Mavericks, MATLAB and Long Computations

ok I reboot the machine right now, hoping that turning off app nap would take any effect.

however, right now I am not anymore able to use this computer to do any analysis withing reasonable times...

it is horribly slow!!! normal computations that are usually done in seconds, takes loooooong time

I noticed this line in the Console:

3/31/14 03:16:06.318 ReportCrash[554]: Invoking spindump for pid=431 thread=4802 percent_cpu=98 duration=92 because of excessive cpu utilization

pid=431 is Matlab...

basically the OS is slowing down my analyses...

any help is appreciated

thanks

here is the output from etrecheck

Hardware Information:

MacBook Pro (Retina, 15-inch, Late 2013)

MacBook Pro - model: MacBookPro11,3

1 2.3 GHz Intel Core i7 CPU: 4 cores

16 GB RAM

Video Information:

Intel Iris Pro - VRAM: 1024 MB

NVIDIA GeForce GT 750M - VRAM: 2048 MB

System Software:

OS X 10.9.2 (13C64) - Uptime: 0 days 0:5:11

Disk Information:

APPLE SSD SM0512F disk0 : (500.28 GB)

EFI (disk0s1) <not mounted>: 209.7 MB

Macintosh HD (disk0s2) / [Startup]: 499.42 GB (195.33 GB free)

Recovery HD (disk0s3) <not mounted>: 650 MB

USB Information:

Apple Internal Memory Card Reader

Apple Inc. BRCM20702 Hub

Apple Inc. Bluetooth USB Host Controller

Apple Inc. Apple Internal Keyboard / Trackpad

FireWire Information:

Thunderbolt Information:

Apple Inc. thunderbolt_bus

Configuration files:

/etc/hosts - Count: 61

Kernel Extensions:

com.nvidia.CUDA (1.1.0)

Startup Items:

CUDA: Path: /System/Library/StartupItems/CUDA

Launch Daemons:

[System] com.adobe.fpsaud.plist 3rd-Party support link

[System] com.adobe.SwitchBoard.plist 3rd-Party support link

[System] com.google.keystone.daemon.plist 3rd-Party support link

[System] com.microsoft.office.licensing.helper.plist 3rd-Party support link

[System] org.macosforge.xquartz.privileged_startx.plist 3rd-Party support link

Launch Agents:

[System] com.adobe.AAM.Updater-1.0.plist 3rd-Party support link

[System] com.google.keystone.agent.plist 3rd-Party support link

[System] com.nvidia.CUDASoftwareUpdate.plist 3rd-Party support link

[System] jp.co.canon.CUPSPS2.BG.plist 3rd-Party support link

[System] org.macosforge.xquartz.startx.plist 3rd-Party support link

User Launch Agents:

[not loaded] com.google.keystone.agent.plist 3rd-Party support link

User Login Items:

iTunesHelper

Degrees

Internet Plug-ins:

FlashPlayer-10.6: Version: 12.0.0.44 - SDK 10.6 3rd-Party support link

QuickTime Plugin: Version: 7.7.3

Flash Player: Version: 12.0.0.44 - SDK 10.6 Outdated! Update

Default Browser: Version: 537 - SDK 10.9

o1dbrowserplugin: Version: 5.2.4.18058 3rd-Party support link

SharePointBrowserPlugin: Version: 14.3.9 - SDK 10.6 3rd-Party support link

googletalkbrowserplugin: Version: 5.2.4.18058 3rd-Party support link

Silverlight: Version: 5.1.20913.0 - SDK 10.6 3rd-Party support link

JavaAppletPlugin: Version: 14.9.0 - SDK 10.7 Outdated! Update

Safari Extensions:

feedly: Version: 16.0.521

clea.nr Videos: Version: 5.0

autocomplete: Version: 1.0

Zotero Connector: Version: 4.0.8

AdBlock: Version: 2.6.18

Alexa Site Info: Version: 1.0

Audio Plug-ins:

BluetoothAudioPlugIn: Version: 1.0 - SDK 10.9

AirPlay: Version: 2.0 - SDK 10.9

AppleAVBAudio: Version: 203.2 - SDK 10.9

iSightAudio: Version: 7.7.3 - SDK 10.9

iTunes Plug-ins:

Quartz Composer Visualizer: Version: 1.4 - SDK 10.9

3rd Party Preference Panes:

CUDA Preferences 3rd-Party support link

Flash Player 3rd-Party support link

Old Applications:

None

Time Machine:

Skip System Files: NO

Auto backup: YES

Volumes being backed up:

Macintosh HD: Disk size: 465.12 GB Disk used: 283.20 GB

Destinations:

My Passport [Local] (Last used)

Total size: 2

Total number of backups: 22

Oldest backup: 2014-01-07 08:48:12 +0000

Last backup: 2014-03-27 19:25:51 +0000

Size of backup disk: Excellent

Backup size 2 > (Disk size 465.12 GB X 3)

Time Machine details may not be accurate.

All volumes being backed up may not be listed.

Top Processes by CPU:

26% com.apple.WebKit.WebContent

13% Safari

5% WindowServer

4% com.apple.WebKit.Networking

1% hidd

Top Processes by Memory:

469 MB Safari

279 MB com.apple.WebKit.WebContent

180 MB mds_stores

147 MB Dock

131 MB com.apple.quicklook.satellite

Virtual Memory Information:

10.84 GB Free RAM

3.40 GB Active RAM

515 MB Inactive RAM

1.26 GB Wired RAM

1.14 GB Page-ins

0 B Page-outs

Please either output something useful to this forum or don't bother answering, because like this you are of no help... go get yourself a cafe from starbucks...

THIS IS NOT A MATLAB RELATED PROBLEM, or if you think it is, then EXPLAIN WHY...

Matlab was working perfectly fine so far and the speed of the computations were much faster in the last few days.

Anyway this is the main observation when matlab start my analysis:

When I lunch my analysis script, it starts very fast, as usual, and then following few seconds, the speed slows down and concomitantly I receive this spindump message on the console...

I am trying to do my job here and the operating system is not allowing me to do this. This is supposedly related to some configuration changes (that occurred) on how the processes gather their priorities from the operating system...

I recovered from time machine the system state from 3 days ago, and guess what? Matlab works again like a charm... I can hear the fans turning full speed, and CPU is >100%...

any ideas what might have gone wrong?

best

this thread is discontinued, please see the new one here:

https://discussions.apple.com/thread/6048601

thanks for your interest...

One time, I was having again 4-5 MATLABs working during the night and when I came back in the morning, the disk space was nearly totally used up (because I need to save lot of data to the disk), and that time I realized that MATLABs were actually already running very very slowly. At that point I was thinking "hmm intelligent 10.9.2 it can predict the catastroph i.e. no diskspace, so therefore it decreases the priority of MATLABs." And I think since then I have this issue with MATLAB.

Other than this, I am pretty much doing office stuff, meaning that Safari, Preview, Mail, iTunes, Calendar are open nearly always... Actually nothing like crapware, I take care of my machine...

I restored the whole system, including Matlab. At this point, probably it is not possible to distangle where the error is located...

You might well be right, but what I observed when I started a new analysis, matlab starts with normal speed and slows down within few seconds to a very slow state. And this occurs in the same time as the Console message. If Matlab was corrupt would it rather just crash instead of being super slow... I don't know, it is beyond my knowledge...

If I observe the same symptoms I will re-install Matlab and see whether there is a chance...

yes you are right.

I don't think there is caching, but I am not sure if I understand it the way you mean it.

My computations are extremely disk access intensive, it is basically read, compute and write, and this many many many times. Reading slices from MRT data, computing something interesting out of it, and writing in back as another volume file.

(So right now, since this morning (i.e. system recovery), I have 4 matlabs running on parallel, so far without any problem.)

I don't think so because the problem occurred right after I started matlab freshly.