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On 10/04/2011 6:04 PM, mohsen ramezanpour wrote:
<blockquote
cite="mid:BANLkTimr5b3o5DTnhDV2o6nb0VFiAMwDbg@mail.gmail.com"
type="cite">Dear Dr.Mark<br>
<br>
<div class="gmail_quote">On Sun, Apr 10, 2011 at 12:20 PM, Mark
Abraham <span dir="ltr"><<a moz-do-not-send="true"
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>
</div>
</div>
</blockquote>
<br>
You seem to have used mpirun to run four different mdrun processes,
each using the same .tpr, one on each cpu. You should be trying to
run one mdrun_mpi using that .tpr, but all four cpus working on the
same run.<br>
<br>
Look at the top few lines of your .log. That will tell you how many
nodes mdrun thought it was running on. I think you will see
"NNODES=1". If so, don't use this mdrun with mpirun.<br>
<br>
<blockquote
cite="mid:BANLkTimr5b3o5DTnhDV2o6nb0VFiAMwDbg@mail.gmail.com"
type="cite">
<div class="gmail_quote">
<div>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>
</div>
</div>
</blockquote>
<br>
Not strictly true. See
<a class="moz-txt-link-freetext" href="http://www.gromacs.org/Documentation/Terminology/Reproducibility">http://www.gromacs.org/Documentation/Terminology/Reproducibility</a><br>
<br>
<blockquote
cite="mid:BANLkTimr5b3o5DTnhDV2o6nb0VFiAMwDbg@mail.gmail.com"
type="cite">
<div class="gmail_quote">
<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>
</div>
</div>
</blockquote>
<br>
The averages being the same or different merely reflect whether your
run was reproducible. Assuming there was no output files in your
working directory to start with, you've run the same irreproducible
run four times, because you're using a non-MPI mdrun.<br>
<br>
Mark<br>
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