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

Mark Abraham Mark.Abraham at anu.edu.au
Thu Apr 19 17:23:53 CEST 2007

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.


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