Older blog entries for nutella (starting at number 40)

Today
Yikes! I received two telephone calls today. The first was from my friend in Chicago who basically confirmed what I had heard on 3/8/01 about the probable substantial delay before my start. He was basically just telling me that they needed the extra pair of hands and that my desk was already filling up with work to do(!). On a lighter note he was able to give me some good news from both himself and his wife. The second call was from Human Resources at the company and in a nice balance they told me that they thought I could start immediately. I gave them my earlier hearsay which raised some doubts but the gentleman there seemed fairly sure of my current status and told me to start making plans to start ASAP. I should find out the bottom line tomorrow but instinct says that this is actually it. Easter in Chicago (probably). Gosh. The annoying thing is that if I had heard this a week ago I could have planned to be out of my apartment by the end of the month and saved myself a month's rent. Ah, who cares.

17 Mar 2001
Beannachtai na Feile Padraig!
I managed to get a large amount of overdue housework completed. I have a huge pile of papers that I am trying to parse into suitably informative groups or to dump and managed to reduce it considerably. I did very little to acknowledge the day, not even with a small drink as I had run the fridge down to empty for defrosting and wasn't in the mood for Bushmills. I suppose I wore something green so that will have to do.

On the trail of building NAMD and VMD, I tried to compile charm++ upon which NAMD depends but this proved to be a problem for my current environment. Since I was busy with the aforementioned housework I couldn't spare the time for analysing the problem. For VMD at its best I need XFree 4 and so I downloaded the sources for 4.02 and built the world. This took an impressive amount of time (hours) dwarfing a mere kernel compilation. By the time it had finished I didn't have the energy to try it out. I did find that SuperProbe crashes completely, but then again the one for 3.3 did the same thing (this is the sparc64 version).

I also built a few programs I find useful such as tacg and meme. It was nice to see that the maintainers of the latter had incorporated my suggestions and bugfixes (described here) so that it would build under Linux.

.

18 Mar 2001

Determined not to waste the good weather I headed out to Point Reyes and decided to hike the Mount Wittenberg trail to the highest point (1407 ft.) in the park. This is steep, but not overly so and winds up from the vistor centre (elevation 80 ft.) over about 2.2 miles. The views on the way up were very nice which is just as well as the ranger who had claimed a "panoramic view" from the summit had clearly not been up there recently as the bulk of the vista is blocked by recently planted fir trees. Being pestered by large amounts of insects did not help matters. I loathe doubling back and so decided to make the trip a loop by taking the Sky trail towards the ocean and then rejoining the Bear Valley trail back to the headquarters. My enthusiasm got the better of me so I ended up staying on the trail for the full 4.5 miles to the coast. The views from Baldy were particularly nice as this was down on to the cliffs and then down on to the ocean below them. The cloud building off shore messed up my timing so that darkness fell much earlier and faster than I anticipated. I thought I had compensated for this by choosing the Bear Valley trail for the return as this is wide and supposedly comparatively well maintained but it turned out to be under tree cover for most of the way. For about the first 2 miles I was hurrying through what passed for twilight but then the coastal fog began drifting down through the trees and making navigation extremely difficult. After that point, still about 2.5 miles from the car, I had to rely on the half-glimpsed pale gravel of the path and this disappeared completely under the heaviest tree cover so I had to rely on my crunching the soles of my boots down to find that the surface was a real trail and not the bed of the Coast Creek. It didn't help that some part of my mind was trying to worry me with the idea that *Bear* Valley wasn't just a name so I was racking my brain for what little I knew about bear habits. I had previously been spooked when out hiking in Sequoia National Park when I blundered into a mother and cubs out in the woods. At this particular time all I could remember was scenes from Yogi Bear and from the latest adverts for Volkswagen and Smirnoff. The light level was so low that my vision was "pixellating" so I had to weave my head around like a bird to keep the coincidence circuits working and preventing what little I could "see" from turning into a completely formless mess. The luminous hands and spots on my watch seemed painfully bright. I also knew that I couldn't stop as I could only see the trail when I was moving, even when it was agonisingly stepwise movement. After about 40 minutes of stumbling I was rewarded by a brief flash of light up ahead as presumably someone pulled their car from the car park and I knew I didn't have far to go. Fifteen minutes later I was driving home, out of the main bank of fog, down to the bridge and then back in to the fog hugging the west side of the city.

Edited 3/21/01 to fix the broken Volkswagen URL (Woohoo!)

TN[IW][CP]NAZ
I had thought that yesterday was going to be a triple-Moffitt day as I left through the Herbert C. Moffitt building on the way to Nick and (supposedly) Jack but Moffitt no.3 was a no- show. Still, it was still a rare and enjoyable week as I managed to see crackmonkey, spicemonkey, stephane and elise for the second time. The crackmonkey contingent was also joined by schoen, GothMonkey, CzechMonkey and demonishi. This being a combined event the PigDogs were also there, including half-breeds like myself, but there were no more than the usual numbers of fatalities on both sides. Another positive sign was that although Expensive-Candy-Man made an early appearance our heroine, Tamale-Lady, beat him off with her carriers of wares and then proceeded to converse in broken Esperanto.

Mr.Bad arrived dressed as "Where's Waldo" and claimed that he was going to kill himself off and be reincarnated - one suggestion from schoen was "Mr. Worse". Mr.B also wanted to use this as a splash page for a new site which would then bounce viewers to a new one. I suggested the up and coming bear fighting site as a suitable target and this was considered a good thing. Get ready to place your bets. Off-shore grizzly smackdown will become a reality. The PigDogs handed out suitably-labeled nametags to all and sundry. Mine was blank.

We baled out at about half past yesterday, growled our farewells and separated. I wisely chose not to wait for the N-Judah but headed for Haight Street and soon caught a 6 which was good as far as 9th Avenue. Again, I chose not to wait for the N which was a good plan as I didn't see any sign of it for another thirty minutes and thirty blocks westward which meant I was nearly home. One occurrence which amused me is that as I stepped from the bus out to the almost deserted 9th and Judah junction I came across someone loudly performing rap (pretty badly) on the street corner. As I walked past he looked rather self-conscious and dropped his volume by about 90%. So much for street cred.

Good company. Good fun. Good Guinness. No spills (!).

In a much more serious but eerie parallel to the event I describe at the start of here I had a call from my brother today describing another bad luck/good luck spill. Chris was helping out on the factory floor where they make high voltage insulators and was moving a freshly-filled mould of resin. One of the chains supporting the mould failed and so the resin (eg. 150degC) was spilt. Thankfully he managed to leap out of the way but still managed to catch a splash in the "funnel" of his protective glove that resulted in severe blistering of his hand. The chemicals in the resin may also have neurotoxic effects as he now has a couple of numb white spots as well as a large chunk of skin missing from his palm. Always one to count his blessings Chris is philosophic about it as he still has full motion in the hand and full sensation in his finger tips. It is his left hand (and he is right handed). Plus clearly this could have been much worse than it was. Chris thinks that the member of staff who would normally have been there, who is shorter and a good deal less athletic, would have fared much worse. I pray for his quick and complete recovery.

Makes a change from those RSI stories, huh?

GAR! Writing manuscripts for publication is a pain when you work for a boss who is a control freak. I did all the practical work, wrote all the methodology and generated all the figures and tables but they insist on writing the bulk of the paper. In my previous jobs I've had two really great supervisors who are either at least as good as me at both science and grammar (and have a good grasp of the current literature), or they just let me do my own thing and then give *constructive* criticism for the paper. My current boss has atrocious grammar and punctuation and simply copies disconnected sentences from the literature and sews them together with flights of fantasy. Any suggestion I give is taken as a personal attack. A great example is a preference for the word "quantitated". I claimed that this does not exist and that the correct word is "quantified". An argument ensues and I bring out dictionaries and hordes of prior publications all of which support me. The boss agrees grudgingly. When I see the final draft of the paper it has "quantitated" throughout. When quizzed the boss claims that "it just feels right" and that they have used that word in the past. This fun is apparently due to the fact that I am the one and only senior postdoc that this person has ever tried to supervise. Secretaries have stopped me in the corridor to ask me why the heck I am in this particular lab as it only ever employs the most naiive people, fresh from their Ph.D.s and "fresh off the boat". The boss is a known problem to the faculty. I am advised to just bite my tongue and wait to get out. One comfort is that those who know me will know that, although I am an author on the eventual paper, I did not write it as wild extrapolation is not my style.

Good luck...? Bad luck...?
I am an incredibly clumsy person, especially in social settings. My childhood memories of formal teas at my grandmother's are of me sitting with my elbows clenched to my sides and my hands barely above tabletop level. I am not sure if this was because I was ordered to do this or if I adopt the style naturally. I don't know if sitting like this has now ruined any chance I may have in the future of developing the coordination required for reaching coolly across the table to accept the plate of thinly cut cucumber sandwiches with the crusts cut off, or if I failed so miserably at an early age that it is a mercy I am so inhibited.

Anyway, the bad luck is that I managed to knock over a large, freshly-filled teapot. The good luck is that: a) it didn't break, b) the tea didn't harm anyone, c) the tea largely hit easily wiped surfaces, d) the group I was with chose not to ridicule and shun me, and (maybe best of all) e) we were given a fresh pot of tea. I am leaning more towards the interpretation that this was good luck overall but not something I would care to rely on in the future. Maybe when at home I should stop eating food directly from the saucepan while sitting on the sofa, or maybe I should curb my habit of making windmill gesticulations when trying to make a conversational point. Maybe I should stick to the wide open spaces of Zeitgeist as the clement weather ushers in another season of TNICNAZ .

Thanks to all (especially elise) for a fun afternoon and apologies to crackmonkey as I had no idea it was (or was near) your birthday.

Okay, maybe in my previous post I should not have said NAMD *AND* VMD. This is because the former should be relatively easy to install and configure while the latter (ideally) requires XFree 4.0. So, I am looking into upgrading. So NAMD has not been touched yet. Anyway, just to show that my mentioning things in advogato does chide me into working on them, I followed up (partially) on something I mentioned here. As I had the case open I swapped a hard drive around and convinced myself that I can actually activate the HPT370 UDMA100 controller by passing an appropriate kernel parameter at boot time. I was only able to activate the primary channel (ide2) as I could not divine the address of ide3 from /proc/pci and most of the web instructions are for the HPT366 controller which is a little different. I was all set to patch the kernel source and fully activate the controller when I found that the Abit motherboard shares the IRQ for the HPT370 with one of the only two PCI slots I can use (just a reminder that this is a low profile case and I am using risers). Both the SMC ethernet card and the CardExpert video card are bus mastering and so are incompatible. Actually I could do without the video card at a pinch as I only need video for diagnosing boot failures as the box lives under my bed and is only connected to the outside world with power and ethernet cables. If I can find a dumb old PCI video card (probably second hand) I might consider stuffing my old hard drive on it for swap/backup/whatever.

"There is no end to madness."
I received an e-mail from my employers to be. Still no idea when the paperwork will finally be processed and a hint that it could take longer than we thought. This makes dealing with my rental agency somewhat delicate as they are keen to know my departure date (as am I). Thankfully I am on good terms with them.

I downloaded the latest versions of NAMD and VMD again (after being reminded of their existence by my having to mention them in a reply to a badvogato post) and want to expend the effort required to get them working (I never fully completed this in the past). I have found that if I mention a task here on advogato I am actually more likely to complete it (out of shame, of course).

The best computer in our lab at work is a 266 MHz G3 running MacOS 8.1 so the best version of Communicator I can use is 4.7 (6.0 requires OS 8.5 or better) this means I am susceptible to redirection here which is annoying as their "Reaction" page does not allow me to give them any feedback. I wish I could simply disable JavaScript but this is a heavily shared computer and it becomes too much effort. I'll just have to rely on Lynx.

I bought some fresh guitar strings (the old ones were almost rusty) and bought a harmonica on impulse. My neighbours must hate me. Actually the walls between my place and their apartment are fairly thin so when I listen to music I use headphones (or wait until I am travelling in my car) and I necessarily favour a "heavily damped finger picking" guitar style. My last apartment was in a basement under the kitchen and utility area of a house and the sound insulation was wonderful (I could only hear the folks upstairs through the window). I miss the freedom that gave me.

I was at a very interesting seminar today at UCSF as Dr. Walter Pitman III talked on his book "Noah's flood" in a lecture entitled "Noah's flood: the science behind the myth". This is another in the same seminar series that previously had us fascinated by Jared Diamond talking on "Guns, germs and steel" and again on "The lethal gift of livestock". One thing Dr. Pitman's talk brought home to me is just how narrow my exposure to such talks has become. I consider it a big change to sit in on a neurophysiology talk rather than confining myself to pharmacology, pharmacy and pharmaceutical chemistry, but today's lecture covered geography, geology, anthropology and mythology.

The focus of Dr. Pitman's talk was that he had good evidence that 7,600 years ago the Black Sea was a much smaller freshwater lake that underwent cataclysmic flooding over a short period of time. The course of events would see the peak of polar glaciation draining the world's oceans and resulting in a Black Sea considerably less expansive than today e.g. the Sea of Azov would be dry land and the Crimea would not be a peninsula. The Black Sea would become an independent body of water as the level dropped below that of the Bosphorus. When the glaciers melted, their outflow was to areas other than the Black Sea so that the oceans level rose until that point 7,600 years ago when they broke through the Bosphorus and linked the Black Sea again. This would have had to happen in a very short period of time and the flow of water through the Bosphorus would have been approximately 200x that at Niagara so the perimeter of the sea would have advanced at 0.5 - 1 mile/day (!). While he believed that this scenario explained the geological findings he also found that this event was also consistent with the migration of various people in all directions away from the Black Sea area so that historians noted the appearance of new peoples in other areas at about that time. Just to add the final flourish this also ties in nicely with the oral tradition/legend of a big flood held by several different religions/mythologies.

My appetite for this sort of thing has been throughly whetted so hopefully I will be able to attend such seminars in the future.

Sunday
As a farewell treat this weekend I was introduced to a San Francisco tradition, Sunday Brunch at Ella's. Despite the fairly heavy rain the queue was as long as ever but we had the definite advantage that one of my hosts actually works at Ella's part time and so were seated within about five minutes (yes, we are darned queue-jumpers). I heartily recommend the chicken hash and the french toast. I know I have now been spoiled for life for these two previously mundane items. If you are vegetarian or vegan they also do a very nice potato scramble with/without eggs. I'm told that part of the reason the place is so popular is because of the staff and can certainly see why as our (very busy) waitress was polite, attentive and hilarious company. Mike and Christy I definitely owe you a meal in Chicago.

I'm especially glad that we managed to do this before I have my get-out date and so before the inevitable rush. When I left Maryland I had promised numerous friends that we would have to do something sociable before I vanished but my departure was so abrupt I either had to cancel or was too stressed to enjoy myself fully. I am hoping for a crackmonkey teaparty in the near future so that this is similarly enjoyable.