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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

Avogadro Paper Published Open Access

In January of last year I was invited to attend the Semantic Physical Science Workshop in Cambridge, England. That was a great meeting where I met like-minded scientists and developers working on adding semantic structure to data in the physical sciences. Peter managed to bring together a varied group with many backgrounds, and so the discussions were especially useful. I was there to think about how our work with Avogadro, and the wider Open Chemistry project might benefit from and contribute to this area.

Avogadro graphical abstract

My thanks go out to Peter Murray-Rust for inviting me to the Semantic Physical Science meeting and helping us to get the Avogadro paper published in the Journal of Cheminformatics as part of the Semantic Physical Science collection. Noel O'Boyle wrote up a blog post summarizing the Avogadro paper accesses in the first month (shown below - thanks Noel) compared to the Blue Obelisk paper and the Open Babel paper. We only just got the final version of the PDF/HTML published in early January, but already have 12 citations according to Google scholar, showing as the second most viewed article in the last 30 days, and the most viewed article in the last year. The paper made the Chemistry Central most accessed articles list in October and November.

I made a guest blog post talking about open access and the Avogadro paper, which was later republished for a different audience. I would like to thank Geoffrey Hutchison, Donald Curtis, David Lonie, Tim Vandermeersch and Eva Zurek for the work they put into the article, along with our contributors, collaborators and the users of Avogadro. If you use Avogadro in your work please cite our paper, and get in touch to let us know what you are doing with it. As we develop the next generation of Avogadro we would appreciate your input, feedback and suggestions on how we can make it more useful to the wider community.

Open Science, Open Access and Open Source

I have been thinking this over for quite a while, and have written this post several times over in my mind. As an undergraduate student I remember admiring scientists and imagining how amazing it must be to have a job where you got to discover new things, think of better solutions to problems facing our society and making the world a better place. As my studies continued I aspired to become one of those researchers, and made the decision to take my studies further and applied to do a PhD.

As a PhD student I enjoyed learning more about materials, and was excited to be working with gold nanoparticles and research into how we might make real devices out of this novel new material in the Nanomaterial Engineering Group. It was exciting, challenging and fascinating using techniques such as X-ray and neutron reflectometry, electron and atomic force microscopy and Langmuir-Blodgett troughs. As I learned more through my work I became frustrated with the quality of the software I used, and had always imagined that "real scientists" had better tools available to them. It became even more frustrating when I realized how bad some of the instrument control software was, and how so many of the file formats could only be used in one or two expensive and hard to use programs that only worked on one or two platforms.

Towards the end of my PhD I decided I would like to take some action. I had been trying to draw and render images of molecular structures, and wanted a way to do simple geometry optimizations for posters, papers and web pages. At first I tried to do some of this using an existing commercial package, but it only worked on Windows and we only had one license for the department. The training provided to me as a researcher in areas such as programming and analysis were disappointing and all too often generic tools such as Word, Powerpoint and Excel were the most viable choice for preparing, analyzing and presenting our work. I began writing more software, but much of it was written from scratch with little guidance. As I searched for a better way I came across some open source libraries and tools.

I found a program run by Google called "Summer of Code" where they offered me the opportunity to "flip bits not burgers". I was extremely lucky to find an idea on KDE's idea page for a molecule editor in Kalzium. I was very excited, and had been using KDE for many years. This was a pivotal moment for me, where my life and career took a twist I never expected into the world of open science - and I have loved every minute of it.

It was through that work that I became involved in the Avogadro project, and later Open Babel and met Geoff who later that year offered me a position in his new research group. This was an exciting opportunity as not only did we share a passion for correlating experimental and computational techniques, Geoff was also very active in open chemistry. After I moved out to Pittsburgh Geoff introduced me to the Blue Obelisk, and I now proudly count myself as one of their un-members. We published an open access paper on the Blue Obelisk five years on last year.

After a two year postdoctoral position with Geoff, who was extremely supportive of my work in open chemistry, I met Bill Hoffman from Kitware. I knew that Kitware developed CMake, but beyond that was not really aware of what they did. It turned out that they were involved in much more than just CMake, with open source tools and frameworks such as VTK, ParaView, ITK, CDash and more. They had been working on open scientific software for over a decade, and they were hiring! They weren't just making applications either, they were tackling the whole problem including development, testing and validation of open-source, cross-platform applications and frameworks.

After accepting a position with Kitware in 2009 one thing I never really appreciated was just how poor access is to publicly funded research. I can no longer access scientific papers I and others wrote, that were funded with tax payer money from both the UK and the US! I think that is terrible, and later realized I had become part of the scholarly poor, Peter wrote a follow up detailing the plight of those of us in industry. There is currently raging debate on open access, and campaigns such as The Cost of Knowledge need our support. The products of publicly funded research should be available to all, whether they are in academia, industry, government or anywhere else.

There are too many black boxes in science today, too much published work that is not available to all or reproduced by others. Mathematics used to be the language of science, but more and more it is computer software that is needed to learn more, and too much of this code is closed, unpublished and poorly shared. Papers must include mathematical proofs, or refer to proofs already published, but it is common to see work published that used closed, proprietary package X to conduct a simulation. This is changing, and Scientific American recently published an article on how "Secret Computer Code Threatens Science". Science also published an article about "Shining Light into Black Boxes", detailing the growing problem of witheld source code preventing meaningful peer review and reproducibility of research.

Michael Nielsen published a book called "Reinventing Discovery" that talks about the value of networked science, and is well worth a read if you have not yet had a chance. The Panton Principles outline the need to make scientific data open, and the Science Code Manifesto calls for openly available code in science. The core goals of the Blue Obelisk are open data, open standards and open source. I think for science to progress we must embrace openness, and sharing and resist the urge to hoard data building up small empires on proprietary code and data.

One thing I hope to see come from all of the controversy of the Research Works Act is a clarification that publicly funded research should be available to all, whether you think they will understand it or not. Scientists need to get better at communicating with the general public, and being more transparent about how research is done. I think open science will give us a chance to increase public engagement in science, which seems to be a growing problem in an age where we can all access the internet and a wealth of knowledge available on it.

I think that we need to figure out sustainable ways to fund the development of open software platforms to enable the next generation of researchers to push back the frontiers of science. We need to remember that we are publishing to share the results of (often publicly funded) research, and so we should be using liberal licenses such as CC-BY, CC0 that allow reuse and further analysis. We also need liberally licensed software that allow those same things, with simple licenses such as BSD and Apache 2.0. These libraries should contain well-tested implementations of data structures, algorithms and best structures, along with training for researchers to help them take advantage of these resources. If there is a better way to do something, contributions and integration should be encouraged as is the case in most open source communities.

Our Open Chemistry project recently got Phase II SBIR funding, and I am very excited to be leading that work at Kitware. It is part of a collaborative, open effort to improve the tools and frameworks available in the area leveraging new software processes to enable wider community involvement.

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.

Visualization Toolkit (VTK) in the Google Summer of Code

As I already mentioned on the Kitware blog, the Visualization Toolkit (VTK) has been accepted as a mentoring organization for Google Summer of Code this year. You can see the VTK entry in Melange, and browse through our project ideas. I have taken part in the Google Summer of Code program since 2007 (first as a student, and later as a mentor) as part of the KDE project. I still maintain close ties to KDE, and work on several related projects such as Avogadro, CMake and VTK. VTK has Qt integration, and ParaView builds on both VTK and Qt for the visualization of large scientific data sets.

If you are a student, and would like to work on an exciting open source project, processing and visualizing some of the largest scientific data sets in the world, take a look at the Visualization Toolkit. There are a wide range of ideas, and if you have an idea you think would fit then please feel free to discuss it with me. I will let you know if it would be a good fit, and whether we have available mentors for the proposed project. We have mentors available who are experts in visualization, large data, parallel algorithms and related technologies. The core of VTK is written in portable C++, with new changes being tested daily. Our API is automatically wrapped in Python, TCL and Java.

I am very excited about VTK's first year in the Google Summer of Code, this represents a unique way for students to get involved in a large, well tested open source project. We have started using Gerrit for code review, and you can view build and test results on many platforms for VTK both continuously and nightly. We have a well established software process which will serve you well in any project where software quality is important, with nearly 1400 unit and regression tests. This is a large, collaborative project with more than 100 contributors last year (as measured by Ohloh).

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.

Avogadro Nominated for SourceForge Community Choice Awards

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.

Avogadro collage

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.

Vote for Avogadro

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

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.

Group shot of KDE GSoC Boston sprint attendees

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.

Boston panorama from the bridge

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!

Road Trip to Canada

So last weekend Louise and I went on our first big road trip to Canada. Neither of us have been to Canada before, and with Benoit now living in Toronto it seemed like a great opportunity to go and catch up. Back in July 2007 I visited Benoit in Paris during my GSoC where we met for the first time in person. Now, two years on we met for the second time in person and introduced our partners to each other too.

Niagara Falls Canada

We left at around 4pm on Friday, I think we crossed the border at about 9pm and got almost all the way there before getting lost in Toronto. Our friend's GPS failed us once we crossed the border and Toronto is a pretty big place. I think we finally arrived just before midnight, tired after the long drive. The next day we drove back down to almost the border to check out the Niagara Falls, which we had never seen before. It rained almost the entire day but we still had a really nice day out.

As well as checking out Niagara Falls on the Canadian side in the rain, we found some very expensive shops in Niagara on the Lake, I bought some maple syrup and some maple spread (still not quite sure what to do with that). We discovered that if you get bored of the main attraction you can always check out one of the many casinos too.... We decided to forgo the gambling and instead headed back to Toronto.

Dinner in Toronto

Once we had dried off a little we all headed out to get some dinner in Toronto's chinatown. We enjoyed some great Vietnamese food and compared notes on moving continents, life in academia, Google Summer of Code and life in general. It is great to still be in touch with many of the people I made friends with during my Google Summer of Code and I hope others get as much out of it as I did.

On Sunday we lost an hour to daylight savings time, wish we could stop doing the clock change thing twice a year... We decided to head back as Louise was tired (she is conducting a geek cloning experiment for me). It rained for most of the drive back too, we did another border crossing and got back home at around 7pm. I do not think our carbon footprint is looking great for the weekend but it was great to catch up and see where Benoit is living now. My thanks to Benoit and Irene for being such great hosts.

Back to work this week, preparing for a big conference next week. I still love to travel, it was great to avoid the airports for once!


Avogadro, OpenGL and Display Bugs

Before last summer I had never really done any OpenGL programming. Now I feel like I know a reasonable amount but certainly still have a lot to learn. I have an Acer Ferrari laptop with an ATI Radeon X700 discrete graphics card in it. I was using the proprietary driver for a while but it was so unstable it just wasn't worth using. I was hopeful after reading about AMD opening up the specs so that good 3D support can be added to the open source driver.

Avogadro showing a filled surface with incorrect colouring on ATI open source driverAvogadro showing a surface with correct colouring on ATI open source driver

I have to say on the whole the 3D support has been getting better and better for the r300 chipset. I cannot enable the desktop effects in KDE 4.1 trunk without losing my OpenGL apps though. As you can see in the above screen shots filled surfaces also do not work. For some reason the colouring of the surface is incorrect, i.e. the colour is never changed. I am running the latest git sources of xorg, the ati drivers, x11-drm, mesa etc, thanks to Donald Berkholz. Avogadro seems hit File r300_render.c function r300Fallback line 360, Software fallback:ctx->RenderMode != GL_RENDER every time too.

There is an open bug report that appears to be describing the same situation. I do wonder if it is possible that our OpenGL code could be improved to avoid this bug. I would love any tips on ensuring our OpenGL code is as compatible as possible. The surface rendering works correctly on all other platforms (Linux, Mac, Windows) and with other drivers as far as I know.

We also have an open bug report where Avogadro segfaults on Linux systems using the savage driver. This seems to be a consistent problem. I am afraid I do not have the hardware to test further, I have added further debug output to our initialisation routines - Avogadro crashes very early on. Again, any ideas on how I might fix this bug or at least exit gracefully would be great. Backtraces may help to at least see what functions are called before the crash but this might just be a driver bug.