Marcus D. Hanwell's Blog

We continue our push forward with Avogadro with the release of Avogadro 0.9.1 on 16 February. There are lots of new features that made it in recently and we are still stabilizing many of them. This release has featured lots of experimentation with CPack, along with me getting more familiar than perhaps I ever wanted to with Windows packaging. CMake makes things easier but there are some things it cannot fix, such as the manifest issues we hit.

This is the second of our final beta series before our 1.0 release. We hope to make a release roughly once a month until we release Avogadro 1.0. During this period some new features will be added. Our main focus will be on improving the API, fixing crashers, ensuring all platforms have stable packages with full functionality and improving fault tolerance. To this end we will be adding to our (currently) quite small test suite and making use of CDash in order for all developers to be able to see issues on all targeted platforms.

Since the release I found a few small bugs and so already want to make a new release. I fixed a bug when calculating electron density cubes from formatted checkpoints - it was one stray line of code! There is a super cell builder that can do rebonding on the super cell in the works and I recently committed some code to use relative paths to find our plugins. This seems to work really well and with a little tinkering should allow us to run off a USB stick without installation.

While working on our Windows build I realized I have been neglecting our Linux build a little. So I have an avogadro.desktop file and some mime type files to give us a menu entry and associate with some file types. I may not have chance to finish them up and commit until I get back on Sunday.

On that note I will likely be offline until Sunday/Monday. I have my first big job interview tomorrow - wish me luck! Like several people on Planet KDE I am currently in the market for a job. I am going to be all mysterious and not give any more details, other than to say I am excited and nervous!

So it is Friday the 13th... At about 5am this morning my server emailed me to tell me one of its disks was down... It is all RAID1 (apart from swap) and so it is mostly OK. I think having half its swap removed upset it quite a bit though, and so almost all services died. I think they are all back up and running again, but if you emailed anything in the last day or so you might want to resend it.

This week has not been my finest - hopefully next week will be much better! Here's hoping nothing else went terribly wrong this week, and that it is just the disk and not the whole server that is having trouble. So much to do, I did not need this.

Camp KDE is over now, I managed to squeeze in a couple of dives before leaving. Our trip back was quite uneventful, the free wireless in Charlotte was nice, and a friend very kindly picked us up from the airport. We got back to a snow covered Pittsburgh yesterday evening. It was good to be back home but the cold weather was quite a shock to the system. I think that Camp KDE was a great success, and thoroughly enjoyed meeting everyone there, and learning a lot from Till and the other Trolls (do they need renaming now?).

It is my birthday today, scarily the next one is the big 30! There were quite a few birthdays in and around the Camp KDE period. I got into work to discover our espresso machine died while I was away - hopefully this will not impact productivity too much... Looks like I have a really busy month ahead of me but will likely take some time out this evening to have a small celebration.

Big KDE 4.2 release tomorrow too - the RC has been working great on my Eee PC while I was away at Camp KDE. The new laptop features are working great and sleep seems to be working flawlessly. I think that 4.2 will be a great release, and on a personal level find that it is now very usable on a day to day basis. I hope Jos and Sebas make it back OK - I think they are the last Camp KDE attendees to leave Jamaica.

For the past couple of weeks Louise and I have been travelling visiting family and friends back in England. It was quite possibly one of the busiest trips I have ever made. Starting out with a good friend's wedding the first weekend we were back where I had the opportunity to take lots of photographs for them. Then down to London on the Sunday for our appointment at the US consulate on Monday. Then we were back up to Sheffield on Tuesday, giving a talk at the University of Sheffield on some of the work I have been doing since I left last year.

On the way back up to Sheffield I managed to pick up a horrible stomach bug and thought I would have to cancel the talk but felt reasonably OK on the day. That was all in the first week back! After that we got a chance to catch up with friends and family. A friend got us a room in the heart of Kelham Island, making it much more convenient to visit several of the best public houses in the city to catch up on some long missed real ale

We managed to catch a nephews birthday and the following week headed north to visit a friend in Leeds and another in Edinburgh. After that it was back down to Sheffield for one last day before spending our final night in England in a hotel in Manchester. We tried a new way back to Pittsburgh which involved three flights and an overnight stay in Philadelphia. We got a flight from Manchester to London Heathrow, spent over five hours in the new Terminal 5 before taking our flight to Philadelphia International.

We arrived late and tired. Thankfully all the visa stuff was fine, arriving in Philadelphia was all OK and the hotel in Philadelphia was pretty nice. At this point to be honest we couldn't wait to get back to our apartment in Pittsburgh and see our dog again. Our first time on Southwest and their boarding system is pretty stupid but they got us home.

Just in time to see the US election unfold. So tonight we have some beers and are settling in to watch it all unfold. I have no vote but do have my fingers crossed that Obama will get in. We will see if I can stay up until it is over as I have been up since 5am this morning. Keep your fingers crossed, it is pretty nice to be in the middle of it all.

Yesterday my wife was supposed to be travelling back to England. She had been planning the trip for over half a year and was looking forward to attending her friend's wedding as well as catching up with friends and family for a couple of weeks. The day started off early as her flight with Delta from Pittsburgh, PA to JFK, New York, NY left at 10:00am.

About an hour after she had left I got an automated call from Delta saying that her flight had been cancelled and they had booked her onto a flight at 6pm that evening! I knew that her British Airways from JFK to Manchester, UK was due to leave at 6:05pm. This was obviously a problem and so we started looking for alternatives to get her there on time.

I called a friend who offered to drive me to the airport to meet her and try to get this sorted out. Delta were less than helpful and claimed weather which apparently means they are not obligated to help. Checking the weather reports confirmed that storms were predicted that afternoon but offered no explanation why they were grounding flights that morning. After talking to them it seemed clear they were not going to get her there in time.

So we called British Airways. We have been loyal customers for years, taken more flights with them than I remember and had always been very happy with the service. We had never had cause to use their customer service but assumed it would be good as every other dealing we had with them was always positive.

After speaking with a customer service agent she assured us that there was nothing to worry about. She advised us to try and get to JFK today, but if we couldn't make it they could put Louise on the flight tomorrow for a fee of approximately $120. This made us feel much better and we thought worst case the journey was just going to be delayed by a day. We abandoned the plan of attempting to hire a car and drive to JFK which according to Google and MapQuest would have taken just shy of seven hours.

After confirming with Delta that there was little chance of them getting my wife to JFK in time for her flight we accepted the flight the next day on the proviso that Louise could get a refund if she found an earlier flight with a competitor. So we headed back home, scoured the travel sites and Louise called British Airways back to see about getting her flight switched to one tomorrow.

To her horror the second representative told her that this was not possible and no changes could be made to her ticket on the day of travel. She then proceeded to very unhelpfully quote that it was in the terms and conditions and that the previous agent was incorrect. We talked with the first person at about 8:20am when we might have had a shot at making it to JFK by car but being at home at around 10:30am we knew that we have no chance of making it.

I made the point that it was their previous agent that had given us incorrect information and that they should take some responsibility and work with us. My wife was obviously really upset by this and so I tried to talk with the woman who just kept repeating that it was in the terms and conditions and that if my wife didn't make it to JFK that day then her ticket would be forfeit and she would need to buy a new ticket.

I quite honestly couldn't believe it and after speaking with this woman it became clear that she thought she was in the right, I couldn't speak to anyone else about the matter and the previous agent was wrong. I was apparently free to make a complaint about this but beyond that she simply didn't care. When I asked her whether she thought it was fair that we pay for the poor training of the previous agent she went on to repeat that it was clear in the terms and conditions. I made the point that the previous agent didn't seem to know it but apparently I should know it myself.

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...

What a hectic week. I never got chance to record our first all American weekend on the long weekend. We started off on Saturday morning shopping in the sales and found a great BBQ at Wal-Mart. It is nearly twice the size of the one we had back in the UK with a great labour saving ash collector at the bottom. We then loaded up on meat and other BBQ essentials.

Had lots of friends over on Saturday evening and then exposed our American friends to the Eurovision song contest! It was very hard to explain this phenomenon to them but it was as amusing as ever with expert commentary by Terry Wogan

Then on Sunday we went along to our first ever baseball game and saw the Pittsburgh Pirates beat the Chicago Cubs. It was a really fun day out, beautiful sunny weekend and then we had another BBQ when we got back. I have always loved BBQs and our new one works great.

This weekend we are heading out on a road trip with a few friends from work. I haven't really taken any photos for about a year now so I am really hoping we can see a little of the country around us and get some photos I can show off. I would love more time for hacking on code too, may be Sunday evening when we get back. I have been seriously neglecting my new game too - GTA IV.

I haven't been keeping up with XKCD since my laptop stopped working - never set up my RSS feeds for the few comics I used to regularly read. I thought I would catch up and this one really made me laugh - I guess geek humour is alive and well!

Along with the one linked to from slashdot about the Googlebomb caused by the died in a blogging accident which I may have just added to now I guess.

I thought I would join in, a little late, with the posts about 2007. I think it is good to reflect at times. Please feel free to skip this whole post if you were hoping for something more focussed. For me 2007 has really been a roller coaster of a year filled with highs and lows. If I were ever to write my memoirs this one would probably go down as the most surreal so far.

At the start of October I began my first postdoctoral position, at the University of Pittsburgh in the Chemistry Department working in the newly formed Hutchison Group for Geoffrey Hutchison. Life has been so hectic these last few months finishing my doctorate and preparing for my biggest move ever.

Louise and I arrived on the 27th of September and had less than a week to find a suitable apartment out here ready for me to start work. I am now a legal non-resident alien (I think - someone correct me if I got it wrong). I am very excited to be starting this new job, the move has been really tough but the research looks very interesting and I am sure that my time here will be very productive.

I have already been to quite a few interesting talks in the department and am making the transition from physics to chemistry. It is OK though as I get to do lots of physics and programming along with some more chemistry. Exciting times and I am sure I will talk more about my work in future. I have already posted a tutorial article on installing Sun Grid Engine on a Mac OS X cluster.

Dax made it out here and we are both enjoying the recent snow. This entry sat in drafts for about a month or so as I have been so busy sorting things out, coding, reading and going to physio for my high ankle sprain which I am told is both unusual and the worst kind of sprain...

On Wednesday Dax, my overgrown German Shepherd dog, took his first ever flight. Originally they were supposed to fly him into Pittsburgh International Airport but apparently there were no carriers that could accommodate such an overgrown dog!

So eventually they gave up and told us that they couldn't get him to Pittsburgh as promised. I think it was Thursday night last week I had a voice mail left from what sounded like Dallas International Airport asking me to call them back and confirm that I would take delivery of Dax. I nearly had kittens of my own as I saw how far away this was!

It turned out that there is a Dulles International Airport, and the way it is pronounced sounds very much like Dallas. That was a much more manageable four hour drive away near Washington DC. So I hired a large pickup truck for Wednesday of this week.

Since moving out to Pittsburgh I have been using my Acer Ferrari laptop at home for development, keeping in touch with people back home and trying to figure out some of the weirder rules out here such as driving licenses in this state. Last night I booted up when I got home and after logging in everything went a little funky - got I/O errors when typing ls for example.

I tried rebooting but it wouldn't even get to the GRUB prompt. So I got out an old Gentoo LiveCD which I had luckily left in my laptop bag. That got so far then failed to mount the drive. After a few reboots and a little wine (to calm my nerves ) I managed to access the drive. I thought I would try copying some stuff across to my external hard drive and ended up getting more I/O errors and some memory errors for good measure. Half the time when I booted from the LiveCD the kernel panicked when attempting to mount the hard drive partitions.

So today I am a very unhappy English man in Pittsburgh. Due to me having spent far more than I budgeted for moving out here, and then more again on flying my dog out, I don't foresee being able to replace it any time soon. This means my development activity will be limited. Not sure if compiling part of a KDE 4 checkout might have been what finished it off. Looks like some kind of motherboard issue. The trackpad stopped working months ago, now I am getting random memory and I/O errors and the CPU has been running hotter and hotter recently. It served me for just over two years which isn't great but I worked it pretty hard and it travelled a fair part of the globe with me too.

Still can't help being cheered up a little as I will be picking Dax, my overgrown German Shepherd dog up from Dulles Washington International Airport tomorrow (not Dallas as it sounded like on the message they left me which made me very unhappy when I first heard).

Update: My very nice and generous new boss has very kindly offered to let me use the group laptop in the interim. It is a MacBook Pro though using something called Mac OS X Leopard. I can keep hacking on Avogadro with it and I even know how to take screen shots with it now too! It is also capable of checking email and browsing the web so my Internet connection in the apartment won't go to waste. I am considerably happier now but will miss my KDE 4 and Linux fix

So I had my first experience of Halloween in the US tonight. As I went grocery shopping I saw all the shops with big bowls full of sweets handing them out to passing children. Dozens of children dressed up as various ghoulish characters wandering around with their parents in toe, helping them to carry their swag.

I walked back to my apartment to witness yet more children wandering the streets with their parents and people up and down my street handing out sweets (or candy as it is known over here). I got home to meet a few of my neighbours work colleagues handing out treats on our doorstep. Lots of the houses around here have been decorated for weeks and it amazes me what a big thing Halloweeen is.

I am really going to miss Guy Fawkes Night on the 5th of November - don't think anyone knows about it over here We always had great parties and gatherings on Bonfire night, although currently my social calendar is emptier than it has ever been due to me being very new in town. Hope you have all enjoyed your Halloween and have a great Bonfire night if you celebrate it!

As I moved continent I guess it is only right I move servers too I have spent most of the weekend backing up, transferring and restoring email, web sites and other assorted services over to a different server I will be sharing access to. Thankfully it is still a Gentoo Linux based server that I will be sharing with my brother-in-law.

The move has taken a lot longer than I anticipated but I think everything is over now. Still some cleaning up tasks to perform. Hopefully this blog hasn't been kicked off planets or spammed them during the move over. If you notice any problems with anything feel free to poke me. Hoping I have finished moving for quite some time now - it isn't much fun and reduces productivity...

What a hectic few months it has been. This year has been really tough on many levels but also very rewarding in other ways. I never really got chance to write up my final thoughts on my Google Summer of Code project and will hopefully get the time to do that soon. Still working on it adding new functionality and fixing bugs where I can.

I completed my thesis over the summer and did my viva which went very well. Managed to hand in the final library copy of my thesis the day after my viva before leaving for a two week diving holiday. Louise won the holiday at the London International Dive Show in March of this year. It was an awesome week away in Curacao and a second week in Bonaire with some amazing diving, although I sprained my ankle really badly at the end of the last week.

Then we returned home for a couple of days before leaving for Pittsburgh via JFK. Got to Pittsburgh on 26 September to start my postdoctoral position at the University of Pittsburgh on 1 October (or October 1 as they say over here). Louise came out with me on the first week and helped me look for a place to live and everything.

Life has been amazingly hectic and I am still feeling very displaced and missing many of the creature comforts I am used to such as money, a car, furniture, good beer... I did get cable, internet and phone on Monday and brought my laptop out with me so things are picking up a little. Hopefully I will be able to write more soon about the dive holiday, my new job, GSoC and continuing work on Avogadro.

For now I am going to hobble to the shops to find some dinner - still not used to eating out alone... Lots of work to get on with that will keep me occupied at least!