<br><br><div class="gmail_quote">On Sat, Jun 4, 2011 at 9:09 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="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div text="#000000" bgcolor="#ffffff"><div><div></div><div class="h5">
On 5/06/2011 3:11 AM, Dimitar Pachov wrote: </div></div></div></blockquote><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div text="#000000" bgcolor="#ffffff">
<div><div class="h5"><span class="Apple-style-span" style="border-collapse: collapse; color: rgb(80, 0, 80); font-family: arial, sans-serif; font-size: 13px; ">On Fri, Jun 3, 2011 at 9:24
PM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au" style="color:rgb(0, 0, 204)" target="_blank">Mark.Abraham@anu.edu.au</a>></span> wrote:</span><blockquote type="cite"><span style="border-collapse:collapse;font-family:arial,sans-serif;font-size:13px"><div style="color:rgb(80, 0, 80)">
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204, 204, 204);padding-left:1ex">
<div text="#000000" bgcolor="#ffffff">
<div>On 4/06/2011 8:26 AM, Dimitar Pachov wrote<br><br></div></div></blockquote><div><br>
</div>
</div>
<div>Here is an example:</div>
<div><br>
</div>
<div>========================</div>
<div>
<div><font size="1">[dpachov]$ ll -rth run1* \#run1*</font></div>
<div><font size="1">-rw-rw-r-- 1 dpachov dpachov 11K May 2
02:59 run1.po.mdp</font></div>
<div><font size="1">-rw-rw-r-- 1 dpachov dpachov 4.6K May 2
02:59 run1.grompp.out</font></div>
<div><font size="1">-rw-rw-r-- 1 dpachov dpachov 3.5M May 13
19:09 run1.gro</font></div>
<div><font size="1">-rw-rw-r-- 1 dpachov dpachov 2.3M May 14
00:40 run1.tpr</font></div>
<div><font size="1">-rw-rw-r-- 1 dpachov dpachov 2.3M May 14
00:40 run1-i.tpr</font></div>
<div><font size="1">-rw-rw-r-- 1 dpachov dpachov 0 May 29
21:53 run1.trr</font></div>
<div><font size="1">-rw-rw-r-- 1 dpachov dpachov 1.2M May 31
10:45 run1.cpt</font></div>
<div><font size="1">-rw-rw-r-- 1 dpachov dpachov 1.2M May 31
10:45 run1_prev.cpt</font></div>
<div><font size="1">-rw-rw-r-- 1 dpachov dpachov 0 Jun 3
14:03 run1.xtc</font></div>
<div><font size="1">-rw-rw-r-- 1 dpachov dpachov 0 Jun 3
14:03 run1.edr</font></div>
<div><font size="1">-rw-rw-r-- 1 dpachov dpachov 15M Jun 3
17:03 run1.log</font></div>
</div>
<div>========================</div>
<div><br>
</div>
<div>Submitted by:</div>
<div>========================</div>
<div><font size="1">ii=1</font></div>
<div><font size="1">ifmpi="mpirun -np $NSLOTS"</font></div>
<div><font size="1">--------</font></div>
<div><font size="1"> if [ ! -f run${ii}-i.tpr ];then</font></div>
<div>
<div><font size="1"> cp run${ii}.tpr run${ii}-i.tpr </font></div>
<div><font size="1"> tpbconv -s run${ii}-i.tpr -until
200000 -o run${ii}.tpr </font></div>
<div><font size="1"> fi</font></div>
<div><font size="1"><br>
</font></div>
<div><font size="1"> k=`ls md-${ii}*.out | wc -l`</font></div>
<div><font size="1"> outfile="md-${ii}-$k.out"</font></div>
<div><font size="1"> if [[ -f run${ii}.cpt ]]; then</font></div>
<div><font size="1"> </font></div>
<div><font size="1"> $ifmpi `which mdrun` -s
run${ii}.tpr -cpi run${ii}.cpt -v -deffnm run${ii} -npme 0
> $outfile 2>&1 </font></div>
<div><font size="1"><br>
</font></div>
<div><font size="1"> fi</font></div>
</div>
<div>=========================</div>
</span></blockquote>
<br></div></div>
This script is not using mdrun -append. </div></blockquote><div><br></div><div>-append is the default, it doesn't need to be explicitly listed. </div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div text="#000000" bgcolor="#ffffff">Your original post suggested
the use of -append was a problem. Why aren't we seeing a script with
mdrun -append? Also, please provide the full script - it looks like
there might be a loop around your tpbconv-then-mdrun fragment.<br></div></blockquote><div><br></div><div>There is no loop; this is a job script with PBS directives. The header of it looks like:</div><div>===========================</div>
<div><div><font class="Apple-style-span" size="1">#!/bin/bash</font></div><div><font class="Apple-style-span" size="1">#$ -S /bin/bash</font></div><div><font class="Apple-style-span" size="1">#$ -pe mpich 8</font></div><div>
<font class="Apple-style-span" size="1">#$ -ckpt reloc</font></div><div><font class="Apple-style-span" size="1">#$ -l mem_total=6G</font></div></div><div>===========================</div><div><br></div><div>as usual submitted by:</div>
<div><br></div><div><font class="Apple-style-span" size="1">qsub -N aaaa myjob.q</font></div><div><br></div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div text="#000000" bgcolor="#ffffff">
<br>
Note that a useful trouble-shooting technique can be to construct
your command line in a shell variable, echo it to stdout (redirected
as suitable) and then execute the contents of the variable. Now,
nobody has to parse a shell script to know what command line
generated what output, and it can be co-located with the command's
stdout.</div></blockquote><div><br></div><div>I somewhat understand your point, but could give an example if you think it is really necessary?</div><div><br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div text="#000000" bgcolor="#ffffff"><div class="im"><blockquote type="cite"><span style="border-collapse:collapse;font-family:arial,sans-serif;font-size:13px"><div>
<font size="1"></font>
</div>
</span></blockquote></div>
<snip><br>
<blockquote type="cite"><span style="border-collapse:collapse;font-family:arial,sans-serif;font-size:13px">
<div><div class="im">
<div><font size="1">Writing checkpoint, step 51879590 at Tue
May 31 10:45:22 2011<br>
</font></div>
</div><div class="im"><div><font size="1"> Energies (kJ/mol)</font></div>
<div><font size="1"> U-B Proper Dih. Improper
Dih. CMAP Dih. LJ-14</font></div>
<div><font size="1"> 8.33208e+03 4.72300e+03
5.31983e+02 -1.21532e+03 2.89586e+03</font></div>
<div><font size="1"> Coulomb-14 LJ (SR) Disper.
corr. Coulomb (SR) Coul. recip.</font></div>
<div> <font size="1"> 3.00900e+04 9.31785e+04
-3.87790e+03 -7.40841e+05 -8.36838e+04</font></div>
<div><font size="1"> Potential Kinetic En. Total
Energy Temperature Pres. DC (bar)</font></div>
<div><font size="1"> -6.89867e+05 1.28721e+05
-5.61146e+05 2.99472e+02 -1.24229e+02</font></div>
<div><font size="1"> Pressure (bar) Constr. rmsd</font></div>
<div><font size="1"> -1.03491e+02 2.99840e-05</font></div>
</div></div>
<div>====================================</div>
</span></blockquote>
<br>
So the -append restart looks like it did fine here.<div><div></div><div class="h5"><br>
<br>
<blockquote type="cite"><span style="border-collapse:collapse;font-family:arial,sans-serif;font-size:13px">
<div>Last output files from restarts:</div>
<div>====================================</div>
<div>
<div><font size="1">[dpachov]$ ll -rth md-1-*out | tail -10</font></div>
<div><font size="1">-rw-rw-r-- 1 dpachov dpachov 6.1K Jun 3
16:40 md-1-2428.out</font></div>
<div> <font size="1">-rw-rw-r-- 1 dpachov dpachov 6.2K Jun 3
16:44 md-1-2429.out</font></div>
<div><font size="1">-rw-rw-r-- 1 dpachov dpachov 5.9K Jun 3
16:46 md-1-2430.out</font></div>
<div><font size="1">-rw-rw-r-- 1 dpachov dpachov 5.9K Jun 3
16:48 md-1-2431.out</font></div>
<div><font size="1">-rw-rw-r-- 1 dpachov dpachov 6.1K Jun 3
16:50 md-1-2432.out</font></div>
<div><font size="1">-rw-rw-r-- 1 dpachov dpachov 0 Jun 3
16:52 md-1-2433.out</font></div>
<div><font size="1">-rw-rw-r-- 1 dpachov dpachov 6.2K Jun 3
16:55 md-1-2434.out</font></div>
<div><font size="1">-rw-rw-r-- 1 dpachov dpachov 6.2K Jun 3
16:58 md-1-2435.out</font></div>
<div><font size="1">-rw-rw-r-- 1 dpachov dpachov 5.9K Jun 3
17:03 md-1-2436.out</font></div>
<div><font size="1"><b>-rw-rw-r-- 1 dpachov dpachov 5.8K Jun
3 17:04 md-1-2437.out</b></font></div>
</div>
<div>====================================</div>
<div>+ around the time when the run1.xtc file seems to have been
saved:</div>
<div>====================================</div>
<div>
<div><font size="1">[dpachov]$ ll -rth md-1-23[5-6][0-9]*out</font></div>
<div><font size="1">-rw-rw-r-- 1 dpachov dpachov 6.2K Jun 3
13:37 md-1-2350.out</font></div>
<div><font size="1">-rw-rw-r-- 1 dpachov dpachov 6.1K Jun 3
13:39 md-1-2351.out</font></div>
<div><font size="1">-rw-rw-r-- 1 dpachov dpachov 6.2K Jun 3
13:43 md-1-2352.out</font></div>
<div><font size="1">-rw-rw-r-- 1 dpachov dpachov 6.2K Jun 3
13:45 md-1-2353.out</font></div>
<div><font size="1">-rw-rw-r-- 1 dpachov dpachov 5.9K Jun 3
13:46 md-1-2354.out</font></div>
<div><font size="1">-rw-rw-r-- 1 dpachov dpachov 0 Jun 3
13:47 md-1-2355.out</font></div>
<div><font size="1">-rw-rw-r-- 1 dpachov dpachov 6.1K Jun 3
13:49 md-1-2356.out</font></div>
<div><font size="1">-rw-rw-r-- 1 dpachov dpachov 6.1K Jun 3
13:52 md-1-2357.out</font></div>
<div><font size="1">-rw-rw-r-- 1 dpachov dpachov 12K Jun 3
13:57 md-1-2358.out</font></div>
<div><font size="1"><b>-rw-rw-r-- 1 dpachov dpachov 12K Jun
3 14:02 md-1-2359.out</b></font></div>
<div><font size="1"><b>-rw-rw-r-- 1 dpachov dpachov 6.0K Jun
3 14:03 md-1-2360.out</b></font></div>
<div><font size="1">-rw-rw-r-- 1 dpachov dpachov 6.2K Jun 3
14:06 md-1-2361.out</font></div>
<div><font size="1">-rw-rw-r-- 1 dpachov dpachov 5.8K Jun 3
14:09 md-1-2362.out</font></div>
<div><font size="1">-rw-rw-r-- 1 dpachov dpachov 5.9K Jun 3
14:10 md-1-2363.out</font></div>
<div><font size="1">-rw-rw-r-- 1 dpachov dpachov 6.1K Jun 3
14:11 md-1-2364.out</font></div>
<div><font size="1">-rw-rw-r-- 1 dpachov dpachov 5.8K Jun 3
14:12 md-1-2365.out</font></div>
<div><font size="1">-rw-rw-r-- 1 dpachov dpachov 6.1K Jun 3
14:13 md-1-2366.out</font></div>
<div><font size="1">-rw-rw-r-- 1 dpachov dpachov 6.1K Jun 3
14:14 md-1-2367.out</font></div>
<div><font size="1">-rw-rw-r-- 1 dpachov dpachov 6.0K Jun 3
14:17 md-1-2368.out</font></div>
<div><font size="1">-rw-rw-r-- 1 dpachov dpachov 5.9K Jun 3
14:18 md-1-2369.out</font></div>
</div>
<div>====================================</div>
</span></blockquote>
<br></div></div>
I don't understand why you have so many restarts only a minute or
two apart. Checkpoints are only written (by default) every 15
minutes, and no job seems to run that long, so all of these will
start from the same point. If they're running simultaneously then
it's conceivable that multiple processes trying to use the same
output file could be a problem, as suggested by Jussi. You say
that's not the case. So why are there so many restarts?</div></blockquote><div><br></div><div>As I said, the queue is like this: you submit the job, it finds an empty node, it goes there, however seconds later another user with higher privileges on that particular node submits a job, his job kicks out my job, mine goes on the queue again, it finds another empty node, goes there, then another user with high privileges on that node submits a job, which consequently kicks out my job again, and the cycle repeats itself ... theoretically, it could continue forever, depending on how many and where the empty nodes are, if any. These many restarts suggest that the queue was full with relatively short jobs ran by users with high privileges. Technically, I cannot see why the same processes should be running simultaneously because at any instant my job runs only on one node, or it stays in the queuing list. </div>
<div><br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div text="#000000" bgcolor="#ffffff"><div><div class="h5"><blockquote type="cite"><div><br>
</div>
<div style="border-collapse: collapse; font-family: arial, sans-serif; font-size: 13px; ">
<div>From md-1-2360.out:</div>
<div>=====================================</div>
<div>
<div><font size="1">:::::::</font></div>
</div>
</div>
<div style="border-collapse: collapse; font-family: arial, sans-serif; font-size: 13px; ">
<div><font size="1">Getting Loaded...</font></div>
<div><font size="1">Reading file run1.tpr, VERSION 4.5.4
(single precision)</font></div>
<div><font size="1"><br>
</font></div>
<div><font size="1">Reading checkpoint file run1.cpt
generated: Tue May 31 10:45:22 2011</font></div>
<div><font size="1"><br>
</font></div>
<div><font size="1"><br>
</font></div>
<div><font size="1">Loaded with Money</font></div>
<div><font size="1"><br>
</font></div>
<div><font size="1">Making 2D domain decomposition 4 x 2 x 1</font></div>
<div><font size="1"><br>
</font></div>
<div><font size="1">WARNING: This run will generate roughly
4915 Mb of data</font></div>
<div><font size="1"><br>
</font></div>
<div><font size="1">starting mdrun 'run1'</font></div>
<div><font size="1">100000000 steps, 200000.0 ps (continuing
from step 51879590, 103759.2 ps).</font></div>
</div>
<div style="border-collapse: collapse; font-family: arial, sans-serif; font-size: 13px; ">=====================================</div>
</blockquote>
<br></div></div>
These aren't showing anything other than that the restart is coming
from the same point each time.<div class="im"><br>
<br>
<blockquote type="cite"><span style="border-collapse:collapse;font-family:arial,sans-serif;font-size:13px">
<div>And from the last generated output md-1-2437.out (I think I
killed the job at that point because of the above
observed behavior):</div>
<div>=====================================</div>
<div>
<div><font size="1">:::::::</font></div>
</div>
<div><font size="1">
<div>Getting Loaded...</div>
<div>Reading file run1.tpr, VERSION 4.5.4 (single precision)</div>
</font></div>
<div><font size="1"><span style="font-size:small">=====================================</span></font></div>
<div><br>
</div>
<div>I have at least 5-6 additional examples like this one. In
some of them the *xtc file does have size greater than zero
yet still very small, but it starts from some random frame
(for example, in one of the cases it contains frames from
~91000ps to ~104000ps, but all frames before 91000ps are
missing).</div>
</span></blockquote>
<br></div>
I think that demonstrating a problem requires that the set of output
files were fine before one particular restart, and weird afterwards.
I don't think we've seen that yet.<div class="im"><br></div></div></blockquote><div><br></div><div>I don't understand your point here. I am providing you with all info I have. I am showing the output files of 3 restarts, and they are different in a sense that the last two did not progress further enough before another job restart occurred. The first was fine before the restart, and the others were not exactly fine after the restart. At this point I realize that what I call "restart" and what you call "restart" might be two different things. And here is where the problem might be lying. </div>
<div><br></div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div text="#000000" bgcolor="#ffffff"><div class="im">
<br>
<blockquote type="cite"><span style="border-collapse:collapse;font-family:arial,sans-serif;font-size:13px">
<div>I realize there might be another problem, but the bottom
line is that there is no mechanism that can prevent this from
happening if many restarts are required, and particularly if
the timing between these restarts is prone to be small
(distributed computing could easily satisfy this condition).</div>
<div><br>
</div>
<div>Any suggestions, particularly related to the minimum
resistance path to regenerate the missing data? :)</div>
<div style="color:rgb(80, 0, 80)">
<div><br>
</div>
<div> </div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204, 204, 204);padding-left:1ex">
<div text="#000000" bgcolor="#ffffff">
<div><br>
<blockquote type="cite">
<div>Using the checkpoint capability & appending
make sense when many restarts are expected, but
unfortunately it is exactly then when these options
completely fail! As a new user of Gromacs, I must
say I am disappointed, and would like to obtain an
explanation of why the usage of these options is
clearly stated to be safe when it is not, and why
the append option is the default, and why at least a
single warning has not been posted anywhere in the
docs & manuals?</div>
</blockquote>
<br>
</div>
I can understand and sympathize with your frustration if
you've experienced the loss of a simulation. Do be careful
when suggesting that others' actions are blame-worthy,
however.</div>
</blockquote>
<div><br>
</div>
</div>
<div>I have never suggested this. As a user, I am entitled to
ask. </div>
</span></blockquote>
<br></div>
Sure. However, talking about something that can "completely fail"</div></blockquote><div><br></div><div>This is a fact, backed up by my evidences => I don't see anything bad directed to anybody. </div>
<div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div text="#000000" bgcolor="#ffffff">
which makes you "disappointed"</div></blockquote><div><br></div><div>This is me being honest => again not related to anybody else. </div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div text="#000000" bgcolor="#ffffff"> and wanting to "obtain an
explanation"</div></blockquote><div><br></div><div>Well, this even is funny :) - many people want this, especially in science. Is that bad?</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div text="#000000" bgcolor="#ffffff"> about why something doesn't work as stated and lacks "a
single warning"</div></blockquote><div><br></div><div>Again a fact => again nothing bad here.</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div text="#000000" bgcolor="#ffffff"> suggests that someone has done something less than
appropriate</div></blockquote><div><br></div><div>This is a completely personal interpretation, and I am personally not responsible of how people perceive information. For unknown to me reason you moved into a very defensive mode. What could I do? </div>
<div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div text="#000000" bgcolor="#ffffff">, and so blame-worthy. It also assumes that the actions
of a new user were correct, and the actions of a developer with long
experience were not. </div></blockquote><div><br></div><div>Sorry, this is too much. Where was this suggested? It seems to me you took it too personally. </div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div text="#000000" bgcolor="#ffffff">This may or may not prove to be true. Starting
such a discussion from a conciliatory (rather than antagonistic)
stance is usually more productive. The shared objective should be to
fix the problem, not prove that someone did something wrong.<br></div></blockquote><div><br></div><div>Agree, and I did it. Again, your perception does not seem to be correlated with my intended approach. </div><div>
</div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div text="#000000" bgcolor="#ffffff">
<br>
An alternative way of wording your paragraph could have been:<br>
"<span style="border-collapse:collapse;font-family:arial,sans-serif;font-size:13px">Using the checkpoint
capability & appending make sense when many restarts are
expected, however I observe that under such circumstances this
capability can fail. I am a new user of GROMACS, might I have been
using them incorrectly? Are the developers aware of any situations
under which the capability is unreliable? If so, should the
default behaviour be different, and should this issue be
documented somewhere?"</span></div></blockquote><div><br></div><div>This is helpful, but again a bit too much. I don't tell you how to write, please do the same. </div><div>Moreover, how could I ask questions the answers to which were mostly known to me before sending my post? </div>
<div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div text="#000000" bgcolor="#ffffff"><div class="im"><br>
<br>
<blockquote type="cite"><span style="border-collapse:collapse;font-family:arial,sans-serif;font-size:13px">
<div>And since my questions were not clearly answered, I will
repeat them in a structured way:</div>
<div><br>
</div>
<div>1. Why is the usage of these options (-cpi and -append)
clearly stated to be safe when in fact it is not?</div>
</span></blockquote>
<br></div>
Because they are believed to be safe. Jussi's suggestion about file
locking may have merit.<div class="im"><br>
<br>
<blockquote type="cite"><span style="border-collapse:collapse;font-family:arial,sans-serif;font-size:13px">
<div>2. Why have you made the -append option the default in the
most current GMX versions?</div>
</span></blockquote>
<br></div>
Because it's the most convenient mode of operation.</div></blockquote><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div text="#000000" bgcolor="#ffffff"><div class="im">
<br>
<br>
<blockquote type="cite"><span style="border-collapse:collapse;font-family:arial,sans-serif;font-size:13px">
<div>3. Why has not a single warning been posted anywhere in the
docs & manuals? (this question is somewhat clear - because
you did not know about such a problem, but people say "<span style="font-family:sans-serif;font-size:13px;line-height:20px">ignorance of the law excuses no one</span>",
which means ignoring to put a warning for something that you
were not 100% certain it would be error-free could not be an
excuse)</div>
</span></blockquote>
<br></div>
Because no-one is aware of a problem to warn about.</div></blockquote><div><br></div><div>No, people are aware, they just do not think it is a problem, because there is an easy work-around (-noappend), although not as convenient and clean. Ask users of the Condor distributed grid using Gromacs.</div>
<div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div text="#000000" bgcolor="#ffffff"><div class="im"><br>
<br>
<blockquote type="cite"><span style="border-collapse:collapse;font-family:arial,sans-serif;font-size:13px">
<div>I am blame-worthy - for blindly believing what was written
in the manual without taking the necessary precautions. Lesson
learned. </div>
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<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204, 204, 204);padding-left:1ex">
<div text="#000000" bgcolor="#ffffff">However, developers'
time rarely permits addressing "feature X doesn't work,
why not?" in a productive way. Solving bugs can be hard,
but will be easier (and solved faster!) if the user who
thinks a problem exists follows good procedure. See <a href="http://www.chiark.greenend.org.uk/%7Esgtatham/bugs.html" style="color:rgb(0, 0, 204)" target="_blank">http://www.chiark.greenend.org.uk/~sgtatham/bugs.html</a><br>
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<div>Implying that I did not follow a certain procedure related
to a certain problem without you knowing what my initial
intention was is just a speculation. <br>
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I don't follow your point. If your intent is to get the problem
being fixed, the advice on that web page is useful.</div></blockquote><div><br></div><div>My intend was clearly stated before, but for the sake of clarification, let's repeat it again:</div><div><br></div><div><meta http-equiv="content-type" content="text/html; charset=utf-8"><div>
1. To let you know about the existence of such a problem.</div><div>2. To find out why I encountered the problem, although I have read and followed all of the Gromacs documentation related to the used by me features. </div>
</div><div>3. To somewhat improve the way the documentation is written. </div><div><br></div><div>Pay attention to the fact that I did NOT have an incentive to get help in solving my problem. There are always exist many work-arounds. </div>
<div><br></div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div text="#000000" bgcolor="#ffffff"> If your intent
is to prove someone else did something wrong then it's time to stop
the discussion :-)<br></div></blockquote><div><br></div><div>I did not want to prove anything besides that a problem existed. Logically, problems are derived from somewhere, and that somewhere is not nowhere. </div><div>
<br></div><div>Of course, as I also mentioned, this is my problem => I did something wrong, which I already stated. You imply I impose blame, which is again too defensive of a statement, and hence I am just going to leave further conclusions to you. :)</div>
<div><br></div><div>Thanks,</div><div>Dimitar</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div text="#000000" bgcolor="#ffffff">
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Cheers,<br>
<br>
Mark<br><br></div></blockquote></div>