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Hi,<br>
I'm resending the message below from last week because it didn't
make it to the list due to some problem with the server.<br>
Rossen<br>
<br>
-------------------------<br>
<br>
Hi Mark,<br>
<br>
It will be definitely important to have the regressiontests working
properly and extended as the development of Gromacs continues. We
discussed that with Berk, and here are some suggestions about the
structure of the suite.<br>
<br>
1. Make all current tests 3.3.4 compliant. There _is_ actually such
a release :) but it hasn't been really announced. <br>
<br>
I put a link to the tarball on the website, but also if you checkout
the releases-3-3-patches branch ,the release is the last commit in
that branch: d26be1f4015d974530e8a203e08ade01008e56a8. The bugs that
have been fixed since 3.3.3 are now on the website: <a
class="moz-txt-link-freetext"
href="http://www.gromacs.org/About_Gromacs/Release_Notes/Revisions_in_versions_3.x">http://www.gromacs.org/About_Gromacs/Release_Notes/Revisions_in_versions_3.x</a>.
<br>
<br>
Are there other important issues with that code?<br>
<br>
2. There is not much point in comparing the tpr's themselves. Not
only it becomes problematic with introducing new options etc, but
most of all the important point is to make sure that the simulations
are reproducible. <br>
<br>
So instead, check the development binaries (mdrun-dev, grompp-dev
etc.) like that:<br>
<ul>
<li>run mdrun-dev first with the 3.3.4-reference.tpr and compare
against 3.3.4-reference.trr/.edr<br>
</li>
<li>run grompp-dev to generate a new dev.tpr and <br>
</li>
<li>run mdrun-dev with dev.tpr and compare again against
3.3.4-reference.trr/.edr</li>
</ul>
3. The above will check only features present in 3.3.4 (and before).
New .tpr files will be needed for the new features available in
later releases. But those will fail to run with older mdrun.<br>
<br>
But that's OK - if the error is simply "reading tpx file (topol.tpr)
version 71 with version 40 program", then the test will be skipped
and reported as "N/A" instead of "Failed". In that way the suite can
be run against any version of mdrun.<br>
<br>
It might be better to limit the number of steps, lets say 50, but
have stricter checking of the error. With longer runs the
trajectories will start deviating more anyway. <br>
<br>
Berk modified yesterday the way gmxcheck compares the virials - now
it uses only the diagonal elements of the tensor since the relative
tolerance is very different between them and the off-diagonal ones.<br>
<br>
Also, the .mdp files should be as small as possible. All default
values should be stripped to keep the input easy to read. I already
did that with all grompp4.mdp files in the complex/ and simple/
tests (and removed the grompp.mdp files), the kernel/* ones are
already using very slim inputs. I put the changes in a new branch,
origin/temp_mdp, to keep the master clean before we decide what to
do. <br>
<br>
4. pdb2gmx: There are new FFs in 4.5 that were not present in
previous version which should be checked also. Similarly to the
mdrun checks, if pdb2gmx returns errors like "Library file
ffamber99.rtp not found in current dir nor in default directories."
(in 4.0) or "Could not find force field 'amber98'" (in 4.5), then
skip the test and mark it as "N/A". EncadFF should be removed, and
Amber/CHARMM tests added maybe a little later when we're sure the
inputs are working fine.<br>
<br>
<br>
Finally, when all the tests pass with 4.5 we can incorporate them
within CTest (there is a very basic support at the moment) and we'll
have a nice testing system:)<br>
<br>
Any comments are welcome.<br>
Rossen<br>
<br>
<br>
<br>
On 8/4/10 6:08 PM, Mark Abraham wrote:
<blockquote cite="mid:fbd998a7296d4.4c5a1d02@anu.edu.au" type="cite">I'm
glad there's some interest in the test set. I'm happy to update
what I did for 4.0.7 for 4.5 also, but there are a number of
issues that need attention from someone other than me. I listed
those that occurred to me here <a class="moz-txt-link-freetext"
href="http://lists.gromacs.org/pipermail/gmx-developers/2009-August/003586.html">http://lists.gromacs.org/pipermail/gmx-developers/2009-August/003586.html</a>,
linked also from the Test Set page on the website.<br>
<br>
Among those issues is that we need a single GROMACS version that
produces reliable reference data for all cases we wish to test!
Various of the 3.3.x series have known issues that make test set
maintenance awkward.<br>
<br>
If I do the necessary updates to release-3-3-patches branch to
make a hypothetical GROMACS 3.3.4 that is useful for making test
set reference calculations, should we make such a release?
Alternatively, we can just announce that the reference data was
generated by the 3-3-version with a given git hash and not
release. Thoughts?<br>
<br>
Mark<br>
<br>
----- Original Message -----<br>
From: Rossen Apostolov <a class="moz-txt-link-rfc2396E"
href="mailto:rossen.apostolov@cbr.su.se"><rossen.apostolov@cbr.su.se></a><br>
Date: Wednesday, August 4, 2010 17:56<br>
Subject: Re: [gmx-users] tests for gmx 4.5<br>
To: <a class="moz-txt-link-abbreviated"
href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
<br>
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<p><font style="font-style: normal; font-weight:
normal; background-color: rgb(245, 248, 240);
font-size: 14px;">> </font> Hi,<br>
<font style="font-style: normal; font-weight:
normal; background-color: rgb(245, 248, 240);
font-size: 14px;">> </font><br>
<font style="font-style: normal; font-weight:
normal; background-color: rgb(245, 248, 240);
font-size: 14px;">> </font> The tests haven't
been ported to 4.5 yet but I hope to fix that before
the final release.<br>
<font style="font-style: normal; font-weight:
normal; background-color: rgb(245, 248, 240);
font-size: 14px;">> </font><br>
<font style="font-style: normal; font-weight:
normal; background-color: rgb(245, 248, 240);
font-size: 14px;">> </font> Rossen<br>
<font style="font-style: normal; font-weight:
normal; background-color: rgb(245, 248, 240);
font-size: 14px;">> </font><br>
<font style="font-style: normal; font-weight:
normal; background-color: rgb(245, 248, 240);
font-size: 14px;">> </font> On 7/31/10 7:08
PM, Alan wrote: </p>
<blockquote
cite="mid:AANLkTinoJzx6o=Esfhq4M=sAwtL880SZ6r+GkpanCZgc@mail.gmail.com"
type="cite">Is there a proper set of tests for gmx
4.5 because neither <a moz-do-not-send="true"
href="ftp://ftp.gromacs.org/pub/tests/gmxtest-4.0.4.tgz"
target="1">ftp://ftp.gromacs.org/pub/tests/gmxtest-4.0.4.tgz</a>
or "git clone git://<a moz-do-not-send="true"
href="http://git.gromacs.org/regressiontests.git"
target="1">git.gromacs.org/regressiontests.git</a>"
is working due to the several modifications done in
gmx 4.5 including automatic thread for mdrun (I am
using a Mac with dual core) and more warnings.
<div> <br>
</div>
<div><font style="font-style: normal; font-weight:
normal; background-color: rgb(245, 248, 240);
font-size: 14px;">> </font>Thanks,</div>
<div><font style="font-style: normal; font-weight:
normal; background-color: rgb(245, 248, 240);
font-size: 14px;">> </font><br>
</div>
<div><font style="font-style: normal; font-weight:
normal; background-color: rgb(245, 248, 240);
font-size: 14px;">> </font>Alan<br
clear="all">
<font style="font-style: normal; font-weight:
normal; background-color: rgb(245, 248, 240);
font-size: 14px;">> </font><br>
<font style="font-style: normal; font-weight:
normal; background-color: rgb(245, 248, 240);
font-size: 14px;">> </font> -- <br>
<font style="font-style: normal; font-weight:
normal; background-color: rgb(245, 248, 240);
font-size: 14px;">> </font> Alan Wilter S.
da Silva, D.Sc. - CCPN Research Associate<br>
<font style="font-style: normal; font-weight:
normal; background-color: rgb(245, 248, 240);
font-size: 14px;">> </font> Department of
Biochemistry, University of Cambridge. <br>
<font style="font-style: normal; font-weight:
normal; background-color: rgb(245, 248, 240);
font-size: 14px;">> </font> 80 Tennis Court
Road, Cambridge CB2 1GA, UK.<br>
<font style="font-style: normal; font-weight:
normal; background-color: rgb(245, 248, 240);
font-size: 14px;">> </font> >><a
moz-do-not-send="true"
href="http://www.bio.cam.ac.uk/%7Eawd28"
target="1">http://www.bio.cam.ac.uk/~awd28</a><<<br>
</div>
</blockquote>
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<br>
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