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Old 10-27-2013, 06:34 AM   #1
mcnelson.phd
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Default OSX Mavericks

Hey guys,

Has anyone updated any of their Macs that they use for bioinformatics to Mavericks yet? We have a Mac Pro running 10.6.8 that we use for the heavy data analysis that we don't do on our linux clusters, as well as some iMacs that we use for lighter analyses and I'm considering whether or not it's worth it to upgrade them. The AppNap and compressed memory features in particular seem like they could give those systems a boost and help extend their usable life span.

Given that the upgrade is free, it's very tempting to just go ahead and try it, but my concern is that there will be unknown issues with some of the programs that we rely on for our analyses. Figure it was worth checking to see if others have upgraded yet and what their impressions were before I try it for myself.
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Old 10-27-2013, 07:12 AM   #2
JohnN
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Because on my heavy reliance on MacPorts, I'm waiting for verification that MacPorts works with Mavericks. (I have not checked since Friday).
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Old 10-27-2013, 07:22 AM   #3
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I upgraded my non-critical home laptop to Maverics and didn't have any issues yet. I don't use MacPorts however..
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Old 10-27-2013, 02:18 PM   #4
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There were issues which you could work around by compiling from sources, but i believe macports have released an official installer. as of yesterday i had issues with the mac-qt4 library not compiling. its used for quite a few GUI apps in macports and i'm waiting for them to update. so you've been warned.
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Old 10-27-2013, 02:19 PM   #5
PeteH
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There are known problems with Mavericks and RStudio (http://blog.rstudio.org/2013/10/22/r...0-9-mavericks/). R itself is fine but it's something to bear in mind if you use RStudio and are considering moving to Mavericks.
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Old 10-27-2013, 04:06 PM   #6
jimmybee
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Quote:
Originally Posted by JohnN View Post
Because on my heavy reliance on MacPorts, I'm waiting for verification that MacPorts works with Mavericks. (I have not checked since Friday).
Ive had no issues
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Old 10-27-2013, 05:00 PM   #7
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Waiting for 10.9.1 to show up may be prudent (at the most a couple of months). Apple generally tackles most of the initial bugs with that minor release.

That said, commercial software we support seems to all work with Mavericks (just needed the java install which is still on 1.6). There is an Xcode update to go along as well so there should be compatible compiler/libraries in case you need to recompile things. Between the OS and Xcode you are looking at a ~7 GB download.
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Old 10-27-2013, 10:33 PM   #8
mdobeson
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The todo list...
http://trac.macports.org/wiki/MavericksProblems
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Old 10-28-2013, 12:35 AM   #9
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I have updated my macbook(mid 2010) and i CLC works fine.
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Old 10-28-2013, 01:23 AM   #10
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So far so good, no issues to report yet. GUI one's such as CLC, Tablet etc. seems coped well.Hoping for no dramas.
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Old 10-28-2013, 04:00 AM   #11
mcnelson.phd
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Looks like my best bet may be to update one of our less crucial systems and see what works and what doesn't.

Thanks for the info guys!
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Old 10-31-2013, 05:12 AM   #12
rhinoceros
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I updated my work computer and ran into problems.

Apparently, OS X Mavericks memory management sucks. I can no longer run some scripts I've written for 454-sequence analysis. Instead, in memory heavy phases of these scripts, a warning that I'm out of memory pops up. A few seconds later the computer freezes completely and has to be cold rebooted. Mind you, I never had these problems in Mountain Lion with the same exact parameters and data. The only workaround is to reduce parallelization.

Computer specs:

MacBook Pro
Retina, 15-inch, Early 2013
Processor 2,7 GHz Intel Core i7
Memory 16 GB 1600 MHz DDR3
Graphics NVIDIA GeForce GT 650M 1024 MB
Software OS X 10.9 (13A603)

Oh well, back to Mountain Lion. I'm somewhat sad as Mavericks handles multiple screens way better than its predecessor.
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Old 10-31-2013, 03:05 PM   #13
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Quote:
I can no longer run some scripts I've written for 454-sequence analysis. Instead, in memory heavy phases of these scripts, a warning that I'm out of memory pops up. A few seconds later the computer freezes completely and has to be cold rebooted. Mind you, I never had these problems in Mountain Lion with the same exact parameters and data. The only workaround is to reduce parallelization.
Bugger! What are your scripts written in? What libraries are you using? Are you hitting swap space?

My 454 perl scripts use ForkManager extensively and are pretty cpu intenstive but I'm careful to stay away from hitting swap hard for obvious performance reasons. I've had no memory issues thus far, just missing macports. Looks like we have the same spec macbook.

Mavericks does have that new memory compression feature which seems a possible culprit if this is indeed a mavericks bug. Who knows! YMMV
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Old 10-31-2013, 03:36 PM   #14
jimmybee
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Quote:
Originally Posted by rhinoceros View Post
I updated my work computer and ran into problems.

Apparently, OS X Mavericks memory management sucks. I can no longer run some scripts I've written for 454-sequence analysis. Instead, in memory heavy phases of these scripts, a warning that I'm out of memory pops up. A few seconds later the computer freezes completely and has to be cold rebooted. Mind you, I never had these problems in Mountain Lion with the same exact parameters and data. The only workaround is to reduce parallelization.

Computer specs:

MacBook Pro
Retina, 15-inch, Early 2013
Processor 2,7 GHz Intel Core i7
Memory 16 GB 1600 MHz DDR3
Graphics NVIDIA GeForce GT 650M 1024 MB
Software OS X 10.9 (13A603)

Oh well, back to Mountain Lion. I'm somewhat sad as Mavericks handles multiple screens way better than its predecessor.
Do you use chrome by any chance?

I had similar issues with my system but has since cleared when I switched to safari. Ive been really throttling the system recently and its been handling parallelisation better than ever. Specially with high memory tasks
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Old 10-31-2013, 11:44 PM   #15
rhinoceros
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Quote:
Originally Posted by mdobeson View Post
Bugger! What are your scripts written in? What libraries are you using? Are you hitting swap space?

My 454 perl scripts use ForkManager extensively and are pretty cpu intenstive but I'm careful to stay away from hitting swap hard for obvious performance reasons. I've had no memory issues thus far, just missing macports. Looks like we have the same spec macbook.

Mavericks does have that new memory compression feature which seems a possible culprit if this is indeed a mavericks bug. Who knows! YMMV
These are shell scripts that are basically wrappers for QIIME and indeed, I'm hitting swap space. I think running pick_open_reference_otus.py script from QIIME with 8 threads against 97_greengenes stayed just a little bit under 16GB in ML, however, for whatever reason Mavericks goes way above it. The memory compression thingy was my first idea too..
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Old 10-31-2013, 11:46 PM   #16
rhinoceros
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Do you use chrome by any chance?

I had similar issues with my system but has since cleared when I switched to safari. Ive been really throttling the system recently and its been handling parallelisation better than ever. Specially with high memory tasks
Nah, I use FireFox. But the thing is, with ML I could have had like 10 programs open and not run into memory problems. With Mavericks, I get memory problems even if I have nothing else running..
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Old 11-01-2013, 08:34 AM   #17
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Quote:
Originally Posted by mcnelson.phd View Post
The AppNap and compressed memory features in particular seem like they could give those systems a boost and help extend their usable life span.
I have to second waiting for the 10.9.1 release at minimum. Often times Apple gets that out inside a month.

Also, are you running out of RAM? Do you have 96GB installed? I can't imagine that this whole compressed memory thing does much good for serious work. Maybe it saves the OS a GB or 2 for lightly used things that load up in RAM, but in general, if you need stuff in RAM, why would you want it compressed? Then you have to uncompress and recompress it upon every use? If that's how you cram something that needs 128GB into 96GB, its going to be painfully slow. And I don't think that's even what it is doing. This is probably a feature for machines with <8GB of RAM....
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Old 11-01-2013, 10:53 AM   #18
mcnelson.phd
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Quote:
Originally Posted by Wallysb01 View Post
Also, are you running out of RAM? Do you have 96GB installed? I can't imagine that this whole compressed memory thing does much good for serious work. Maybe it saves the OS a GB or 2 for lightly used things that load up in RAM, but in general, if you need stuff in RAM, why would you want it compressed? Then you have to uncompress and recompress it upon every use? If that's how you cram something that needs 128GB into 96GB, its going to be painfully slow. And I don't think that's even what it is doing. This is probably a feature for machines with <8GB of RAM....
We're currently OK with RAM usage and capacity, and my intention wasn't that compressed memory would allow us to analyze a larger dataset than the system is capable of handling.

My main line of thought was that compressed memory and AppNap would help keep systems like our iMacs, which are used for light analyses by multiple users, to last longer between hardware replacements. Basically, these systems are used for small genome assemblies, light 16S analysis, Sanger sequence analysis, etc. along with basic things like using MS Office doing statistical analyses. Because most users would have multiple programs open as they work on and analyze their data, something like AppNap could help extend the usable lifespan of these systems so we don't have to buy a whole new system every year or two.

For heavier analyses we would rely on our linux clusters, so we're not trying to skimp on our computing capabilities.

And as I thought when I first posted, it looks like I'm better off waiting to see what happens with the first few point updates to stabilize the OS. I've also heard from some colleagues that some older applications that they and we use are no longer supported, so we'll have to look at whether or not we still need them and if it's worth paying for upgrades or if something else is available that we might try instead.
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