Segmentation fault 11

[Ilya Temkin]

Dear POY Developers -

I keep getting “Segmentation fault: 11”; it occurs when I’m trying to swap a single (and rather tiny) tree under iterative pass. Running POY 5.1.1 on Mac OS 10.9.5.
I would appreciate any advise.

Best,

ilya

[Nick Lucaroni]

Hey Ilya,

OSX switched their standard C compiler to cLang in OSX 10.5 or about. Our inline directives we use mean something subtly different to that compiler than to gcc, I have a branch on the mercurial repo on google-code that removes those directives. Ward hasn't had any problems compiling and running with that version and even on the new OSX Yosemite. 

hg cone http://code.google.com/p/poy

hg update clang-compatibility

then you should be good to go. In the near future I'd like to take the diff that gets applied, and package that into the configure script and run it when using clang. But for now, as it was just a test to see if this was the only issue, and it looks like it is.

nick

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[Ward C Wheeler]

Illya—You are probably hitting a memory limit on your computer.  How long are the sequences?  How much 

memory do you have on your machine?

W

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Ward Wheeler

Division of Invertebrate Zoology

American Museum of Natural History

Central Park West at 79th Street

New York, NY 10024-5192

USA

whe...@amnh.org

http://www.amnh.org/our-research/staff-directory/ward-wheeler

http://www.amnh.org/our-research/computational-sciences/research/projects/systematic-biology/poy/download

http://www.wiley.com/WileyCDA/WileyTitle/productCd-047067170X.html

[ilya temkin]

Hello, Ward -

My dataset consists of 18 terminals / 31 sequence fragments (the longest fragment is 346); I'm running it on a MacBook Air with 8 GB memory (1.7 GHz, dual core). I did ran a similar dataset a few months ago and do not recall getting the seg fault error at that time.

Best regards and many thanks,

ilya

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From: whe...@amnh.org
To: po...@googlegroups.com
Subject: Re: [POY] Segmentation fault 11
Date: Mon, 24 Nov 2014 16:56:44 +0000

[Nick Lucaroni]

hmm, so what changed? OS upgrade? Are you using clang now?

nick