strange error in Simbiology

Hi,

I have some strange error (maybe bug) in Simbiology. I run a GlobalSearch optimization algorithm, and usually it runs fine, for many hours (~10, depending on the tolerances that I choose), but sometimes it crashes unexpectedly.

When it crashes I see first some message related with java: Opening log file: /home/rchereji/java.log.608 Then very soon I get some strange error from Simbiology (something like this):

??? Error using ==> sbioloadproject>createMATFile at 182 Error opening project file "/net/nikkafs/fs2/rchereji/Matlab/Projects/V218G/Mutant_V218G_v2.sbproj".

Error in ==> sbioloadproject at 83 tempfilename = createMATFile(projfilename, 'simbiodata\d*.mat');

Error in ==> computeResiduals_threeDataSets_v2 at 11 sbioloadproject(model);

I uploaded all the relevant files/error logs here: http://www.mediafire.com/?3xvc5cmu40g5195

It seems it's a problem with sbioloadproject. Maybe from the error logs someone can figure out if there is a bug in sbioloadproject or java...

Please let me know if you have some suggestions.

Best,

Razvan

Answer 1

[Arthur Goldsipe]

From looking at the Java error log, I suspect it's a bug and/or memory leak in Java's handling of zip files. I'm still trying to confirm that, but given the sporadic nature of the issue that may take some time.

In the meantime, you can work around the problem by using MAT files instead of SBPROJ files. Just change sbiosaveproject and sbiosaveproject to load and save, respectively.

Good luck! -Arthur

[Razvan]

Thanks Arthur!

I didn't know it works with save/load. I'll use these now. Good luck solving the java problem!

Razvan

[Razvan]

I uploaded more of the java error logs here: http://www.mediafire.com/?wkqodgvdkqeya20

These may be helpful.

Cheers,

Razvan

[Razvan]

Hi Arthur,

I changed the load/save functions, but it still crashes. The new error is here (in case it's helpful) http://www.mediafire.com/?lr1eaof4ov83v2j

I hope you'll solve this problem in the next versions of Simbiology. I lost so much time because of this bug... It's very annoying.

Good luck!

Razvan

[Arthur Goldsipe]

Hi Razvan,

Let's continue the investigation offline and see if we can track down the problem.

-Arthur

[Walter Roberson]

Java is known to have bugs in unzip -- a memory leak. But now I can't find the relevant postings :(