Marcus D. Hanwell's Blog - KDE

Another Post About Camp KDE 2010

marcus@cryos.net (Marcus D. Hanwell) — Wed, 20 Jan 2010 11:18:00 -0500

There have been lots of posts about Camp KDE on Planet KDE, along with identi.ca posts and a stream of photos on flickr. It has been a great event so far with some really interesting talks. I especially enjoyed Philip Bourne's talk on open access to data which is very close to my heart, but noted that many parts of the stack used are still closed source. My background in Physics and Chemistry tell me that this needs to change. Open access data without open source tools to create, store and view that data is only addressing one part of the problem. I hope to address other parts of this issue in the work I am doing at Kitware

Celeste's talk was also interesting, and I found out that I may be an OCD interface design guy (many of the points she outlined bugged me in projects I had worked on, especially consistency in interfaces, grammar, etc). Great talk, and illuminating for someone like me who has not worked with anyone in this field before. Then of course there was Till and Alexandra's talk on career opportunities in FOSS, which was a great talk and I found myself nodding along with them. My windy path was not quite so glamourous as rock star or opera singer, but I can certainly identify with them. I instead pursued a degree and a PhD in physics research (largely experimental too), only to find I was extremely passionate about developing software to edit and visualize the data, rather than spending months in the lab.

This is not even the end of the first day, and so you can tell it was a great conference. Jos talked to use about marketing and then Artur presented his take on KDE form the desktop to the pocket. I still really want my own N900 to experiment with taking scientific visualization to the pocket (I have the desktops, laptops and a netbook to play with already). The next morning began with Frank presenting his vision of open source in the cloud, I find myself using the cloud more and more (especially now I have a Droid), but share his concerns and wish to create AGP led alternatives that can be easily deployed by both companies and individuals.

I also really enjoyed Romain's talk on the state of KDE PIM/KDE Windows, with live demos (warts and all). It also nicely segwayed the need for automated testing in order to improve the quality of KDE on other platforms, as well as use our limited resources wisely. I presented my talk on CMake, CTest, CDash and improving the software process in KDE. I think the testing framework can really help KDE developers by providing continuous feedback about platforms not everyone has access to. There are already quite a few KDE projects on my.cdash.org, and I would like to improve that and possibly use subprojects to divide the projects up into manageable pieces.

More great talks from Leo, and we ended the day with plasma talks and demos from Marco and Chani. I don't want to reproduce the schedule, but needless to say we had a great set of talks (all of which were taped and should be available soon). Thanks go out to Jeff and the ground team here for organizing the event so well. Monday was taken up with some more technical talks, Will's talk on the build service is something I would like to use in the future and see if we can get it contributing build/test results to KDE dashboards. The day concluded with CMake training run by me. I really enjoyed the dialog that was present in many of the talks (mine included), and got some great feedback about the training afterwards. I would love to do this again at future KDE events, and from the feedback I received it would seem others would like that to. It was very strange not to talk about any of the scientific visualization work I am doing, one of the first conferences in years where I have not.

Tuesday was the traditional trip day, and we checked out Stone Brewery, tried some excellent ales and then had dinner at one of the longest tables I have ever eaten at. William was of course in attendance, as the youngest attendee. After that we braved the driving rain and winds to get back to the UCSD campus. I took the opportunity to catch up on some work, and recharge my batteries a little ready for the Qt training that is being offered by Till Adam of KDAB today. Looking forward to a day of learning and admiring the sun this morning! The company has been great, and I am very pleased I was able to make it along. This is my first business trip for Kitware, and I am very pleased they sent me along, and that NAMIC sponsored my attendance.

Disclaimer: The opinions and musings in this post are mine, and not those of my employer. Any mistakes/inaccuracies are also mine, that said I would love to hear what people think of this new work.

Kitware at Camp KDE, Software Process Talk and CMake Tutorial

marcus@cryos.net (Marcus D. Hanwell) — Thu, 14 Jan 2010 22:30:26 -0500

Kitware is very kindly sending me to Camp KDE. I will be giving a talk on Sunday about CMake, testing, software process and new features in the recent CMake 2.8.0 release. I will also be running a training session on CMake on Monday afternoon. See you all there!

I will also be available to talk about many other things, such as the migration to git, open source chemistry, open science and scientific visualization. Since I joined Kitware I have been exploring some crazy cool ideas in new areas of visualization too, hopefully my influence has not been too disruptive. I will be on the lookout for potential Qties to join my team of Qties at Kitware - be warned

Looking forward to my second Camp KDE! We should arrive in San Diego Friday afternoon, not looking forward to the security lines... I will of course be bringing my spawned process (now named William), who was but a bump at the last Camp KDE. His Mum will be in attendance too, having to travel on her birthday. I am in the last few weeks of my twenties, so be kind.

Google Tech Talk on CMake

marcus@cryos.net (Marcus D. Hanwell) — Thu, 07 Jan 2010 20:41:35 -0500

Bill Hoffman gave a Google Tech Talk on 7 December 2009 at Google's New York city office on CMake, CTest, CDash and CPack. Google recently made the talk available on YouTube.

I wish I could have made it down with Bill and Will to see Google's New York office. For anyone attending Camp KDE, I will be discussing some of these concepts there too, but with a focus on the software process and testing components of CMake.

I'm Going to Camp KDE 2010

marcus@cryos.net (Marcus D. Hanwell) — Sat, 19 Dec 2009 17:28:02 -0500

Life has been so hectic since I moved to upstate New York to start my new job with Kitware. I am very pleased to say that Kitware is sending me to Camp KDE 2010 in San Diego, CA 15-22 January. I will be presenting a talk on CMake, the new features in the recently released 2.8 version, and some of the less well known features of the CMake package, including CTest, and CDash. In addition I will be running a CMake training session for anyone who would like to learn more about CMake.

I attended the first Camp KDE last year in Jamaica, and am very pleased to be attending the second Camp KDE next year in San Diego. Last year I focused on my work in packaging and open source chemistry visualization. I also met Bill Hoffman, who talked about CMake and am now working with him and many other talented people at Kitware. My wife and unborn child also attended the first Camp KDE. Now we have a six month old in the 97th percentile for length, weight and head size who will be joining my wife and I at Camp KDE 2010. I am trying to teach him to count from zero so that he has a good head start when he starts coding

I won't be talking about any of my work in open source scientific visualization at Camp KDE this time, but if any of the attendees are interested I would love to discuss it and will have a few slides for a short impromptu talk...

Avogadro 1.0.0 Released!

marcus@cryos.net (Marcus D. Hanwell) — Fri, 23 Oct 2009 18:02:00 -0400

It is with great pleasure that I announce the release of Avogadro 1.0.0. After many years of work we have released what we consider to be a stable Avogadro release on Mole Day, which seems appropriate given the projects's name. There are still some rough edges, but I think this is a good release. With your help we can fix bugs in the release while working on new features in trunk.

Avogadro - Code Swarm from Marcus Hanwell on Vimeo.

What better time to look back to the beginnings of Avogadro. There was a blog post made today by Sourceforge about Avogadro detailing a little of that history. I have also made a code_swarm movie visualizing the history of the Avogadro project. There have been quite some changes in that time both at a project level and a personal level.

I would like to thank Google for sponsoring me for a GSoC project in the summer of 2007. Also Geoff Hutchison for giving me the opportunity to work with him at the University of Pittsburgh on interesting computational and visualization projects. Then there is my new employer, Kitware, who have provided me with an exciting opportunity to push scientific visualization and cross platform development to its limits.

To finish off a great day, my wife has informed me my new espresso machine has arrived! I am going to Camp KDE in January too!

The Big Move and New Position at Kitware

marcus@cryos.net (Marcus D. Hanwell) — Wed, 30 Sep 2009 19:40:46 -0400

On Monday 21 September we packed the majority of our belongings into the back of a Penske truck and made the 500 mile drive (in convoy - Louise, William, Dax and myself) from Pittsburgh, PA to Clifton Park, NY. Since then we have been unloading the truck, unpacking our things into our new home and doing all those things you have to do when you move house, and several things necessary when moving between states and jobs.

This is certainly the most rural house I have lived in since I was very young. We found a nice duplex on the outskirts of Clifton Park, it uses well water and I am the proud owner of the contents of two full propane tanks (no natural gas lines run out to the house). We also have a really nice wood fire in the living room, and I snagged the family room and am using it as a large home office! Thankfully they were able to hook up a cable Internet connection on Tuesday last week, and so I was not offline for too long.

Tomorrow is my first day with Kitware, I will be attending a training course being run by Kitware for the remainder of the week and so won't have my first day in the office until next Monday. I will be working in the scientific visualization group on projects such as ParaView, and have had lots of ideas for future Avogadro development over the last few weeks. I am very much looking forward to working in some new areas, but also to enhancing the previous research and development I have done in the area of visualization in chemistry. I am also looking forward to working on CMake.

Avogadro 0.9.7 Released

marcus@cryos.net (Marcus D. Hanwell) — Mon, 20 Jul 2009 01:58:08 -0400

Avogadro 0.9.7 was released on 18 July 2009. You can download Avogadro here. I have been less involved in the development of Avogadro in the last six weeks due to a major event in my personal life. Still this release has some great new features in it, several of which I squeezed the time in to implement.

Some of the highlights include fixing a long standing rendering bug for our Linux users (me included) where garbage would be rendered right below the tab labels. This was a fix added to Qt 4.5.0 that I discovered while looking into the issue. A nice side effect is the new inline close buttons on view tabs. I also finally got detached OpenGL views into Avogadro, as shown in the screenshot to the right. It is a little clunky right now as you need to open a new view, and then detach it. I will clean up the interface for the next release hopefully. This allows for multiple views of the same molecular scene, which can be extremely useful for certain kinds of work.

Another long standing feature I wanted to implement is in too, the inline configuration buttons for our display types. If you can see the little wrenches, you can now click on them to configure that display type. This code was inspired by the inline close buttons that are in the Qt Creator open file list. Geoff worked making the configuration docks easier to hide, we now default to devoting roughly 90% of screen space to the 3D view, which I think is great. There have been several changes to how molecules are loaded/saved too, I am still hunting down some issues but this allows us to read multiple molecule files for example.

Today is the last day that you can vote for Avogadro in the SourceForge Community Choice Awards! Please cast your vote if you think that Avogadro is a great tool for Academia. Tim (one of our other dedicated Avogadro developers) posted about the release and the awards too. I would like to thank several people in the chemistry community who expressed their support for Avogadro on their blogs - Peter Murray-Rust, Richard Apidoca and Jan Jensen, along with so many others who have helped to promote Avogadro on Twitter, FriendFeed and other online services.

We hope you enjoy the release, whatever happens with the SourceForge Community Choice Awards it was an honour to be nominated. It was great to see all the support for the Avogadro project in the wider community too. It has inspired me to go on and do more with Avogadro - thanks to all of you.

Avogadro Auto Optimization Screencast

marcus@cryos.net (Marcus D. Hanwell) — Fri, 10 Jul 2009 19:44:45 -0400

Geoff showed me a new screencast he created recently. It is made using the latest Avogadro, and is one of the first screencasts with our new and improved user interface. Geoff has also added some audio commentary with notes on the chemical relevance of the auto optimization tool. Check it out and let us know what you think - a new release of Avogadro is coming soon.

I will hopefully find the time to make a few new screencasts soon too. Between my one month old son, day job and waiting on my visa application (does not take any real time - some mental drain) I have not had much spare time to code or blog. Remember that Avogadro was nominated for the SourceForge community choice awards too - click on the link below to vote for us.

Avogadro Nominated for SourceForge Community Choice Awards

marcus@cryos.net (Marcus D. Hanwell) — Tue, 23 Jun 2009 23:23:00 -0400

I am very pleased to announce that Avogadro has been nominated as a finalist in the SourceForge community choice awards this year. We are in the "Best Project for Academia" category, and I would like to encourage you to vote for Avogadro.

This is a real honour for all of us, and I appreciate all of you who nominated Avogadro. We are all pushing very hard on polishing Avogadro, getting ready for our 1.0 release. It would be absolutely amazing to see Avogadro win this award, so please vote for us.

There are also some other really nice projects in there too, such as Lancelot, ClamAV, phpMyAdmin and RepRap. So please take a few moments to place your vote, and tell your friends!

Update: You can vote even without a SourceForge account - just enter your email address and verify your vote.

Spawning a New Process: William Aaron Alexander Hanwell

marcus@cryos.net (Marcus D. Hanwell) — Tue, 23 Jun 2009 17:07:34 -0400

Exactly two weeks ago today my son was born, weighing in at 8 lbs 13 oz and measuring 21 inches long. Louise and I have named him William Aaron Alexander Hanwell, our new addition has been thriving after a bumpy start. I would like to claim first foetal attendee of a KDE conference, getting him off to a brilliant start listening to some great technical talks in Jamaica. I know most people play classical music to their unborn children, but we like to be different I need to find him a KDE baby grow!

You can see him in the above photos just minutes after his birth, and a little more relaxed the next day in his hospital crib. Not wanting to be too run of the mill he was consistently breach, delivered by C-section and had his cord wrapped around his neck 2.5 times. Not a problem for that kind of delivery, but it would have been had we had the natural birth we were hoping for. As he was born in the US he also manages to get dual nationality (US by birth, UK from us), whilst his poor old Dad is still waiting to hear back about his H-1B visa...

I think three days prior Carsten's wife gave birth too, and I believe Mauricio will also be growing his family later this year. So the KDE Edu developers all seem to be expanding their families this year, I guess the greater question is whether this was a coordinated effort As with all true geek babies I will be setting him up with his own blog and online photo album, mainly so that our family and friends back home will be able to keep up with him as he grows.

So far I am really enjoying being a new father, although aware that this isn't the only big change over the summer!

Appeal for Help: Avogadro Toolbar Icons

marcus@cryos.net (Marcus D. Hanwell) — Mon, 08 Jun 2009 15:19:52 -0400

Over the last few days we have been working on improving the look and feel of the Avogadro user interface. We owe both Qt Software and the Oxygen icon team a lot for making this process a lot easier. Avogadro uses quite a few Oxygen icons that we have taken and in some cases adapted slightly.

The sliver of screen shot above shows our tools tool bar, along with the tool and display settings buttons. We are pretty happy with the majority of the icons, which are (from left to right) draw, navigate, bond-centric manipulation, atom centric manipulation, selection, auto rotation (animated rotation about axes), auto optimise (continuous optimisation of the molecule geometry), z-matrix, measure and align tools.

I would really welcome any suggestions and/or icon submissions for the auto rotate (the spinny thing near the centre), and the auto optimise (the wand with the circle) tools. I think auto rotate is OK, but it would be better if it conveyed more of a three dimensional rotation. The auto optimise wand is perhaps the worst as it does not suggest optimisation of the geometry, but I am not sure what would. Do any of you more creative types have any suggestions?

I also wonder if there are nice icons we could use for tool and display settings, or a way to make those buttons smaller without losing discoverability. I look forward to hearing people's thoughts. As this is what people see when they first open Avogadro we would like to make the interface as inviting and intuitive as possible.

Avogadro 0.9.5 Released

marcus@cryos.net (Marcus D. Hanwell) — Wed, 03 Jun 2009 20:40:00 -0400

Yesterday I tagged the Avogadro 0.9.5 release, you can grab the latest downloads from here. Life has been hectic this last couple of months, and to be honest I have not gotten as much done as I would have liked. Still there are some great additions such as the experimental cartoon ribbon display ported by Tim from the Zodiac Zeden project.

Geoff also worked on getting more screen real estate for the actual display, after we bounced some ideas around over the last few months. I think that looks great, and have always tried to ensure the maximum amount of screen space was devoted to displaying the molecule. I still have a few more ideas, but fear I do not have the time to implement them. Geoff also added a new peptide builder and David has been working tirelessly on plotting spectra.

I have been working on decidedly less glamorous and less visual aspects of Avogadro. This includes improvements to our build system, I added the infrastructure required to find and build plugins/applications against the system installed Avogadro library. I also uploaded a few examples to GitHub, and David is actively working on an external plugin for a summer project.

I worked on getting a CMake project that included and compiled both Avogadro and OpenBabel. I then turned my attention to making a relocatable, self-contained app bundle for the Mac. This is working quite well, although there are a few parts of the build system I would like to clean up. It does mean we have relocatable applications that can run from a USB stick on both Windows and Apple systems now.

I crushed quite a few bugs too, worked on API improvements and fixed Noel's long standing feature request - to disable the visual cues when navigating around a molecule. The original Windows installer shipped with a data loss bug, when saving a molecule the original could be erased and you would be left with a zero length file. This was a Windows specific bug that slipped through, I spent half of today tracking this issue with a few other Windows bugs and updated installers have been uploaded (Tim made the Python enabled installer). Please ensure you update to Avogadro-0.9.5-win32a.exe or Avogadro-0.9.5-python-win32.exe. Hacking on Windows has to be one of my least favourite activities, and I need a couple of days away from that whole platform before I can go back and finish some of the work I have been doing...

We are pushing to a 1.0.0 release, targeted for July. We would appreciate feedback on the interface, bugs encountered, the public API that is installed along with any other suggestions or offers of help. Our translations are now doing very well too, and any help improving them further would be appreciated.

Enjoy the new release, another is likely only a week or two away as we crush the remaining bugs. I am also fighting to find time to implement a few more features I would really like to see in Avogadro 1.0.0.

Vote for Avogadro

marcus@cryos.net (Marcus D. Hanwell) — Thu, 14 May 2009 15:25:00 -0400

I just got an email from Sourceforge about their community awards. If you are a user, fan or developer please vote for Avogadro in the Best Project for Academia category. They even provided me with a nice graphics to put on the page, you can just click on it to register your vote.

In other news lots of exciting things happening in Avogadro, hopefully I will find some time to blog about them soon!

KDE GSoC Sprint Winding Down

marcus@cryos.net (Marcus D. Hanwell) — Tue, 12 May 2009 20:45:00 -0400

The KDE GSoC sprint is over, and we have all returned to our respective homes. We lost a couple of people who had early flights on Sunday, I snapped a fairly blurred group shot Saturday evening, outside of the MIT Stata Center. After an intense day of hacking we headed out for food in the middle of a torrential down pour. We had some great Indian food, ice cream and then went candle pin bowling before they closed at midnight.

Sunday morning we got back into hacking pretty early on. We debated the merits of different editors, the role of desktop and internet applications and debugged a few issues with development environments. We also got Dunkin' Donuts coffee and some very tasty burritos. Sunday was cut short by flights, but Jeff very kindly ferried the two groups to the airport for flights at around 6pm and 8pm.

As I was in the second group we took the opportunity to walk into Boston from Cambridge and take a look around. As we crossed the river I took the opportunity to take lots of photos and stitch them together into my first panorama. I think it turned out quite well, I am just starting to get familiar with the software.

I spotted a few posts from Chani and Alejandro about the event too. It was great meeting you guys and I hope you all have a great summer of code!

KDE GSoC Sprint in Boston

marcus@cryos.net (Marcus D. Hanwell) — Sat, 09 May 2009 19:30:16 -0400

We all arrived yesterday in Boston, got to know each other and did some hacking. Yesterday evening we all went to an iMax theater to see the new Star Trek movie. We have spent most of the day talking code and hacking in a small room in one of MIT's buildings.

It has been a pretty productive day, and it is always great to meet up with KDE developers old and new. Everyone is heading out at various points throughout tomorrow. Thanks to Jeff and Qt Software for making this event happen.