Dear Dr.Mark<br><br><div class="gmail_quote">On Sun, Apr 10, 2011 at 12:20 PM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div class="im">On 10/04/2011 5:40 PM, mohsen ramezanpour wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Dear All<br>
I used the following commands accoring to Extending Simulation in gromacs/Documentation/how-tos/Extending Simulation<br>
to extend my simulation.<br>
I entered:<br>
<br>
tpbconv -s npt-1.tpr -extend 100 -o npt-1-extend.tpr<br>
<br>
nohup mpirun -np 4 mdrun -s npt-1-extend.tpr -cpi npt-1.cpt<br>
<br>
Ii run this command on a node with 4 cpu.<br>
the result was these files:<br>
confout.gro , state.cpt ,md.log , traj.trr ,state_prev.cpt ,ener.edr ,<br>
#confout.gro.1# ,#confout.gro.2# ,#confout.gro.3# ,# ener.edr.1# ,#ener.edr.2# ,#md.log.1 #,#traj.trr.1# ,#traj.trr.2# ,<br>
<br>
I extended 4 files on 4 distinct nodes!<br>
</blockquote>
<br></div>
That's not the behaviour you were looking for. You've run the same .tpr four times, once on each CPU. This is because mdrun was not compiled with MPI. See the installation instructions.<div class="im"><br></div></blockquote>
<div>I think I explained bad.let me explain it more:<br>Suppose I entered the above commands on just one node(with 4 cpu) for npt-1.tpr (just one time I entered these commands)<br><br>besides if you were right it would result the same outputs when I run it on different nodes with the same commands,please see below!<br>
<br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="im">
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
it is excellent,because the number of outputs was different, for example one node produced 3 md.log and 4 confout.gro !<br>
<br>
The main question is:<br>
which one of the resulted outputs are the main result? on wich do I must analyse?<br>
</blockquote>
<br></div>
They should all be equivalent, but not necessarily binary identical.<br></blockquote><div>Actually I checked all of them,they are different,with different averages of quantities,<br>and all of them show a final text that means the program finished succesfully!<br>
<br>what do you think Dr.Mark?<br>Thanks in advance for your reply <br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
Mark<br><font color="#888888">
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