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Memory Error Question (Read 2435 times)

SamW

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Memory Error Question
Jul 7^th, 2011 at 4:28pm

I have been looping a likelihood optimization routine for codon models (ea loop does the Model, Tree, LikelihoodFunction and Optimize functions).

I have been getting the attached error after it runs for about 24 hrs +/-. The server this is running on has 4GB of ram. The IT person thought it had something to do with the memory being full and this crashing HyPhy. I am getting this issue even using the REPLACE_TREE_STRUCTURE=1 command before each likelihood calculation in the loop.

Can you help possibly??

Thanks,
Sam

The attached error reads:
"The instruction at 0x62483411 referenced memory at 0x00000008. The memory could not be read. Click on OK to terminate the program"

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Sergei

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Re: Memory Error Question
Reply #1 - Jul 7^th, 2011 at 5:08pm

Hi Sam,

No idea what this might be related to. Try

1). Watching memory usage of HyPhy over time to ensure that it is simply running out of RAM.
2). Try to isolate the piece of HyPhy code that causes this behavior. Without knowing what you are doing with the code, I can't be more specific. It is possible that HyPhy has a memory leak that I don't know about.

Can you attach the batch files and data files needed to re-create the behavior?

Sergei

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SamW

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Re: Memory Error Question
Reply #2 - Jul 7^th, 2011 at 6:55pm

Sergei,

Thanks for the help. I guess I was just hoping it was something obvious that I didn't know...
I'll get working on whittling the code down to ID where the issue is.

I've also attached the batch file and data and utility functions to make it all run. The .zip contains the file structure referenced in the code so I think you can just drop it somewhere and run the GA_HYPHY_codon.h and it should get going. Also, the current function settings are what I ran the last time I got the memory error. I totally understand if it's a waste of your time to deal with this code (of course).

Thanks again.
Sam

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SamW YaBB Newbies Offline Feed your monkey! Posts: 18	Re: Memory Error Question Reply #3 - Jul 10^th, 2011 at 12:02pm Sergei, I've been testing with the older HyPhy version 1.0 and the memory error is not occurring when using it. I thought this may be of interest to you. V/R, Sam
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