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I'm runnning Mathematica 9 on Ubuntu 11.10. After installing CDF player I still have problem (most of time) with Manipulate. Only way I'm able to change value of a parameter is by manually entering a value into into an edit field (dragging the slider or pushing buttons doesn't work). Can anyone suggest what I'm doing wrong? (Even simple Manipulate[x, {x, 1, 5}] doesn't work properly.)

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What does this code do on your machine? Slider[Dynamic[x],{0,1}] then Dynamic[x] – Szabolcs Mar 21 '13 at 18:02
First creates slider (like one in Manipulate) which I can not drag. Second returns 0. – ipy Mar 21 '13 at 21:54
Did you modify Mathematica in any way (e.g. changing it to use system Qt libraries)? What desktop environment are you using? – Szabolcs Mar 21 '13 at 21:57
I had the same problem (but using Ubuntu 12.04/x86_64). In my case, I guess it was a configuration-problem, since restarting once with mathematica -cleanStart helped. Did you try that? – Dragos Mar 28 '13 at 0:13
I also have this problem. For me it appears only if Mathematica has been running during a hibernate or sleep. I don't know any way around this beyond restarting Mathematica. – ssch Sep 11 '13 at 19:46

I had some trouble with this and I believe it was because I was using Open JDK. I switched to the official Oracle JDK and that seemed to fix the problem. However, now that I'm running Fedora 19 with OpenJDK 1.7.0_60 Runtime Environment (fedora- I don't see this problem, at least not often. So it might simply go away if you install Oracle's Java or upgrade to a more recent version of Ubuntu with a newer openjdk.

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As far as I know Mathematica uses only the java it comes shipped with in .../SystemFiles/Java/ so I don't think OpenJDK is the problem. – ssch Sep 11 '13 at 19:48

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