search

yarden / MISO

MISO: Mixture of Isoforms model for RNA-Seq isoform quantitation
http://genes.mit.edu/burgelab/miso/index.html
132 stars 74 forks source link

MISO on MAC 10.9: malloc error #67

Open Jerry-Zhao opened 10 years ago

Jerry-Zhao commented 10 years ago

I got a malloc error when running MISO on MAC 10.9.3.

"malloc: *\ error for object 0x208a7614: incorrect checksum for freed object - object was probably modified after being freed "

Based on the error messages ("object was probably modified after being freed"), it is possible that

  1. freeing an object twice,
  2. freeing a pointer that was never allocated
  3. writing through an invalid pointer which previously pointed to an object which was already freed

It is also likely related to the memory sharing and freeing between processors. Maybe some blocks are not always on the main thread.

Because I set the "num_processors" to 1 in the miso_settings.txt, there are no such error messages for some data sets, but remain for other data sets.

Is there a way to fix this problem?

Thanks!

Best, Jerry

Jerry-Zhao commented 10 years ago

Update: I have switched to Linux and everything goes well.

Jerry

yarden commented 10 years ago

terrific. Would still be interested to see the problematic event's BAM if possible - we'll work on addressing this. Best, Yarden

Sent from a mobile device

On Jun 27, 2014, at 4:04 PM, Jerry-Zhao notifications@github.com wrote:

Update: I have switched to Linux and everything goes well.

Jerry

— Reply to this email directly or view it on GitHub.

stephenfloor commented 10 years ago

I am struggling with this issue on OSX 10.9.5. I have tried upgrading python to 2.7.8, building with gcc 4.9, and going down to a single processor, but the issue still appears sometimes. It also seems to appear randomly, even on the same input, which probably makes it a nightmare to debug.

This is the exact error (as in the OP): Python(85890,0x7fff7d8b9310) malloc: *\ error for object 0x7fc642149370: incorrect checksum for freed object - object was probably modified after being freed.

Rarely, I have also seen segmentation faults. I have been trying to pare my input bam down to a minimal file that generates the error with high frequency, but so far this has failed. I am happy to supply my input bam though. Some info below, please let me know if anything else would help.

Config:

pkgutil --pkg-info=com.apple.pkg.CLTools_Executables package-id: com.apple.pkg.CLTools_Executables version: 6.0.0.0.1.1410400753 volume: / location: / install-time: 1413245257 groups: com.apple.FindSystemFiles.pkg-group com.apple.DevToolsBoth.pkg-group com.apple.DevToolsNonRelocatableShared.pkg-group

Python 2.7.8

clang --version Apple LLVM version 6.0 (clang-600.0.51) (based on LLVM 3.5svn) Target: x86_64-apple-darwin13.4.0 Thread model: posix

yarden commented 10 years ago

Hi,

Thanks for this info! I'll look into it, but it's difficult to debug as you noted. The best quick fix I can recommend is to use Linux instead of Mac OS X -- sorry that there's not a more satisfying answer. I'm overhauling some of the code that is likely responsible for these nondeterministic memory leaks but it won't be done for a while. Best, Yarden

Jerry-Zhao commented 10 years ago

Hi, All,

I installed Linux on my MAC Pro and run MISO under Linux. No more error messages since then.

Best, Jerry

On Tue, Oct 28, 2014 at 4:49 PM, Yarden Katz notifications@github.com wrote:

Hi,

Thanks for this info! I'll look into it, but it's difficult to debug as you noted. The best quick fix I can recommend is to use Linux instead of Mac OS X -- sorry that there's not a more satisfying answer. I'm overhauling some of the code that is likely responsible for these nondeterministic memory leaks but it won't be done for a while. Best, Yarden

— Reply to this email directly or view it on GitHub https://github.com/yarden/MISO/issues/67#issuecomment-60828877.