<div dir="ltr"><br><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Nov 26, 2014 at 6:42 PM, Shirts, Michael R. (mrs5pt) <span dir="ltr"><<a href="mailto:mrs5pt@eservices.virginia.edu" target="_blank">mrs5pt@eservices.virginia.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word;color:rgb(0,0,0);font-size:14px;font-family:Calibri,sans-serif">
<div>
<div>Hi, all-</div>
<div>My goals for 5.1:</div>
<ul>
<li>High priority:
<ul>
<li>Resolve any lingering issues with proper framework to do free energy changes, so that everything is better documented and consistent, and addressing lingering questions.
<ul>
<li>Topics include verifying Hamiltonian replica exchange, making sure integrated with pull code, deciding on best practices, clearing out redmine with free energy related issues, partially unifying analysis approaches. Adding a MBAR option into GROMACS would
be nice, but may need to wait. </li></ul></li></ul></li></ul></div></div></blockquote><div><br></div><div>Great. These are things also very important here. It's not healthy for the code to have Shirts-style and old-style implementations not properly integrated, tested and documented.</div><div><br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word;color:rgb(0,0,0);font-size:14px;font-family:Calibri,sans-serif"><div><ul><li><ul><li>
</li></ul>
<ul>
<li>Finally remove the iteration code (literally in the middle of rebasing the removed-iteration code to the current master when receiving this email)</li></ul></li></ul></div></div></blockquote><div><br></div><div>Great. I recently considered throwing a birthday party for this patch :-) The mechanics of the rebase would be very easy for me to do (main issue is the ongoing header file reorganization in master) - but we need more eyes than mine on the result!</div><div><br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word;color:rgb(0,0,0);font-size:14px;font-family:Calibri,sans-serif"><div><ul><li><ul><li> </li></ul>
<ul>
<li>At least partially reorganize the integrator framework bookkeeping to be cleaner and in the Trotter decomposition style. This would be a code reorganization, but should not be a feature change at this point. So the scope would be whatever is manageable.</li></ul></li></ul></div></div></blockquote><div><br></div><div>Good; it will also be easier to see the wood once the iteration trees are gone.</div><div><br></div><div>Mark </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word;color:rgb(0,0,0);font-size:14px;font-family:Calibri,sans-serif"><div><ul><li>
</li><li>Going to try very hard
<ul>
<li>Add an MC Barostat (especially important if removing iterative MTTK in above).</li></ul>
<ul>
<li>Better document existing expanded ensemble framework and adding features from with Viveca's expanded ensemble framework to reduce code duplication and harmonize approaches.</li></ul>
</li></ul>
<div>
<ul>
<li>Priorities for 5.2
<ul>
<li>Fully trotterizing the code to support multiple time steps</li><li>A more complete MC framework</li><li>Free energy calculations using linear basis scheme (requires GPU-accelerated tabulated functions); this should accelerate free energy calculations by removing it form the inner , as well as removing the need to ever write free energy inner loops for SIMD
or GPU.</li><li>Multiple end states (instead of just A and B)</li><li>Enveloping distribution sampling</li></ul>
</li></ul>
</div>
<div>
<div>Best,</div>
~~~~~~~~~~~~<br>
Michael Shirts<br>
Associate Professor<br>
Department of Chemical Engineering<br>
University of Virginia<br>
<a href="http://michael.shirts@virginia.edu" target="_blank">michael.shirts@virginia.edu</a><br>
(434) 243-1821</div>
</div>
<div><br>
</div>
<span>
<div style="font-family:Calibri;font-size:14pt;text-align:left;color:black;BORDER-BOTTOM:medium none;BORDER-LEFT:medium none;PADDING-BOTTOM:0in;PADDING-LEFT:0in;PADDING-RIGHT:0in;BORDER-TOP:#b5c4df 1pt solid;BORDER-RIGHT:medium none;PADDING-TOP:3pt">
<span style="font-weight:bold">From: </span>Mark Abraham <<a href="mailto:mark.j.abraham@gmail.com" target="_blank">mark.j.abraham@gmail.com</a>><br>
<span style="font-weight:bold">Reply-To: </span>"<a href="mailto:gmx-developers@gromacs.org" target="_blank">gmx-developers@gromacs.org</a>" <<a href="mailto:gmx-developers@gromacs.org" target="_blank">gmx-developers@gromacs.org</a>><br>
<span style="font-weight:bold">Date: </span>Wednesday, November 26, 2014 at 12:18 PM<br>
<span style="font-weight:bold">To: </span>Discussion list for GROMACS development <<a href="mailto:gmx-developers@gromacs.org" target="_blank">gmx-developers@gromacs.org</a>>, Christian Wennberg <<a href="mailto:chriwen@kth.se" target="_blank">chriwen@kth.se</a>>, Iman Pouya <<a href="mailto:iman.pouya@gmail.com" target="_blank">iman.pouya@gmail.com</a>>,
Alfredo Metere <<a href="mailto:alfredo.metere@scilifelab.se" target="_blank">alfredo.metere@scilifelab.se</a>>, Anca Hamuraru <<a href="mailto:anca@streamcomputing.eu" target="_blank">anca@streamcomputing.eu</a>>, Vincent Hindriksen <<a href="mailto:vincent@streamcomputing.eu" target="_blank">vincent@streamcomputing.eu</a>><br>
<span style="font-weight:bold">Subject: </span>[gmx-developers] plans for Gromacs 5.1 release<br>
</div><div><div class="h5">
<div><br>
</div>
<div>
<div>
<div dir="ltr">Hi,
<div><br>
</div>
<div>It's time we got organized for the next minor release. Generally policy is unchanged - we do a feature-change release at least once a year, and bugfix releases periodically on the last minor/major release. An "extra" release for some special purpose is
negotiable.</div>
<div><br>
</div>
<div>I propose</div>
<div><br>
</div>
<div>* now:</div>
<div> + get code you want to be considered for 5.1 into gerrit (tag the first line of the commit message [RFC] or [WIP] if you know that the current state of the code is not a serious candidate for merging)</div>
<div> + get your karma up by participating in review of others' code</div>
<div> + reply to this email (or comment on your patches in gerrit) to guide other people about what might be important for them to review</div>
<div><br>
</div>
<div>* mid-January:<br>
</div>
<div> + release 5.0.x</div>
<div> + release 5.1-beta from whatever is the tip of master branch at the time</div>
<div> + fork release-5-1 branch then (still open for functionality changes until the 5.1-rc1 releases; gerrit's feature for cherry picking between branches will make this fork manageable)</div>
<div><br>
</div>
<div>* early-to-mid February:</div>
<div> + release 5.1-rc1</div>
<div> + close release-5-1 to new functionality, it remains open for bug fixes, test cases, and documentation only</div>
<div> + test widely on any plausible machine and compiler for portability and correctness</div>
<div> + release 5.1-rc[234] if that seems like a good idea</div>
<div><br>
</div>
<div>* mid-March:</div>
<div> + release 5.0.x for hopefully the last time, pretty much close release-5-0 branch</div>
<div> + release 5.1</div>
<div> + remove the group cutoff scheme</div>
<div> + ...</div>
<div> + Profit!</div>
<div><br>
</div>
<div>Do speak up if you have a suggestion for a change / request for special consideration / whatever. I've deliberately left the Christmas period open for people who might want to do a last code push at that time, but a huge patch landing without warning on
January 10... will probably get ignored by me.</div>
<div><br>
</div>
<div>Please note that things like ongoing contribution with testing and code review are the primary things that might earn an authorship on Gromacs papers (5.0 is still on my TODO list, sorry) - adding some feature is awesome, but what reward structure we can
offer needs to focus on the large amount of inglorious work that has to happen.</div>
<div><br>
</div>
<div>Things team Stockholm are actively working on that we'd like to have ready for 5.1 (and the names of the primary people involved)</div>
<div>* new DD communication support (Berk)</div>
<div>* enhancements to pull code (Berk)</div>
<div>* Verlet scheme support for tables, vacuum, Generalized Born (Berk, Alfredo)</div>
<div>* GPU support for tabulated interactions (Alfredo)</div>
<div>* GPU acceleration of (at least) dihedral interactions (Iman)</div>
<div>* combined FFTs for LJ-PME (Christian)</div>
<div>* offload of bonded interactions for enhancing load balance (Mark)</div>
<div>* support for latest CUDA offerings (Szilard)</div>
<div>* OpenCL non-bonded support (mostly Anca from <a href="http://www.streamcomputing.eu" target="_blank">
http://www.streamcomputing.eu</a>, Mark)</div>
<div>* support for CPU-based SIMD on everything on the horizon (Erik)</div>
<div><br>
</div>
<div>Like everything else, none of that's going to block releases, but since 5.1 will be the last minor release with the group cutoff scheme, feature completion of the Verlet scheme will be an internal priority for development, review, and testing. Full feature
completion is unlikely to happen, so support for twin-range multiple-time stepping, QM/MM, and AdReS may disappear unless people want to put the work in.</div>
<div><br>
</div>
<div>There's a lot of code already in Gerrit awaiting review, particularly from Teemu on the analysis tools. I need to help out more there, but do check if he's fixing stuff that you might care about!</div>
<div><br>
</div>
<div>If you're working on code that you might want to get into 5.1, speak up!</div>
<div><br>
</div>
<div>Happy reviewing!</div>
<div><br>
</div>
<div>Mark</div>
</div>
</div>
</div>
</div></div></span>
</div>
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