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

pascal.baillod at epfl.ch pascal.baillod at epfl.ch
Thu Apr 19 16:15:42 CEST 2007

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
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:

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!

Pascal Baillod

Pascal Baillod (PhD student) 
Swiss Federal Institute of Technology EPFL	        Tel: +41-(0)21-693-0322
Institute of Chemical Sciences and Engineering ,	Fax: +41-(0)21-693-0320
Laboratory of Computational Chemistry and Biochemistry	pascal.baillod at epfl.ch
Room BCH 4121, Avenue Forel,	                        http://lcbcpc21.epfl.ch
CH-1015 Lausanne	

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