BUCKy error message

[Tom Near]

Dear BUCKy Users: I am new to BUCKy and have been able to perform
analyses on modest datasets (approximately 50 taxa for 9 genes).
However, in runs with larger taxa samples (e.g. >100 taxa) I am
getting the following error message when running bucky.

bucky(1683) malloc: *** mmap(size=2097152) failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
what(): St9bad_alloc
Abort trap


Does anyone have experience with this error message and know what is
the cause?

Thank you for your help!

[Josh Williams]

I actually just got this same message:

*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug

terminate called after throwing an instance of 'std::bad_alloc'
what(): St9bad_alloc
Abort trap


I have no idea what this is, though. Hopefully someone does.

[Colin Dewey]

Dear Tom & Josh,

These error messages are due to BUCKy running out of memory, which is a common problem for large data sets (many taxa, many genes, or both). You can either try running on a machine with more more memory or try using the "--opt-space" option to bucky, which makes it use more space efficient data structures (at the cost of being slightly slower).

Hope that helps,
Colin

[Josh Williams]

Yeah, this error message was definitely a memory issue. I ran the
file on my university's HPC and it worked just fine, with about 34
taxa.

Josh