Jul 102011
 

This week end I updated the blog software to wordpress 3.2, it’s going to be a lot easier to blog since I’ll be able to do it directly from my phone, and can probably link the posts to my Facebook wall and google+, and maybe even twitter; this will the end of my long lasting social networking abstinence. Can’t wait to see that happen!

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.

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Dec 132008
 

So over thanksgiving I’ve taken some time to work a little more on my secret iPhone project (or I should just say “my secret project” abstracting the iPhone altogether since until recently almost no iPhone API’s were called), and I’m pretty glad I’ve made a little progress from the point where I was stuck for a while now. I’ve started implementing things in OpenGL ES in the hopes to see things go very fast and some impressive rendering speeds however I was pretty disappointed by the outcome, I’m guessing the bottleneck is the arithmetic I’m doing so I’ve started considering using the vfp for the iPhone.

Lately as a result I’ve been looking into using the hardware a little more and that probably means that I will have to rewrite some parts of the engine 🙁 to make hardware acceleration more doable. 

I thought I’d share my little bit of research on google which gave me the following pointer to a very good place to start in order to exploit the iPhone vfp:  

update: I’ve been researching a bit more and it seems the iPhone vfp is more specifically a vfp11 co-processor for the iPhone’s processor (ARM1176JZF), for which I pulled the doc on the arm website:

arm 1176jzf-s pdf doc

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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:

http://codeclimber.net.nz/

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.

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 Posted by at 2:17 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

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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 rockclimbing.com 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
 

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 Network.com, 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.

Apr 052008
 

Microsoft / business objects have changed the way Crystal Reports based applications can be deployed. It used to be complicated enough, now things have changed and apparently the documentation is scarce on the subject. I was sitting in a cafe a couple days ago trying to upgrade the source of one of my apps to visual studio 2008, I realized the crystal reports merge modules were not found anymore and wasn’t able to find any info about this in the documentation… god I hate that, everything should be findable in the docs (either the search function or the content have something to do with it, but somehow msdn docs can be unsettling sometimes). I found the solution to the problem as soon as I got connected to the internet.

It used to be be that you could deploy a Crystal Reports based project using merge modules, the new way to deploy crystal reports under visual studio 2008 is to use a redistributable msi package located under “C:Program FilesMicrosoft SDKsWindowsv6.0ABootstrapperPackagesCrystalReports10_5CRRedist2008_x86.msi”. I haven’t figured out a visual studio UI supported way to deploy this package at the same time as my application, and it looks as if, for now, one needs to deploy crystal reports separately. I will post my solution to this problem when I find out how to do this.
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