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
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