[gmx-users] do_dssp crashes on certain machines..

[Florian Haberl]

hi,

On Thursday, 19. April 2007 17:23, Mark Abraham wrote:
> pascal.baillod at epfl.ch wrote:
> > Dear community,
> >
> > I have the following problem with do_dssp, when I try analysing a long 70
> > ns trajectory produced by a REMD calculation. All my previous analysis
> > went fine, when the trajectory had a length of ~= 50ns. However, I now
> > obtain the following errror message, perhaps one hour after launching
> > do_dssp, when the standard error message says frames around 54ns are
> > being analysed:
> >
> >
> > Group    12 (          Cl) has     8 elements
> > Group    13 (         SOL) has 42228 elements
> > Group    14 (       Other) has 42236 elements
> > Select a group: There are 103 residues in your selected group
> > Opening library file
> > /home/coutinho/software/gromacs-3.3.0/icc9.0/share/gromacs/top/ss.map
> > Reading frame       0 time    0.000
> > Back Off! I just backed up ddKGQneH to ./#ddKGQneH.1#
> > Reading frame   36630 time 54945.000
> > -------------------------------------------------------
> > Program do_dssp, VERSION 3.3
> > Source code file: futil.c, line: 340
> >
> > File input/output error:
> > ddr3C7fs
> > -------------------------------------------------------
> >
> >
> > I guess this problem is due to the architecture/memory of the nodes of
> > the cluster I use (where this error occurs whether do_dssp is the only
> > job on the node or not): The same analysis works fine on another machine.
> > The cluster I use is made of Hewlett-Packard ProLiant DL145 G2 AMD
> > Opteron Model 246 nodes. The nodes contain two AMD opteron 2.4GHz cpus
> > and 4*1GB memory.
> >
> > I thank you very much for any suggestions!
>
> Do the analysis piecewise... trjconv to break the .trr into chunks, and
> now you can even do the analysis in parallel.

Could be a nice application for pushing parallel filesystems to its limits!

Perhaps it could be implemented in upcoming gromacs versions, something like 
mpich wrapper for certain analysis tools.
>
> Mark
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Grettings,

Florian

-- 
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 Florian Haberl                        
 Computer-Chemie-Centrum   
 Universitaet Erlangen/ Nuernberg
 Naegelsbachstr 25
 D-91052 Erlangen
 Telephone:  	+49(0) − 9131 − 85 26581
 Mailto: florian.haberl AT chemie.uni-erlangen.de
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