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.