<br><br><div class="gmail_quote">On Mon, Feb 18, 2013 at 2:18 PM, Justin Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
Hi All,<br>
<br>
I'm assuming fixes to the manual are being considered separately then? To me, we really shouldn't release 4.6.1 unless we have a corresponding manual out at least within 24 hr of the code being made public. In my mind, released code necessitates a definitive manual, and there have been questions on the user list related to the manual. There are still some glaring inaccuracies and outdated information, mostly in section 6.12 related to GPU usage (basically it needs to be scrapped, since OpenMM isn't even fully supported any more) and Appendix A. My patch related to environment variables (<a href="https://gerrit.gromacs.org/#/c/2055/" target="_blank">https://gerrit.gromacs.org/#/<u></u>c/2055/</a>) is basically done since Szilard finished off the last few items, but hasn't even been reviewed.<br>
</blockquote><div><br></div><div>I'd certainly like an up-to-date manual to go with code releases. :-) There's a lot of things I have to juggle doing, unfortunately. I'll look at manual issues tomorrow.</div><div>
<br></div><div>Mark</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
-Justin<div><div class="h5"><br>
<br>
On 2/18/13 8:07 AM, Mark Abraham wrote:<br>
</div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div class="h5">
Hi GROMACS developers,<br>
<br>
There's a release branch constructed, containing a number of minor fixes,<br>
documentation updates and a few remaining fixes of critical issues. Below is a<br>
list of commits that are ancestors of the 4.6.1 release patch - please review<br>
things that you know about!<br>
<br>
<a href="https://gerrit.gromacs.org/#q,I60998e3b,n,z" target="_blank">https://gerrit.gromacs.org/#q,<u></u>I60998e3b,n,z</a> New patch release 4.6.1<br>
<a href="https://gerrit.gromacs.org/#q,I9a551260,n,z" target="_blank">https://gerrit.gromacs.org/#q,<u></u>I9a551260,n,z</a> Update outdated admin things<br>
<a href="https://gerrit.gromacs.org/#q,Iba5b4c66,n,z" target="_blank">https://gerrit.gromacs.org/#q,<u></u>Iba5b4c66,n,z</a> Fixes for install guide page.<br>
<a href="https://gerrit.gromacs.org/#q,Ia0a571d2,n,z" target="_blank">https://gerrit.gromacs.org/#q,<u></u>Ia0a571d2,n,z</a> Updated install guide<br>
<a href="https://gerrit.gromacs.org/#q,I33495d57,n,z" target="_blank">https://gerrit.gromacs.org/#q,<u></u>I33495d57,n,z</a> Uncrustified code changes since 4.6<br>
<a href="https://gerrit.gromacs.org/#q,If96fd044,n,z" target="_blank">https://gerrit.gromacs.org/#q,<u></u>If96fd044,n,z</a> Bump shared object version to 8<br>
<a href="https://gerrit.gromacs.org/#q,I79a06b20,n,z" target="_blank">https://gerrit.gromacs.org/#q,<u></u>I79a06b20,n,z</a> fixed issues with FEP soft-core and<br>
cut-off's<br>
<a href="https://gerrit.gromacs.org/#q,Ib90ac4e5,n,z" target="_blank">https://gerrit.gromacs.org/#q,<u></u>Ib90ac4e5,n,z</a> Merge release-4-5-patches into<br>
release-4-6<br>
<a href="https://gerrit.gromacs.org/#q,I146592c3,n,z" target="_blank">https://gerrit.gromacs.org/#q,<u></u>I146592c3,n,z</a> fixed GPU particle gridding<br>
performance issue<br>
<a href="https://gerrit.gromacs.org/#q,I268bbf65,n,z" target="_blank">https://gerrit.gromacs.org/#q,<u></u>I268bbf65,n,z</a> Made g_tune_pme work with 4.6 if<br>
user sets "-p" command line option<br>
<a href="https://gerrit.gromacs.org/#q,I79fd46e1,n,z" target="_blank">https://gerrit.gromacs.org/#q,<u></u>I79fd46e1,n,z</a> Fix CMake namespace pollution<br>
<a href="https://gerrit.gromacs.org/#q,I3c37844c,n,z" target="_blank">https://gerrit.gromacs.org/#q,<u></u>I3c37844c,n,z</a> Issue errors/warnings for ICC before<br>
12.0.0<br>
<a href="https://gerrit.gromacs.org/#q,Ia6157db8,n,z" target="_blank">https://gerrit.gromacs.org/#q,<u></u>Ia6157db8,n,z</a> bugfix for md-vv + nose-hoover +<br>
(nstcalcenergy > nsttcouple)<br>
<a href="https://gerrit.gromacs.org/#q,Ia071c6a1,n,z" target="_blank">https://gerrit.gromacs.org/#q,<u></u>Ia071c6a1,n,z</a> Use explicit kernel pointer typecasts<br>
<br>
Mark<br>
<br>
On Tue, Feb 12, 2013 at 9:15 PM, Mark Abraham <<a href="mailto:mark.j.abraham@gmail.com" target="_blank">mark.j.abraham@gmail.com</a><br></div></div><div class="im">
<mailto:<a href="mailto:mark.j.abraham@gmail.com" target="_blank">mark.j.abraham@gmail.<u></u>com</a>>> wrote:<br>
<br>
Hi GROMACS developers,<br>
<br>
We've made a number of bug fixes to 4.6, and it's time we got those out to<br>
the world in 4.6.1. There's a few bits and pieces still sitting in gerrit,<br>
so please see what you can get done. I'll plan to construct a release branch<br>
on Friday and release Monday Feb 17.<br>
<br>
Cheers,<br>
<br>
Mark<br>
<br>
<br>
<br>
<br>
</div></blockquote><span class="HOEnZb"><font color="#888888">
<br>
-- <br>
==============================<u></u>==========<br>
<br>
Justin A. Lemkul, Ph.D.<br>
Research Scientist<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | <a href="tel:%28540%29%20231-9080" value="+15402319080" target="_blank">(540) 231-9080</a><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br>
<br>
==============================<u></u>==========</font></span><div class="HOEnZb"><div class="h5"><br>
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