  	75124 Uppsala, Sweden
> phone:	46 18 471 4205		fax: 46 18 511 755
> spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
>