Marcus D. Hanwell's Blog - Gentoo

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 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.

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!

Qt Creator, CMake and C++/Qt Development

marcus@cryos.net (Marcus D. Hanwell) — Tue, 28 Apr 2009 11:13:00 -0400

I have been experimenting with Qt Creator since the first release. I have always preferred a minimal editor for development work, with my main needs being good syntax highlighting, the ability to switch between different files quickly and something that stays out of my way as much as possible. Previously I had used Vim, Kate and several konsole instances the majority of the time.

Recently I have been looking for something with better integration, and so had been slowly keeping an eye out for a lightweight IDE. My main requirements were something lightweight, good C++ support, ideally good Qt support and CMake integration. Over the weekend I tried the latest Qt Creator 1.1 release and was really impressed.

Seb Ruiz made a great post on Qt Creator 1.1 that summed up many of my thoughts, and gave a quick walkthrough. It was not immediately obvious how to import a CMake project, I was looking for an import project option. All that is necessary is to go to file and open. You can then open the base CMakeLists.txt file for your project and the CMake plugin will do the rest.

From there on in you get great integration with the build system, version control (Git and friends), and your friendly GDB debugger. Under projects you might want to quickly add -j5 (if you are lucky enough to have a quad core machine) to the additional arguments input for make, and select the main executable target for your project if you also have several other executable targets (unit tests etc).

The first time you debug a project you will be prompted to build the Qt debugger helper. Then the integration with GDB really wins over using GDB directly, or using ddd which I had been using more and more recently. I would highly recommend trying Qt Creator if you are looking for a lightweight, cross platform IDE. There are certainly other great IDEs out there, but I think that Qt Creator is a great fit for my development style (and may be yours).

CMake Performance with Open Babel

marcus@cryos.net (Marcus D. Hanwell) — Sat, 11 Apr 2009 11:17:00 -0400

Recently, Luca made a post comparing the speed of CMake and autotools in which some timings were posted. I have to say that I am not sure I agreed with the conclusion and have had a very different experience with the projects I am involved in. As with anything your mileage may vary, and I have not looked at Wesnoth.

I think it is questionable at best to include the time it takes to build CMake, but not autotools. Seems like this is a one time cost and the build time is not that high for either. All tests were performed on my quad core Gentoo box at work. Each step is for the first cold run as would normally be the case when compiling Open Babel from source. The make step used `time make -j5` and I have listed the real time in each case.

The timings are shown in the table below. They seem somewhat similar to the experiences of the QGIS developers who made this move quite some time ago. All times shown are in seconds and are the real time reported by the time command.

	Autotools	CMake
Configure time	20.39	4.79
Compile time	116.45	102.23
Install time	28.39	4.19
Total time	165.23	111.21

For those interested, on this system the total CMake compilation/installation time (cmake-gui disabled) was 1 minute and 54 seconds. The compilation/installation time for automake, autoconf, libtool, m4 was 2 minute and 14 seconds. I am not sure how relevant either of those times are, other than to show neither of them take that long to compile and install. Gentoo users/developers may or may not have CMake installed, most other developers will install the binary packages for either one and are likely to be much more interested in how well it integrates with their development environment, compile and install times.

As a developer I prefer CMake, and have been using/maintaining the CMake based build system for Open Babel for over a year now. It was originally contributed by the KDE Windows porting team, but I found that I spent less time waiting for it to do things when I was working on code too. Add to that the extras CMake comes with, such as CTest, CDash and CPack I think it makes a very attractive option for many projects. I am also hoping that it will allow Open Babel to drop maintaining a totally separate build system for MSVC.

I am sure the Open Babel autotools build system could be optimized (I never tried), but when you add in the additional benefits mentioned above, support for multiple targets such as makefiles, XCode, MSVC, Eclipse etc, one shared language/syntax for all build files and an increasingly polished competitor to autotools, I honestly think it is a sensible choice for projects to move to CMake. There are a few less well known features such as Fortran module dependency parsing that I think are fairly unique and valuable, in scientific coding at least (and I have used the Fortran module dependency parsing at least once and was pleasantly surprised).

Full disclosure: I recently accepted a job offer with Kitware, and will start in the Fall assuming all the visa paperwork falls into place. The opinions expressed here are my own. I think it is great to discuss issues like this objectively, and hope to be a part of making CMake a better build system. As with most software - there are areas that need improving.

Avogadro 0.9.3 Released

marcus@cryos.net (Marcus D. Hanwell) — Thu, 02 Apr 2009 12:13:00 -0400

Yesterday, on April 1, we tagged and released Avogadro 0.9.3 exactly one calendar month after 0.9.2 was released. This has been quite a big month for Avogadro - I took it to the APS March meeting and the Q-Chem workshop. To the left is a screenshot of the latest release showing the electron density of a vitamin C molecule with the approximated electrostatic surface potential mapped onto it.

We made quite a few fixes and improvements leading up to the APS and Q-Chem meetings. The highlights are in the release notes. Some of my favourites are the animation of molecular vibrations, plotting of IR spectra, improved rendering/handling of surfaces including meshes with colours mapped to their vertices. The Windows build is also fully relocatable, meaning it can even run off of a USB stick. I am hoping to do the same for the Mac and Linux builds too. I made several improvements to the super cell builder, surfaces and even made a start on a z matrix editor (not ready yet).

To the right is the ray traced image of a larger molecule and one of its molecular orbitals. The POV-Ray rendering code has also seen quite a few improvements. I have been experimenting with generating movies from POV-Ray rendered images too. I am planning to make improvements to our build system on Windows and Mac in order to make packaging easier. My main focus is still Linux development, but so many people insist on using other operating systems. Other more exciting things include producing videos of molecules rotating, vibrating, trajectories and using GLSL to improve the rendering performance with big systems (>25,000).

We would appreciate feedback on this release from the wider community. I am really pleased to announce we have gained at least one new contributor this month, David Lonie, who worked on the new IR spectra plotting code. I have made a new ebuild for Gentoo, prepared a Windows installer, Geoff has made a new Mac package and there is ofcourse source. I am sure other distros will have packages ready soon too. Hope you enjoy the graphics - videos to come soon!

Avogadro 0.9.2 Released

marcus@cryos.net (Marcus D. Hanwell) — Sun, 01 Mar 2009 14:50:01 -0500

I just finishing tagging Avogadro 0.9.2 earlier today. I possibly procrastinated on tagging this one a little as February has not been my finest month. I didn't see any reason to make another release in that hellish month when I could wait a day. This release is a little earlier than we had scheduled, but it contains lots of bug fixes and improvements along with a couple of new features.

Among the highlights I tracked down our orphaned tools and extensions, so Avogadro closes down far more gracefully now than it once did. I went hunting for memory leaks and QObjects with no parents. I added some initial support for building supercells such as the zeolite structure shown in the screenshot. I also fixed some bugs with electron density calculation and this works much better and faster now. I also improved the Linux desktop user experience by adding a .desktop file, icon and mime type associations. Looks very swish.

I built a new Windows release without Python, Tim will put one up with Python support soon, bumped the Gentoo ebuild as 0.9.1 was bumped by someone else and it could not locate its plugins. I have made a number of improvements to our plugin loading to ensure that it is relative to the binary location. This should make relocatable binaries on all platforms quite feasible. March is a busy month but I hope to be able to make some more big improvements. If it goes as badly as February I may consider hibernation as an option though!

I will be presenting some of this work at the APS and a quantum chemistry workshop in March too, both here in Pittsburgh. We always love to have feedback, bug reports, patches or be invited to give talks at conferences in far off places! Here is hoping for a better month...

New Addition to the Family

marcus@cryos.net (Marcus D. Hanwell) — Wed, 15 Oct 2008 13:42:15 -0400

On Monday we had a new addition to the family arrive - an Asus Eee PC 1000! So far I am pretty impressed with the hardware. The Linux installation was pretty disappointing but I never really intended to keep that anyway. I played around with it on Monday as I built a chroot for the new arrival (pictured below).

I went for the 10" model as I was worried about the size of the keyboard on the smaller ones. I also liked the sound of the SSD drive and it looked like a great little unit. I ended up building a custom stage 4 Gentoo tarball for it on my desktop and installing it here. I have it running the new KDE 4.1.2 ebuilds along with a few KDE 3 apps I can't do without.

All in all it seems to be working pretty well. I only got round to installing Gentoo on it yesterday. So far I have the webcam, wired and wireless networking working. I am using WICD to control networking. I would love to see a Qt4/KDE 4 frontend that integrates better but it is an awesome little app.

This is my first post on it, the screen isn't a bad size and the battery life seems to be good. I am on the road today and my wife acted as an unwilling hand model. I still haven't managed to get the asus_laptop or asus_acpi modules to load and so am missing all those devices. It claims no such device.

I will hopefully be able to post more at some point in the future. I certainly think this is great for being on the road and Skype is working with the webcam. I did use the 2.6.27 kernel whicih made things a lot easier I suspect. I might try building a vanilla kernel soon to see if that lets me insert the asus_laptop module successfully.

For now I have quite a few hours to kill in the BA lounge at JFK!

KDE 4.1.2 Unmasked in Gentoo

marcus@cryos.net (Marcus D. Hanwell) — Fri, 10 Oct 2008 12:48:00 -0400

FHS where it clearly states, "Large software packages must not use a direct subdirectory under the /usr hierarchy." We currently do, the FHS KDE install really is FHS compliant. Please not that is not the primary reason we would like to do this. It is however one of several benefits.

I thought I had made it quite clear that slotting of minor versions was not going to be removed. Jorge and I have been working hard on getting the KDE 4.1 ebuilds into shape, and after Jorge worked with Zac on a few ideas it appears that new portage behaviours to do with blocking effectively allows us to use the original multislot idea I implemented using a different implementation (avoids variable slots). Some of the changes could do with EAPI 2 but it looks like we can implement much of what we need now and impove things when EAPI 2 is available.

Thanks to those who commented on my post in a constructive fashion. Not sure how to respond to a few of you who just don't seem to have read my post (or the FHS). Just to say that we are working on it. Jorge, myself and several interested users have been doing what we can with the time we have available to get the ebuilds into shape. If you would like to take a look at what we are doing you can check out the kde-testing overlay using layman, otherwise we will be working on getting KDE 4.1 into the tree as soon as we can.

KDE 4.1 Gentoo Ebuilds

marcus@cryos.net (Marcus D. Hanwell) — Sun, 07 Sep 2008 16:55:00 -0400

So there have been quite a few people asking what is happening with KDE 4.1 on Gentoo. There are still no ebuilds in the tree for KDE 4.1 and to be totally honest I have not been actively developing the KDE ebuilds until recently (took quite a long break). It is however something I really feel that we should have and so I have been working with a few other developers and interested users on the new ebuilds in an overlay. I think these ebuilds are almost ready and I am very eager to get them into the tree.

So what have we been doing? We have been working on a set of ebuilds that can be used with portage 2.2, there were a few setbacks when it became clear that EAPI 2 was not likely to be allowed in the tree in the very near term, but good noises are being made on the mailing lists. I think one of the big changes I have been working on is bringing KDE back into the normal file system hierarchy. This means that you will not be able to slot multiple minor versions of KDE such as 4.1 and 4.2 together.

The loss of slotting also means that ebuild maintenance will be significantly easier, externally released packages will automatically relink to the latest kdelibs for example. It also means that users will not build up multiple copies of minor KDE versions such as 4.0, 4.1, 4.2. I think for the majority of our userbase (myself included) this situation is undesirable with few benefits for normal use of KDE. So having one slot for KDE 4 and upgrading in the normal fashion seems to be very beneficial.

This has not been universally accepted as a good thing. I personally think our main tree KDE should always be installed in the normal FHS hierarchy as upstream seems to intend it. I see little benefit for most users, and many developers not closely involved in KDE development, to having multiple minor versions installed. Also having external KDE packages such as k3b and amarok installed in /usr but linking to libraries in a KDE prefix has never been optimal.

My vision is for a default in-tree KDE that installs into the normal FHS tree as Gnome, Qt 4, XOrg etc do. Developers, power users and those that like to tweak would still be free to install slotted versions of KDE in KDE prefixes alongside the FHS KDE. They could also remove the FHS KDE and just use slotted versions too. We discussed during KDE 3.5 bumps how the current slotting was not ideal.

I am certainly open to opinions. It would be good to get wider feedback from the community on which direction they would like to go in and why. This will not affect KDE 3.5 slotting with KDE 4 - they will always be slotted. It will make maintenance of external KDE packages simpler as everything will be in the same tree. Overlays with ebuilds in alternate slots and prefixes are of course still easily possible and people could continue using KDE in this way.

Currently this work is taking place in an overlay. I am quite honestly exhausted discussing why this is or is not a good idea. I hope I have made my position clear and why I think it is a good thing for our user base. I really want to get KDE 4.1 into the tree as soon as possible. I do feel that these changes should be pushed into the tree, defaulting to an FHS compliant install and using a KDE prefix if requested.

What are your thoughts (other than get KDE 4.1 in tree now - we are working on that)?

New Webcam and Linux

marcus@cryos.net (Marcus D. Hanwell) — Mon, 16 Jun 2008 23:29:08 -0400

As my regular readers will know I moved over to Pittsburgh, PA in the USA at the end of September last year. Before I left I got some of mine and Louise's family webcams so that we could stay in touch. Then it took ages to sell our house and the shipping nightmare began (which I will try and bring myself to talk about one of these days). Eventually I actually got my desktop computer back (a little worse for wear after the shippers "carefully packaged it").

Going back to my original point, I had been putting off buying a webcam as I wanted it to work well in Linux, and every time I looked into which webcams might be my best bet it seemed that even individual models had multiple chipsets, which may or may not be supported. On Saturday I bit the bullet as Louise had been asking about getting Skype working.

I chose the Logitech Quickcam Pro 9000 (photo above) as it seemed to be part of the new USB video class standard I had been reading about and saw there was a healthy Linux UVC project already. I still anticipated having trouble getting it working on Gentoo but thought I should be able to get it working eventually.

Imagine my surprise when I just typed emerge -av media-video/linux-uvc media-video/luvcview, modprobed the new kernel module, ran luvcview and I could see me staring at the camera! Sometimes I worry this Linux thing might be getting a little too easy Another five minutes and I had the microphone working (just usb audio) and was testing it out in Skype. On Sunday we had our first intercontinental video chat with my Mum and two nephews. Skype also integrates into my KDE 4 desktop without any trouble.

I am pretty new to the webcam thing and had resisted it for a while but it was great to be able to chat and see family and friends back home. I would rather use an open source, cross platform video conferencing application but have yet to find a viable one. Open Wengo looks like it might be that application one day but I couldn't get it to work reliably last time I tried (although I did like the look of it). I also don't seem to be able to find a nice application that will let me capture video messages easily.

I was very pleasantly surprised by my experience and am very happy with the performance of the Linux drivers for the webcam as well as the camera itself. Any Linux webcam tips would of course be gratefully received!

UPDATE: Forgot to mention this great blog post I spotted that helped me decide this webcam was probably a good bet...