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On 1/02/2011 7:50 AM, Sai Pooja wrote:
<blockquote
cite="mid:AANLkTimjwhUf9KXdRWZCu3TEsRDOqqb6EqCqr-zAjfLD@mail.gmail.com"
type="cite">
<div>I think I have figured out the reason. It is because I am
carrying out replica exchange (manual) after every mdrun. If the
exchange occurs, I exchange the checkpoint files, extend the
simulation by 500 steps and continue. The new simulation starts
from exchanged cptfile. It seems that whenever the exchange
occurs, the earlier log,traj files are not appended. They are
instead overwritten. the obv solution is to save and index these
files with the relevant replicas everytime an exchange occurs. </div>
</blockquote>
<br>
This would have been good to know earlier. If replica-exchange leads
to the ensemble of the .tpr not matching the ensemble of the .cpt,
then IIRC 4.5.3 mdrun will refuse to start from the .cpt, which
means the subsequent mdrun will start from the .tpr only. Certainly
a non-appending mdrun prints a warning (or error, I forget which)
message to the log file, but perhaps the use of -append
(erroneously) doesn't do that. Please have a look and see if that is
the issue. There is an environment variable that can be set to tell
mdrun that you (think you) know what you are doing mismatching .tpr
and .cpt.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:AANLkTimjwhUf9KXdRWZCu3TEsRDOqqb6EqCqr-zAjfLD@mail.gmail.com"
type="cite">
<div>However, i have a more general question. Since mdrun still
runs with the exchanged checkpoint files and starts from the
point where the previous run ended, can I be assured that an
exchange has been affected - since tpr files correspond to the
"replica-box" and cpi to the most recent exchanged replicas?</div>
<div> </div>
<div>Pooja<br>
<br>
</div>
<div class="gmail_quote">On Mon, Jan 31, 2011 at 2:33 PM, Sai
Pooja <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:saipooja@gmail.com">saipooja@gmail.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="padding-left: 1ex;
margin: 0px 0px 0px 0.8ex; border-left: 1px solid rgb(204,
204, 204);">
<div><br>
I manually index checkpoint files after every mdrun. What
troubles me is the randomness with which -append
fails/works.</div>
<div> </div>
<div>For eg, I have a simulation which runs from 3ns, 1ps in 1
mdrun. Now oddly enough, the logfile starts from 1184ps(in
the end, I do remember the one starting from 0 but that was
overwritten it seems) and the rest is appended uptil the
3000ps step. Why would append work from 1184ps to 3000ps but
not for the previous ones?Could it have anything to do with
the network/cluster? If that is the case is it safer to
create a new file everytime and then concatenate them after
say every 100ps?</div>
<div> </div>
<font color="#888888">
<div>Pooja<br>
</div>
</font>
<div class="gmail_quote">
<div>
<div class="h5">On Sat, Jan 29, 2011 at 6:52 PM, Mark
Abraham <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au"
target="_blank">Mark.Abraham@anu.edu.au</a>></span>
wrote:<br>
</div>
</div>
<blockquote class="gmail_quote" style="padding-left: 1ex;
margin: 0px 0px 0px 0.8ex; border-left: 1px solid rgb(204,
204, 204);">
<div>
<div class="h5">
<div bgcolor="#ffffff" text="#000000">
<div>On 30/01/2011 10:39 AM, Sai Pooja wrote:
<blockquote type="cite">I would be happy to supply
more information.. if someone could please look
into this.. otherwise I will have to switch to
storing every file and then just concatenating
them which seems like a rather roundabout way of
doing it.<br>
</blockquote>
<br>
</div>
As I suggested a few emails ago, are you sure that
-cpi file exists? If your numerical suffixes are
indexing restarts, then unless you've done some
manual copying that you haven't told us about, it
won't. Your filename scheme seems a bit contorted -
like you're trying to do the work that GROMACS 4.5.x
will just do for you if you let it.<br>
<br>
Otherwise, you'll have to do some detective work
with gmxcheck on the -cpi to see what might be the
issue.<br>
<br>
In your case, an initial<br>
<br>
mdrun -deffnm rex_3<br>
<br>
(perhaps save some copies while you're
experimenting) and subsequently<br>
<br>
tpbconv -extend <blah> -f rex_3 -o rex_3<br>
mdrun -deffnm rex_3 -append<br>
<br>
will work and be much simpler than whatever you're
trying to do with filenames :-)<br>
<font color="#888888"><br>
Mark</font>
<div>
<div><br>
<br>
<blockquote type="cite"><br>
<div class="gmail_quote">On Fri, Jan 28, 2011
at 4:37 PM, Sai Pooja <span dir="ltr"><<a
moz-do-not-send="true"
href="mailto:saipooja@gmail.com"
target="_blank">saipooja@gmail.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote"
style="padding-left: 1ex; margin: 0px 0px
0px 0.8ex; border-left: 1px solid rgb(204,
204, 204);">
<div>This is the command:</div>
<div> </div>
<div>nbs submit -command
"(/usr/local/gromacs/4.5.1/bin/mdrun_mpi
-s rex_3.tpr -e rex_3 -c after_rex_3
-cpi restart3 -cpo restart3 -ap<br>
pend -g rexlog3 -x rextraj3);" -nproc 1
-name "GENHAM-DIHEDRAL-3" -mail start
end</div>
<div> </div>
<font color="#888888">
<div>Pooja<br>
<br>
</div>
</font>
<div>
<div>
<div class="gmail_quote">On Fri, Jan
28, 2011 at 4:20 PM, Mark Abraham <span
dir="ltr"><<a
moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au"
target="_blank">Mark.Abraham@anu.edu.au</a>></span>
wrote:<br>
<blockquote class="gmail_quote"
style="padding-left: 1ex; margin:
0px 0px 0px 0.8ex; border-left:
1px solid rgb(204, 204, 204);">
<div>
<div>On 29/01/2011 3:56 AM, Sai
Pooja wrote:<br>
<blockquote
class="gmail_quote"
style="padding-left: 1ex;
margin: 0px 0px 0px 0.8ex;
border-left: 1px solid
rgb(204, 204, 204);">Hi,<br>
I am using tpbconv and mdrun
to extend a simulation. I
use it with the append
option but the files still
get overwritten or erased.
Can someone help me in this
regard?<br>
Pooja<br>
Commands (in python)<br>
cmd = '(%s/tpbconv -extend
%f -s rex_%d.tpr -o
rex_%d.tpr)'
%(GROMPATH,dtstep,i,i)<br>
os.system(cmd)<br>
time.sleep(1)<br>
cmd = 'nbs submit
-command "'<br>
cmd += '(%s/mdrun_mpi
-noh -noversion -s
rex_%d.tpr -e rex_%d -c
after_rex_%d -cpi restart%d
-cpo restart%d -append -g
rexlog%d -x rextraj%d
>/dev/null); '
%(GROMPATH,i,i,i,i,i,i,i)<br>
cmd += '" '<br>
cmd += '-nproc 1 '<br>
cmd += '-name
"GENHAM-DIHEDRAL-%d" '%(i)<br>
cmd += '-mail start end
'<br>
cmd += '-elapsed_limit
16h >> rexid'<br>
os.system(cmd)<br>
</blockquote>
<br>
</div>
</div>
More useful for diagnostic and
record-preservation purposes is to
construct the cmd string and print
it to stdout (or something).<br>
<br>
At the moment it is far from clear
that your -cpi file exists for the
new run.<br>
<br>
Mark<br>
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