Marcus D. Hanwell's Blog - General

Leap Day: Never Enough Time

marcus@cryos.net (Marcus D. Hanwell) — Thu, 01 Mar 2012 01:23:15 +0000

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.

Reflections on 2011: Open Source, Open Science and Open Chemistry

marcus@cryos.net (Marcus D. Hanwell) — Sun, 01 Jan 2012 20:40:41 +0000

It has been so long since I uttered a word here, 2011 was certainly a busy year for me and I hope to ensure I dedicate more time telling people about what I am up to in 2012. In preparation for that I have spent some time moving my blog to some new hardware, in the cloud. I also got to the bottom of the poor performance of page loads, and things should be much snappier now. After all that I figured it was time for a cosmetic refresh, so after upgrading the Serendipity I selected a new and hopefully cleaner theme.

As an extra special treat I updated the photo to something a little more recent to - me emerging from my TARDIS with a mug of espresso in hand! Kitware grew a lot last year, so much so that we had to take space in a new building across the road. It was decided that our scientific computing team would move, along with the communications team. In the move I got my own office, with a view of the old office across the street.

VTK was accepted as a mentoring organization in the Google Summer of Code program. We were lucky enough to get two very talented and tenacious students who produced some great work over the summer. We also continued improving and extending Gerrit, and thanks to the Google Summer of Code I had the opportunity to attend both the Mentor Summit and the Git Together (held the day after). Not satisfied with two meetings in one trip I also attended a small portion of the Open Science Summit, and hope to be able to attend the whole thing if it happens again in 2012.

Speaking of Open Science, 2011 was a big year for the area both on a personal level and in the wider community. I talked about our work in open science at several conferences, and more specifically the work we have been doing in Open Chemistry. I wrote a Source article introducing the work that we have done in Open Chemistry since I joined Kitware, and we recently acquired the openchemistry.org domain and have begun populating it. We were also awarded a Phase II SBIR which gives us two years of funding to develop many of the applications and libraries that I mentioned in the article.

The Science Code Manifesto was conceived in 2011, and Michael Nielsen released his new book Reinventing Discovery. There was also Open Access Week which highlighted the need for open access to scientific journals and data. I was very pleased to be a coauthor on two open access articles in 2011, the Quixote project and the Blue Obelisk five years on. I was also honored to receive my own Blue Obelisk award in 2011 from Peter Murrary-Rust!

There is so much else, but I am out of time for now and this post is already very long. Google+ was released to the masses, you can see a little more of me there, and I have created an Open Chemistry page that I will try to keep updated over the coming year. I was invited to a workshop on Semantic Physical Science in Cambridge, England and so I will be starting my traveling very much earlier than usual - leaving next Thursday. Here is to a great new year, one in which I hope we as a community can make significant progress in opening science for the world, and creating a truly shared set of tools for all!

I hope that 2012 is the year more of us start sharing in meaningful ways.

One Year at Kitware...Already?!?

marcus@cryos.net (Marcus D. Hanwell) — Sun, 31 Oct 2010 19:23:00 +0000

It is hard to believe, but I have been at Kitware for just over a year now. How are things going? I would say very well...I am very pleased I made the move, and that Bill Hoffman pushed me into applying after meeting him at the first Camp KDE. Kitware is growing fast, we are always on the lookout for new talent and I am already starting to feel like an old timer with all of the new employees joining.

I had my first ever annual review, which went well. We received word in September that my first SBIR proposal had been accepted, and we are working on getting the contract in place for that. So watch this space - a great collaboration coming up working on open source chemistry visualization, editing, database integration, and computational chemistry input file generation along with analysis of the outputs. I think this is a great opportunity to extend VTK, and Avogadro.

I took a very active role in our migration to Git, and I am pleased to say that it has been going well. I also more recently got Gerrit up and running, introducing tightly integrated code review to some of our open source projects at Kitware. I played a large role in setting up one of our most complex build systems to date for Titan, where it can build Qt, Boost and VTK (among other dependencies) using CMake's external project features. I have also had the opportunity to work with some of the Boost developers, and am helping with their build system work.

I have mostly concentrated on 2D rendering in VTK, using OpenGL. I replaced the existing 2D charts in VTK and ParaView with new charts using a new 2D rendering abstraction. So we now have a selection of chart types, with interactivity, that can be used on both client and server side. More recently I have been going even lower level, and working on FreeType font rendering in VTK, and seeing what I can do to improve the capabilities there.

There is lots of other stuff, some of it I have talked about here, and other bits I will when I find time. It has been a great first year, and looks like it is shaping up to be an even better second year. I feel very lucky to be getting paid to work on open source, open science and I get to work on some very interesting problems that help real scientists. Going forward I hope to introduce more scientists to open source, open data, open standards and collaboration platforms. I am very privileged to have worked with so many forward looking scientists over the last few years, and am a proud unmember of the Blue Obelisk.

I think Kitware is the perfect place for me to push forward open source in science, and am refreshed that I rarely need to push anyone here in that direction. I have been driven to learn a lot of new things in the past year, and it has been tough at times, but I have thoroughly enjoyed it. There are some really amazing projects coming up in the next year - so watch this space!

Back in England

marcus@cryos.net (Marcus D. Hanwell) — Tue, 31 Aug 2010 09:40:26 +0000

We are back in England after nearly two years away, we landed yesterday morning at London Heathrow. We flew with American Airlines this time (my first time with them), and I must say that I still prefer British Airways - they give you free drinks and I remember the staff being friendlier. The flight went well, and they got us in on time, immigration and baggage claim was all very simple, and so I was pleased the travel went well. William was a little angle on the flight, after letting him run around the airport for a few hours.

This is William's first time in England, so after getting the Underground to St Pancras Louise and I parted ways. She headed up to Sheffield with William, and I headed up to Chester to get my geek on. I will be spending the next couple of days talking with Noel, Tim and Chris about Open Babel development, CMake, Git, Gerrit and open source chemistry software i general. It should be a lot of fun, and while I have not had anywhere near the time I would like to work on open source projects in general, I think some of the things I am doing at Kitware might be useful.

Then Louise and I will be meeting up in London, staying with friends so that we can make our third trip to the US embassy to ask for another visa stamp. All of the forms have changed since we last went in 2008, and our visa type has changed. Hopefully that will all go smoothly, then we will visit another friend before returning up t'North together. I should finally make it up to Sheffield myself on Saturday, but plan on heading out on the Sunday. I have a week of meeting with chemists, physicists and materials scientists, mainly of the computational persuasion, to talk about cool stuff I am doing and what they are doing.

There will be a short intermission on the weekend for a friend's wedding, before continuing another week of talking to scientists. One of these visits will take me down to Cardiff, where Torchwood was filmed. So I am doubly excited by seeing the city where one of my favorite Doctor Who spinoffs was filmed, and meeting with more people to talk about quantum chemistry, electronic structure and visualization. I will be ending my time in England on this trip in Sheffield, meeting with old supervisors, friends and coworkers, talking about what I am doing now and how we might work together in the future.

I am also hoping to squeeze in a generous helping of real ale, some fish and chips, a few full English breakfasts and time to catch up with family and friends. Despite being back for quite a long time, and initially wondering what we would do, I find I don't have nearly enough time to meet with everyone I would like to and catch up with all of my old friends. We should try to make sure we come back more often! I think this post is long enough already - looking forward to getting out and about in England after my long absence. We will be looking around Chester later, before getting down to business.

Returning From Hibernation...

marcus@cryos.net (Marcus D. Hanwell) — Sun, 23 May 2010 21:46:23 +0000

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 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.

Avatar and 3D

marcus@cryos.net (Marcus D. Hanwell) — Tue, 05 Jan 2010 00:48:20 +0000

The Wednesday before Christmas several of my new coworkers from Kitware went to see the new Avatar movie in 3D. I haven't been to the movies much recently, generally just using Netflix to watch movies at home. I have to say it was well worth it, and I have been trying to talk Louise into going to see it with me again. We saw it at the local IMAX, and the images really popped out of the screen. It was a little off putting that they use linearly polarized light, so that the effect is lost when tilting your head. I would highly recommend that you make the trip out to see it in 3D, and hope to figure out babysitters and all that stuff so that Louise and I can go and see it before it leaves the big screen.

The story was quite engaging, but I did find it really quite lame that the mineral they were mining was called "unobtanium", or that is what is sounded like. They could have chosen a better name, but it at least it seems to have been used tongue in cheek. That said I moved my head out of the way once or twice when an object swung around. It was also amazing how much emotion was conveyed in the characters, and how tough it was to tell where the CG and real sequences were joined.

I would love to have access to 3D of this quality on my desktop. When are the 30" 3D monitors due out with Linux and OpenGL support?!?

The End of the Noughties

marcus@cryos.net (Marcus D. Hanwell) — Sat, 02 Jan 2010 04:08:48 +0000

It is hard to believe the noughties are over - happy new year! It has been a decade of extremes for me on a personal level. It started with me going back to university, which was very challenging and rewarding. I attained a first class degree in Physics, and enjoyed it so much that I decided to stay and study for a research doctorate in nanomaterials. I was very look to work with Tim Richardson and Neil Cowlam who really allowed me to explore the field and go off on some really interesting tangents.

During my Ph.D. research I found the time to get involved in open source development, first with GentooKDE. I was lucky enough to be selected for a Google Summer of Code project in 2007 right at the end of my Ph.D. research. I spent most of my time working on Avogadro, Kalzium and Open Babel.

After that I was really hooked on open source development, and was offered a position as a postdoc by Geoff Hutchison in his new research group at the University of Pittsburgh in the chemistry department. This was a really big move from Sheffield, UK to Pittsburgh, PA in the USA. I learned more than I ever wanted to know about visas and working as an immigrant in another country.

These were certainly some of the high points of the decade, but it wasn't all good. In the middle of the final semester of my undergraduate degree we lost my little brother. This was a very difficult time for us all, and influenced my decision to stay in Sheffield over the next few years with my family. Then on the day I found out that I had been accepted into the Google Summer of Code program, as I was writing up my thesis for my Ph.D., we lost my sister unexpectedly too. I found out just how trusting and understanding relative strangers in the KDE community could be, and will always be thankful to them. Of course my friends and family were all there for us too.

During all this I met Louise (at the end of the nineties), and in 2005 we got married. Weeks before our wedding I attended a conference in Japan, and London was bombed the day before I returned from Japan. Roughly a week before our wedding Sharm el Sheikh in Egypt was bombed (our honeymoon destination). Even days before we weren't sure if we would be able to go on honeymoon. In the end we had a great wedding and an amazing honeymoon.

So much more happened, I think I have some great material for memoirs. I do worry whether people will really believe it all happened - the noughties were a real roller coaster ride. In 2009 my son was born, the birth did not go as planned, then at nine weeks he got a UTI that turned into E. Coli in his blood. I found out that I am an overprotective father, and that the doctors and nurses at the Childrens hospital in Pittsburgh are very good.

I also attended Camp KDE, met loads of amazing people including my future boss. Even that was far from simple, from an amazing start, to a suboptimal interview (I will tell you over beers), to the decision to hire me, then the visa gauntlet I ran to our eventual move more than six months later.

I have to say that we are extremely happy now we are in Clifton Park, NY. I love my new job at Kitware, the area is great and we have been made to feel very welcome by everyone at Kitware - especially Bill and Naomi. I think the next decade is going to be a good one, and have my fingers crossed for no really bad things.

I wish everyone a very happy new year. I feel very lucky to have such a great job working on open source code, with a generous hardware budget to buy new toys. If I could just talk them into getting an espresso machine everything would be perfect! We are on the look out for more Qties (pronounced "cuties"), and I am hoping to become lead Qtie I am really looking forward to Camp KDE in a few weeks, and all the work I will be doing at Kitware in the new year.

Big Snow!

marcus@cryos.net (Marcus D. Hanwell) — Wed, 09 Dec 2009 15:15:00 +0000

As some of you may remember we moved up to Clifton Park, NY in September. From when I first met Bill at Camp KDE in January he told me about all the snow they got up here. To be honest I was starting to doubt him, and then we got some snow on the weekend and I was really excited. Today I woke up, looked out and saw we got a lot of snow! I am not disappointed, possibly a little overwhelmed...

I think I am going to like it up here, Dax loves it and William is not too sure what to make of it right now. They just plowed the road (not our big drive though), and so I may try to venture into work soon. Of course Dax and I had a big play in the snow, and I think we are going to have to buy a sledge as soon as possible.

The Big Move and New Position at Kitware

marcus@cryos.net (Marcus D. Hanwell) — Wed, 30 Sep 2009 23:40:46 +0000

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.

What a Crazy August

marcus@cryos.net (Marcus D. Hanwell) — Sun, 06 Sep 2009 18:36:00 +0000

August was without doubt one of the craziest months in the last few years. It started off with the normal "getting used to being a new Dad" type of stuff. Then as we were thinking about our upcoming trip to find a new house our car started acting funny. Long story short it was not good, and we made the decision to get a new one. We should have probably done that in the first place, hindsight is always a great thing...

So we had some fun and games as we picked out a new car, checked our already stretched summer finances and finally took delivery of a shiny Subaru Forester on Wednesday 5 August. It immediately produced some awful, loud static noise as we drove it home from the showroom. By Friday they had given us a courtesy car while they figured out what was wrong. Friday night they had it back to us with a new audio system installed.

Then we figured it would be great to catch up with Adam in Washington DC, and to iron out any further car bugs before our house hunting trip. So 8-9 August we stayed with Adam and checked out the Air and Space Museum. We also took William to the White House, and a few other touristy spots. He won't remember it, but he got to see the capital, along with lots of rockets, planes and satellites.

On Monday I went back into work, left a little early and William was making some strange noises. When we got home I felt his head, and it was really hot. As Louise was getting the thermometer William was sick for the first time ever - all over me. When I checked his temperature it was up at 39.8C, in excess of 103F (checked with two thermometers). This scared us so we rushed him to the children's hospital, as any nervous first time parent would.

As they were looking at him we started to realise that it might be quite serious. They ran a battery of tests, including urine and blood tests, cultures, X-rays, spinal fluid and constant vitals. They found a bacterial infection, I have never been so scared and stressed before. I found out that I am a very protective father, and was disheartened as more and more tests came in and we were admitted for an extended stay.

All of our friends were out of town at the time too, which made things more difficult. It turned out he had an E. Coli infection in his blood. We were lucky in some senses, the antibiotic they started him on as we were admitted was one of the best for the strain of E. Coli he had been infected with. His blood only showed bacteria in the first culture they took. Still, they were talking about 14 days on IV antibiotics using a central line as an inpatient.

Thankfully after talking with them they found an alternative oral antibiotic therapy that recent studies showed were just as effective. So he could come home on the Thursday evening. It was great to be home again, although very stressful to have William get so ill so quickly. I had never imagined he could get so ill so quickly, it reminded me off the waiting for them to tell us he was OK after he was born.

After that we tried to get back to life as normal. Until the end of the month when we had our big trip up to Clifton Park, NY to look for houses. Friday went very badly, we saw one house which was terrible and everything else we had lined up had been rented before we got into town. Saturday we saw another house before leaving for Boston - it was OK, but not really what we were looking for.

Saturday afternoon we drove over to Boston, MA to go to Jeff's wedding. It was great to have a break from looking at houses. We had a great time looking around Cambridge and Boston, the wedding was really nice and William managed to get lots of attention. Thanks for inviting us Jeff - it was a really nice day. William's first formal event. Before leaving on Sunday we visited the Harpoon brewery to sample some of their beers.

We found several new places listed on Sunday before leaving Boston, so we set up appointments for Monday. Monday was something of a three bears type of day. The first house we saw was close to work, but too small. The second house we saw was about the right size, good state of repair but a little expensive and too far from work. The third place we saw advertised as we were thinking about how to compromise, saw it at 6:30pm and it was just right.

So in the end we didn't have to extend our stay, found a nice place that is close to where I will work and Louise really likes it. We just had a 500 mile drive back home. That was pretty much August, I did manage to squeeze some time in for hacking on code, taking care of the cluster at work, and general work stuff. September we just need to do our first 500 mile interstate move. It should be relatively simple after an intercontinental move surely

Avogadro Nominated for SourceForge Community Choice Awards

marcus@cryos.net (Marcus D. Hanwell) — Wed, 24 Jun 2009 03:23:00 +0000

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

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

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

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

Spawning a New Process: William Aaron Alexander Hanwell

marcus@cryos.net (Marcus D. Hanwell) — Tue, 23 Jun 2009 21:07:34 +0000

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

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

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

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

New Job at Kitware

marcus@cryos.net (Marcus D. Hanwell) — Wed, 06 May 2009 22:51:07 +0000

In January I started looking for a job as my postdoctoral position at the University of Pittsburgh was due to end in September. I took a break from this to attend Camp KDE, the first KDE meeting held west of the Atlantic. I gave two halves of two talks (so a whole talk in total) where I talked about two things I work on in the open source world - scientific visualization and packaging.

Bill Hoffman also attended the meeting and gave a talk about CMake. While watching his talk (and I think the same happened while he was watching my talks) it clicked that Kitware would be a great fit. Once I got back to Pittsburgh I sent off a copy of my CV, and they very quickly set up some phone interviews. After that they flew me out to Clifton Park for quite an interview, if you get me over a few beers I might tell you all about it...

The more I learned about Kitware the more I liked it. Their language of choice is C++, they do a lot of scientific visualization, such as ParaView, work with national labs, academics and companies on interesting scientific problems. Then there are the software process, cross platform build, test and packaging projects. They even use Qt, and will likely use it more now the license has changed. Most of their software is released under an open source license too! I really got on with Bill and his family when I met them at Camp KDE, and came away with a very good impression of Kitware after the interview.

I accepted a job offer for the position of research and development engineer at Kitware in Clifton Park, NY. Due to being British, and various visa issues I will not be starting there until October (assuming all the visa paperwork falls into place). My wife and I are very excited about this opportunity at Kitware. So wish me luck, I am leaving academia after quite a long stay. Don't tell anyone at Kitware, but most of the stuff they want me to do I would gladly do in my spare time They are still looking for more developers, especially people with C++ and Qt experience if you are on the job market too.

CMake Performance with Open Babel

marcus@cryos.net (Marcus D. Hanwell) — Sat, 11 Apr 2009 15:17:00 +0000

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.

Road Trip to Canada

marcus@cryos.net (Marcus D. Hanwell) — Tue, 10 Mar 2009 12:37:33 +0000

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.

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.

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!