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<div class="moz-cite-prefix">Hi,<br>
<br>
Are you running all these runs with domain decomposition?<br>
If you are running in parallel, the local order of atoms (in md.c)
can be different, depending on the kernel. So that could explain
your different forces.<br>
The forces in the trr, however, will always be ordered as in the
topology, and thus they should match with -rerun.<br>
<br>
Cheers,<br>
<br>
Berk<br>
<br>
On 06/13/2013 10:46 AM, francesco oteri wrote:<br>
</div>
<blockquote
cite="mid:CAFQcp-OKp6y6SAW5Tn-Y8LqsGDbu7hHepv+9QkSJkrEFSE--VA@mail.gmail.com"
type="cite">
<meta http-equiv="Content-Type" content="text/html;
charset=ISO-8859-1">
<div dir="ltr">Hi Tianwu,
<div style="">just to be sure, can you try to compile with
CMAKE_BUILD_TYPE=Debug</div>
<div style="">and repeating again the runs?</div>
<div style=""><br>
</div>
<div style="">Francesco</div>
</div>
<div class="gmail_extra">
<br>
<br>
<div class="gmail_quote">2013/6/13 Mark Abraham <span dir="ltr"><<a
moz-do-not-send="true"
href="mailto:mark.j.abraham@gmail.com" target="_blank">mark.j.abraham@gmail.com</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr"><br>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">
<div class="im">On Wed, Jun 12, 2013 at 10:58 PM,
Tianwu Zang <span dir="ltr"><<a
moz-do-not-send="true"
href="mailto:tz4@rice.edu" target="_blank">tz4@rice.edu</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">Hi all,
<div>I am using a very common system for
testing, with only one protein (~1000+ atoms)
and ~7000+ water atoms with box size = 4.5</div>
<div>When I tried rerun the simulation, results
kept the same with the last run for the same
kernel, but became quite different (even at
step=0) for different kernel, like using
generic kernel in the first run and specific
kernel in the second run..</div>
<div>In my case, for specific kernel, f[0]~884
and for generic kernel f[0]~337, which is a
huge difference..</div>
<div>I have already set the variable gen_seed in
my .mdp file so there shouldn't be any problem
of random seed.</div>
<div>Now I am wondering if these force results
should not differ from each other, where I am
doing wrong?</div>
</div>
</blockquote>
<div><br>
</div>
</div>
<div>OK. What's your .mdp file?</div>
<span class="HOEnZb"><font color="#888888">
<div>
<br>
</div>
<div>
Mark</div>
</font></span>
<div>
<div class="h5">
<div> </div>
<blockquote class="gmail_quote" style="margin:0 0
0 .8ex;border-left:1px #ccc
solid;padding-left:1ex">
<div dir="ltr">
<div>Thanks again,</div>
<div>-Mark</div>
</div>
<div>
<div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">
On Wed, Jun 12, 2013 at 8:05 AM,
francesco oteri <span dir="ltr"><<a
moz-do-not-send="true"
href="mailto:francesco.oteri@gmail.com"
target="_blank">francesco.oteri@gmail.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote"
style="margin:0 0 0
.8ex;border-left:1px #ccc
solid;padding-left:1ex">
<div dir="ltr">Hi,
<div>Marc said it is using -rerun
and, as far as I know and basing
on my experience, </div>
<div>it gives exactly the same
reults. Of course, also the seed
has to be the same :D</div>
<span><font color="#888888">
<div>
<br>
</div>
<div>Francesco</div>
</font></span></div>
<div>
<div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">2013/6/12
Berk Hess <span dir="ltr"><<a
moz-do-not-send="true"
href="mailto:hess@kth.se"
target="_blank">hess@kth.se</a>></span><br>
<blockquote
class="gmail_quote"
style="margin:0 0 0
.8ex;border-left:1px #ccc
solid;padding-left:1ex">
<div bgcolor="#FFFFFF"
text="#000000">
<div>Hi,<br>
<br>
You haven't said at what
step this happens.<br>
At step zero the forces
should match, except for
the last decimal(s).<br>
But since MD is chaotic,
trajectories diverge
exponentially, which is
very fast.<br>
This usually means
forces are significantly
decorrelated after 100
to 1000 steps.<br>
<br>
Cheers,<br>
<br>
Berk
<div>
<div><br>
<br>
On 06/12/2013 01:50
PM, Mark Abraham
wrote:<br>
</div>
</div>
</div>
<div>
<div>
<blockquote
type="cite">
<div dir="ltr"><br>
<div
class="gmail_extra"><br>
<br>
<div
class="gmail_quote">On
Wed, Jun 12,
2013 at 3:28
AM, Mark
Tianwu Zang <span
dir="ltr"><<a
moz-do-not-send="true" href="mailto:zangtw@gmail.com" target="_blank">zangtw@gmail.com</a>></span>
wrote:<br>
<blockquote
class="gmail_quote"
style="margin:0px
0px 0px
0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div dir="ltr"><span
style="font-family:arial,sans-serif;font-size:13px">Hi Francesco and
Mark,</span>
<div
style="font-family:arial,sans-serif;font-size:13px">
Thanks for
your precious
advice. Now
this time I
didn't insert
any code but
use the .mdp
options
instead. I
used the
following
steps: first
set the
environment
variable
GMX_NB_GENERIC=1,
run the
GROMACS, and
run again with
the same input
but
GMX_NB_GENERIC
unset. Next,
compare two
force.xvg
generated from
two traj.trr
using g_traj.
However, I
still found
the results
different from
each other..
My gcc version
is
4.6.3(almost
the newest),
my fftw
version is
3.3.3(double
precision, and
GROMACS is
also build in
double-precision)
and I use the
argument
--reprod to
make sure the
calculation of
PME is
reproducible. </div>
<div
style="font-family:arial,sans-serif;font-size:13px">My
running
command for
GROMACS is</div>
<div
style="font-family:arial,sans-serif;font-size:13px">mpirun
-np 2
mdrun_mpi -s
test.tpr -v
-reprod</div>
</div>
</blockquote>
<div><br>
</div>
<div>That's
better, but
the advice
here is worth
following: <a
moz-do-not-send="true"
href="http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy"
target="_blank">http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy</a></div>
<div> </div>
<blockquote
class="gmail_quote"
style="margin:0px
0px 0px
0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div dir="ltr">
<div
style="font-family:arial,sans-serif;font-size:13px">
I tried to
attach my test
tpr and mdp
file in this
email but my
attempt was
not approved
by
administrator
because the
email would be
oversized..</div>
</div>
</blockquote>
<div><br>
</div>
<div>Describing
in words what
your system is
doing would be
a good start
;-)</div>
<div><br>
</div>
<div>Mark</div>
<div><br>
</div>
<blockquote
class="gmail_quote"
style="margin:0px
0px 0px
0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div dir="ltr">
<span><font
color="#888888">
<div
style="font-family:arial,sans-serif;font-size:13px"><br>
</div>
<div
style="font-family:arial,sans-serif;font-size:13px">
-Mark</div>
</font></span></div>
<div>
<div>
<div
class="gmail_extra"><br>
<br>
<div
class="gmail_quote">On
Sat, Jun 8,
2013 at 7:25
AM, francesco
oteri <span
dir="ltr"><<a
moz-do-not-send="true" href="mailto:francesco.oteri@gmail.com"
target="_blank">francesco.oteri@gmail.com</a>></span>
wrote:<br>
<blockquote
class="gmail_quote"
style="margin:0px
0px 0px
0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div dir="ltr">In
my case the
excuse was
that the
system
administrator
never updated
the compiler.
<div> So I
after a couple
of days I
installed the
new compiler.</div>
<div>In any
case, I
noticed that
the
problem disappeared using
the "Debug"
version so I
guess </div>
<div>it is
something
related either
to the
optimized
kernel or the
optimization
strategy used
by the
compiler. </div>
<span><font
color="#888888">
<div><br>
</div>
<div><br>
</div>
<div>Francesco</div>
</font></span></div>
<div>
<div>
<div
class="gmail_extra">
<br>
<br>
<div
class="gmail_quote">2013/6/8
Mark Abraham <span
dir="ltr"><<a
moz-do-not-send="true" href="mailto:mark.j.abraham@gmail.com"
target="_blank">mark.j.abraham@gmail.com</a>></span><br>
<blockquote
class="gmail_quote"
style="margin:0px
0px 0px
0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div dir="ltr"><br>
<div
class="gmail_extra"><br>
<br>
<div
class="gmail_quote">
<div>On Sat,
Jun 8, 2013 at
12:59 PM,
francesco
oteri <span
dir="ltr"><<a
moz-do-not-send="true" href="mailto:francesco.oteri@gmail.com"
target="_blank">francesco.oteri@gmail.com</a>></span>
wrote:<br>
<blockquote
class="gmail_quote"
style="margin:0px
0px 0px
0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div dir="ltr">H
Mark,
<div>I had a
similar
problem
recently and,
eventually, I
figured out
the cause was
the compiler
version.</div>
<div>I was
using gcc4.1
and my problem
got solved
using a more
recent
version.
Actually, this
issue </div>
<div>in the
website is
clearly
stated. So,
which compiler
are you using?</div>
<div>Could you
report an
example
of inconsistency?</div>
</div>
</blockquote>
<div><br>
</div>
</div>
<div>That
warning has
been there
many years,
but AFAIK
nobody ever
identified the
real problem
(if it
exists).
Nevertheless,
there is no
excuse for
using both
GROMACS and
such an old
compiler! :-)</div>
<span><font
color="#888888">
<div><br>
</div>
<div>Mark</div>
</font></span>
<div>
<div>
<div><br>
</div>
<blockquote
class="gmail_quote"
style="margin:0px
0px 0px
0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div dir="ltr">
<div><br>
</div>
<div>Francesco </div>
</div>
<div
class="gmail_extra">
<div>
<div> <br>
<br>
<div
class="gmail_quote">2013/6/8
Mark Abraham <span
dir="ltr"><<a
moz-do-not-send="true" href="mailto:mark.j.abraham@gmail.com"
target="_blank">mark.j.abraham@gmail.com</a>></span><br>
<blockquote
class="gmail_quote"
style="margin:0px
0px 0px
0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div dir="ltr"><br>
<div
class="gmail_extra"><br>
<br>
<div
class="gmail_quote">On
Sat, Jun 8,
2013 at 1:44
AM, Mark
Tianwu Zang <span
dir="ltr"><<a
moz-do-not-send="true" href="mailto:zangtw@gmail.com" target="_blank">zangtw@gmail.com</a>></span>
wrote:<br>
<blockquote
class="gmail_quote"
style="margin:0px
0px 0px
0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div dir="ltr">Dear
all,
<div>I have
inserted only
a few lines
after update()
in md.c to
monitor how
forces change
after every
step. My codes
are very
simple, just
like:</div>
<div> </div>
<div>for i=0
to
md->nalloc</div>
<div>
<div> fprintf
f[i][0],
f[i][1],
f[i][2]</div>
</div>
</div>
</blockquote>
<div><br>
</div>
<div>That
seems like the
hard way to do
it, with
nstfout
available in
the .mdp
file. </div>
<div><br>
</div>
<blockquote
class="gmail_quote"
style="margin:0px
0px 0px
0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div dir="ltr">
<div>
<div>However,
I found the
results of my
output become
quite
different
after
exporting
GMX_NB_GENERIC=1,
which means
the forces
calculated by
generic kernel
and
interaction-specific
kernel are not
the same. I am
a little
confused now..
It this
phenomena
quite normal
or I ignored
something
important?</div>
</div>
</div>
</blockquote>
<div><br>
</div>
<div>AFAIK the
generic kernel
should serve
as a reference
for the
interaction-specific
kernels. If
not, there
might a
problem to
fix. Hard to
say without
context.</div>
<div><br>
</div>
<div>Mark</div>
<div><br>
</div>
<blockquote
class="gmail_quote"
style="margin:0px
0px 0px
0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div dir="ltr">
<div>
<div>Thanks a
lot!</div>
<span><font
color="#888888">
<div>-Mark</div>
<div><br>
</div>
</font></span></div>
<div><br>
</div>
</div>
<span><font
color="#888888">
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<span><font
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<br>
Cordiali
saluti,
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Francesco </font></span></div>
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-- <br>
Cordiali saluti, Dr.Oteri Francesco
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