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Running EGO

Now we are ready to run EGO. If you are using the sequential version of EGO just type ego_seq.

If you use PVM you have to specify which and how many nodes should be used for EGO. This may be done by entering the PVM console by typing
Now you can add your nodes by typing
add node1 node2 node3
(Substitute your local machine names for node1, node2, etc.). Exiting the PVM console with
will leave that configuration active for your calculation. If you add fewer nodes than you requested in your ctl.lis file, EGO spawns some ``virtual nodes'' on the existing nodes[*]. Always remember that one node is used as a master node. This node controls the worker nodes, writes analysis output, etc. So if you request
N nodes for calculation in ctl.lis you should reserve N+1 ``physical nodes'' of your parallel computer for EGO to get best performance. To start calculation type

If you use PARIX you start the calculation by typing
ppx run -f0 4 4 /ego/PARIX/ego.px
This command starts EGO via the link 0 (-f0) on a Parsytec PowerXplorer with
4*4=16 nodes which are connected via a 2-dimensional mesh having 4 nodes on each side.

If you use MPI calculation is started usually by a mpirun command. Depending on your MPI implementation you specify as argument either the program name or a configuration file which gives information on the hosts to use for your run, pathes and the program name. For further details look at the documentation of your MPI implementation.

The startup of EGO looks like:

EGO_VIII.2   A Molecular Dynamics Program
C by M. Eichinger, H. Grubmueller and H. Heller, 1988-1995

Reading control file      : </home/mol/eichi/trans/data/pti/ctl.lis>

No of nodes used in calculation = 2 (out of 1 available nodes)
Found NO restart file     : </home/mol/eichi/trans/data/pti/restart.lis>
Lis-files are in directory: </home/mol/eichi/trans/data/pti/>
Writing data to directory : </home/mol/eichi/trans/data/pti/out/>
Current working directory : </home/mol/eichi/trans/data/pti/>

========== Start of control file =============================
2               Requested no of nodes.
568             Number of atoms.
========== End of control file ===============================

568 atoms will be written to output files.
Bounding-Box:  X: -6.9109 	  27.965 	 dx=  34.876
               Y:  10.077 	  34.601 	 dy=  24.524
               Z: -11.487 	  24.238 	 dz=  35.726
Level  0: Nr_of_clusters  105    Nr_of_Children  568   (Time:  0.1074) 
Cl.-Statistic-file <cluster0.out> written: <RGyr>= 1.408 Sig = 0.236
Cl.-Statistic-file <cluster1.out> written: <RGyr>= 4.032 Sig = 0.4205
Number of atoms on Node   1:   300
Number of atoms on Node   2:   268
Reading bondfile ...
Reading exclusion-file ...
Reading exclusion-14-file ...
Reading angle-file ...
Reading dihedral-file ...
Reading improper-file ...
Reading shake-file ...
Found  114 hydrogen-atoms in shake-list.

Start now distributing data to nodes ...
Node number   1 is being loaded with  300 atom-coordinates now.
EXCLUSION list             :  1496
1-4 EXCLUSION list         :  1044
SHAKE list                 :  132
BOND list   (intern/extern):  226     24
ANGLE list  (intern/extern):  395     81
DIHEDRAL l. (intern/extern):  151     67
IMPROPER l. (intern/extern):  109     33
Branch for node  1 loaded.

Reading van der Waals parameters
Reading 1-4 van der Waals parameters
Reading bond potential parameters
Reading angle potential parameters
Reading dihedral potential parameters
Reading improper potential parameters

Switched over to calculation phase!

The last line signals that EGO's startup has finished. All necessary initialization of the master node and worker nodes has been done and EGO starts now to calculate the trajectory.

next up previous contents
Next: EGO Output Up: Getting Started - Computing Previous: Example: A Fraction of
Helmut Heller