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Using VTK's Image Regression Tests in Avogadro 2

One of the really nice features of VTK's testing framework is the use of image-based regression tests. These allow developers to write tests that result in a final image, which can be recorded and compared to known baseline images in order to verify that the OpenGL rendering code is rendering the same (or similar) image on all platforms. If this fails then CDash will display the image the test produced, the baseline image it was compared to and an image difference. Any project that performs rendering or visualization needs tests like these in addition to unit tests if they want to assure visualization code continues to function as expected across a range of platforms.

We recently extracted the relevant code from the VTK testing framework to perform image based regressions in Avogadro 2, with the bulk of that code living in utilities/vtktesting/imageregressiontest.h. This is currently used in one of the tests, with plans to extend it to cover all major types of rendering, this can in seen in action intests/qtopengl/glwidgettest.cpp with the important lines that take the snapshot/do the image comparison being:

  // Grab the frame buffer of the GLWidget and save it to a QImage.
  QImage image = widget.grabFrameBuffer(false);
  // Set up the image regression test.
  Avogadro::VtkTesting::ImageRegressionTest test(argc, argv);
  // Do the image threshold test, printing output to the std::cout.
  return test.imageThresholdTest(image, std::cout);

The CMake code that feeds in the command line arguments, and ensures the test runs correctly is in tests/qtopengl/CMakeLists.txt, and largely involves passing in paths to the baseline directory, a temporary directory and the test name (using the standard CMake generated test driver).

  add_test(NAME "QtOpenGL-${test}"
    COMMAND
      AvogadroQtOpenGLTests "${testname}test"
      "--baseline" "${AVOGADRO_DATA_ROOT}/baselines/avogadro/qtopengl"
      "--temporary" "${PROJECT_BINARY_DIR}/Testing/Temporary")
Valid baseline image

The above is the baseline image, that is stored in a known location and compared with the image produced by the test (shown below).

Test image image produced

If the images don't match a difference image is produced and uploaded (shown below). In this case you can see that an extra sphere was rendered, and this can clearly be seen in the difference image. There is also a numerical difference returned by the test, which is a measure of how much the images differ. The tolerance can be tweaked depending on the test to allow some minor pixel differences, although care must be taken not to raise the number too high.

Image difference from test to valid

We have not implemented it in Avogadro 2 yet, but VTK can use multiple baselines and returns the smallest image difference. This allows for OS/GPU specific baselines to be uploaded where necessary as an alternative to increasing the tolerance. Using special tags returned by the tests in the standard output will prompt the ctest command to upload the image files when necessary (in the case the baseline image cannot be found, or the image comparison fails).

First Open Chemistry Beta Release

Open Chemistry

We are pleased to announce the first beta release of the Open Chemistry suite of cross platform, open-source, BSD-licensed tools and libraries - Avogadro 2, MoleQueue and MongoChem. They are being released in beta, before all planned features are complete, to get feedback from the community following the open-source mantra of “release early, release often”. We will be making regular releases over the coming months, as well as automatically generating nightly binaries. A Source article from 2011 introduced the project, slides from FOSDEM describe it more recently, and the 0.5.0 release binaries can be downloaded here.

Open Chemistry workflow

These three desktop applications can each be used independently, but also have the capability of working together. Avogadro 2 is a rewrite of Avogadro that addresses many of the limitations we saw. This includes things such as the rendering code, scalability, scriptability, and increased flexibility, enabling us to effectively address the current and upcoming challenges in computational chemistry and related fields. MoleQueue provides desktop services for executing standalone programs both locally and on remote batch schedulers, such as Sun Grid Engine, PBS and SLURM. MongoChem provides chemically-aware search, storage, and informatics visualization using MongoDB and VTK.

Open Chemistry library organization

Avogadro 2

Avogadro 2 is a rewrite of Avogadro; please see the recently-published paper for more details on Avogadro 1. Avogadro has been very successful over the years, and we would like to thank all of our contributors and supporters, including the core development team: Geoff Hutchison, Donald Curtis, David Lonie, Tim Vandermeersch, Benoit Jacob, Carsten Niehaus, and Marcus Hanwell. We also recently obtained permission from almost all authors to relicense the existing code under the 3-clause BSD license, which will make migration of code to the new architecture much easier.

Avogadro 2 rendering a molecular orbital

Some notable new features of Avogadro 2 include:

  • Scalable data structures capable of addressing the needs of large molecular systems.
  • A flexible file I/O API supporting seamless addition of formats at runtime.
  • A Python-based input generator API, creating an input for a range of quantum codes.
  • A specialized scene graph for supporting scalable molecular rendering.
  • OpenGL 2.1/GLSL based rendering, employing point sprites, VBOs, etc.
  • Unit tests for core classes, with ongoing work to improve coverage.
  • Binary installers generated nightly.
  • Use of MoleQueue to run computational codes such as NWChem, MOPAC, GAMESS, etc.

Avogadro is not yet feature complete, but we invite you to try it out along with the suite of applications as we continue to improve it. The new Avogadro libraries feature much finer granularity; whereas before we provided a single library with all API, there is now a layered API in multiple libraries. The Core and IO libraries have minimal dependencies, with the rendering library adding a dependence on OpenGL, and the Qt libraries adding Qt 4 dependencies. This allows us to reuse the code in many more places than was possible before, with rendering possible on a server without Qt/X, and the Core/IO libraries being suitable for command line use or integration into non-graphical applications.

MoleQueue

MoleQueue is a new application developed to satisfy the need to execute computational chemistry codes locally and remotely. Rather than adding this functionality directory to Avogadro 2, it has been developed as a standalone system-tray resident application that runs a graphical application and a local server (using local sockets for communication). It supports the configuration of multiple queues (local and remote), each containing one-or-more programs to be executed. Applications communicate with MoleQueue using JSON-RPC 2.0 over a local socket, and receive updates as the job state changes. A recent Source article describes MoleQueue in more detail.

MoleQueue queue configuration

In addition to the system-tray resident application, MoleQueue provides a Qt 4-based client library that can easily be integrated into Qt applications, providing a familiar signal-slot based API for job submission, monitoring, and retrieval. The project has remained general in its approach, containing no chemistry specific API, and has already been used by several other projects at Kitware in different application domains. Communicating with the MoleQueue server from other languages is quite simple, with the client code having minimal requirements for connecting to a named local socket and constructing JSON strings conforming to the JSON-RPC 2.0 specification.

MongoChem

MongoChem is another new application developed as part of the Open Chemistry suite of tools, leveraging MongoDB, VTK, and AvogadroLibs to provide chemical informatics on the desktop. It seeks to address the need for researchers and groups to be able to effectively store, index, search and retrieve relevant chemical data. It supports the use of a central database server where all data can be housed, and enables the significant feature set of MongoDB to be leveraged, such as sharding, replication and efficient storage of large data files. We have been able to reuse several powerful cheminformatics libraries such as Open Babel and Chemkit to generate identifiers, molecular fingerprints and other artifacts as well as developing out features in the Avogadro libraries to support approaches to large datasets involving many files.

MongoChem

We have taken advantage of the charts developed in VTK and 2D chemical structure depiction in Open Babel to deliver immersive charts that are capable of displaying multiple dimensions of the data. Linked selection allows for selection in one view, such as parallel coordinate; views of that selection in a scatter plot matrix, and the table view. The detail dialog for a given molecule shows 2D structure depiction, an interactive 3D visualization when geometry is available and support for tagging and/or annotation. We have also developed an early preview of a web interface to the same data using ParaViewWeb, enabling you to share data more widely if desired. This also features a 3D interactive view using the ParaViewWeb image streaming technology which works in almost all modern browsers.

Putting Them Together

Each of the applications in the Open Chemistry suite listens for connections on a named local socket, and provides a simple JSON-RPC 2.0 based API. Avogadro 2 is capable of generating input files for several computational chemistry codes, including GAMESS and NWChem, and can use MoleQueue to execute these programs and keep track of the job states. Avogadro 2 can also query MongoChem for similar molecules to the one currently displayed, and see a listing sorted by similarity. MongoChem is capable of searching large collections of molecules, and can use the RPC API to open any selected molecule in the active Avogadro 2 session.

Acknowledgements

The development of the Open Chemistry workbench has been funded by a US Army SBIR with the Engineering Research Development Center under contract (W912HZ-12-C-0005) at Kitware, Inc.

Originally published on the Kitware blog

FOSDEM: Open Science and Open Chemistry

I will be talking about the Open Chemistry Project at FOSDEM this year in the FOSS for scientists devroom at 12:30pm on Saturday. I will discuss the development of a suite of tools for computational chemists and related disciplines, which includes the development of three desktop applications addressing 3D molecular structure editing, input preparation, output analysis, cheminformatics and integration with high-performance computing resources.

Open Chemistry

On Sunday Bill Hoffman will be speaking in the main track about Open Science, Open Software, and Reproducible Code at 3pm on Sunday. Bill and Alexander Neundorf will also be talking about Modern CMake in the cross desktop devroom on Saturday.

FOSDEM is one of the first conferences I attended (possibly the first, I can't remember if I went to a science conference before this). It will be great to return after so many years, and hopefully meet old colleagues and a few new ones. Please find me, Bill or Alex if you would like to discuss any of this work with us. I fly out tomorrow, and hope to get over jet lag quickly. Once FOSDEM is over we will be visiting Kitware SAS in Lyon, France for a couple of days (this is my first trip to our new office).

Then I have a few days in England visiting friends and family before heading back to the US.

Leap Day: Never Enough Time

What a busy year it has been so far, a leap day hardly seems enough to help me catch up! I started off the year with a meeting in Cambridge, England on Semantic Physical Science which was hosted by Peter Murray-Rust. I ended up leading the working group on CML and the developing a roadmap to move forward. Peter blogged about this on my birthday (by chance) and you can see the video of my summing up of the results, along with all the other videos from the final day.

While I was back in England I took the opportunity to visit friends and family, along with a day trip to Liverpool to meet with Abbie and Jens. While I was there we discussed some plans around alternate inputs for Avogadro for an upcoming MP visit at the end of January. I found some time to blog about that on the Kitware blog, and Abbie wrote up the visit on their site. I think engaging more people in chemistry is important, and whilst I don't think the interaction is ideal at the moment I was pleased to see them enjoying it. The Kinect is something that many groups can purchase, and if it helps engage a wider audience in science I think that is a great thing.

I am very excited about the work we are doing in Open Chemistry at Kitware. We have been bringing web sites and testing online, and have begun engaging more people in the development process. The official announcement of our Phase II funding went out in January too, and I set up an Open Chemistry group on Google+ if you would like to follow new developments there.

I am especially excited after meeting some people from EMSL at the Semantic Physical Science meeting in Cambridge about the possibilities of working with NWChem more in the future. The open source license they switched to last year is of a very similar liberal nature to that of many of the open source projects we work on at Kitware. There are a large array of techniques available in NWChem, and interest in correlating computational and experimental observables.

We have also been extending Gerrit to support topic branch reviews, and switched VTK to use it for all code submissions. You can see proposed topics and they will trigger automatic build tests using CDash@Home for members of the core group. The Open Chemistry projects are also using the same Gerrit server for code review, and I am adding automated build testing of topics as I find time (any more leap days would help).

As my extra day draws to a close I realize there is still so much more I should get down. I will aim for more discipline in adding more regular entries here, you can follow my Google+ updates if you would like more updates on open source, open science and the life of a scientific software developer.

Conferences: Talking Open Science at OSCON, Desktop Summit and Chemical Databases Meeting

Over the last two months I have had one of my most hectic travel schedules ever. It started withOSCON, and a panel discussion about "Practicing Open Science". This one was a bit of a surprise, as Bill Hoffman was originally presenting with Will Schroeder and Brian Wylie, from Sandia National Laboratories. As Bill couldn't make it we decided to change the content of my section, and talk about the new open chemistry area that I have been working on for about four years now. Will went first, followed by me and a wrap up from Brian, with a nice flow between Kitware working on open science for over a decade, me growing a new area of open science (now at Kitware) and Brian giving a government perspective on open source and open science. The slides are below and on slideshare if you would like to take a look.

I thoroughly enjoyed OSCON, and would love to attend future events. The toughest thing was deciding which talks to attend as there were often multiple tracks with talks of interest to me. This was also by far the largest and most commercialized open source event I have attended so far, in the beautiful city of Portland, OR. I couldn't stick around for long after the conference as I was flying out to England on the following Tuesday, and on to Berlin, Germany Friday to attend the Desktop Summit. This was my first time in Germany, and I was looking forward to exploring Berlin a little, along with some time to catch up with a few family and friends in England before and after the conference. I talked about "Open Source Visualization of Scientific Data" on the final day of the main conference, and was very pleased to have a large and interested audience. Here I also discussed my work in open chemistry, along with a lot of the other work we do at Kitware in the Scientific Computing group.

I stayed for the remainder of the conference, attending my first KDE e.V. meeting, and was joined by Bill Hoffman towards the end of the week. Bill gave a workshop on using CMake, and I helped out with that, along with taking part in several BoF sessions and meetings. It was a very hectic week, very different feel to OSCON with a lot of great presentations, BoFs and hacking sessions. I also had the opportunity to meet up with Alexander Neundorf who was an intern at Kitware for half a year, and several other KDE developers interested in build systems, software process, testing, coverage and related areas.

Then I was back home for just over a week before braving the elements and heading straight for the path of hurricane Irene. I was invited to the 5th Meeting on U.S. Government Chemical Databases and Open Chemistry where I talked about "Chemical Databases and Open Chemistry on the Desktop". This meeting was very focused on chemical databases and the open chemistry I have been working on so hard for the last few years. It was a great experience to be able to see what others are working on, and discuss possible points for future collaboration. There is some amazing work happening in this area, and this meeting helped me gain greater clarity on how my work at Kitware can fit into the larger picture to significantly improve the landscape in open chemistry.

Thanks to Kitware for allowing me to attend, and funding my travel/other expenses, and to my wife and son for tolerating my long absences over the last couple of months. An even bigger thank you to my wife, Louise, for letting me off the hook on my first missed wedding anniversary so that I could present at OSCON! I had some great news about funding for the continued development of many of the ideas discussed in the slides, and so hope to have much more to talk about over the coming months (and years). This post is already pretty long, I hope to continue developing this work and promoting open science, especially in chemistry, materials science, physics and the bio areas. There are lots of other amazing people working in these areas too, and I feel like we are getting to a point where we can create real change to improve the outlook in scientific research.

Talking About Open Source Visualization of Scientific Data at the Desktop Summit

I have begun my journey to the Desktop Summit, making the flight over from the US to Manchester yesterday. A short stay in Sheffield, and catch up with family before heading out to get my flight to Berlin tomorrow. I will be talking about the work I have done both at and before joining Kitware with the title "Open Source Visualization of Scientific Data". I plan to talk about a range of work from my Google Summer of Code project on Kalzium back in 2007, through to some of the exciting work at Kitware in VTK, ParaView and Titan looking at the challenges of large data, remote visualization and how to integrate the web and smartphones/tablets into the scientific data visualization workflow.

Desktop Summit 2011

Bill Hoffman is also planning to attend, and we will be running a workshop introducing CMake on Thursday. This is my first Desktop Summit, although Bill and I have both attended previous aKademy and Camp KDE meetings. I should be in on time to attend the pre-registration event, and will not be leaving until Saturday. Looking forward to a great summit, catching up with some old friends and making some new ones. Now, I think I should try to get some sleep before my flight tomorrow!


Talking at OSCON 2011 about Open Science

I am currently on a plane bound for Portland, Oregon enjoying the in-plane wi-fi. Will Schroeder, Brian Wylie and I will be talking about "Practicing Open Science" on Friday in the government track. I am standing in for Bill Hoffman who unfortunately could not make it, and will be discussing the work I have been doing to grow open chemistry both at Kitware and outside of Kitware with many amazing collaborators scattered around the world. I am really excited to have the opportunity to talk at OSCON, and would be happy to meet up and discuss this work if you are at OSCON. Will and Brian are both very passionate about open science too, they will both give their unique perspectives on practicing open science. I will be there from this evening and don't fly out until early Saturday morning.

OSCON 2011

I am very much looking forward to OSCON, and the major difficulty I have had is choosing between the talks that are all happening at the same time. In some cases there are two or three I would like to see in any given slot. I am hoping to attend the KDE release party tomorrow too, please join us there if you would like to celebrate with us.

Avogadro 1.0.3 Released

I am pleased to be able to announce the availability of Avogadro 1.0.3! What happened to Avogadro 1.0.2 I hear you ask...shortly after tagging Michael reported an issue with i18n building/installations. So 1.0.3 contains a couple of very small build system fixes, but see the 1.0.2 release notes for details of most of the fixes.

As always, we appreciate your feedback. There are still a few issues outstanding, but many things were fixed. These binaries are also built against much newer versions of Qt and Open Babel where significant improvements have also been made. There may be one or two more releases of the 1.0 line if necessary (I have streamlined the release process with a view to making more releases), but I would like to focus our efforts on an unstable release for 1.1. Once 1.1 is stable, a 1.2.0 release will be cut and branched. There are lots of new features in master that we would love more feedback on.

Blue Obelisk Award

At the recent ACS Spring meeting I attended the Blue Obelisk dinner, where I was honored to receive a Blue Obelisk award, pictured below, for my contributions to Open Data, Open Standards and Open Source. This is largely due to the work I have done on Avogadro, Open Babel and other open source chemistry tools.

Blue Obelisk award

This was one of the biggest dinners I have had the opportunity to attend, and I got to meet many of the people I have worked with (or used their work), along with several people I had not had the opportunity to work with yet, but hope to in the future. We presented the work we had been doing on Quixote project at the chemical information symposium on chemistry and the internet, after attending the first Quixote meeting the previous week (thank you to Hartree Centre for inviting me to speak there, and sponsoring the event).

These are exciting times, thank you very much to Peter Murray-Rust for presenting me with the award, and all of the support he has shown, along with his relentless passion for open science. I have only been a part of this for a few years, but Peter has been working on opening up chemistry for decades now.

CMake External Projects: Building Project Dependencies

Historically projects have attempted to minimize their dependency list, and often bundle in small third party libraries in an attempt to make things easier for new developers/users to compile their code. In the Avogadro project we have bundled a few really small libraries, but on the whole have maintained a dependency list and tried to keep it smaller. As I work on new code, I see opportunities to break off bits of functionality, such as with OpenQube, but don't want to add yet another thing a new user or developer must download, compile and install somewhere.

Linux packagers, myself included, dislike the practice of bundling in libraries. It means that instead of patching one libxml2, we get to patch one plus the three or four in our tree that have been bundled (often with different version, some local patches). The problem is less pronounced on Linux where package managers are ubiquitous and we are able to provide a list of packages to install, but even there we might be developing against versions not yet in the main distribution repository. This is one of the reasons I have always favored rolling release distributions over the periodic.

CMake's external project module helps us to deal with this issue in quite an elegant fashion. Coupled with meta repositories to bring several source trees together, CMake is able to direct the build of several projects, passing locations between projects and expressing dependencies between the projects being built. This means that something like Open Babel can build zlib and libxml2 before building the main Open Babel library. External projects and CMake allow us to download the source, create the build trees and even direct the build of non-CMake based projects like libxml2.

I have a prototype of this that I just put up to build the core of Avogadro, its working name is Avogadro Squared as I was feeling geeky that day and had no good names. One thing you should note is that everything in there is an external project, and Avogadro is the last one to be built (it depends on all of the other projects). It requires minimal changes to the projects it contains, it uses git submodules for some of the source, and CMake's download and tar functionality for zlib and libxml2. I will be adding options to simply use system versions of the libraries it can build, but Linux distributions etc can continue using the Avogadro repository directly.

As a new developer or user I can checkout the meta repository, have git download the submodules and CMake download the source tarballs. I can then build the entire project, and then continue to work in the Avogadro subdirectory of the build tree after that. That build tree is almost identical to the one I would have ended up with had I not used the meta repository, except it points to the dependencies I just built. I can then use vim, and IDE or whatever I choose to work on the inner projects. This works across Linux, Mac and Windows to get new users and developers up and running very quickly while only loosely coupling the dependencies to the Avogadro project.

I have worked on other larger projects, such as Titan and ParaView that are using this approach to a greater or lesser extent. Titan can actually built Qt, Boost, VTK, protobuf, Trilinos and a host of other dependencies before building the Titan libraries and applications. I think Avogadro Squared is an example of just how minimal a meta repository can be, although I will be extending it with more dependencies it really is just a glue repository.

Volume Rendering in Avogadro

Since joining Kitware I have had limited spare time to work on Avogadro, and for various reasons my spare time has been more limited than usual too. Since the new year I have been able to start spending more time working on Avogadro, and open source chemistry in general, thanks to an SBIR phase I proposal that was funded last year with the US Army Corps of Engineers. This is exciting for a number of reasons, including the fact that I have the opportunity to prototype exciting new features for chemistry visualization, workflow and data management.

One of the new bits of work I have been doing is to use some of the advanced visualization techniques in VTK such as GPU accelerated volume rendering. Now the code is still pretty rough, and is more a proof of concept. I wrote a simple external Avogadro extension that links to and uses VTK to render the first volume found in the current Avogadro molecule. All of the parameters are currently fixed, I am hoping to get the time to add in more options along with some integration of the Avogadro rendered molecule in the VTK render window. You can view the code here, please bear in mind it is at a very early stage.

I have also been working on several other things such as splitting out the quantum calculation code from the Avogadro plugins, and putting it in a small library. I have called the library OpenQube, right now it only has the base functionality that was in Avogadro but I will be extending it with more features, regression tests and I am hoping due to the decoupled nature and liberal BSD license it will encourage wider collaboration in this field.

There is also the Quixote project which I am very excited about. Meaningfully storing the results of quantum calculations, annotating them and retrieving them within an open framework. This is a growing problem in todays world, and I am working on extensions to Avogadro to allow it to fully exploit the semantic chemical web. This includes some of the previous work to access the PDB and other public resources as well as private databases within groups and organizations.

I think this is going to be a very exciting year for Avogadro, and open source chemistry in general.

Returning From Hibernation...

Wow, I just looked and I haven't written a thing since January! For those of you who might have been worried, or just wondered what I was up to...here is a quick run down. I am going to start with a little advice, combining starting a new family with moving from academia to industry and moving house it tough ;-) I have been really focused on work, home and one big conference, and kinda shut down otherwise.

I hope to remedy that in the coming months, and have started by doing some development for Avogadro and Open Babel. I also got Kalzium in KDE trunk ported to use the system Avogadro library, with some help from Pino Toscano. So KDE 4.5 will feature a Kalzium using the system installed Avogadro, this prompted a couple of bug fixes in Avogadro. So after that I tagged and released a much delayed Avogadro 1.0.1 with several bug fixes.

Way back in March Kitware was kind enough to send me out to the March ACS meeting, where I presented a talk on VTK, ParaView and its use in chemistry. I also gave a talk on Avogadro, and its use as a framework in chemistry visualization, which Geoff followed up with a talk on some applications of the Avogadro framework in his research.

The ACS conference deserves a full post of its own, but I feel like it has been so long I will just summarize a few of my thoughts. There were some other really interesting talks on visualization, and how it can be applied in chemistry. I got a general feeling that commercial software still has too much of a stranglehold, and hope to see that change as we develop powerful open source platforms that can be shared by all. There is a definite need for this in chemistry, and I am doing everything I can to seek some funding to further that cause, failing that I will continue to do what I can in my spare time.

I was honored to meet members of the Blue Obelisk for the first time. Saw some great talks about open science, open data, open standards and open access. I especially enjoyed meeting and seeing Peter Murray-Rust talk for the first time, I found that I share many of his ideals. I think we differ in some places, but life would be boring if that were not the case!

Our son, William, is nearly one year old already! He might be a big part of the reason why I have been inactive. The kinds of sleep deprivation torture you go through with children are indescribable :-P He is thankfully sleeping quite well now, and even took his first two steps yesterday.

We had our first visitors in our new home - friends from Pittsburgh and Washington DC all came up for a weekend. I fired up our new BBQ, an enormous American style with offset fire box. Made some amazing ribs, and shared some of the home brew I made - a portable porter, and an English brown ale (first two batches). We are just getting ready for a trip to Pittsburgh, and then William's first birthday (planning a small party at our place).

Then there is work, lots of exciting things are happening there. I taught my first course at Kitware, going through ParaView plugins. The new CMake book came out (I am one of the contributors to the new edition), and the new VTK book came out at around the same time. Kitware is hiring, so please let me know if you are interested in applying. We have some really interesting projects to work on, most of my time is spent on something called Titan. Last Friday I also pumped the tyres up on my bike, and rode into work for "Bike to Work Day".

I have skipped loads of stuff, but already wrote more than I intended. I will see if I can be a little more disciplined and write more frequently. My current problem is finding time to fit everything in, but I have a new strategy I am working on in order to do better. Life after the big 30 is certainly different. I feel energized again, and hope to be writing about more fun and interesting stuff I am doing over the coming months.

Another Post About Camp KDE 2010

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

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 ;-)

Camp KDE

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

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.