Saturday, February 16, 2008

Installing MEEP on CYGWIN

Well, after finding no online tutorial that explains how one can install MEEP on WinDoze using Cygwin, and being unable to edit the MEEP wiki page, I am posting this here.


On your windoze workstation, first install Cygwin. I used the cygwin setup to install all available packages which took a hefty few GB. 
MEEP installation then pretty-much follows the original instructions,  except for a few changes that could save major headaches later!

Create a folder MEEP in /home/username (where username is your current Windows login username) and download and extract all .tar.gz files here. 

Compile and install BLAS, LAPACK. There is apparently something wrong with Cygwin's libtool repository. So MEEP won't compile unless the fix below is applied before installing harminv:

Change the last line in your /usr/lib/gcc/i686-pc-cygwin/3.4.4/libg2c.la 
from
    libdir='/usr/lib/gcc/i686-pc-cygwin/'
to
    libdir='/usr/lib/gcc/i686-pc-cygwin/3.4.4'
Now compile and install harminv, Guile, libctl and HDF5.

In order to avoid an error message about an undefined 'timezone' variable while compiling HDF5 (see here), you may want to configure HDF5 as follows (thanks to Mark Hadfield):
CC=gcc CFLAGS=-ansi ./configure --prefix=/usr/local
make

Now compile and install HDF5, and finally of course MEEP (hopefully, it works?).

But then, Meep installation will fail as the HDF guys (NCSA) changed the programming interface incompatibly in HDF5 ver 1.8. For example, the prototype for the H5Eget_auto function changed and this causes compilation of Meep to fail.

Thanks to the workaround from Steven Johnson, Meep successfully installs by configuring it as:
./configure CPPFLAGS="-DH5_USE_16_API"

Although, I am having trouble doing 'make check' on Meep. This fails with the error:
> bragg_transmission.cpp: In function `double distance_from_curve(int, double, double*, double, double)':
> bragg_transmission.cpp:186: error: `infinity' undeclared (first use this function)
> bragg_transmission.cpp:186: error: (Each undeclared identifier is reported only once for each function it appears in.)

Apparently,  INFINITY is originally declared in meep.hpp and so, if you hardwire INFINITY to be 1e-20 in the bragg_transmission.cpp, which is it's usual definition in MEEP, it may work.

Friday, June 29, 2007

Novaeseelandiae (Jun 9 - Jun 20, 2007)

Day 1

I flew from JFK into Auckland (via LA) at 4.45 AM. It was quite funny to see all the beagles they were using at the airport as sniffer dogs to sniff out that orange peel in your bag that you forgot to declare. Apparently they take Biosecurity very seriously indeed. I hit the ground running so to say. I took the AIRBUS into town and checked into the YHA. I hopped onto the Kawau Kat ferry at 9:00 to goto the Tiritiri Matangi, this open bird sanctuary off the coast of Auckland in the Huaraki Gulf.




Downtown Auckland


Sky Casino


Auckland has apparently some 20 denuded volcanic peaks.


Auckland harbor


A native 'takapu' Australasian Gannet (Morus serrator: Sulidae).


Spur-Wattled Plover (Vanellus miles: Charadriidae)


'torea' South Island Pied Oystercatcher (Haematopus ostralegus: Haematopodidae)




The sea at Tiritiri Matangi was amazingly blue - almost tropical, not totally unlike Zanzibar.


Tiri turned out to be a veritable bird paradise. The 5 hour amble through the island was led by the able ladies from the Friends of Tiritiri Matangi, steeped in bird lore as they were. As soon as I stepped off the ferry, I began to tick off lifebirds. Here's the 'kotare' Sacred kingfisher (Todiramphus sanctus : Alcedinidae), a native.


and a 'kakariki' Red-crowned parakeet (Cyanoramphus novaezelandiae novaezelandiae: Psittacidae), another rare native


Besides the birds, the island is also rich in flora. here's the majestic 'pohutukawa' (Metrosideros excelsa) NZ Christmas tree




'manuka' tea tree (Leptospermum scoparium) flowers


'ti kouka' Cabbage tree (Cordyline australis)


Tree ferns




One of the two extant species of the ancient clade of "wattlebirds", the 'Tieke' North Island Saddleback (Philesturnus carunculatus rufusater: Callaeidae). Only 5000 are left of this threatened endemic now extinct on mainland NZ, of which there are apparently 600 in Tiri.




The ubiquitous 'korimako' Bellbird (Anthornis melanura melanura: Meliphagidae), an endemic honeyeater. A male pictured here.


A male 'hihi' Stitchbird (Notiomystis cincta: Meliphagidae) It is apparently New Zealand's only known polygynandrous breeding bird. There are only some 3000 of this threatened endemic left in the wild, with ~100 in Tiri, but are now extinct on mainland NZ.


A Stitchbird nest.


Listen to the bellbird evenchorus.


'tiwakawaka' Grey Fantail (Rhipidura fuliginosa : Dicruridae)


'pukeko' Purple Swamphen (Porphyrio porphyrio melanotus: Rallidae), a partially protected native


A flock of foraging 'popokatea' Whiteheads (Mohua albicilla: Pachycephalidae).




This is Greg, an eligible single male I should add, for those interested. Greg is an endemic 'takahe' (Porphyrio hochstetteri: Rallidae), an endangered endemic with only 243 left!






' toutouwai' North Island Robin (Petroica longipes: Petroicidae), another protected endemic.


'Tui' (Prosthemadera novaeseelandiae novaeseelandiae: Meliphagidae), one of the 3 endemic NZ honeyeaters.




Finally we ambled past an open field to reach the gift shop for some complimentary tea, courtesy of the Friends of Tiritiri Matangi.


Returning to the "wharf", we bumped into the Brown Teal (Anas aucklandica chlorotis: Anatidae), yet another endangered endemic.

Day 2

The weather in the North Island turned out to be abysmal. I had originally planned to visit Tongariro or Egmont National Park to do at least one alpine dayhike, either the Tongariro crossing or climb Mt. Egmont/Taranaki (site of the Last Samurai), if not both, but they both got so much snow that even the year-round shuttle to Tongariro crossing was cancelled.


Lake Taupo on a miserable day

I decided to cut my losses as the weather looked all set to get worse. So I took the overnight bus to Wellington and then caught the 9:25 ferry to Picton the next day, as ironically the weather was fine in the South Island. But the local YHA wouldn't even let me hang out in the lounge even though I had stayed in the Auckland YHA only the night before. However, they had such generosity to let me store my backpack in a coin-op locker. So I had a nice Thai entree (Lotus Thai Restaurant) despite the abrupt service, wandered in Taupo till 10pm, got back just in time to the YHA to catch Meet the Fockers, and then I was off on the 1AM Intercity bus to Wellington.

Day 3


en route from Wellington on the Picton 9:30 ferry.




The views were breath-taking and the sea was so blue.

I got into Picton around 13:00 and my first stop was the visitor center and then the Dept. of Conservation (DOC) office to plan for the next step. I have to say that in general the Maoris who predominantly work in the visitor center are a bit gruff and disgruntled for the right reasons, decades of oppression and assimilation. But the DOC office populated by the pakehas are a bit on the friendlier side for the most part. It was clear that the only place to head to was the Nelson/Marlborough Sounds area with its 270+ days of sunshine. Nelson Lakes National Park seemed like an attractive choice, however, my hopes of staying overnight in an alpine hut (Angelus Hut) were dashed, as I didn't have ice axes or crampons and more importantly any previous experience hiking in alpine environments.

In Picton, I stayed in what is easily the best youth hostel in NZ - the Sequoia Lodge, run by a friendly bloke Peter, the only place so far to offer complimentary breakfast and everyday social events.


Tirohanga track.


Bird's eye view of Picton harbour from a lookout on the Tirohanga track, a "fairly strenous" 6km roundtrip hike with 300m ascent/ 1.5 hours. The track was lush with bellbirds, and 'tauhou' Silvereyes (Zosterops lateralis lateralis: Zosteropidae?), but it rained all day without any respite :(

Day 4

The next day I caught the first bus (nakedbus.com can get you NZ$1 fares if booked early)  from Picton to the sleepy hamlet of St. Arnaud (pronounced Arnard) perched at ~800m ASL on the foothills of the Southern Alps. En route I passed several vineyards such as the one below. It was a glorious sunny day for a welcome change.



Hobbitonesque or not, I pretty soon got disgusted at the scenery - endless rolling sheep pastures - and at the mindless destruction of habitat, thanks to the pakeha settlers.


Interface I. How many interfaces can you detect in this picture?




The northern tip of the Southern Alps.


South Island Pied Oystercatchers on an impressive backdrop!


The eroded north face of Mt. Robert (~1500m) seen from the state highway 63, St. Arnaud.

I got into town around 13:30 and my first stop was the DOC office where I unloaded non-essentaial stuff into a smaller backpack and stored it. The DOC guy assured me that my best bet was the relatively "easy" 700m ascent to Bushline hut almost on the summit of Mt. Robert, but warned that the track was icy above the snowline. But by the time I made arrangements for my onward travel at the Yellow House backpackers, where I booked a NZ$1 online ticket for the bus back to Picton, it was already 2:45 PM. I walked over to the St. Arnaud alpine village store - the combined convenience store and petrol (yeees, Kiwis are more British) station - and bought some exorbitantly priced water to augment my meager supply. It was 3PM when I officially started the hike. I took a bit of a detour along the Peninsula Walk to catch some birds and beautiful vistas of Lake Rotoiti (literally mini Rotorua), and crashed over towards the Mt. Robert Car Park. Apparently it is an hour to the car park from the DOC office and a 2.5 hour hike to the Hut via Lakeside and Paddy's track. And this being close to the winter solstice, the days were extremely short - just 9 hours - and it gets dark by 17:15. So it was really stupid of me to try to make it up to the hut with poor light and with snow on the track, but I had no other choice and I am far too determined and hardy than you might otherwise think.


The aptly named Bushline hut can be barely seen at the left of Mt. Robert, just where the bush starts.


A panorama from the shores of L. Rotoiti.




The hike was through a dense Manuka and Kanuka growth full of bellbirds, tuis, robins and fantails.


Welcome Swallows (Hirundo tahitica neoxena: Hirundinidae) self-introduced from Australia, apparently unwelcome in New Zealand.


A couple of couple of Grey Fantails gleaning off insects disturbed by trampers like me.


Bird's eye view of L. Rotoiti from Paddy's track.




You can see that it was getting dark. The winding track never seemed to end, but I finally reached the hut at 18:15 when the stars had already risen, aided by my torch and the albedo of snow. Thankfully, as snow reflects almost all the light that falls on it, I was able to discern the snow free areas on the path where I can safely trod. Nevertheless, it was hard going on the slippery ice with a large backpack though. I wasn't alone at the hut, there was a young German couple and a bunch of Kiwi high school kids on a summer camp who were merry playing "scum" (their polite version of Arschloch). It was toasting inside thanks to the wood-burning kiln and I had my meager dinner consisting of a Clif Bar and Fig Newmans. There were pretty comfy mattresses on the bunk beds and with a down mummy bag, I was cozy and would have slept like a log, but for the Stentorian snoring of the kids!

Day 5


There was about 6in to a foot of snow around the hut.


Sunrise!




A panorama at sunrise from Bushline hut.



I waited for the Sun to rise sufficiently high enough to melt away some ice on the track and it was 8:30 AM when I finally set out on what promised to be a day of long hike. The summit of Mt. Robert was supposedly just another half-hour from the Bushline hut, but I didn't bother as the track got a bit too icy. I got back down to Lakeside track by 10AM keeping well ahead of the kids who were racing to beat me via Paddy's track. Lakeside track as the name suggests, follows the lake all the way around to Coldwater Hut at its head on the West Bay where the Travers river flows into the lake. The track winds its way through the beautiful beech forests crossing several alpine streams and the Whiskey Falls.


Another view of L. Rotoiti from Paddy's track.




Racing to keep ahead of the kids.
















Paradise Shelducks, with Black Swans in the background.


At the head of L. Rotoiti, the lake gives way to a flat tussock habitat and the braided river bed of Travers river. I reached Cold Water Hut around 13:00 and had my CLIF bar resting on a table overlooking the lake and the small kayak jetty.


I was told at the DOC office that there was a footbridge to cross the Travers river to get over to the Lakeside Hut. I had planned my day on this. I come to find out that the bridge was actually another 1.5 hours further down. I was aghast as it was already 14:00 when I got to the supposed river crossing and there was no way to use the foot bridge to get to Lakeside hut as it will be dusk by then. So I decided to cross the river barefoot, but not only was the water freezing but it was also impossible to walk across the rough gravel. Fortunately the river was not swift and only knee-deep in places and so I finally reached the Lakeside hut at 14:30. I refilled my bottles and I changed into a fresh pair of socks that immediately got sodden, as my "breathable" DRILEX boots were completely soaked. I set off at 3PM with a wet feet, racing to get to St. Arnaud before dusk. I would have stayed at the Lakeside hut except for the fact that it was already cramped with a bunch of American collegers and that I didn't buy a permit to stay in the hut overnight.


view from L. Rotoiti, east bay.






South Island Robin (Petroica australis australis) now considered a separate species from the North Island Robin.


An eroded face of the St. Arnaud Range.

I finally reached Yellow House at 6PM after 10 hours of hiking. I warmed up after a nice hot shower, but it was just a great relief to get the backpack off my back. My dinner would have consisted of dry bread with Marmite, except that my debut with Marmite produced consequences of a nauseous nature.

Day 6


Still Life: Silvereye at the backpackers.


The guardian spirit of L. Rotoiti. The Maoris believe that this ancestor of theirs dug a hole in the ground that filled with water forming the lake.

I caught the noon Southern Link K-bus service to Greymouth. There's basically only two options to get out of St. Arnaud, either to Greymouth or back to Picton. I really wanted to goto Rakiura National Park in Stewart Island, the only place to watch untranslocated Kiwis in the wild. But since I missed my bus to Picton, it became nigh impossible. But it turned out to be for the better in retrospect, for it would have entailed a 20+ hour bus travel (Picton - Christchurch, and an overnight Knightrider bus to Dunedin or Invercagill and then a ferry to Stewart Island the next day) and would have barely given me half a day at Ulva Island where I would have stayed overnight and then a sprint back to Christchurch the next day to be in time for the opening reception of the Evolution meeting. Not to mention that all this was entirely contingent on fine weather and on timely bus connections.


The road from St. Arnaud followed the course of the amazingly blue Buller River and then the Grey River near Greymouth. It was beautiful with the river on one side and the mountains on the other.


Buller River


Grey River near Greymouth




Sunset across Greymouth from my YHA room.

At the YHA, I made arrangements to goto Franz Josef glacier the next day with this nice Quebecois lad Pierre-Luc. After a tasty pizza at the Bonsai cafe, and trying out a few local brews (Monteith's Original, and Dark), I was ready to call it a day.

Day 7

The next day Pierre-Luc and I got picked up from the YHA at 7:00 by Atomic Shuttle. We got into Franz Josef around 10:00. My first stop as usual was the helpful and usually well-stocked DOC office. But they were out of stock with the trail map I was interested in. So I photographed the "type" maps on display instead.




The endemic 'miromiro' Tomtit (Petroica macrocephala: Petroicidae) at the DOC office in Franz Josef.



I checked into the YHA there and wandered out to get some energy bars at the convenience store, but instead got whisked into the 10:45 shuttle van that drops hikers at the trailheads. The next shuttle was only at 13:00. I decided not to do a guided glacier walk ($150) or a heli-hike ($300) for the obvious reason that I was on a shoe-string budget and it certainly cuts down on my carbon footprint somewhat by refraining from the heli-flights, even though I flew 10, 000 miles to get here, right? I decided instead to go on the 8-hr return strenuous sub-alpine Alex Knob track with its spectacular views of the glacier. I have had only a modest breakfast that day and I was starting to catch a cold and worst of all, I had only 6 hours of daylight to complete an 8 hour hike, so I decided to go easy and time myself. I decided to go as far as I can until 14:00 and then turn back giving me ample time to catch my scheduled return shuttle at 17:00. Besides, neither did I have a torch, nor leave an intention form with the DOC office for the unlikely event of needing a search and rescue. But the shuttle driver kindly decided to pass on my hiking plans to the YHA and the DOC, should I get delayed or lost.


The threatened endemic 'kereru' New Zealand Pigeon ( Hemiphaga novaeseelandiae novaeseelandiae: Columbidae)


The Alex Knob track started out as a pretty flat gravel affair and soon became hard going, but it was uplifting to be tramping in a dense pristine forest.




And once above the snow line, of course there was snow on the ground


The Franz Josef glacier is named after the Austro-Hungarian Emperor by the explorer and geologist Julius von Haast. This is apparently one of two places in the world where the glacier comes so close to the sea (level), the other being in Argentina. In the 19th century, the glacier used to extend all the way to where the approach road to the Alex Knob trailhead is, but has receded dramatically now. 



Franz Josef Glacier from the Rata Lookout (zoomed in).


A glacial stream


At the Christmas Lookout.




I was a bit far from the glacier but with a 12x zoom camera and a pair of Zeiss binoculars, nothing could be too far. I was even able to appreciate the blueness of the ice.






The helicopters were whizzing past, back and forth - it was quite annoying both to me and the birds.




The west coast from Alex Knob track.


This is not a seething mass of worms, but some kind of epiphyte!


This is probably the most memorable moment of the hike, besides the glacier views. I was keeping my eyes peeled for geckos, when I noticed some movements in the bush. But the movement was persistent and in the same spot. It turned out to be an endemic South Island Kaka (Nestor meridionalis: Psittacidae) directly overhead peeling barks to expose insects.



I was able to do almost 80-85% of the hike to the top and I got back down at 16:30, which gave me enough time to goto the car park and do a short hike to the Peter's Pool giving spectacular reflections of the glacier. And the timing couldn't have been more perfect: Sunset.





I got back totmüde and with a nasty cold. But then the local Priya Indian Restaurant was a lifesaver. I surfed for a while at this rather cool old party bus converted into an internet cafe with thumping techno, before crashing.


Day 8

The next day I got on the 9:25 Atomic Shuttle service to Greymouth and then on the 13:00 bus to Christchurch.


The picturesque town of Hokitika en route to Greymouth from Franz Josef.




We passed through Arthur's Pass from Greymouth to Christchurch. The views were breath-taking for want of a better word. But it was starting to snow. Apparently even buses need chains to get through in the winter.


I could almost picture the Riders of Rohan gathering here!


I got into Christchurch at 17:30 just in time for the Opening reception of Evolution 2007 at the Christchurch Convention Center!

Days 9-12

The conference was fun, well organized, probably the best conference one could ever goto. They fed us amazingly good food twice a day. They even had gluten-free food, let alone vegetarian or vegan. The conference began with a traditional Powhiri ceremony. It is the bizzare yet beautiful ceremony of encounter to assess the visitor's intent intersperesed with haka and music. Puny and most awkward looking president of the SSE, and local conference organizers took the challenge that ended with the hongi or a gentle pressing of noses. My talk was very generally well received. I even got a strange request from an electronica music composer to send him some of my bellbird vocalizations.

I stayed with my main hombre Jon Marshall at the Stonehurst hostel on Gloucester St. It was the worst accomodation thus far. We paid some 60$ for a super-cramped double room and the heat stopped working. As it is, the heat turns off after 15-30 minutes but having to go without even this was terrible indeed. And as it turned out, the environs was a bit seedy with hookers on the prowl nearby. The one mitigating aspect was the proximity to this cool bar, Winnie Bagoes.

Christchurch and Auckland were both cool cities. Everything was very walkable. The younger Maoris I met were all chill. They usually streaked or bleached their hair and looked like Bené from Cidade de Deus (City of God). I was surprised to find that there were so many Japanese in the big cities that even the Telecom booths and some other public places have multilingual text in Japanese as well.



There was this cool evolution themed art exhibition in a private art gallery, with free beer (they had great 1/2 litre micro-brewed Pilsner!) and wine tasting. Alas, none of the evolutionary biologists at the conference came. Casting pearls at swine, I should say. On display were cool but weird bird-cat combo skins such as this by Claire Hobbs and a kitten with wings dubbed "pegapuss".


Christ College, Christchurch - the most elite school in town. Very reminiscent of Cambridge.


The native 'tarapunga' Red-billed Gull (Larus novaehollandiae scopulinus: Laridae)


A female ' putangitangi' Paradise Shelduck (Tadorna variegata: Anatidae)


A male Paradise Shelduck.


Song Thrush (Turdus philomelos: Turdidae), introduced from England


The Christchurch Botanic gardens had an excellent collection of native and non-native flora. It was weird to find a cherry blossom tree in bloom in the winter.


They even had a few massive Sequoia trees.


The quaint Christchurch Arts centre, once the University of Canterbury.




Rutherford's Den. The very classroom where young Ernest had history lessons.


The 'Chalice' sculpture in the backdrop of the Cathedral. Apparently since it was dedicated in the week of Sep. 11 terrorist attacks , it became a symbol of 911.


The Cathedral




The stylish Christchurch Art Gallery.




Interface II. Inside the Christchurch Art Gallery.

Overall, my impression is that the Kiwi society is very Anglicized and apparently not as Americanized as Australia, but way progressive than any other English-speaking country. But you have McDonald and KFCs and the usual crap every corner you turn in all big cities. And not surprisingly both the people who work or those who eat there were obese or overweight, go figure. I didn't see very many homeless on the streets, although I feel Maoris in general still do not have access to good education and high-paying jobs, barring those rugby players. But irrespective of the way the Maoris may languish, at least the government makes a gesture by adopting Maori as an official language and most official mottoes are in Maori like the DOC's - Te papa atawhai (The Land is for the People or somesuch triteness - ironically the people in question are the pakehas). In spite of all this, things are at least somewhat better than Australia, IMHO.

I was also disappointed, that most of the souvenir stuff was made in China, and even more puzzling is why Helen Clark's labour government is interested in signing "free" trade deals with the US and China. It is about time the Labour stopped calling themselves "Labour" worldwide, now that they have stopped representing their constituents.

In the end, I didn't see a Kiwi, a Wrybill, Penguins, or even a Kea and didn't get to do the best one-day hike in NZ, the Tongariro crossing. I, however, did see a congener of the Kea, a South Island Kaka. But was the three grand I spent overall worth it? The jury is still out on this...

Here's my bird list from New Zealand: