[gmx-users] re:multi problem again

[David van der Spoel]

Andrei Neamtu wrote:
> Dear Mark,
> 
> Thank you for your reply!
> 
> I thought that maybe the accessibility were the problem. I don't figure 
> how to set the working directory of say node 1 to my current working 
> directory on node 0.
> I setup node 1 to be able to access node 0 through ssh with no password 
> but the problem remains. So .. I'm stuck here.
> Any idea where to start digging solving the most probable accessibility 
> problem?
> 
> In short there is how I made the GROMACS installation:
> 
> 1. I installed GROMACS (serial and parallel version) on every node
> 2. I setup the node 0 to be able to access all other nodes through ssh 
> without password
> 3. generated on node 0 the nodesfile file for lam booting
> 
> I must say that parallel simulations run fine on the entire cluster (I 
> mean a single system split on all nodes). The only problem appears when 
> I try using -multi to simulate several copies of the system along the 
> nodes.
> 
> Do I have to use a file sharing system or something like this ...?
> It is the first time I try to use the -multi option.
> 
> Thank you a lot,
> Andrei
> 
> 

you have to look into your queueing system. alternatively you can use 
the complete path e.g. /home/andrei/simulation/sim.tpr

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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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