Mar 182009

Last Saturday I got my head shaved with Bottlewine and a few other co-workers from my past job at Children’s Hospital for a fund raiser to help research on infantile cancer, here are some pictures, I raised close to 700$. The fundraiser is still going on, here is a link to my st baldrick’s page if you would like to give some money:

st baldrick 004.JPGst baldrick 023.JPGst baldrick 080.JPGst baldrick 103.JPG

Dec 302008

The other day I found out that XCode breakpoints were not working anymore under iPhone Simulator, still worked fine with the device. Reinstalled XCode: nothing better. Removed all XCode settings files in the user directory as well as the /Library/Preferences directory: nothing better. Looking at the output from gdb I found it was reporting a certain number of errors related to finding symbols for the iPhone framework libraries: the messages read like this:

Unable to read symbols for "/System/Library/Frameworks/UIKit.framework/UIKit" (file not found).
warning: Unable to read symbols from "UIKit" (not yet mapped into memory).
warning: Unable to read symbols for "/System/Library/Frameworks/CoreGraphics.framework/CoreGraphics" (file not found).
warning: Unable to read symbols from "CoreGraphics" (not yet mapped into memory).
warning: Unable to read symbols for "/System/Library/Frameworks/OpenGLES.framework/OpenGLES" (file not found).
warning: Unable to read symbols from "OpenGLES" (not yet mapped into memory).
Program loaded.
Pending breakpoint 1 - ""aPointSystem.m:395" resolved
sharedlibrary apply-load-rules all

After a few google searches I realized a lot of people are reporting the same messages, but there was never a real solution on how to get rid of this and the rare solutions suggested to remove some rogue breakpoints and everything would be solved… So not so surprisingly I focused on solving this problem first because i thought it was very likely to be the reason for my breakpoints not working. Well yeah indeed if I remove all breakpoints all ‘file not found’ messages go away, but all debugging also goes away, as soon as the breakpoints are back, so are the messages !!

So after a couple days of scrambling I still had in the back of my mind the idea that the only thing I had done lately to the system was to upgrade the mac os X kernel to the newest voodoo kernel. Some rare intermittent crashes (see screenshots) occuring while debugging, together with the problem occuring only on the iphone smulator (hence host code and possible kernel hooks failures) and reinstallation/settings erasure independent it seemed to be a consistent explanation to my woes….

occasional Voodoo kernel panic

Sure enough, after I returned to the old kernel the breakpoints started working again, it turns out the ‘file not found’ messages are completely normal the reason being the iphone framework code is private to apple and therefore debug symbols are inexistent. You got to admit the ‘file not found’ messages are somewhat misleading.


Jul 222008

My boss walked up to me about naming the project I’m working on, then I was wondering “why the heck do we need to have codenames for projects” anyways, the answer to this question aside, I decided I’d google a bit about this and see what I fell on:

I never thought I’d be able to tag together any post with the main topics of my blog: C# coding and Rock Climbing, well I was wrong… watch me.


 Posted by at 2:17 pm
Jul 122008

Just received my new D300 camera this week, I’ve been like a kid playing with it all of yesterday and today. I pass on the features my goal is not to do a review since there are thousands out there; however I’m pretty happy I’ll finally be able to post some decent quality pictures here. Let’s start with some pictures I took today (3 Megapixels only since I haven’t received my memory card yet and I would only be able to take one shot in full resolution!)

Lucia working on her breakpoints at Dolores Park Cafe

d300 first shots 006.JPG

the line in front of the apple store after the iphone 2.0 (3g iphone) was released

d300 first shots 015.JPG


 Posted by at 4:40 pm
Jul 122008

As promised I’m posting the necessary files to get 10.5.3 keyboard and mouse working for my vaio sz120p hackintosh; unfortunately I had several rounds of trial and error, and I don’t remember which extension I have used to make things working. The only things I know for sure is that it is one of the files in this archive.

link to zip download


Jun 152008

It’s been a while I haven’t come back here but hey… life is busy. Among other things I got a new job… I’m now working at Illumina in Hayward, Ca, who is in the business of sequencing DNA. So far I’m pretty happy with the environment they provide, everything I’ve ever dreamed of for a long time, lots of smart people, lots of nice technology, and a true enterprise setting… At last I can see what it’s like ! They are the current leaders in the market, let’s hope this is going to last and single molecule sequencing technologies are not going to hit us pretty hard. I’ve already completed a couple projects in Perl and Bash, however I will spend most of the time doing C# development.

I went for a few trips: for Damien’s birthday party I went to do some class 4 white water rafting in Auburn, it was pretty fun and scary in the rapids, especially this “tunnel chute” which is totally impressive, most of the time was spent paddling however, but it was still fun since we kept going at each other and sink each others out of the boats. There were some totally climbable boulders in the valley we rafted down, but they’re probably very inaccessible, but I could totally see some quality problems. Other than that I was surprised to see that some people are still looking for gold along the American River.

Last week we went to Mount Diablo and did some climbs that we don’t usually do, so it was a bit of a change from always going to the lower tier and climb the 90 foot wall.
We were supposed to drive up to Donner lake this week end and do some sport climbs up there, but we didn’t really get through with it, since we didn’t realize it was that far and half a week end is kinda short for such a trip. next time we’ll get it right…

Climbing wise I haven’t done so bad lately, last week I managed to send my first V9 and I also sent a V8 during that same session.

As far a software projects go, I’ve been kindda lousy lately and haven’t been able to finish anything while at the same time starting more things. A facebook app called sentit (i realized later does the same thing in better), and also my iphone Etcho App, which is still at the same point. Well I’m back on macOSX this week end and have taken forever to fix up my hackintosh bugs, but hopefully now we’re on the right track. My next post is about fixing those bugs, I don’t want to have to search everywhere again…

update: well I got the keyboard working yesterday but now it’s not working so my next article is going to have to wait…

 Posted by at 5:49 pm  Tagged with:
Apr 052008

I went to TBS 3 series Rock Climbing competition yesterday evening, in Iron Works, Berkeley. I’m pretty happy with what I was able to climb. As always it was bit difficult to start and get the blood pumping in my body, I’m a lot better now at dealing with this than in my first comps. Still it took more than 2 hours to start feeling comfortable on the climbs and not to have to wait 10-20 minutes between climbs to get my arms to recover fully. Like I said I was pretty happy about my performance overall, this was definitely the comp at which I performed best, I was able to flash a V5, three V6s and a V7 unlike the other comps I went to in the past where I usually performed less well than my usual level this time I was right on! At the end of the comp while working on a V6 and after almost finishing it and everybody yelling in the background “finish !!!, come on !!”, because I was first one to arrive at this point, the weirdest thing happened, I was so pumped out that both my arms started cramping, biceps, shoulders and forearms !!! when I went down the climb my arms went upwards in the airs elbows flexed (my biceps contracting) and my hands were closing in a fist without me commanding it, although I didn’t feel pain as you usually do when you get cramps… Totally weird… But I called it quits at this point.

Apr 052008

In my previous posts about running Blat searches on the Sun Grid Engine, I mentioned I would follow up to report what kind of money we’re looking into when running such searches for mapping large amounts of sequences. The results were pretty impressive and nothing like my first benchmarks suggested. At first I reported that it would cost approximately 730$ to map about 280Mb of dna sequence. This was sort of expensive, but not expensive enough to prevent us from running it. However I inferred this only on the results of one run where the best thing to do would have been to base myself on running 2 runs because of the overhead costs of starting a program (and loading all the needed resources). It turns out that the test program run time was mostly due to overhead costs. To my great surprise when I did the actual blat run on the 280Mb of sequences which I expected to be roughly $400-500 or cpu hours it turned out it took only 11 cpu hours !! In addition surprisingly the Repeat Masker step is the one that is now more costly: where as it used to cost roughly a third or a fourth of the compute time of blat on a standalone workstation, it is now costing about 3 times more in the grid engine setup.

Under the grid engine setup on, we can not only run blat on several hundreds of nodes, it also will run roughly 10 times faster on each node than it does on my workstation. It seems blat benefits a lot from being run in 64 bit mode, or the memory installed on the sun hardware is top of the line, since blat is mostly memory accesses.