Archive for April, 2009

April Thank-You Notes

Thursday, April 30th, 2009

To start with an aside, let me say that I have made the move from “thank yous” to “thank-you notes,” thus avoiding a “word” I didn’t like to see in print, but had nonetheless used a few times here. Sometimes the obvious solution to a problem takes a while to become visible. I will not be giving any “shout-outs.”

As usual, this blog got a ten-fold increase in daily visitors while MacSurfer’s Headline News™ had a link to a post (What a Relief! MacBook Pro Overheating Problem Cured—Really) here. Thank you, Darren.

Other Mac sites that continue to send visitors here are PowerBook Central, and LowEnd Mac. Thanks, folks. I’m so glad that I actually have a solution to the MacBook overheating problem to point to now.

My post Some Observations on College Guides and Their Usefulness was included in the Carnival of College Admission: Kick A@$ College Links. Thank you, Elizabeth.

Joe, aka Coonass in italy, referenced and commented on Dante’s Heavenly Vision and the Physics of the Proton in his March 13 post “religion and science.” Thank you again, Joe.

David of D Dubs Reads found a lot to think about in the Dante post and added On-Screen Scientist to his blogroll. Much appreciated, David.

Denyse posted a long excerpt from the Dante piece on her Colliding Universes blog and linked to it. Thanks again, Denyse.

Harry of The Kudzu Files has placed this blog on his Blogopedia list. Thank you, Harry.

I’m programming an iPhone app (baseball related), which is taking a lot of my time, so posting will no doubt continue to be less frequent for a while. I’ll probably record another of the oldies for an audio post before long. Requests welcomed at the email address toward the upper right of this page.

Oh yes, I’m now on twitter as onscrn.

Only Three More Shopping Days Until DNA Day! Save Big!

Wednesday, April 22nd, 2009

Let’s face it: knowing the structure and workings of DNA is part of basic scientific literacy these days, which is why, after all, millions of us celebrate DNA Day. If you’re still doing last-minute DNA Day shopping, do we have a great deal for you! OnScreen DNA, the world’s best three-dimensional computer model of the double helix structure of DNA, complete with on-screen, tutorial-based simulations of how DNA works, is on sale at 50% off.

And what better way could there be to celebrate fifty-six years since the 1953 publication of the Watson and Crick paper elucidating DNA’s double-helix structure than buying OnScreen DNA for only $19.53? It’s perfect for those students, teachers, and science lovers of all ages on your shopping list. And don’t forget to treat yourself.

Don’t worry if you don’t see this until DNA Day itself—the online offer and the ability to get the software immediately by download will still be available right through April 25. Yes, we are celebrating with the “traditional” April 25 instead of moving to April 24, as many national national organizations, evidently wanting to avoid a weekend day, have done this year.

Seriously, there is nothing that I know of that teaches DNA structure and functioning in such a complete and thoroughly three-dimensional way as OnScreen DNA, which I designed and programmed myself. The software runs on Macintosh OS X or Windows XP/Vista. The on-screen tutorials explain everything you’re seeing, and practically no prior knowledge is assumed.

The animations of DNA and RNA chain-construction in OnScreen DNA are a lot of fun. I still enjoy them after having gone through them countless times during programming, debugging, testing, and just playing. You really need to see the three-dimensional structure of DNA, not just the two-dimensional ladders which animations encountered on the internet seem to invariably fall back on. Having programmed the OnScreen DNA animations, I can see why they do that—it’s a pain to do the three-dimensional programming. But it is worth it. Take a look at the results and judge for yourself. Just go to <onscreen-dna.com/buy_dna_online.php> to take advantage of this special offer.

What a Relief! MacBook Pro Overheating Problem Cured—Really.

Friday, April 17th, 2009

Just in case anyone has arrived here desperate for a solution to MacBook overheating, let me put it in this first sentence: CoolBook is what you need. I last wrote about the ever-worsening tendency of my first-generation MacBook Pro to go into a runaway heating mode back on November 22 of last year in an optimistically titled post called New Firefox Cures Overheating? I knew better than to be confident that something as simple as a browser upgrade could have taken care of my overheating problems, but I wanted so much to believe it. The Firefox upgrade probably did alleviate overheating associated with Firefox, but before long it became obvious that it was only a small part of the problem.

Since my lonely corner of the blogosphere receives several visits daily from unfortunates with the same overheating problems (I can tell from the logs of their visits: Google search terms), I’ve felt bad that all I was really offering them was the knowledge that they were not alone, even if Apple has never said anything about the problem. My computer got a slight amount of symptomatic relief by using the Fan Control utility, which goes into the System Preferences panel. With Fan Control, I was able to control the fan speed versus temperature profile to some degree, but the maximum fan speed, no matter what temperature it kicks in at, is no match for a true runaway heating episode.

The overheating problem only got worse for me with the 10.5.6 OS upgrade. Some apps became completely unusable. For example, Winclone, a great program for backing up your Boot Camp Windows partition to a compressed file on your Mac partition, thus allowing you to have a Windows backup on your Time Machine drive, would reach 100° C before 5% of the Windows partition had been read! The temperature never reached a plateau, and the high temperature caused a shutdown the one time I decided to let it keep going and hope for the best. I tried reverting back to an earlier version of Winclone, which had never caused a problem before, but that didn’t help.

The funny thing was that the runaway heating often seemed to be associated with periods where one might expect the computer to be cooly twiddling its thumbs. For example, EPSON Scan, the software that runs my excellent Epson Perfection 2450 Photo Scanner, would operate at a reasonable temperature when actually scanning, but once I clicked to tell it that, yes, I wanted it to scan another page, it seemed to go into a rage for some reason, and I heard, not the purr of a resting Mac, but the ever loudening buzz of the cooling fans, which were vainly trying to get it to cool down. Click to begin the next scan, and the temperature would drop. Similar odd behavior was observed with the Microsoft Office upgrade installer. Once the installation, which occurred coolly enough, had finished, the fans would start to buzz; and quitting the installer was the only way to bring the temperature back down.

There were also certain websites that would cause both Safari and Firefox to get a fever that ramped up rapidly and could only be stopped by jumping to another site. This could happen on certain sites without any video or anything I’d seen associated with the problem before. A web site featuring high school athletic event schedules was one such innocuous looking site with pyromaniacal pages.

At some point a few weeks ago Safari became completely useless, as it would invariably start up the runaway heating ramp within seconds after launch. How can it happen that a program permanently changes its behavior? I don’t know, but reinstalling with a freshly downloaded copy of Safari 3.2 did not help. Ordinarily I wouldn’t have tried the Safari 4 beta, but I had nothing to lose at that point, so I installed it, and it ran normally. I believe running Safari 4 instead of its formerly stable predecessor actually caused an overall lowering of the average temperature at which my MacBook Pro ran, but it by no means cured the overheating problem. I was pretty well resigned to having it indefinitely until the day before yesterday, when I got my hopes up again.

I can’t remember how I came across CoolBook, but I downloaded and installed it yesterday, and it has really solved my problem. Hopefully it has no undiscovered side effects. How does CoolBook work? In a word: undervolting. CoolBookController (to use the program’s full name) allows you to scale down the operating voltages assigned to different frequencies, thus allowing the computer to run at a cooler temperature without reducing the computing power, which depends on the frequency. Apple has set a default table of these voltage and frequency pairs that is quite conservative. Chips vary, and Apple must have chosen the voltages so that almost no cpus will be unstable for any frequency. This makes life easier for Apple, from the warranty standpoint no doubt, but in the case of the laptops it sells, it makes for a lot of unnecessarily high operating temperatures. So why doesn’t Apple do a chip-by-chip calibration to minimize the number of hot MacBooks? Well, it probably took me at least two hours to get CoolBook all set up for my MacBook Pro. First, it takes a while to figure out what to do, though everything you really need can be found in the instructions.

Then it’s just a matter of trial and error to determine what is the lowest voltage you can use with a given frequency on your machine. A utility called CPUTest is provided to verify cpu stability for the voltage/frequency combination you choose. This utility evidently does uninterrupted heavy-duty computations until it catches an error or until you decide it’s run long enough to call it a successful combination. The documentation recommends running the test for at least ten minutes; so you can see how an hour can easily be used up. In my experience, failures usually occurred in the first minute or so though.

I followed the recommendation to determine the maximum frequency at which my machine could run without trouble at the lowest voltage setting of 0.95V. Following the result reported in the documentation I tried 1.837 GHz for this voltage and got an immediate black-screen shutdown. i should have known mine couldn’t match that. I cut the trial frequency way down and worked my way up. I found 1.503 GHz was the highest stable frequency. Apple’s default frequency for the lowest voltage is 1.0 GHz.

Here are the frequency/voltage pairs that my formerly hot MacBook Pro ended up with (original Apple voltage settings in parentheses):  1.503 GHz, 0.95 V (1.1125 V); 1.67 GHz, 0.9625 V (1.1625 V); 1.837 GHz, 1.0125 V (1.2125 V); 2.004 GHz, 1.0875 V (1.2625 V).

How much difference do the lower voltage settings make? A very big difference in operating temperature for my machine. It has cool (58° C) and silent operation during times of cpu-loafing such as the computer is experiencing while I type this piece. During the stress of the CPUTest, I saw the temperature reach 98° C for the 2.004 GHz frequency, but it stopped there, and I know from experience it would only have been stopped by a computer shutdown at 115° C using the Apple default voltage.

The fix of the overheating problem still doesn’t explain why the computer thinks it needs to go to to maximum frequency for no apparent reason. CoolBook’s cpu-frequency monitor allows you to see what the current frequency is. Sure enough, it goes to the maximum 2.004 GHz on that baseball schedule page. I think I may just now have seen the culprit though. That page has one of those continually scrolling stock-ticker-like message things, which perhaps eats up computer cycles somehow. If that’s it, it doesn’t even have to be visible to cause the effect.

I also see that gathering permissions info in Disk Utility throws it into the highest frequency mode, as I would have expected from previous temperature rise observations. Why is that, I wonder? Quitting Disk Utility in midstream had no immediate effect on the computing frequency though. It’s stuck there at the highest frequency, though no running program is doing anything I’m aware of. I think this must really be an OS X issue. Fortunately, instead of being in the upper nineties, the temperature is around 70° C. That’s still high enough to cause an annoying fan noise though. Already complaining!

Anyway, the $10 I spent on CoolBook was nothing for the amount of relief it has brought. I’d have spent ten times that much to be guaranteed a solution to the overheating problem, which was ongoing and had become quite limiting, witness my not being able to run Winclone. This time, there really has been a solution. I successfully made a backup with Winclone yesterday at around 70° C. Unless Apple breaks CoolBook with its next update (and the danger of that will give me pause), I’m set for being a normal Mac user for the foreseeable future. CoolBook is evidently the creation of Magnus Lundholm and is found on a web site with an se domain. Hats off to the guy in Sweden!